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Posts Tagged ‘Genome-wide association study’

Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation: a Compilation of Articles in the Journal http://pharmaceuticalintelligence.com


Compilation of References by Leaders in Pharmaceutical Business Intelligence in the Journal http://pharmaceuticalintelligence.com about
Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation

Curator: Larry H Bernstein, MD, FCAP

Proteomics

  1. The Human Proteome Map Completed

Reporter and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/28/the-human-proteome-map-completed/

  1. Proteomics – The Pathway to Understanding and Decision-making in Medicine

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/06/24/proteomics-the-pathway-to-
understanding-and-decision-making-in-medicine/

3. Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/10/22/advances-in-separations-technology-for-the-omics-and-clarification-         of-therapeutic-targets/

  1. Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-                metabolome/

5. Genomics, Proteomics and standards

Larry H Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/06/genomics-proteomics-and-standards/

6. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

 

Metabolomics

  1. Extracellular evaluation of intracellular flux in yeast cells

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

https://pharmaceuticalintelligence.com/2014/08/25/extracellular-evaluation-of-intracellular-flux-in-yeast-cells/

  1. Metabolomic analysis of two leukemia cell lines. I.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

https://pharmaceuticalintelligence.com/2014/08/23/metabolomic-analysis-of-two-leukemia-cell-lines-_i/

  1. Metabolomic analysis of two leukemia cell lines. II.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

https://pharmaceuticalintelligence.com/2014/08/24/metabolomic-analysis-of-two-leukemia-cell-lines-ii/

  1. Metabolomics, Metabonomics and Functional Nutrition: the next step in nutritional metabolism and biotherapeutics

Reviewer and Curator, Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/22/metabolomics-metabonomics-and-functional-nutrition-the-next-step-          in-nutritional-metabolism-and-biotherapeutics/

  1. Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

https://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle-              metabolism-provides-homeomeostatic-regulation/

Metabolic Pathways

  1. Pentose Shunt, Electron Transfer, Galactose, more Lipids in brief

Reviewer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/21/pentose-shunt-electron-transfer-galactose-more-lipids-in-brief/

  1. Mitochondria: More than just the “powerhouse of the cell”

Ritu Saxena, PhD

https://pharmaceuticalintelligence.com/2012/07/09/mitochondria-more-than-just-the-powerhouse-of-the-cell/

  1. Mitochondrial fission and fusion: potential therapeutic targets?

Ritu saxena

https://pharmaceuticalintelligence.com/2012/10/31/mitochondrial-fission-and-fusion-potential-therapeutic-target/

4.  Mitochondrial mutation analysis might be “1-step” away

Ritu Saxena

https://pharmaceuticalintelligence.com/2012/08/14/mitochondrial-mutation-analysis-might-be-1-step-away/

  1. Selected References to Signaling and Metabolic Pathways in PharmaceuticalIntelligence.com

Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/14/selected-references-to-signaling-and-metabolic-pathways-in-                     leaders-in-pharmaceutical-intelligence/

  1. Metabolic drivers in aggressive brain tumors

Prabodh Kandal, PhD

https://pharmaceuticalintelligence.com/2012/11/11/metabolic-drivers-in-aggressive-brain-tumors/

  1. Metabolite Identification Combining Genetic and Metabolic Information: Genetic association links unknown metabolites to functionally related genes

Writer and Curator, Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/10/22/metabolite-identification-combining-genetic-and-metabolic-                        information-genetic-association-links-unknown-metabolites-to-functionally-related-genes/

  1. Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation

Larry H Bernstein, MD, FCAP, author and curator

https://pharmaceuticalintelligence.com/2012/09/26/mitochondria-origin-from-oxygen-free-environment-role-in-aerobic-            glycolysis-metabolic-adaptation/

  1. Therapeutic Targets for Diabetes and Related Metabolic Disorders

Reporter, Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/08/20/therapeutic-targets-for-diabetes-and-related-metabolic-disorders/

10.  Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

https://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle-              metabolism-provides-homeomeostatic-regulation/

11. The multi-step transfer of phosphate bond and hydrogen exchange energy

Larry H. Bernstein, MD, FCAP, Curator:

https://pharmaceuticalintelligence.com/2014/08/19/the-multi-step-transfer-of-phosphate-bond-and-hydrogen-                          exchange-energy/

12. Studies of Respiration Lead to Acetyl CoA

https://pharmaceuticalintelligence.com/2014/08/18/studies-of-respiration-lead-to-acetyl-coa/

13. Lipid Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/15/lipid-metabolism/

14. Carbohydrate Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/13/carbohydrate-metabolism/

15. Update on mitochondrial function, respiration, and associated disorders

Larry H. Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated-                   disorders/

16. Prologue to Cancer – e-book Volume One – Where are we in this journey?

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/04/13/prologue-to-cancer-ebook-4-where-are-we-in-this-journey/

17. Introduction – The Evolution of Cancer Therapy and Cancer Research: How We Got Here?

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/04/04/introduction-the-evolution-of-cancer-therapy-and-cancer-research-          how-we-got-here/

18. Inhibition of the Cardiomyocyte-Specific Kinase TNNI3K

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/11/01/inhibition-of-the-cardiomyocyte-specific-kinase-tnni3k/

19. The Binding of Oligonucleotides in DNA and 3-D Lattice Structures

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/05/15/the-binding-of-oligonucleotides-in-dna-and-3-d-lattice-structures/

20. Mitochondrial Metabolism and Cardiac Function

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-metabolism-and-cardiac-function/

21. How Methionine Imbalance with Sulfur-Insufficiency Leads to Hyperhomocysteinemia

Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/04/04/sulfur-deficiency-leads_to_hyperhomocysteinemia/

22. AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Author and Curator: Stephen J. Williams, PhD

https://pharmaceuticalintelligence.com/2013/03/12/ampk-is-a-negative-regulator-of-the-warburg-effect-and-suppresses-         tumor-growth-in-vivo/

23. A Second Look at the Transthyretin Nutrition Inflammatory Conundrum

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/12/03/a-second-look-at-the-transthyretin-nutrition-inflammatory-                         conundrum/

24. Mitochondrial Damage and Repair under Oxidative Stress

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

25. Nitric Oxide and Immune Responses: Part 2

Author and Curator: Aviral Vatsa, PhD, MBBS

https://pharmaceuticalintelligence.com/2012/10/28/nitric-oxide-and-immune-responses-part-2/

26. Overview of Posttranslational Modification (PTM)

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/29/overview-of-posttranslational-modification-ptm/

27. Malnutrition in India, high newborn death rate and stunting of children age under five years

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/15/malnutrition-in-india-high-newborn-death-rate-and-stunting-of-                   children-age-under-five-years/

28. Update on mitochondrial function, respiration, and associated disorders

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated-                  disorders/

29. Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

Larry H. Bernstein, MD, FCAP, Curator

https://pharmaceuticalintelligence.com/2014/07/06/omega-3-fatty-acids-depleting-the-source-and-protein-insufficiency-         in-renal-disease/

30. Introduction to e-Series A: Cardiovascular Diseases, Volume Four Part 2: Regenerative Medicine

Larry H. Bernstein, MD, FCAP, writer, and Aviva Lev- Ari, PhD, RN

https://pharmaceuticalintelligence.com/2014/04/27/larryhbernintroduction_to_cardiovascular_diseases-                                  translational_medicine-part_2/

31. Epilogue: Envisioning New Insights in Cancer Translational Biology
Series C: e-Books on Cancer & Oncology

Author & Curator: Larry H. Bernstein, MD, FCAP, Series C Content Consultant

https://pharmaceuticalintelligence.com/2014/03/29/epilogue-envisioning-new-insights/

32. Ca2+-Stimulated Exocytosis:  The Role of Calmodulin and Protein Kinase C in Ca2+ Regulation of Hormone                         and Neurotransmitter

Writer and Curator: Larry H Bernstein, MD, FCAP and
Curator and Content Editor: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/12/23/calmodulin-and-protein-kinase-c-drive-the-ca2-regulation-of-                    hormone-and-neurotransmitter-release-that-triggers-ca2-stimulated-exocy

33. Cardiac Contractility & Myocardial Performance: Therapeutic Implications of Ryanopathy (Calcium Release-                           related Contractile Dysfunction) and Catecholamine Responses

Author, and Content Consultant to e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC
Author and Curator: Larry H Bernstein, MD, FCAP
and Article Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/08/28/cardiac-contractility-myocardium-performance-ventricular-arrhythmias-      and-non-ischemic-heart-failure-therapeutic-implications-for-cardiomyocyte-ryanopathy-calcium-release-related-                    contractile/

34. Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

Author and Curator: Larry H Bernstein, MD, FCAP Author: Stephen Williams, PhD, and Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/08/26/role-of-calcium-the-actin-skeleton-and-lipid-structures-in-signaling-and-cell-motility/

35. Identification of Biomarkers that are Related to the Actin Cytoskeleton

Larry H Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2012/12/10/identification-of-biomarkers-that-are-related-to-the-actin-                           cytoskeleton/

36. Advanced Topics in Sepsis and the Cardiovascular System at its End Stage

Author: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/08/18/advanced-topics-in-Sepsis-and-the-Cardiovascular-System-at-its-              End-Stage/

37. The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

Demet Sag, PhD, Author and Curator

https://pharmaceuticalintelligence.com/2013/08/04/the-delicate-connection-ido-indolamine-2-3-dehydrogenase-and-               immunology/

38. IDO for Commitment of a Life Time: The Origins and Mechanisms of IDO, indolamine 2, 3-dioxygenase

Demet Sag, PhD, Author and Curator

https://pharmaceuticalintelligence.com/2013/08/04/ido-for-commitment-of-a-life-time-the-origins-and-mechanisms-of-             ido-indolamine-2-3-dioxygenase/

39. Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Homeostasis of Immune Responses for Good and Bad

Curator: Demet Sag, PhD, CRA, GCP

https://pharmaceuticalintelligence.com/2013/07/31/confined-indolamine-2-3-dehydrogenase-controls-the-hemostasis-           of-immune-responses-for-good-and-bad/

40. Signaling Pathway that Makes Young Neurons Connect was discovered @ Scripps Research Institute

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/06/26/signaling-pathway-that-makes-young-neurons-connect-was-                     discovered-scripps-research-institute/

41. Naked Mole Rats Cancer-Free

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/06/20/naked-mole-rats-cancer-free/

42. Late Onset of Alzheimer’s Disease and One-carbon Metabolism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

https://pharmaceuticalintelligence.com/2013/05/06/alzheimers-disease-and-one-carbon-metabolism/

43. Problems of vegetarianism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

https://pharmaceuticalintelligence.com/2013/04/22/problems-of-vegetarianism/

44.  Amyloidosis with Cardiomyopathy

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/03/31/amyloidosis-with-cardiomyopathy/

45. Liver endoplasmic reticulum stress and hepatosteatosis

Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2013/03/10/liver-endoplasmic-reticulum-stress-and-hepatosteatosis/

46. The Molecular Biology of Renal Disorders: Nitric Oxide – Part III

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/11/26/the-molecular-biology-of-renal-disorders/

47. Nitric Oxide Function in Coagulation – Part II

Curator and Author: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/11/26/nitric-oxide-function-in-coagulation/

48. Nitric Oxide, Platelets, Endothelium and Hemostasis

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/11/08/nitric-oxide-platelets-endothelium-and-hemostasis/

49. Interaction of Nitric Oxide and Prostacyclin in Vascular Endothelium

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/09/14/interaction-of-nitric-oxide-and-prostacyclin-in-vascular-endothelium/

50. Nitric Oxide and Immune Responses: Part 1

Curator and Author:  Aviral Vatsa PhD, MBBS

https://pharmaceuticalintelligence.com/2012/10/18/nitric-oxide-and-immune-responses-part-1/

51. Nitric Oxide and Immune Responses: Part 2

Curator and Author:  Aviral Vatsa PhD, MBBS

https://pharmaceuticalintelligence.com/2012/10/28/nitric-oxide-and-immune-responses-part-2/

52. Mitochondrial Damage and Repair under Oxidative Stress

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

53. Is the Warburg Effect the cause or the effect of cancer: A 21st Century View?

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/10/17/is-the-warburg-effect-the-cause-or-the-effect-of-cancer-a-21st-                 century-view/

54. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                  proteolysis-and-cell-apoptosis/

55. Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2013/02/14/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                   proteolysis-and-cell-apoptosis-reconsidered/

56. Nitric Oxide and iNOS have Key Roles in Kidney Diseases – Part II

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/11/26/nitric-oxide-and-inos-have-key-roles-in-kidney-diseases/

57. New Insights on Nitric Oxide donors – Part IV

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/11/26/new-insights-on-no-donors/

58. Crucial role of Nitric Oxide in Cancer

Curator and Author: Ritu Saxena, Ph.D.

https://pharmaceuticalintelligence.com/2012/10/16/crucial-role-of-nitric-oxide-in-cancer/

59. Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/09/16/nitric-oxide-has-a-ubiquitous-role-in-the-regulation-of-glycolysis-with-         a-concomitant-influence-on-mitochondrial-function/

60. Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

Curator and Author: Ziv Raviv, PhD, RN 04/06/2013

https://pharmaceuticalintelligence.com/2013/04/06/targeting-mitochondrial-bound-hexokinase-for-cancer-therapy/

61. Biochemistry of the Coagulation Cascade and Platelet Aggregation – Part I

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/11/26/biochemistry-of-the-coagulation-cascade-and-platelet-aggregation/

Genomics, Transcriptomics, and Epigenetics

  1. What is the meaning of so many RNAs?

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/06/what-is-the-meaning-of-so-many-rnas/

  1. RNA and the transcription the genetic code

Larry H. Bernstein, MD, FCAP, Writer and Curator

https://pharmaceuticalintelligence.com/2014/08/02/rna-and-the-transcription-of-the-genetic-code/

  1. A Primer on DNA and DNA Replication

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/29/a_primer_on_dna_and_dna_replication/

4. Synthesizing Synthetic Biology: PLOS Collections

Reporter: Aviva Lev-Ari

https://pharmaceuticalintelligence.com/2012/08/17/synthesizing-synthetic-biology-plos-collections/

5. Pathology Emergence in the 21st Century

Author and Curator: Larry Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/03/pathology-emergence-in-the-21st-century/

6. RNA and the transcription the genetic code

Writer and Curator, Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/02/rna-and-the-transcription-of-the-genetic-code/

7. A Great University engaged in Drug Discovery: University of Pittsburgh

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2014/07/15/a-great-university-engaged-in-drug-discovery/

8. microRNA called miRNA-142 involved in the process by which the immature cells in the bone  marrow give                              rise to all the types of blood cells, including immune cells and the oxygen-bearing red blood cells

Aviva Lev-Ari, PhD, RN, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/24/microrna-called-mir-142-involved-in-the-process-by-which-the-                   immature-cells-in-the-bone-marrow-give-rise-to-all-the-types-of-blood-cells-including-immune-cells-and-the-oxygen-             bearing-red-blood-cells/

9. Genes, proteomes, and their interaction

Larry H. Bernstein, MD, FCAP, Writer and Curator

https://pharmaceuticalintelligence.com/2014/07/28/genes-proteomes-and-their-interaction/

10. Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator    Aviva Lev-Ari, PhD, RN, Curator

https://pharmaceuticalintelligence.com/2014/07/29/regulation-of-somatic-stem-cell-function/

11. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

https://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in-           adult-organisms/

12. Bzzz! Are fruitflies like us?

Larry H Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/07/bzzz-are-fruitflies-like-us/

13. Long Non-coding RNAs Can Encode Proteins After All

Larry H Bernstein, MD, FCAP, Reporter

https://pharmaceuticalintelligence.com/2014/06/29/long-non-coding-rnas-can-encode-proteins-after-all/

14. Michael Snyder @Stanford University sequenced the lymphoblastoid transcriptomes and developed an
allele-specific full-length transcriptome

Aviva Lev-Ari, PhD, RN, Author and Curator

https://pharmaceuticalintelligence.com/014/06/23/michael-snyder-stanford-university-sequenced-the-lymphoblastoid-            transcriptomes-and-developed-an-allele-specific-full-length-transcriptome/

15. Commentary on Biomarkers for Genetics and Genomics of Cardiovascular Disease: Views by Larry H                                     Bernstein, MD, FCAP

Author: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/16/commentary-on-biomarkers-for-genetics-and-genomics-of-                        cardiovascular-disease-views-by-larry-h-bernstein-md-fcap/

16. Observations on Finding the Genetic Links in Common Disease: Whole Genomic Sequencing Studies

Author an curator: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/05/18/observations-on-finding-the-genetic-links/

17. Silencing Cancers with Synthetic siRNAs

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

https://pharmaceuticalintelligence.com/2013/12/09/silencing-cancers-with-synthetic-sirnas/

18. Cardiometabolic Syndrome and the Genetics of Hypertension: The Neuroendocrine Transcriptome Control Points

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/12/12/cardiometabolic-syndrome-and-the-genetics-of-hypertension-the-neuroendocrine-transcriptome-control-points/

19. Developments in the Genomics and Proteomics of Type 2 Diabetes Mellitus and Treatment Targets

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

https://pharmaceuticalintelligence.com/2013/12/08/developments-in-the-genomics-and-proteomics-of-type-2-diabetes-           mellitus-and-treatment-targets/

20. Loss of normal growth regulation

Larry H Bernstein, MD, FCAP, Curator

https://pharmaceuticalintelligence.com/2014/07/06/loss-of-normal-growth-regulation/

21. CT Angiography & TrueVision™ Metabolomics (Genomic Phenotyping) for new Therapeutic Targets to Atherosclerosis

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/11/15/ct-angiography-truevision-metabolomics-genomic-phenotyping-for-           new-therapeutic-targets-to-atherosclerosis/

22.  CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics & Computational Genomics

Genomics Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/30/cracking-the-code-of-human-life-the-birth-of-bioinformatics-                      computational-genomics/

23. Big Data in Genomic Medicine

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/12/17/big-data-in-genomic-medicine/

24. From Genomics of Microorganisms to Translational Medicine

Author and Curator: Demet Sag, PhD

https://pharmaceuticalintelligence.com/2014/03/20/without-the-past-no-future-but-learn-and-move-genomics-of-                      microorganisms-to-translational-medicine/

25. Summary of Genomics and Medicine: Role in Cardiovascular Diseases

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/01/06/summary-of-genomics-and-medicine-role-in-cardiovascular-diseases/

 26. Genomic Promise for Neurodegenerative Diseases, Dementias, Autism Spectrum, Schizophrenia, and Serious                      Depression

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/02/19/genomic-promise-for-neurodegenerative-diseases-dementias-autism-        spectrum-schizophrenia-and-serious-depression/

 27.  BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

Sudipta Saha, PhD

https://pharmaceuticalintelligence.com/2012/12/04/brca1-a-tumour-suppressor-in-breast-and-ovarian-cancer-functions-         in-transcription-ubiquitination-and-dna-repair/

28. Personalized medicine gearing up to tackle cancer

Ritu Saxena, PhD

https://pharmaceuticalintelligence.com/2013/01/07/personalized-medicine-gearing-up-to-tackle-cancer/

29. Differentiation Therapy – Epigenetics Tackles Solid Tumors

Stephen J Williams, PhD

      https://pharmaceuticalintelligence.com/2013/01/03/differentiation-therapy-epigenetics-tackles-solid-tumors/

30. Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment

     Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/17/mechanism-involved-in-breast-cancer-cell-growth-function-in-early-          detection-treatment/

31. The Molecular pathology of Breast Cancer Progression

Tilde Barliya, PhD

https://pharmaceuticalintelligence.com/2013/01/10/the-molecular-pathology-of-breast-cancer-progression

32. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-                   signatures-2/

33. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine –                                                       Part 1 (pharmaceuticalintelligence.com)

Aviva  Lev-Ari, PhD, RN

http://pharmaceuticalntelligence.com/2013/01/13/paradigm-shift-in-human-genomics-predictive-biomarkers-and-personalized-medicine-part-1/

34. LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer                                         Personalized Treatment: Part 2

A Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-       drug-selection-in-cancer-personalized-treatment-part-2/

35. Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-        research-part-3/

36. Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of                           Cancer Scientific Leaders @http://pharmaceuticalintelligence.com

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/13/7000/Harnessing_Personalized_Medicine_for_ Cancer_Management-      Prospects_of_Prevention_and_Cure/

37.  GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico
effect of the inhibitor in its “virtual clinical trial”

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2012/11/14/gsk-for-personalized-medicine-using-cancer-drugs-needs-alacris-             systems-biology-model-to-determine-the-in-silico-effect-of-the-inhibitor-in-its-virtual-clinical-trial/

38. Personalized medicine-based cure for cancer might not be far away

Ritu Saxena, PhD

  https://pharmaceuticalintelligence.com/2012/11/20/personalized-medicine-based-cure-for-cancer-might-not-be-far-away/

39. Human Variome Project: encyclopedic catalog of sequence variants indexed to the human genome sequence

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2012/11/24/human-variome-project-encyclopedic-catalog-of-sequence-variants-         indexed-to-the-human-genome-sequence/

40. Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/10/inspiration-from-dr-maureen-cronins-achievements-in-applying-                genomic-sequencing-to-cancer-diagnostics/

41. The “Cancer establishments” examined by James Watson, co-discoverer of DNA w/Crick, 4/1953

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/09/the-cancer-establishments-examined-by-james-watson-co-discover-         of-dna-wcrick-41953/

42. What can we expect of tumor therapeutic response?

Author and curator: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/12/05/what-can-we-expect-of-tumor-therapeutic-response/

43. Directions for genomics in personalized medicine

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/01/27/directions-for-genomics-in-personalized-medicine/

44. How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis.

Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/2012/10/31/how-mobile-elements-in-junk-dna-prote-cancer-part1-transposon-            mediated-tumorigenesis/

45. mRNA interference with cancer expression

Author and Curator, Larry H. Bernstein, MD, FCAP

 https://pharmaceuticalintelligence.com/2012/10/26/mrna-interference-with-cancer-expression/

46. Expanding the Genetic Alphabet and linking the genome to the metabolome

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-               metabolome/

47. Breast Cancer, drug resistance, and biopharmaceutical targets

Author and Curator: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/09/18/breast-cancer-drug-resistance-and-biopharmaceutical-targets/

48.  Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression                            Analysis

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/12/24/breast-cancer-genomic-profiling-to-predict-survival-combination-of-           histopathology-and-gene-expression-analysis

49. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva  Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-                   signatures-2/

50. Genomic Analysis: FLUIDIGM Technology in the Life Science and Agricultural Biotechnology

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/08/22/genomic-analysis-fluidigm-technology-in-the-life-science-and-                   agricultural-biotechnology/

51. 2013 Genomics: The Era Beyond the Sequencing Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2013_Genomics

52. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/Paradigm Shift in Human Genomics_/

Signaling Pathways

  1. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Curator

https://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

  1. A Synthesis of the Beauty and Complexity of How We View Cancer:
    Cancer Volume One – Summary

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/03/26/a-synthesis-of-the-beauty-and-complexity-of-how-we-view-cancer/

  1. Recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes in
    serous endometrial tumors

Sudipta Saha, PhD

https://pharmaceuticalintelligence.com/2012/11/19/recurrent-somatic-mutations-in-chromatin-remodeling-ad-ubiquitin-           ligase-complex-genes-in-serous-endometrial-tumors/

4.  Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition

Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/2012/11/30/histone-deacetylase-inhibitors-induce-epithelial-to-mesenchymal-              transition-in-prostate-cancer-cells/

5. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Author and Curator: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                   proteolysis-and-cell-apoptosis/

6. Signaling and Signaling Pathways

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2014/08/12/signaling-and-signaling-pathways/

7.  Leptin signaling in mediating the cardiac hypertrophy associated with obesity

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2013/11/03/leptin-signaling-in-mediating-the-cardiac-hypertrophy-associated-            with-obesity/

  1. Sensors and Signaling in Oxidative Stress

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2013/11/01/sensors-and-signaling-in-oxidative-stress/

  1. The Final Considerations of the Role of Platelets and Platelet Endothelial Reactions in Atherosclerosis and Novel
    Treatments

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2013/10/15/the-final-considerations-of-the-role-of-platelets-and-platelet-                      endothelial-reactions-in-atherosclerosis-and-novel-treatments

10.   Platelets in Translational Research – Part 1

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2013/10/07/platelets-in-translational-research-1/

11.  Disruption of Calcium Homeostasis: Cardiomyocytes and Vascular Smooth Muscle Cells: The Cardiac and
Cardiovascular Calcium Signaling Mechanism

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to e-SERIES A:
Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/09/12/disruption-of-calcium-homeostasis-cardiomyocytes-and-vascular-             smooth-muscle-cells-the-cardiac-and-cardiovascular-calcium-signaling-mechanism/

12. The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and
Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia,
Similarities and Differences, and Pharmaceutical Targets

     Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to
e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and
Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/09/08/the-centrality-of-ca2-signaling-and-cytoskeleton-involving-calmodulin-       kinases-and-ryanodine-receptors-in-cardiac-failure-arterial-smooth-muscle-post-ischemic-arrhythmia-similarities-and-           differen/

13.  Nitric Oxide Signalling Pathways

Aviral Vatsa, PhD, MBBS

https://pharmaceuticalintelligence.com/2012/08/22/nitric-oxide-signalling-pathways/

14. Immune activation, immunity, antibacterial activity

Larry H. Bernstein, MD, FCAP, Curator

https://pharmaceuticalintelligence.com/2014/07/06/immune-activation-immunity-antibacterial-activity/

15.  Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator    Aviva Lev-Ari, PhD, RN, Curator

https://pharmaceuticalintelligence.com/2014/07/29/regulation-of-somatic-stem-cell-function/

16. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

https://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in-adult-organisms/

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Blood Pressure Response to Antihypertensives: Hypertension Susceptibility Loci Study

Reporter: Aviva Lev-Ari, PhD, RN

 

Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives

Results From the Pharmacogenomic Evaluation of Antihypertensive Responses Study

Yan Gong, PhD, Caitrin W. McDonough, PhD, Zhiying Wang, MS, Wei Hou, PhD,Rhonda M. Cooper-DeHoff, PharmD, MS, Taimour Y. Langaee, PhD, Amber L. Beitelshees, PharmD, MPH, Arlene B. Chapman, MD, John G. Gums, PharmD, Kent R. Bailey, PhD, Eric Boerwinkle, PhD, Stephen T. Turner, MD and Julie A. Johnson, PharmD

Author Affiliations

From the Department of Pharmacotherapy and Translational Research (Y.G., C.W.M., R.M.C.-D., T.Y.L., J.G.G., J.A.J.), Department of Biostatistics, College of Medicine (W.H.), Division of Cardiovascular Medicine, College of Medicine (R.M.C.-D., J.A.J.), and Department of Community Health and Family Medicine (J.G.G.), University of Florida, Gainesville, FL; Division of Epidemiology, University of Texas at Houston, Houston, TX (Z.W., E.B.); Division of Endocrinology, Diabetes and Nutrition, University of Maryland, Baltimore, MD (A.L.B.); Renal Division, Emory University, Atlanta, GA (A.B.C.); and Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN (S.T.T.).

Correspondence to Yan Gong, PhD, Department of Pharmacotherapy and Translational Research, University of Florida, PO Box 100486, 1600 SW Archer Rd, Gainesville, FL 32610. E-mail gong@cop.ufl.edu.

Abstract

Background—To date, 39 single nucleotide polymorphisms (SNPs) have been associated with blood pressure (BP) or hypertension in genome-wide association studies in whites. Our hypothesis is that the loci/SNPs associated with BP/hypertension are also associated with BP response to antihypertensive drugs.

Methods and Results—We assessed the association of these loci with BP response to atenolol or hydrochlorothiazide monotherapy in 768 hypertensive participants in the Pharmacogenomics Responses of Antihypertensive Responses study. Linear regression analysis was performed on whites for each SNP in an additive model adjusting for baseline BP, age, sex, and principal components for ancestry. Genetic scores were constructed to include SNPs with nominal associations, and empirical Pvalues were determined by permutation test. Genotypes of 37 loci were obtained from Illumina 50K cardiovascular or Omni1M genome-wide association study chips. In whites, no SNPs reached Bonferroni-corrected α of 0.0014, 6 reached nominal significance (P<0.05), and 3 were associated with atenolol BP response at P<0.01. The genetic score of the atenolol BP-lowering alleles was associated with response to atenolol (P=3.3×10–6 for systolic BP; P=1.6×10–6 for diastolic BP). The genetic score of the hydrochlorothiazide BP-lowering alleles was associated with response to hydrochlorothiazide (P=0.0006 for systolic BP; P=0.0003 for diastolic BP). Both risk score P values were <0.01 based on the empirical distribution from the permutation test.

Conclusions—These findings suggest that selected signals from hypertension genome-wide association studies may predict BP response to atenolol and hydrochlorothiazide when assessed through risk scoring.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 686-691

Published online before print October 19, 2012,

doi: 10.1161/ CIRCGENETICS.112.964080

 

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Genomics of Incident Ischemic Stroke Events, Stroke and Cardiovascular Disease

Reporter: Aviva Lev-Ari, PhD, RN

 

Associations Between Incident Ischemic Stroke Events and Stroke and Cardiovascular Disease-Related Genome-Wide Association Studies Single Nucleotide Polymorphisms in the Population Architecture Using Genomics and Epidemiology Study

Cara L. Carty, PhD, Petra Bůžková, PhD, Myriam Fornage, PhD, Nora Franceschini, MD, Shelley Cole, PhD, Gerardo Heiss, MD, PhD, Lucia A. Hindorff, PhD, MPH, Barbara V. Howard, PhD, Sue Mann, MPH, Lisa W. Martin, MD, Ying Zhang, PhD, Tara C. Matise, PhD, Ross Prentice, PhD, Alexander P. Reiner, MD, MS and Charles Kooperberg, PhD

Author Affiliations

From the Public Health Sciences, Fred Hutchinson Cancer Research Center (C.L.C., S.M., R.P., C.K.); Department of Biostatistics, University of Washington, Seattle, WA (P.B.); Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX (M.F.); Division of Epidemiology, School of Public Health, University of Texas Health Sciences Center, Houston, TX (M.F.); Department of Epidemiology, University of North Carolina, Chapel Hill, NC (N.F., G.H.); Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (S.C.); Office of Population Genomics, National Human Genome Research Institute, Bethesda, MD (L.A.H.); Medstar Health Research Institute, Washington, DC (B.V.H.); George Washington University School of Medicine, Washington, DC (B.V.H., L.W.M.); University of Oklahoma Health Sciences Center, Oklahoma City, OK (Y.Z.); Department of Genetics, Rutgers University, Piscataway, NJ (T.C.M.); Department of Epidemiology, University of Washington, Seattle, WA (A.P.R.).

Correspondence to Dr Cara L. Carty, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N./M3-A410, Seattle, WA 98109. E-mail ccarty@fhcrc.org

Abstract

Background—Genome-wide association studies (GWAS) have identified loci associated with ischemic stroke (IS) and cardiovascular disease (CVD) in European-descent individuals, but their replication in different populations has been largely unexplored.

Methods and Results—Nine single nucleotide polymorphisms (SNPs) selected from GWAS and meta-analyses of stroke, and 86 SNPs previously associated with myocardial infarction and CVD risk factors, including blood lipids (high density lipoprotein [HDL], low density lipoprotein [LDL], and triglycerides), type 2 diabetes, and body mass index (BMI), were investigated for associations with incident IS in European Americans (EA) N=26 276, African-Americans (AA) N=8970, and American Indians (AI) N=3570 from the Population Architecture using Genomicsand Epidemiology Study. Ancestry-specific fixed effects meta-analysis with inverse variance weighting was used to combine study-specific log hazard ratios from Cox proportional hazards models. Two of 9 stroke SNPs (rs783396 and rs1804689) were associated with increased IS hazard in AA; none were significant in this large EA cohort. Of 73 CVD risk factor SNPs tested in EA, 2 (HDL and triglycerides SNPs) were associated with IS. In AA, SNPs associated with LDL, HDL, and BMI were significantly associated with IS (3 of 86 SNPs tested). Out of 58 SNPs tested in AI, 1 LDL SNP was significantly associated with IS.

Conclusions—Our analyses showing lack of replication in spite of reasonable power for many stroke SNPs and differing results by ancestry highlight the need to follow up on GWAS findings and conduct genetic association studies in diverse populations. We found modest IS associations with BMI and lipids SNPs, though these findings require confirmation.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 210-216

 

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Cardiovascular Genetics: Functional Characterization and Clinical Applications  @ 2013 Annual Conference of American Society of Human Genetics in Boston, 10/22-26, 2013

Reporter: Aviva Lev- Ari, PhD, RN

Sessions and Events 

The 63rd Annual Conference of American Society of Human Genetics in Boston, 10/22-26, 2013

http://www.ashg.org/cgi-bin/2013/ashg13SOE.pl 

PLATFORM ABSTRACTS

http://www.ashg.org/2013meeting/pdf/46025_Platform_bookmark%20for%20Web%20Final%20from%20AGS.pdf

We express a special interest in Session 58

Friday, October 25, 2013 Boston Convention Center 

2:00 PM–4:15 PM

Concurrent Platform (abstract-driven) Session E (54-62)

SESSION 58 – Cardiovascular Genetics: Functional Characterization and Clinical Applications

Room 205, Level 2, Convention Center

Moderators: Dan E. Arking, Johns Hopkins Univ. Sch. of Med.
Myriam Fornage, Univ. of Texas Hlth Sci. Ctr. at Houston

Human Syndromic Atrioventricular Septal Defect

367/2:00 A homozygous mutation in Smoothened, a member of the Sonic hedgehog (SHH)-GLI pathway is involved in human syndromic atrioventricular septal defect. W. S. Kerstjens-Frederikse, Y. Sribudiani, M. E. Baardman, L. M. A. Van Unen, R. Brouwer, M. van den Hout, C. Kockx, W. Van IJcken, A. J. Van Essen, P. A. Van Der Zwaag, G. J. Du Marchie Sarvaas, R. M. F. Berger, F. W. Verheijen, R. M. W. Hofstra.

A homozygous mutation in Smoothened, a member of the Sonic Hedgehog (SHH)-GLI pathway is involved in human syndromic atrioventricular septal defect.

W.S. Kerstjens-Frederikse1, Y. Sribudiani2, M.E. Baardman1, L.M.A. Van Unen2, R. Brouwer2, M. van den Hout2, C. Kockx2, W. Van IJcken2, A.J. Van Essen1, P.A. Van Der Zwaag1, G.J. Du Marchie

Sarvaas3, R.M.F. Berger3, F.W. Verheijen2, R.M.W. Hofstra2.

1) Dept Gen, Univ of Groningen, Univ Med Ctr Groningen, Netherlands;

2) Dept Gen, Erasmus Med Ctr, Rotterdam, Netherlands; 3) Dept Ped Cardiol, Univ of Groningen, Univ Med Ctr Groningen, Netherlands.

Introduction: Atrioventricular septal defect (AVSD) is a common congenital heart disease with a high impact on personal health. It is often accompanied by other congenital anomalies and in many of these syndromic AVSDs, defects in the sonic hedgehog (SHH)-GLI signalling pathway have been detected. SMO codes for the transmembrane protein smoothened (SMO), which is active in cells with a primary cilium and is located on the ciliary membrane. SMO is a key protein in the SHH-GLI signaling cascade.

Methods: Two probands, a twin boy and girl, presented with an AVSD, large fontanel, postaxial polydactyly and skin syndactyly of the second and third toes of both feet. The boy also had hypospadias. The parents were consanguineous and they had one healthy older child. Karyotyping was normal and Smith-Lemli-Opitz syndrome (SLOS) was excluded. Exome sequencing was performed and candidate variants were validated by Sanger sequencing.

Results: A novel homozygous missense mutation c.1725C>T (p.R575W) in SMO (7q32.3) was detected. Functional studies in fibroblasts of the patients showed normal expression of SMO protein but an abnormal localization of SMO, outside the cilia. Moreover we show severely reduced downstream GLI1 mRNA expression after stimulation with the SMO agonist purmorphamine. These results, together with the previously described association of SHH signalling defects with AVSD and SLOS, suggest that this SMO mutation is involved in syndromic AVSD in these patients.

Conclusion: We present the first reported smoothened mutation in humans, in two patients with an AVSD and a phenotype resembling Smith-Lemli-Opitz syndrome

Left Ventricular Noncompaction – Model in Zebrafish

368/2:15 Identification of PRDM16 as a disease gene for left ventricular non-compaction and the efficient generation of a personalized disease model in zebrafish. A.-K. Arndt, S. Schaefer, R. Siebert, S. A. Cook, H.-H. Kramer, S. Klaassen, C. A. MacRae.

 

Identification of PRDM16 as a disease gene for left ventricular noncompaction

and the efficient generation of a personalized disease

model in zebrafish. A.-K. Arndt1,2, S. Schaefer3, R. Siebert4, S.A. Cook5,

H.-H. Kramer2, S. Klaassen6, C.A. MacRae1. 

1) Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA;

2) Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig- Holstein, Kiel, Germany,;

3) Max-Delbruck-Center for Molecular Medicine, Berlin, Germany; 4) Institute of Human Genetics, University Hospital Schleswig Holstein, Kiel, Germany;

5) National Heart Centre, Singapore;

6) Department of Pediatric Cardiology, Charité, Berlin, Germany.

Using our own data and publically available array comparative genomic hybridization data, we identified the transcription factor PRDM16(PR domain containing 16) as a causal gene for the cardiomyopathy associated with monosomy 1p36, and confirmed its role in individuals with non-syndromic left ventricular noncompaction cardiomyopathy (LVNC) and dilated cardiomyopathy (DCM). In a cohort of 75 non-syndromic patients with LVNC we detected 3 sporadic mutations, including 1 truncation mutant, 1 frameshift null mutation, and a single missense mutant. In addition, in a series of cardiac biopsies from 131 individuals with DCM, we found 5 individuals with 4 previously unreported non-synonymous variants in the coding region of PRDM16. None of the PRDM16 mutations identified were observed in over 6500 controls.

PRDM16 has not previously been associated with cardiovascular disease. Modeling of PRDM16 haploinsufficiency and a human truncation mutant in zebrafish resulted in impaired cardiomyocyte proliferation with associated physiologic defects in cardiac contractility and cell-cell coupling.

Using a phenotype-driven screening approach in the fish, we have identified 5 compounds that are able to rescue the physiologic defects associated with mutant or haploinsufficient PRDM16. Notably, all of the compounds had the capacity to restore cardiomyocyte proliferation and to prevent apoptosis in the model. Wildtype zebrafish also demonstrated a significant increase in cardiomyocyte numbers after treatment with the compounds suggesting a pro-proliferative effect of the compounds. In addition, the compounds also rescued the contractile and electrical defects observed in these disease models. These findings underline the importance of personalized disease models for specific pathways, to accelerate the exploration of disease biology and the development of innovative therapeutic approaches.

Genetics of Cerebral Small Vessel Disease

369/2:30 Mutation and copy number variation of FOXC1 causes cerebral small vessel disease. C. R. French, S. Seshadri, A. L. Destefano, M. Fornage, D. J. Emery, M. Hofker, J. Fu, A. J. Waskiewicz, O. J. Lehmann.

Mutation and copy number variation of FOXC1 causes cerebral small vessel disease. C.R. French1, S. Seshadri2, A.L Destefano3, M. Fornage4, D.J. Emery5, M. Hofker6, J. Fu6, A.J. Waskiewicz7, O.J. Lehmann1, 8.

1) Ophthalmology, University of Alberta, Edmonton, AB, Canada;

2) Department of Neurology, Boston University, Boston, MA, U. S. A;

3) School of Public Health, Boston University, Boston, MA, U. S. A;

4) Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences

Center, Houston, TX, U.S.A;

5) Department of Radiology, University of Alberta, Edmonton, AB, Canada;

6) Department of Medical Genetics, University Medical Center Groningen, Groningen, The Netherlands;

7) Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada;

8) Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.

Cerebral small vessel disease (CSVD) represents a major risk factor for stroke and cognitive decline in the elderly. The ability to readily visualize its microangiopathic features by magnetic resonance imaging provides opportunities for using markers of CSVD to identify novel stroke associated pathways. Using targeted genome-wide association analysis we identified CSVD associated single nucleotide polymorphisms (SNPs) adjacent to the forkhead transcription factor FOXC1, and using eQTL analysis in two independent data sets, demonstrate that such SNP’s are associated with FOXC1 expression levels.

We further demonstrate, using magnetic resonance imaging, that patients with either FOXC1 mutation or copy number variation exhibit CSVD. These findings, present in patients as young as two years of age and observed with missense and nonsense mutations as well as FOXC1-encompassing segmental deletion and duplication, demonstrate FOXC1 dysfunction induces cerebral small vessel pathology. A causative role for FOXC1 in the development and maintenance of cerebral vasculature is supported by the cerebral hemorrhage generated by morpholino-induced suppression of FOXC1 orthologs in a zebrafish model system. Furthermore, in vivo imaging demonstrates profoundly impaired migration of neural crest cells and their subsequent association with nascent vasculature, a process required for the differentiation of perivascular mural cells. In addition, foxc1 inhibition reduces the expression of pdgfra, a gene critically required for vascular stability via its role in mural cell recruitment. Taken together, these data support a requirement for Foxc1 in stabilizing newly formed vasculature via recruitment of neural crest derived mural cells, and define a casual role for FOXC1 in cerebrovascular pathology.

Genetics & Brugada Syndrome

370/2:45 Genetic association of common variants with a rare cardiac disease, the Brugada syndrome, in a multi-centric study. C. Dina, J. Barc, Y. Mizusawa, C. A. Remme, J. B. Gourraud, F. Simonet, P. J. Schwartz, L. Crotti, P. Guicheney, A. Leenhardt, C. Antzelevitch, E. Schulze-Bahr, E. R. Behr, J. Tfelt-Hansen, S. Kaab, H. Watanabe, M. Horie, N. Makita, W. Shimizu, P. Froguel, B. Balkau, M. Gessler, D. Roden, V. M. Christoffels, H. Le Marec, A. A. Wilde, V. Probst, J. J. Schott, R. Redon, C. R. Bezzina.

Genetic association of common variants with a rare cardiac disease,

the Brugada Syndrome, in a multi-centric study. C. Dina1,2, J. Barc3, Y.

Mizusawa3, C.A. Remme3, J.B. Gourraud1,2, F. Simonet1, P.J. Schwartz4,

L. Crotti4, P. Guicheney5, A. Leenhardt6, C. Antzelevitch7, E. Schulze-Bahr8,

E.R. Behr9, J. Tfelt-Hansen10, S. Kaab11, H. Watanabe12, M. Horie13, N.

Makita14, W. Shimizu15, P. Froguel 16, B. Balkau17, M. Gessler18, D.

Roden19, V.M. Christoffels3, H. Le Marec1,2, A.A. Wilde3, V. Probst1,2, J.J.

Schott1,2, R. Redon1,2, C.R. Bezzina3.

1) Thorx Inst, INSERM UMR 1087, CNRS, Nantes, France;

2) CHU Nantes, l’institut du thorax, Nantes, France;

3) Heart Failure Research Center, Academic Medical Center, Amsterdam, Netherlands;

4) University of Pavia, Pavia, Italy;

5) InsermUMR956, UPMC, Paris, France;

6) Cardiology Unit, Hôpital Bichat, Assistance Publique- Hôpitaux de Paris, Nantes, France;

7) Department of Experimental Cardiology, Masonic Medical Research Laboratory, Utica, NY, United States;

8) Department of Cardiovascular Medicine, University Hospital, Münster, Germany;

9) Cardiovascular Sciences Research Centre, St George’s University, London, United Kingdom;

10) Laboratory of Molecular Cardiology, University of Copenhagen, Copenhagen, Denmark;

11) 1Department of Medicine I, Ludwig-Maximilians University, Munich, Germany;

12) Department of Cardiovascular Biology and Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan;

13) Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan;

14) Department of Molecular Physiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan;

15) Division of Arrhythmia and Electrophysiology, Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan;

16) CNRS UMR 8199, Pasteur Institute, Lille, France;

17) Inserm UMR 1018, Centre for research in Epidemiology and Population Health, Villejuif, France;

18) Theodor-Boveri-Institute, University of Wuerzburg, Wuerzburg, Germany;

19) Department of Medicine and Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, United States.

The Brugada Syndrome (BrS) is considered as a rare Mendelian disorder with autosomal dominant transmission. BrS is associated with an increased risk of sudden cardiac death and specific electrocardiographic features consisting of ST-segment elevation in the right precordial leads. Loss-of-function mutations in SCN5A, encoding the pore-forming subunit of the cardiac sodium channel (Nav1.5), are identified in ~20% of patients. However, studies in families harbouring mutations in SCN5A have demonstrated low disease penetrance and in some instances absence of the familial SCN5A mutation in some affected members. These observations suggest a more complex inheritance model. To identify common genetic factors modulating disease risk, we conducted a genome-wide association study on 312 individuals with BrS and 1115 ancestry-matched controls. Two genomic regions displayed significant association. Both associations were replicated on two independent case/control sets from Europe (598/855) and Japan (208/1016) and a third locus emerged, all three with extremely significant p-values (1.10-14 down to 1.10-68). To our knowledge, this is the first time that several common variants are associated with a rare disease, with very high effect (Osdds-ratio) ranging from 1.58 to 2.55. While two loci displaying association hits had already been shown to influence ECG parameters in the general population, the third one encompasses a transcription factor which had never been related to cardiac arrhythmia. We showed that this factor regulates Nav1.5 channel expression in hearts of homozygous knockout embryos and influence cardiac conduction velocity in adult heterozygous mice. At last, we found that the cumulative effect of the 3 loci on disease susceptibility was unexpectedly large, indicating that common genetic variation may have a strong impact on predisposition to rare disease.

Mutations, Vasculopathy with Fever and Early Onset Strokes

371/3:00 Loss-of-function mutations in CECR1, encoding adenosine deaminase 2, cause systemic vasculopathy with fever and early onset strokes. Q. Zhou, A. Zavialov, M. Boehm, J. Chae, M. Hershfield, R. Sood, S. Burgess, A. Zavialov, D. Chin, C. Toro, R. Lee, M. Quezado, A. Ombrello, D. Stone, I. Aksentijevich, D. Kastner.

Loss-of-Function Mutations in CECR1, Encoding Adenosine Deaminase

2,Cause Systemic Vasculopathy with Fever and Early Onset

Strokes. Q. Zhou1, A. Zavialov2, M. Boehm3, J. Chae1, M. Hershfield4, R.

Sood5, S. Burgess6, A. Zavialov2, D. Chin1, C. Toro7, R. Lee8, M. Quezado9,

A. Ombrello1, D. Stone1, I. Aksentijevich1, D. Kastner1.

1) Inflammatory Disease Section, NHGRI, Bethesda, USA;

2) Turku Centre for Biotechnology, University of Turku, Turku, Finland;

3) Laboratory of Cardiovascular Regenerative Medicine, NHLBI, Bethesda, USA;

4) Department of Medicine, Duke University Medical Center, Durham, USA;

5) Zebrafish Core, NHGRI, Bethesda, USA;

6) Developmental Genomics Section, NHGRI, Bethesda, USA;

7) NIH Undiagnosed Diseases Program, NIH, Bethesda, USA;

8) Translational Surgical Pathology Section, NCI, Bethesda, USA;

9) General Surgical Pathology Section, NCI, Bethesda, USA.

We recently observed 5 unrelated patients with fevers, systemic inflammation, livedo reticularis, vasculopathy, and early-onset recurrent ischemic strokes. We performed exome sequencing on affected patients and their unaffected parents. The 5 patients shared 3 missense mutations in CECR1, encoding adenosine deaminase 2 (ADA2), with the genotypes A109D/ Y453C, Y453C/G47A, G47A/H112Q, R169Q/Y453C, and R169Q/28kb genomic deletion encompassing the 5’UTR and first exon of CECR1.

All mutations are either novel or present at low frequency (<0.001) in several large databases, consistent with the recessive inheritance. The Y453C mutation was present in 2/13004 alleles in an NHLBI database. Both alleles are found in 2 affected siblings who suffered from late-onset ischemic stroke, indicating that heterozygous mutations in ADA2 might be associated with susceptibility to adult stroke. Computer modeling based on the crystal structure of the human ADA2 suggests that CECR1 mutations either disrupt protein stability or impair ADA2 enzyme activity. All patients had at least a 10-fold reduction in serum and plasma concentrations of ADA2, and reduced ADA2-specific adenosine deaminase activity. Western blots showed a decrease in protein expression in supernatants of cultured patients’ cells. ADA2 is homologous to ADA1, which is mutated in some patients with SCID.

In contrast to ADA1, ADA2 is expressed predominantly in myeloid cells and is a secreted protein, and its affinity for adenosine is much less than ADA1. Animal models suggest that ADA2 is the prototype for a family of growth factors (ADGFs).Although there is no mouse homolog of CECR1, there are 2 zebrafish homologs, Cecr1a and Cecr1b. Using morpholino technology to knock down the expression of the ADA2 homologs, we observed intracranial hemorrhages in approximately 50% of the zebrafish embryos harboring the knockdown construct, relative to 3% in controls. Immunohistochemical studies of endothelial cells from patients’ skin biopsies demonstrate a diffuse systemic vasculopathy characterized by impaired endothelial integrity, endothelial cellular activation, and a perivascular infiltrate of CD8 T-cells and CD163-positive macrophages. ADA2 is not expressed in the endothelial cells. Our data suggest that ADA2 may be necessary for vascular integrity in the developing zebrafish as an endothelial cell-extrinsic growth factor, and that the near absence of functional ADA2 in patients may lead to strokes by a similar mechanism.

Genetics of Atherosclerotic Plaque in Patients with Chronic Coronary Artery Disease

372/3:15 Genetic influence on LpPLA2 activity at baseline as evaluated in the exome chip-enriched GWAS study among ~13600 patients with chronic coronary artery disease in the STABILITY (STabilisation of Atherosclerotic plaque By Initiation of darapLadIb TherapY) trial. L. Warren, L. Li, D. Fraser, J. Aponte, A. Yeo, R. Davies, C. Macphee, L. Hegg, L. Tarka, C. Held, R. Stewart, L. Wallentin, H. White, M. Nelson, D. Waterworth.

Genetic influence on LpPLA2 activity at baseline as evaluated in the exome chip-enrichedGWASstudy among ~13600 patients with chronic coronary artery disease in the STABILITY (STabilisation of Atherosclerotic plaque By Initiation of darapLadIb TherapY) trial.

L. Warren1, L. Li1, D. Fraser1, J. Aponte1, A. Yeo2, R. Davies3, C. Macphee3, L. Hegg3,

L. Tarka3, C. Held4, R. Stewart5, L. Wallentin4, H. White5, M. Nelson1, D.

Waterworth3.

1) GlaxoSmithKline, Res Triangle Park, NC;

2) GlaxoSmithKline, Stevenage, UK;

3) GlaxoSmithKline, Upper Merion, Pennsylvania, USA;

4) Uppsala Clinical Research Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden;

5) 5Green Lane Cardiovascular Service, Auckland Cty Hospital, Auckland, New Zealand.

STABILITY is an ongoing phase III cardiovascular outcomes study that compares the effects of darapladib enteric coated (EC) tablets, 160 mg versus placebo, when added to the standard of care, on the incidence of major adverse cardiovascular events (MACE) in subjects with chronic coronary heart disease (CHD). Blood samples for determination of the LpPLA2 activity level in plasma and for extraction of DNA was obtained at randomization. To identify genetic variants that may predict response to darapladib, we genotyped ~900K common and low frequency coding variations using Illumina OmniExpress GWAS plus exome chip in advance of study completion. Among the 15828 Intent-to-Treat recruited subjects, 13674 (86%) provided informed consent for genetic analysis. Our pharmacogenetic (PGx) analysis group is comprised of subjects from 39 countries on five continents, including 10139 Whites of European heritage, 1682 Asians of East Asian or Japanese heritage, 414 Asians of Central/South Asian heritage, 268 Blacks, 1027 Hispanics and 144 others. Here we report association analysis of baseline levels of LpPLA2 to support future PGx analysis of drug response post trial completion. Among the 911375 variants genotyped, 213540 (23%) were rare (MAF < 0.5%).

Our analyses were focused on the drug target, LpPLA2 enzyme activity measured at baseline. GWAS analysis of LpPLA2 activity adjusting for age, gender and top 20 principle component scores identified 58 variants surpassing GWAS-significant threshold (5e-08).

Genome-wide stepwise regression analyses identified multiple independent associations from PLA2G7, CELSR2, APOB, KIF6, and APOE, reflecting the dependency of LpPLA2 on LDL-cholesterol levels. Most notably, several low frequency and rare coding variants in PLA2G7 were identified to be strongly associated with LpPLA2 activity. They are V279F (MAF=1.0%, P= 1.7e-108), a previously known association, and four novel associations due to I1317N (MAF=0.05%, P=4.9e-8), Q287X (MAF=0.05%, P=1.6e-7), T278M (MAF=0.02%, P=7.6e-5) and L389S (MAF=0.04%, P=4.3e-4).

All these variants had enzyme activity lowering effects and each appeared to be specific to certain ethnicity. Our comprehensive PGx analyses of baseline data has already provided great insight into common and rare coding genetic variants associated with drug target and related traits and this knowledge will be invaluable in facilitating future PGx investigation of darapladib response.

Genetics of influence IL-18 regulation in patients with Acute Coronary Syndrome

373/3:30 Genome-wide association study identifies common and rare genetic variants in caspase-1-related genes that influence IL-18 regulation in patients with acute coronary syndrome. A. Johansson, N. Eriksson, E. Hagström, C. Varenhorst, A. Åkerblom, M. Bertilsson, T. Axelsson, B. J. Barratt, R. C. Becker, A. Himmelmann, S. James, H. A. Katus, G. Steg, R. F. Storey, A. Syvänen, L. Wallentin, A. Siegbahn.

Genome-wide association study identifies common and rare genetic

variants in caspase-1-related genes that influence IL-18 regulation in

patients with Acute Coronary Syndrome. A. Johansson1, 2, N. Eriksson1,

E. Hagström1,3, C. Varenhorst1,3, A. Åkerblom1,3, M. Bertilsson1, T. Axelsson4,

B.J. Barratt5, R.C. Becker6, A. Himmelmann7, S. James1,3, H.A.

Katus8, G. Steg9, R.F. Storey10, A. Syvänen4, L. Wallentin1,3, A. Siegbahn1,11.

1) Uppsala Clinical Research Center, Uppsala University, Sweden;

2) Department of Immunoloy, Genetics and Pathology, Uppsala University, Sweden;

3) Department of Medical Sciences, Cardiology, Uppsala University, Sweden;

4) Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Sweden;

5) AstraZeneca R&D, Alderley Park, Cheshire, UK;

6) Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA;

7) AstraZeneca Research and Development, Mölndal, Sweden;

8) Medizinishe Klinik, Universitätsklinikum Heidelberg, Heidelberg, Germany;

9) INSERM-Unité 698, Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France; Université Paris-Diderot, Sorbonne-Paris Cité, Paris, France;

10) Department of Cardiovascular Science, University of Sheffield, Sheffield, UK;

11) Department of Medical Sciences, Clinical Chemistry, Uppsala University, Sweden.

 

Interleukin 18 (IL-18) levels are increased in patients with acute coronary syndromes (ACS) and correlated with myocardial injury. We performed a genome-wide association study (GWAS) to identify genetic determinants of IL-18 levels in patients with ACS. In the PLATelet inhibition and patient Outcomes (PLATO) trial, enrolling a broad selection of ACS patients, baseline plasma IL-18 levels were measured in 16633 patients. Of these, 9340 were successfully genotyped using Illumina HumanOmni2.5 or HumanOmniExpressExome BeadChip and SNPs imputed using 1000 Genomes Phase I integrated variant set. Seven independent associations, in five chromosomal regions, were identified. The first region, with two independent (r2 = 0.11) association signals (rs34649619, p = 1.17*10−50 and rs360718, p = 2.03*10−12), is located within IL18. Both top SNPs are located in predicted promoter regions, and the insertion polymorphism rs34649619 (T/TA) disrupts a transcription factor binding site for FOXI1, FOXD3 and FOXA2. The second region, also represented by two independent (r2 = 0.003) association signals (rs385076, p = 6.99*10−72 and rs149451729, p = 3.79*10−16), is located in NLRC4. While rs385076 overlaps with a regulatory region, rs149451729 is a rare coding variant resulting in an amino acid substitution, predicted to be deleterious. The third region is located upstream of CARD16, CARD17, and CARD18 and one of the top SNPs (rs17103763, p = 6.19*10−9) has previously been associated with expression levels of CARD16. The two remaining chromosomal regions are located within GSFMF/MROH6 (rs2290414, p = 5.66*10−17) and RAD17 (rs17229943, p = 5.00*10−12).

While the latter genes have not been associated with IL-18 production previously, others are known to be involved in IL-18 release. NLRC4 is an inflammasome that activates the inflammatory cascade in the presence of bacterial molecules. It recruits and activates procaspase-1, which in its turn is responsible for the maturation of pro-IL-18. CARD16-18, also known as COP1, INCA and ICEBERG, encode caspase inhibitors, known to bind to and prevent procaspase-1 activation. Our results suggest that SNPs in IL18 and caspase-1-associated genes are important for IL-18 production. By combining the identified SNPs in a Mendelian randomization study, the causal effect of IL-18 on clinical endpoints could be further evaluated in a longitudinal study.

Thoracic Aortic Aneurysmal Genes

374/3:45 Prevalence and predictors of pneumothorax in patients with connective tissue disorders enrolled in the GenTAC (National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions) Registry. J. P. Habashi, G. L. Oswald, K. W. Holmes, E. M. Reynolds, S. LeMaire, W. Ravekes, N. B. McDonnell, C. Maslen, R. V. Shohet, R. E. Pyeritz, R. Devereux, D. M. Milewicz, H. C. Dietz, GenTAC Registry Consortium.

Prevalence and Predictors of Pneumothorax in Patients with Connective Tissue Disorders Enrolled in the GenTAC (National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions) Registry.

J.P. Habashi1, G.L. Oswald2, K.W. Holmes1,5, E.M.

Reynolds10, S. LeMaire3, W. Ravekes1, N.B. McDonnell4, C. Maslen5, R.V.

Shohet6, R.E. Pyeritz7, R. Devereux8, D.M. Milewicz9, H.C. Dietz2, GenTAC

Registry Consortium.

1) Dept Pediatric Cardiology, Johns Hopkins Univ, Baltimore, MD;

2) Dept. Medical Genetics, Johns Hopkins Univ, Baltimore, MD;

3) Baylor College of Medicine, Houston TX;

4) NIA at Harbor Hospital, Baltimore, MD;

5) Oregon Health & Science University, Portland, OR;

6) Queen’s Medical Center, Honolulu, HI;

7) The University of Pennsylvania, Philadelphia, PA; 8) Weill Cornell Medical College of Cornell University, New York NY;

9) University of Texas Medical School at Houston, Houston, TX;

10) University of Maryland, Baltimore, MD.

Spontaneous pneumothorax—described as escape of air into the pleural space surrounding the lung in the absence of traumatic injury—is a rare occurrence in the general population (0.1-0.5%), however is well recognized in Marfan syndrome (MFS)(4-5%). Associations between pneumothorax and other connective tissue disorders (CTDs) are less well recognized. We sought to examine potential associations of

  • pneumothorax with MFS,
  • vascular Ehlers-Danlos syndrome (vEDS) and other CTDs.

 

Phenotypic data were analyzed on all GenTAC patients with confirmed diagnoses of

  • MFS,
  • vEDS,
  • Loeys-Dietz syndrome (LDS),
  • bicuspid aortic valve with aortic enlargement (BAVe) or
  • familial thoracic aortic aneurysm and dissection (FTAAD)

to assess the prevalence of pneumothorax and associated features (1918 total pts).

Of 695 patients with Ghent criteria-confirmed MFS, 73 had experienced a spontaneous pneumothorax (prevalence 10.5%), higher than reported in the literature. The frequency of pneumothorax in vEDS patients (16/107, 15%) was similar to the frequency in the MFS group. The prevalences of pneumothorax in LDS (4/73, 5.5%), FTAAD (13/237, 5.5%), and BAVe (19/ 806, 2.4%) were significantly less than that for MFS and vEDS (p<0.001), yet greater than reported for the general population. In MFS patients with a pneumothorax, there was a three-fold increase in reported skeletal features of pectus carinatum, pectus excavatum, scoliosis and/or kyphosis compared to those without pneumothorax. Similarly, in vEDS, there was a four-fold increase in pectus carinatum, scoliosis and kyphosis in those patients with a pneumothorax compared to those without pneumothorax. In a subset of patients with self-reported data (n=846), smoking was not associated with increased prevalence of pneumothorax. Gender was not a predictor of pneumothorax in any of the diagnostic categories analyzed despite literature reports of increased prevalence in males. In patients enrolled in the GenTAC registry with a diagnosis of MFS, vEDS, BAVe, FTAAD or LDS, the prevalence of pneumothorax was significantly increased in all CTDs analyzed as compared to the general population. The prevalence of pneumothorax was significantly higher in patients with MFS or vEDS than in the other CTDs.

These data suggest that skeletal features may be a predictor for pneumothorax. Patients presenting with a spontaneous pneumothorax should be evaluated for several potential CTDs; such an evaluation could unmask an undiagnosed aortic aneurysm.

 

375/4:00 Surprising clinical lessons from targeted next-generation sequencing of thoracic aortic aneurysmal genes. B. Loeys, D. Proost, G. Vandeweyer, S. Salemink, M. Kempers, G. Oswald, H. Dietz, G. Mortier, L. Van Laer.

Surprising clinical lessons from targeted next generation sequencing of thoracic aortic aneurysmal genes. B. Loeys1,2, D. Proost1, G. Vandeweyer1, S. Salemink2, M. Kempers2, G. Oswald3, H. Dietz3, G. Mortier1, L. Van Laer1.

1) Center for Medical Genetics, University of Antwerp/ Antwerp University Hospital, Antwerp, Belgium;

2) Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands;

3) Mc Kusick Nathans Institute for Genetic Medicine, Johns Hopkins University Hospital, Baltimore, USA.

Thoracic aortic aneurysm/dissection (TAA), an important cause of death in the industrialized world, is genetically heterogeneous and at least 14 causative genes have been identified, accounting for both syndromic and non-syndromic forms. The diagnosis is not always straightforward because a considerable clinical overlap exists between patients with mutations in different genes, and mutations in the same gene cause a wide phenotypic variability. Molecular confirmation of the diagnosis is becoming increasingly important for gene-tailored patient management but consecutive, conventional molecular TAA gene screening is expensive and labor-intensive. To shorten the turn-around-time, to increase mutation-uptake and to reduce the overall cost of molecular testing, we developed a TAA gene panel for next generation sequencing (NGS) of 14 TAA genes (ACTA2, COL3A1, EFEMP2, FBN1, FLNA, MYH11, MYLK, NOTCH1, SKI, SLC2A10, SMAD3, TGFB2, TGFBR1 and TGFBR2). We obtained enrichment with Haloplex technology and performed 2×150 bp paired-end runs on a Miseq sequencer in a series of 57 consecutive TAA patients, both syndromic and non-syndromic.

The sensitivity and false positive rate were previously shown to be 100% and 3%, respectively. Applying our NGS approach, we identified a causal mutation in 16 patients (28%). This uptake is really high as on average one molecular study per patient (range 0-6) was performed prior to inclusion in this study. One mutation was found in each of the 6 following genes: ACTA2, COL3A1, TGFBR1, MYLK, SMAD3, SLC2A10 (homozygous); two mutations inNOTCH1and eight in FBN1. An additional 6 variants of unknown significance were identified: 2 in FLNA, 2 in NOTCH1, 1 in FBN1 and 1 heterozygous in EFEMP2. All variants were confirmed by Sanger sequencing.

Remarkably, from the eight FBN1 positive patients, three patients had previously been tested FBN1 negative by certified labs, indicating that the sensitivity of Sanger sequencing is not 100%. Interestingly, in two FBN1 mutation positive patients

  • the clinical diagnosis of Marfan syndrome was unsuspected. Similarly,
  • the clinical diagnosis of vascular Ehlers-Danlos syndrome (COL3A1) had not been made. Finally,
  • the ACTA2 mutation was identified postmortem from paraffin-embedded extracted DNA.

We conclude that our NGS approach for TAA genetic testing overcomes the intrinsic hurdles of Sanger sequencing and becomes a powerful tool in the elaboration of clinical phenotypes assigned to different genes.

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Finding the Genetic Links in Common Disease:  Caveats of Whole Genome Sequencing Studies

Writer and Reporter: Stephen J. Williams, Ph.D.

In the November 23, 2012 issue of Science, Jocelyn Kaiser reports (Genetic Influences On Disease Remain Hidden in News and Analysis)[1] on the difficulties that many genomic studies are encountering correlating genetic variants to high risk of type 2 diabetes and heart disease.  At the recent American Society of Human Genetics annual 2012 meeting, results of several DNA sequencing studies reported difficulties in finding genetic variants and links to high risk type 2 diabetes and heart disease.  These studies were a part of an international effort to determine the multiple genetic events contributing to complex, common diseases like diabetes.  Unlike Mendelian inherited diseases (like ataxia telangiectasia) which are characterized by defects mainly in one gene, finding genetic links to more complex diseases may pose a problem as outlined in the article:

  • Variants may be so rare that massive number of patient’s genome would need to be analyzed
  • For most diseases, individual SNPs (single nucleotide polymorphisms) raise risk modestly
  • Hard to find isolated families (hemophilia) or isolated populations (Ashkenazi Jew)
  • Disease-influencing genes have not been weeded out by natural selection after human population explosion (~5000 years ago) resulted in numerous gene variants
  • What percentage variants account for disease heritability (studies have shown this is as low as 26% for diabetes with the remaining risk determined by environment)

Although many genome-wide-associations studies have found SNPs that have causality to increasing risk diseases such as cancer, diabetes, and heart disease, most individual SNPs for common diseases raise risk by about only 20-40% and would be useless for predicting an individual’s chance they will develop disease and be a candidate for a personalized therapy approach.  Therefore, for common diseases, investigators are relying on direct exome sequencing and whole-genome sequencing to detect these medium-rare risk variants, rather than relying on genome-wide association studies (which are usually fine for detecting the higher frequency variants associated with common diseases).

Three of the many projects (one for heart risk and two for diabetes risk) are highlighted in the article:

1.  National Heart, Lung and Blood Institute Exome Sequencing Project (ESP)[2]: heart, lung, blood

  • Sequenced 6,700 exomes of European or African descent
  • Majority of variants linked to disease too rare (as low as one variant)
  • Groups of variants in the same gene confirmed link between APOC3 and higher risk for early-onset heart attack
  • No other significant gene variants linked with heart disease

2.  T2D-GENES Consortium: diabetes

Sequenced 5,300 exomes of type 2 diabetes patients and controls from five ancestry groups
SNP in PAX4 gene associated with disease in East Asians
No low-frequency variant with large effect though

3.  GoT2D: diabetes

  • After sequencing 2700 patient’s exomes and whole genome no new rare variants above 1.5% frequency with a strong effect on diabetes risk

A nice article by Dr. Sowmiya Moorthie entitled Involvement of rare variants in common disease can be found at the PGH Foundation site http://www.phgfoundation.org/news/5164/ further discusses this conundrum,  and is summarized below:

“Although GWAs have identified many SNPs associated with common disease, they have as yet had little success in identifying the causative genetic variants. Those that have been identified have only a weak effect on disease risk, and therefore only explain a small proportion of the heritable, genetic component of susceptibility to that disease. This has led to the common disease-common variant hypothesis, which predicts that common disease-causing genetic variants exist in all human populations, but each individual variant will necessarily only have a small effect on disease susceptibility (i.e. a low associated relative risk).

An alternative hypothesis is the common disease, many rare variants hypothesis, which postulates that disease is caused by multiple strong-effect variants, each of which is only found in a few individuals. Dickson et al. in a paper in PLoS Biology postulate that these rare variants can be indirectly associated with common variants; they call these synthetic associations and demonstrate how further investigation could help explain findings from GWA studies [Dickson et al. (2010) PLoS Biol. 8(1):e1000294][3].  In simulation experiments, 30% of synthetic associations were caused by the presence of rare causative variants and furthermore, the strength of the association with common variants also increased if the number of rare causative variants increased. “

one_of_many rare variants

Figure from Dr. Moorthie’s article showing the problem of “finding one in many”.

(please   click to enlarge)

Indeed, other examples of such issues concerning gene variant association studies occur with other common diseases such as neurologic diseases and obesity, where it has been difficult to clearly and definitively associate any variant with prediction of risk.

For example, Nuytemans et. al.[4] used exome sequencing to find variants in the vascular protein sorting 3J (VPS35) and eukaryotic transcription initiation factor 4  gamma1 (EIF4G1) genes, tow genes causally linked to Parkinson’s Disease (PD).  Although they identified novel VPS35 variants none of these variants could be correlated to higher risk of PD.   One EIF4G1 variant seemed to be a strong Parkinson’s Disease risk factor however there was “no evidence for an overall contribution of genetic variability in VPS35 or EIF4G1 to PD development”.

These negative results may have relevance as companies such as 23andme (www.23andme.com) claim to be able to test for Parkinson’s predisposition.  To see a description of the LLRK2 mutational analysis which they use to determine risk for the disease please see the following link: https://www.23andme.com/health/Parkinsons-Disease/. This company and other like it have been subjects of posts on this site (Personalized Medicine: Clinical Aspiration of Microarrays)

However there seems to be more luck with strategies focused on analyzing intronic sequence rather than exome sequence. Jocelyn Kaiser’s Science article notes this in a brief interview with Harry Dietz of Johns Hopkins University where he suspects that “much of the missing heritability lies in gene-gene interactions”.  Oliver Harismendy and Kelly Frazer and colleagues’ recent publication in Genome Biology  http://genomebiology.com/content/11/11/R118 support this notion[5].  The authors used targeted resequencing of two endocannabinoid metabolic enzyme genes (fatty-acid-amide hydrolase (FAAH) and monoglyceride lipase (MGLL) in 147 normal weight and 142 extremely obese patients.

These patients were enrolled in the CRESCENDO trial and patients analyzed were of European descent. However, instead of just exome sequencing, the group resequenced exome AND intronic sequence, especially focusing on promoter regions.   They identified 1,448 single nucleotide variants but using a statistical filter (called RareCover which is referred to as a collapsing method) they found 4 variants in the promoters and intronic areas of the FAAH and MGLL genes which correlated to body mass index.  It should be noted that anandamide, a substrate for FAAH, is elevated in obese patients. The authors did note some issues though mentioning that “some other loci, more weakly or inconsistently associated in the original GWASs, were not replicated in our samples, which is not too surprising given the sample size of our cohort is inadequate to replicate modest associations”.

PLEASE WATCH VIDEO on the National Heart, Lung and Blood Institute Exome Sequencing Project

https://www.youtube.com/watch?v=-Qr5ahk1HEI

REFERENCES

http://www.phgfoundation.org/news/5164/  PHG Foundation

1.            Kaiser J: Human genetics. Genetic influences on disease remain hidden. Science 2012, 338(6110):1016-1017.

2.            Tennessen JA, Bigham AW, O’Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G et al: Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012, 337(6090):64-69.

3.            Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB: Rare variants create synthetic genome-wide associations. PLoS biology 2010, 8(1):e1000294.

4.            Nuytemans K, Bademci G, Inchausti V, Dressen A, Kinnamon DD, Mehta A, Wang L, Zuchner S, Beecham GW, Martin ER et al: Whole exome sequencing of rare variants in EIF4G1 and VPS35 in Parkinson disease. Neurology 2013, 80(11):982-989.

5.            Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Sipe JC, Murray SS et al: Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome biology 2010, 11(11):R118.

Other posts on this site related to Genomics include:

Cancer Biology and Genomics for Disease Diagnosis

Diagnosis of Cardiovascular Disease, Treatment and Prevention: Current & Predicted Cost of Care and the Promise of Individualized Medicine Using Clinical Decision Support Systems

Ethical Concerns in Personalized Medicine: BRCA1/2 Testing in Minors and Communication of Breast Cancer Risk

Genomics & Genetics of Cardiovascular Disease Diagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013

Genomics-based cure for diabetes on-the-way

Personalized Medicine: Clinical Aspiration of Microarrays

Late Onset of Alzheimer’s Disease and One-carbon Metabolism

Genetics of Disease: More Complex is How to Creating New Drugs

Genetics of Conduction Disease: Atrioventricular (AV) Conduction Disease (block): Gene Mutations – Transcription, Excitability, and Energy Homeostasis

Centers of Excellence in Genomic Sciences (CEGS): NHGRI to Fund New CEGS on the Brain: Mental Disorders and the Nervous System

Cancer Genomic Precision Therapy: Digitized Tumor’s Genome (WGSA) Compared with Genome-native Germ Line: Flash-frozen specimen and Formalin-fixed paraffin-embedded Specimen Needed

Mitochondrial Metabolism and Cardiac Function

Pancreatic Cancer: Genetics, Genomics and Immunotherapy

Issues in Personalized Medicine in Cancer: Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Quantum Biology And Computational Medicine

Personalized Cardiovascular Genetic Medicine at Partners HealthCare and Harvard Medical School

Centers of Excellence in Genomic Sciences (CEGS): NHGRI to Fund New CEGS on the Brain: Mental Disorders and the Nervous System

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

Consumer Market for Personal DNA Sequencing: Part 4

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

Whole-Genome Sequencing Data will be Stored in Coriell’s Spin off For-Profit Entity

 

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Genetics of Conduction Disease: Atrioventricular (AV) Conduction Disease (block): Gene Mutations – Transcription, Excitability, and Energy Homeostasis

Curator: Aviva Lev-Ari, PhD, RN

UPDATED on 6/13/2013

with a CASE of  Anti-Ro Antibodies and Reversible Atrioventricular Block

N Engl J Med 2013; 368:2335-2337 June 13, 2013 DOI: 10.1056/NEJMc1300484

As an Introduction to the Genetics of Conduction Disease, we selected the following article which represents the MOST comprehensive review of the Human Cardiac Conduction System presented to date:

Circulation.2011; 123: 904-915 doi: 10.1161/​CIRCULATIONAHA.110.942284

The Cardiac Conduction System

  1. David S. Park, MD, PhD;
  2. Glenn I. Fishman, MD

+Author Affiliations


  1. From the Leon H. Charney Division of Cardiology, New York University School of Medicine, New York, NY.
  1. Correspondence to Glenn I. Fishman, MD, Leon H. Charney Division of Cardiology, New York University School of Medicine, 522 First Ave, Smilow 801, New York, NY 10016. E-mail glenn.fishman@med.nyu.edu

Key Words:

The human heart beats 2.5 billion times during a normal lifespan, a feat accomplished by cells of the cardiac conduction system (CCS). The functional components of the CCS can be broadly divided into the impulse-generating nodes and the impulse-propagating His-Purkinje system. Human diseases of the conduction system have been identified that alter impulse generation, impulse propagation, or both. CCS dysfunction is primarily due to acquired conditions such as myocardial ischemia/infarct, age-related degeneration, procedural complications, and drug toxicity. Inherited forms of CCS disease are rare, but each new mutation provides invaluable insight into the molecular mechanisms governing CCS development and function. Applying a multidisciplinary approach, which includes human genetic screening, biophysical analysis, and transgenic mouse technology, has yielded a broad array of gene families involved in maintaining normal CCS physiology (Figure 1). In this review, we discuss gene families that have been implicated in human CCS diseases of rhythm, conduction block, accessory conduction, and development (Table). We also investigate evolving therapeutic strategies that may serve as adjuvant or replacement therapy to current implantable pacemakers.

Figure 1.

View larger version:

Figure 1.

Cardiac conduction system cell. Genes identified in human cardiac conduction system disease are highlighted.

Table.

Genetic Basis of Conduction System Disease

Diseases of Automaticity

The human sinoatrial node (SAN) is a crescent-shaped, intramural structure with its head located subepicardially at the junction of the right atrium and the superior vena cava and its tail extending 10 to 20 mm along the crista terminalis.26 The SAN has complex 3-dimensional tissue architecture with central and peripheral components made up of distinct ion channel and gap junction expression profiles.27 Central and peripheral cells have different action potential characteristics and conduction properties (Figure 2).27Experimental and computational models have demonstrated that SAN heterogeneity is necessary to maintain normal automaticity and impulse conduction.28,,30

Figure 2.

Figure 2.

Electrophysiological heterogeneity of the sinoatrial node (SAN). The central SAN, the site of dominant pacemaking, is electronically insulated from the hyperpolarizing atrial myocardium through the differential expression of connexins and ion channels. Peripheral SAN cells are electrophysiologically intermediate between central cells and atrial cardiomyocytes. SR indicates sarcoplasmic reticulum.

Pacemaker automaticity is due to spontaneous diastolic depolarization of phase 4, which depolarizes the membrane to threshold potential generating rhythmic action potentials. The current paradigm of SAN automaticity has been modeled as 2 clocks that function in concert, the “membrane voltage clock” and the “calcium clock.” The membrane voltage clock is produced by the net disequilibrium between the decay of outward potassium currents (IK) and the activation of inward currents that include, but are not limited to, background sodium-sensitive current (Ib Na), L- and T-type calcium currents (ICa,L,ICa,T), sustained inward (Ist) current, and hyperpolarization-activated current (If) (Figure 2).27,31,,33

The subsarcolemmal calcium clock contributes to SAN diastolic depolarization through the spontaneous, rhythmic release of Ca2+ from the sarcoplasmic reticulum (SR) via the ryanodine type 2 receptor (RYR2).34 The local intracellular calcium (Cai) elevations drive the sodium-calcium exchange current (INCX) to substitute 1 intracellular Ca2+ for 3 extracellular Na+. The net gain in positive charge results in membrane depolarization.35The elevation of intracellular Ca2+ occurs in the latter third of diastolic depolarization and is sensitive to β-adrenergic stimulation.36

Human mutations affecting the voltage clock

  • (SCN5A and HCN4),

  • calcium clock (RYR2 and CASQ2), or both mechanisms

  • (ANKB) have been identified that negatively affect sinus node function.37,38

Diseases of Conduction BlockConduction block can occur at any level of the CCS and can manifest as sinoatrial exit block, atrioventricular block, infra-Hisian block, or bundle branch block. Impaired conduction can be caused by ion channel defects that alter action potential shape or by defective coupling between cardiomyocytes. Inherited defects in cardiac conduction have been linked to mutations in SCN5A and SCN1B (both affect phase 0) and KCNJ2 (affects phase 3 and 4). 

The cardiac sodium channel consists of the pore-forming α-subunit (encoded by SCN5A) and a modulatory β-subunit (encoded by SCN1B). The α-subunit contains a voltage sensor that allows for rapid activation in response to membrane depolarization. After depolarization, the sodium channel undergoes a period of inactivation, in which it is refractory to further impulses. SCN5A requires membrane repolarization to relieve the inactivated state. The inward rectifier potassium channel, Kir2.1, encoded by KCNJ2, maintains the resting membrane potential. Therefore, proper functioning of Nav1.5 and Kir2.1 is necessary for normal cardiac excitability.

SCN5A

Progressive cardiac conduction defect, or Lev-Lenègre disease, is characterized by age-related, fibrosclerotic degeneration of the His-Purkinje system.6 Impulse propagation through the proximal ventricular conduction system progressively declines, resulting in bundle branch blocks and eventually complete atrioventricular block. An inherited form of Lev-Lenègre disease is associated with loss of function mutations in SCN5A and can exist alone or as overlap syndromes with Brugada or long QT syndrome 3.6 Inherited progressive cardiac conduction defect is associated with a high risk of complete atrioventricular block and Stoke-Adams syncope without ventricular dysrhythmia.7 Schott et al8 identified a mutation in SCN5A that cosegregates with Lenègre disease in a large French family. Affected individuals had variable degrees of conduction block requiring pacemaker implantation in 4 family members because of syncope or complete heart block. Linkage analysis and candidate gene sequencing identified a T>C substitution at position +2 of the donor splice site of intron 22 (IVS22+2 T>C), which results in a mutant lacking the voltage-sensitive segment.8 Functional analysis demonstrated no transient inward sodium current in response to depolarization, consistent with a loss-of-function mutation.6

SCN1B

The majority of patients with Brugada and conduction disease do not have SCN5Amutations. Therefore, modifiers of Nav1.5 expression or function have become the target of candidate gene sequencing approaches. Watanabe et al9 identified SCN1B mutations in 3 families with conduction disease with or without Brugada syndrome. Coexpression of mutant β-subunits with Nav1.5 resulted in diminished sodium current.

KCNJ2

Mutations in KCNJ2 have been found in a rare autosomal dominant condition called Andersen-Tawil syndrome, characterized by periodic paralysis, dysmorphic features, polymorphic ventricular tachycardia, and cardiac conduction disease.10,11 ECG evaluation of 96 patients with Andersen-Tawil syndrome from 33 unrelated kindreds revealed conduction defects at multiple levels from the atrioventricular node to the distal conduction system.55 Cardiomyocytes expressing a dominant-negative subunit of Kir2.1 exhibited a 95% reduction in IK1, resulting in significant action potential prolongation. Mouse models of Andersen-Tawil syndrome exhibited a slower heart rate and significant slowing of conduction.56,57

Diseases of Accessory Conduction

Wolff-Parkinson-White (WPW) syndrome is characterized by preexcitation of ventricular myocardium via an accessory pathway (bundle of Kent) that bypasses the normal slow conduction through the atrioventricular node. Ventricular preexcitation is common, with a disease prevalence of 1.5 to 3 per 1000 people.22,58 Histological evaluation of Kent bundles resected from human subjects displayed features of typical ventricular myocytes with expression of connexin 43 (Cx43).59 The expression of high-conductance gap junctions in bypass tracts enables them to preexcite ventricular myocardium, manifesting as a short PR and a slurred QRS complex, or “delta wave,” on the ECG. The vast majority of WPW cases are sporadic, and the underlying mechanism remains unknown; however, rare inherited forms have been reported. Vidaillet et al60 determined that 3.4% of probands with WPW had 1 or more first-degree relatives with accessory conduction.

PRKAG2

A familial form of WPW with an autosomal dominant mode of transmission was identified in 2 families. Thirty-one affected individuals had evidence of preexcitation and cardiac hypertrophy. A missense mutation in PRKAG2 was identified that results in a constitutively active form of the γ2 regulatory subunit of AMP-activated protein kinase.22,23 Under normal conditions, AMP-activated protein kinase responds to energy-depleted states by increasing glucose uptake and promoting glycolysis. Transgenic mice expressing a heart-restricted, constitutively active mutant, PRKAG2N488I, recapitulated the human WPW phenotype of cardiac hypertrophy, preexcitation, and conduction defects. The predominant histological finding was ventricular myocyte engorgement with glycogen-laden vacuoles. The disruption of the annulus fibrosus by vacuolated ventricular myocytes resulted in the preexcitation phenotype.61 Using a mouse model of reversible glycogen-storage defect, Wolf et al62 demonstrated that the cardiomyopathy and CCS degeneration seen in PRKAG2N488I mice were reversible processes.

BMP2

Lalani et al24 reported a novel WPW syndrome associated with microdeletion of the bone morphogenetic protein-2 (Bmp2) region within 20p12.3 that is characterized by variable cognitive deficits and dysmorphic features. The BMPs are members of the transforming growth factor-β superfamily and play a critical role in cardiac development. Mice with cardiac deletion of BMP receptor type Ia (Bmpr1a) were embryonic lethal before E18.5 because of abnormal development of trabecular and compact myocardium, interventricular septum, and endocardial cushion.63 More restricted deletion of Bmpr1a in the atrioventricular canal resulted in defective atrioventricular valve formation and maturation defects in the annulus fibrosus, resulting in preexcitation.64,65

 

Diseases of CCS Development

Congenital heart disease is the most common form of birth defect, affecting 1% to 2% of live births.66 Arrhythmias may result from defective CCS specification/patterning, malformation or displacement of the conduction system, altered hemodynamics, prolonged hypoxic states, or postoperative sequelae.67,68 Developmentally, the conduction system derives from myocardial precursor cells within the fetal heart.69,,71The process by which conduction cells are specified or recruited into a “conduction” versus “working myocyte” lineage is determined by the regional expression of transcription factors.69,,74 The main transcription factors identified in human CCS development are the T-box and homeobox factors.

TBX5

Holt-Oram syndrome is an autosomal dominant condition characterized by preaxial radial ray limb deformities (defects of the radius, carpal bones, and/or thumbs) and cardiac septation defects. The septal defects are typically ostium secundum atrial septal defects, muscular ventricular septal defects, and atrioventricular canal defects. Patients with Holt-Oram syndrome manifest variable degrees of CCS dysfunction, such as sinus bradycardia and atrioventricular block, even in the absence of overt structural heart disease. In 1997, Basson et al18 screened 2 families with Holt-Oram syndrome and identified mutations in the T-box transcription factor, TBX5. The T-box transcription factors can function as transcriptional activators or repressors and are known to be critical regulators of cardiac specification and differentiation. Seven TBX family members are expressed in the developing heart, 3 of which (TBX1, TBX5, TBX20) have been linked to human congenital heart disease.75

Mice deficient in Tbx5 were embryonic lethal at E10.5 because of arrested development of the atria and left ventricle. Tbx5+/− mice recapitulated the upper limb and cardiac manifestations of human Holt-Oram syndrome, including the conduction abnormalities.72,76 Significant maturation defects in the atrioventricular canal and ventricular conduction system were present.76 Moskowitz et al76 demonstrated thatTbx5+/− mice have maturation failure of the atrioventricular canal manifesting as persistent atrioventricular rings around the tricuspid and mitral valves. Patterning defects were noted in the His bundle and bundle branches, including complete absence of right bundle branch formation in some cases. Expression of CCS-enriched markers, such as atrial natriuretic factor and Cx40, were found to be significantly downregulated, implicating TBX5 as a transcriptional activator of these genes. TBX5 and the homeobox transcription factor NKX2-5 were found to act synergistically in upregulating atrial natriuretic factor and Cx40 expression.76

Conduction Disease Associated With Neuromuscular Disorders

Neuromuscular disorders represent a diverse collection of diseases that commonly present with cardiac involvement. Mutations have been identified in genes involved in the cytoskeleton, nuclear envelope, and mitochondrial function. Cardiac involvement typically manifests as dilated or hypertrophic cardiomyopathy, atrioventricular conduction defects, and atrial and ventricular dysrhythmias.82

EMD and LMNA

Mutations affecting the nuclear envelope have been associated with significant CCS dysfunction. The inner membrane of the nuclear envelope is a highly organized structure, composed of integral membrane proteins and nuclear cytoskeletal proteins that function together in higher-order chromatin structure and transcriptional regulation. The lamins (A, B, and C) are an integral part of an intermediate filament network that imparts structural rigidity to the inner nuclear membrane. Emerin, a member of the nuclear lamina-associated protein family, putatively mediates anchoring of chromatin to the cytoskeleton. Mutations in emerin (EMD) or lamin A/C (LMNA) result in X-linked Emery-Dreifuss muscular dystrophy and autosomal dominant Emery-Dreifuss muscular dystrophy,20respectively. Individuals with Emery-Dreifuss muscular dystrophy develop progressive skeletal muscle weakness in the first decade of life and cardiac involvement (dilated cardiomyopathy and atrioventricular block) in the second decade.82,83

Arimura et al84 engineered a mouse model of autosomal dominant Emery-Dreifuss muscular dystrophy by knocking-in an Lmna missense mutation (H222P) previously identified from a family with typical autosomal dominant Emery-Dreifuss muscular dystrophy. The mouse model faithfully recapitulated the human disease with LmnaH222P/H222P mice exhibiting locomotive defects, dilated cardiomyopathy, and CCS dysfunction. Telemetric evaluation of the mutant mice revealed PR prolongation and QRS complex widening. A similar CCS defect was seen in mice haploinsufficient in the Lmna gene. Lmna+/− mice exhibited sinus bradycardia with variable degrees of atrioventricular block. Histological evaluation of these mice revealed nuclear deformation and apoptosis in atrioventricular node cells.85 Another engineered mouse line expressing LmnaN195K, known to cause autosomal dominant dilated cardiomyopathy with conduction disease in humans,86 exhibited high-grade atrioventricular block and complete heart block. Biochemical evaluation revealed reduced expression and mislocalization of Cx40 and Cx43 in mutant atrial tissue.87 Desmin staining also revealed structural defects of the sarcomere and intercalated discs.87

Genome-wide expression profiling of Lmna H222P mouse hearts revealed significant increases in mitogen-activated protein kinase (MAPK) signaling pathways.88Hyperactivation of MAPK pathways is associated with cardiomyopathy and CCS dysfunction. A significant increase of the activated forms of 2 MAPKs, JNK and ERK1/2, was noted in mutant hearts that predated the onset of overt or molecularly defined cardiomyopathy.88 Treatment of Lmna H222P mice with an inhibitor of ERK phosphorylation abrogated the increase in biomarkers of cardiomyopathy and restored ejection fraction to normal levels. These findings directly link MAPK hyperactivation to the cardiomyopathic phenotype in Lmna H222P mice.89

On the basis of the phenotypes of these mouse models, lamin A/C appears to maintain the functional integrity of the CCS in 2 ways: (1) protection of the nucleus against mechanical stress and (2) maintenance of proper chromatin organization to ensure accurate gene expression, such as in connexin expression and MAPK signaling pathways.83

Future Directions

Linkage analysis with positional cloning has been a highly effective means of identifying gene mutations within kindreds of monogenic disease. More than 1000 genes have been identified with this approach, including those in this review. With the sequencing of the human genome, the promise of identifying genetic causes of complex, multifactorial diseases is becoming more of a reality. One major step in this direction was the development of genome-wide association studies.94

The genome-wide association study is a test of association between a disease and genetic markers that span the entire genome. The technique relies on the fact that variance at one locus predicts with high probability variance of an adjacent locus because of linkage disequilibrium. In other words, there is nonrandom cosegregation of a series of genetic markers that are close together in the genome. This cluster of linked markers is known as a haplotype. The first study of haplotype structure within 4 populations (Yoruban, Northern/Western Europeans, Chinese, and Japanese) was published in Naturein 2005 by the International HapMap Consortium. Their work reported that individual genetic markers (single nucleotide polymorphisms) predict adjacent markers typically with a resolution of ≈30 000 bp. Considering that the human genome is ≈3×109 bp, they projected that <500 000 single nucleotide polymorphisms would be needed to survey the entire genome for all common genetic variants.94,95

Genome-wide association studies have now been used to identify genetic variants that influence ECG parameters in different populations. Intermediate parameters, such as heart rate or PR interval, were used as surrogate markers of disease for 2 reasons: (1) They have an association with cardiovascular morbidity and atrial fibrillation, and (2) they have tighter associations with gene variants than the actual disease. Holm et al96reported several genome-wide associations using a cutoff P value <1.6×10−9. One locus harboring MYH6 was associated with heart rate, 4 loci (TBX5SCN10ACAV1, andARHGAP24) were associated with PR interval, and 4 loci (TBX5SCN10A6p21, and10q21) were associated with QRS duration. They went on to test these associations with individuals manifesting different arrhythmias in an Icelandic and Norwegian population. Correlations were found between atrial fibrillation and TBX5 and CAV1 (P=4.0×10−5 andP=0.00032, respectively), between advanced atrioventricular block and TBX5 (P=0.0067), and between pacemaker implantation and SCN10A (P=0.0029).

Similar loci were identified by 2 additional independent genome-wide association studies in a European population and an Indian Asian population. Pfeufer et al97 reported 9 loci that were highly associated with PR interval (P<5×10−8) from a meta-analysis of the CHARGE Consortium with >28 000 European subjects. One locus had associations with 2 sodium channels (SCN10A and SCN5A), and 6 loci were near genes involved in cardiac development (CAV1-CAV2NKX2-5SOX5WNT11MEIS1and TBX5-TBX3). Of these,SCN10ASCN5ACAV1-CAV2NKX2-5, and SOX5 were found to be associated with atrial fibrillation. Chambers et al98 also reported the association between SCN10A and PR interval in 6543 Indian Asians. Physiological testing of Scn10a-deficient mice revealed shortened PR intervals in knockout mice with no significant difference in all other ECG and echocardiographic parameters.

The discovery of novel gene families associated with human conduction and arrhythmic diseases with the use of genome-wide association studies is well under way. Identification of SCN10A by 3 independent groups studying different populations confirms the fidelity of this approach. Further experiments confirming the significance of these associations will need to be performed. In addition to identifying novel gene targets, this technique will also aid in the discovery of new associations with noncoding regions in which new epigenetic modifiers and transcriptional/translational regulators, such as microRNAs, will be identified.

Therapeutic Strategies

The current standard of care for symptomatic bradycardia due to conduction system disease is the implantation of an electronic pacemaker. Despite their success, electronic pacemakers have limitations, which include lead complications, finite battery life, potential for infection, lack of autonomic responsiveness, and size restriction in younger patients. These limitations have spurred on the development of biological pacemakers, the premise of which is to restore pacemaking activity with the use of viral-based or stem cell–based gene delivery systems.99 The identification and characterization of genes involved in generating pacemaker currents have allowed biological pacemaker technology to become a reality.

The restoration of sinus pacing rates can be achieved by modulating inward and outward currents to establish or increase the slope of diastolic depolarization in cardiac tissue. Increasing inward currents and/or decreasing outward currents increase the slope of diastolic depolarization and therefore the pacing rate. Genes that have been investigated or are under current investigation include the following: (1) β2-adrenergic receptor,100,101(2) dominant-negative Kir2.1 mutants,102 (3) adenylate cyclase type VI (ACVI),103,104and (4) HCN channels.105 The β2-adrenergic receptor and adenylate cyclase type VI both increase cAMP levels, leading to activation of endogenous HCN channels and calcium clock mechanisms. Although initial animal models using the β2-adrenergic receptor showed promise with transient increases in heart rate, the potential for proarrhythmia and the inability of this approach to establish de novo pacemaker activity limited its efficacy.101

Another approach focused on modifying ionic currents that convert working myocardial cells, which have relatively stable diastolic potentials, into cells with phase 4 diastolic depolarization. It was postulated that atrial and ventricular myocytes have the potential for automaticity, but that hyperpolarizing currents, such as IK1, prevent diastolic depolarization by stabilizing the resting membrane potential. Miake et al102 confirmed this hypothesis when they demonstrated that adenoviral delivery of a dominant-negative Kir2.1 construct into the left ventricle of guinea pigs resulted in conversion of quiescent myocytes into pacemaker cells. Unfortunately, significant action potential prolongation limited the clinical utility of this treatment strategy.102

Rosen and colleagues105,106 demonstrated that automaticity could be induced in quiescent myocardium with the use of heterologous expression of HCN channels that produce the pacemaker current If. Qu and Plotnikov et al demonstrated that stable autonomous rhythms could be generated when adenovirus encoding HCN2 was injected into the left atrium105 or left bundle branch106 of a canine heart. To bypass the limitations of viral-based systems, such as host immune response, several groups reported the successful use of cell-based delivery systems. Plotnikov et al107 reported the successful implantation of human mesenchymal stem cells expressing HCN2 in the left ventricle of a canine model of atrioventricular block. Dogs maintained stable ectopic pacemaker activity for >6 weeks without the use of immunosuppression.107 Human mesenchymal stem cells electronically couple to host myocardium through gap junctions; therefore, conditions with significant gap junction remodeling may affect the efficacy of this method.

Although standalone biological pacemakers may be far into the future, adjuvant biological pacemakers may find real-world utility for current deficiencies of electronic pacemakers, such as limited battery life and device infections. For example, biological preparations used in conjunction with device therapy may be used to extend battery life, decreasing the frequency of generator changes. Transient injectable pacemakers may also function as bridge therapy after lead extraction of an infected device. The need for adjuvant biological pacemakers is clear, but continued refinement of gene- and cell-based delivery systems will be necessary to make this technology a reality.99

Conclusion

Although rare, inherited arrhythmias have become an invaluable tool in identifying the genetic determinants of CCS function. Each new mutation enhances our understanding and appreciation of the biochemical and structural complexity needed for cardiac impulse generation and propagation. This methodology is hampered, however, by the relative scarcity of inherited conditions affecting the CCS. The addition of genome-wide association studies has broadened this search for novel genes beyond rare familial afflictions to include common, multifactorial conditions. It is hoped that this exciting new frontier will bring to light the complex interplay of genes and genetic/epigenetic modifiers that influence the prevalence of common diseases. These genetic screens will ultimately yield a bevy of new gene targets for pharmaceutical or gene-based therapeutics of the future.

Sources of Funding

Studies in the Fishman laboratory are supported by National Institutes of Health grants HL64757, HL081336, and HL82727 and a New York State STEM award (to Dr Fishman) and a Heart Rhythm Foundation Fellowship (to Dr Park).

Genetics of Atrioventricular Conduction Disease in Humans.

Benson DW.

Source

Division of Cardiology, ML7042, Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA. woody.benson@cchmc.org

Abstract

Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV block has unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with disease gene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics.

http://www.ncbi.nlm.nih.gov/pubmed/15372490

Additional Studies on Genetic Congenital AV Block

1) 12738236
Na+ channel mutation leading to loss of function and non-progressive cardiac conduction defects.
BACKGROUND: We previously described a Dutch family in which congenital cardiac conduction disorder has clinically been identified. The ECG of the index patient showed a first-degree AV block associated with extensive ventricular conduction delay. Sequencing of the SCN5A locus coding for the human cardiac Na+ channel revealed a single nucleotide deletion at position 5280, resulting in a frame-shift in the sequence coding for the pore region of domain IV and a premature stop codon at the C-terminus. METHODS AND RESULTS: Wild type and mutant Na+ channel proteins were expressed in Xenopus laevis oocytes and in mammalian cells. Voltage clamp experiments demonstrated the presence of fast activating and inactivating inward currents in cells expressing the wild type channel alone or in combination with the beta1 subinut (SCN1B). In contrast, cells expressing the mutant channels did not show any activation of inward current with or without the beta1 subunit. Culturing transfected cells at 25 degrees C did not restore the Na+ channel activity of the mutant protein. Transient expression of WT and mutant Na+ channels in the form of GFP fusion proteins in COS-7 cells indicated protein expression in the cytosol. But in contrast to WT channels were not associated with the plasma membrane. CONCLUSIONS: The SCN5A/5280delG mutation results in the translation into non-function channel proteins that do not reach the plasma membrane. This could explain the cardiac conduction defects in patients carrying the mutation.
2) 12956334
The genetic origin of atrioventricular conduction disturbance in humans.
Atrioventricular (AV) conduction disturbance (block) describes impairment of the electrical continuity between the atria and ventricles. Clinical classification of AV block has utilized biophysical characteristics, usually the extent (1st, 2nd, 3rd degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is not known. In some casesAV block occurrence is associated with intrauterine exposure to maternal antibody (anti-Ro, anti-La), and other cases are associated with injury (e.g. surgery). Based on familial clustering of idiopathic AV block, a genetic cause has also been suspected. Published pedigrees show autosomal dominant inheritance, and associated heart disease is common (e.g. congenital heart malformation, cardiomyopathy, etc.). The latter finding is not unexpected given the common origin of working myocytes and elements of the specialized conduction system. Using genetic models incorporating reduced penetrance (presence of disease genotype in absence of phenotype), variable expressivity (presence of a disease genotype with variable phenotypes) and genetic heterogeneity (similar phenotypes, different disease genotypes), molecular genetic causes of AV block are being identified. These findings are significant as they provide insight into the molecular basis of a clinical condition previously defined only by biophysical characteristics.
3) 15372490
Genetics of atrioventricular conduction disease in humans.
Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV blockhas unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with disease gene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics.

SOURCE:

Anti-Ro Antibodies and Reversible Atrioventricular Block

N Engl J Med 2013; 368:2335-2337 June 13, 2013DOI: 10.1056/NEJMc1300484

To the Editor:

Transplacental transfer of anti-Ro antibodies is a well-known cause of conduction defects and permanent atrioventricular block in newborns.1 In adults, conduction disturbances related to these antibodies are rare.2

We report a case of a 26-year-old woman with no history of this condition who was admitted to the hospital through the emergency department after having several syncopal episodes. Electrocardiography (ECG) performed while the patient was at rest showed complete atrioventricular block and ventricular escape rhythm associated with left bundle-branch block (Figure 1AFIGURE 1Electrocardiographic Findings.). Laboratory evaluation included a positive test for antinuclear antibodies (with the HEp-2 cell substrate) at a titer of 1:320, with a speckled pattern and specificity for extractable nuclear antigens, including antibodies against Ro52 confirmed by means of immunoblot and enzyme-linked immunosorbent assays (first measurement of antibodies, 1.2 U per milliliter). No clinical manifestations of rheumatologic disease were present. Other causes of reversible atrioventricular block were ruled out. The patient had no history of cardiac surgery, ablation procedures, or drug use. There was no evidence of infiltrative diseases (e.g., sarcoidosis or amyloidosis) or myocardial ischemia, nor was there clinical suspicion of infectious diseases that cause conduction disturbances (e.g., Lyme disease or Chagas’ disease). Levels of electrolytes and thyrotropin were normal. Transthoracic echocardiography and magnetic resonance imaging were unremarkable.

During the first 4 days after admission, the patient had varying degrees of atrioventricular block. An electrophysiological study showed a mildly prolonged HV interval of 62 msec during sinus rhythm (normal values, 35 to 55 msec) and a pathologic response to atrial pacing, with atrioventricular block occurring after the deflection of the bundle of His during continuous stimulation at a fixed cycle length of 490 msec (Figure 1B). Intravenous methylprednisolone was initiated at a dose of 1 mg per kilogram of body weight per day, and 1:1 atrioventricular conduction was subsequently maintained on surface ECG. A second electrophysiological study during treatment showed normal atrioventricular conduction.

Maintenance immunosuppressive therapy with azathioprine (at a dose of 100 mg daily) and methylprednisolone (at a dose of 4 mg daily) was initiated and continued for 12 months. Serial anti-Ro (SS-A) levels fluctuated during follow-up and became negative after 1 year. Because of the uncertainty of the outcome, a backup pacemaker was implanted. The patient remained completely asymptomatic for 12 months with sustained normal atrioventricular conduction.

In this case of atrioventricular block in an adult patient with positive anti-Ro antibodies, we used electrophysiological testing to localize the conduction defect below the atrioventricular node. This finding, together with left bundle-branch block detected on ECG, suggests specific involvement of the Purkinje fibers. The pathogenesis of cardiac conduction disturbances in adults with positive anti-Ro (SS-A) antibodies remains unclear.3 Experimental studies suggest that anti-Ro antibodies interact with calcium channels and cause reversible inhibition of calcium currents. In fetal hearts, the internalization of these channels leads to apoptosis and fibrosis of the conduction tissue. The presence of a fully developed sarcoplasmic reticulum and the apparent lack of antibody-induced apoptosis in adult cardiomyocytes may explain the differential susceptibility of adult hearts to anti-Ro antibodies2 and, conceivably, the reversibility of the conduction disease in such persons.

Irene Santos-Pardo, M.D.
Melania Martínez-Morillo, M.D.
Roger Villuendas, M.D.
Antoni Bayes-Genis, M.D., Ph.D.
Hospital Universitari Germans Trias i Pujol, Badalona, Spain
abayes.germanstrias@gencat.cat

REFERENCES

1

Chameides L, Truex RC, Vetter V, Rashkind WJ, Galioto FM Jr, Noonan JA. Association of maternal systemic lupus erythematosus with congenital complete heart block. N Engl J Med 1977;297:1204-1207
Full Text | Web of Science | Medline

Lazzerini PE, Capecchi PL, Laghi-Pasini F. Anti-Ro/SSA antibodies and cardiac arrhythmias in the adult: facts and hypotheses. Scand J Immunol 2010;72:213-222
CrossRef | Web of Science | Medline

Costedoat-Chalumeau N, Georgin-la-Vialle S, Amoura Z, Piette J-C. Anti-SSA/Ro and anti-SSB/La antibody-mediated congenital heart block. Lupus 2005;14:660-664
CrossRef | Web of Science | Medline

SOURCE

http://www.nejm.org/doi/full/10.1056/NEJMc1300484?query=TOC

New Research on the Genetics of Conduction Disease

2010  
Heart failure clinics

  

conduction diseases (CD) include defects in impulse generation and conduction. Patients with CD may manifest a wide range of clinical presentations, from asymptomatic to potentially life-threatening arrhythmias. The pathophysiologic mechanisms underlying CD are diverse and may have implications for diagnosis, treatment, and prognosis. Known causes of functional CD include cardiac ion channelopathies or defects in modifying proteins, such as cytoskeletal proteins. Progress in molecular biology and genetics along with development of animal models has increased the understanding of the molecular mechanisms of these disorders. This article discusses the genetic basis for CD and its clinical implications.
(Beinart et al. 2010)
Beinart R, Ruskin J, et al. (2010). The genetics of conduction disease. Heart Fail Clin 6 (2): 201-14.
PMID: 20347788  DOI: 10.1016/j.hfc.2009.11.006  PII: S1551-7136(09)00108-1
2012  
PLoS genetics

  

(Curran and Mohler 2012)
Curran J and Mohler PJ (2012). Defining the Pathways Underlying the Prolonged PR Interval in Atrioventricular Conduction Disease. PLoS Genet. 8 (12): e1003154.
PMID: 23236297  DOI: 10.1371/journal.pgen.1003154  PII: PGENETICS-D-12-02668
2003  
BMC medical genetics

  

BACKGROUND: Mutations in the gene encoding the nuclear membrane protein lamin A/C have been associated with at least 7 distinct diseases including autosomal dominant dilated cardiomyopathy withconduction system disease, autosomal dominant and recessive Emery Dreifuss Muscular Dystrophy, limb girdle muscular dystrophy type 1B, autosomal recessive type 2 Charcot Marie Tooth, mandibuloacral dysplasia, familial partial lipodystrophy and Hutchinson-Gilford progeria.METHODS: We used mutation detection to evaluate the lamin A/C gene in a 45 year-old woman with familial dilated cardiomyopathy and conduction system disease whose family has been well characterized for this phenotype 1.RESULTS: DNA from the proband was analyzed, and a novel 2 base-pair deletion c.908_909delCT in LMNA was identified.CONCLUSIONS: Mutations in the gene encoding lamin A/C can lead to significant cardiac conductionsystem disease that can be successfully treated with pacemakers and/or defibrillators. Genetic screening can help assess risk for arrhythmia and need for device implantation.
(MacLeod et al. 2003)
MacLeod HM, Culley MR, et al. (2003). Lamin A/C truncation in dilated cardiomyopathy with conduction disease. BMC Med. Genet. 4: 4.
PMID: 12854972  DOI: 10.1186/1471-2350-4-4
2012  
Heart (British Cardiac Society)

  

(MacRae 2012)
MacRae CA (2012). Pattern recognition: combining informatics and genetics to re-evaluate conduction disease. Heart 98 (17): 1263-4.
PMID: 22875820  DOI: 10.1136/heartjnl-2012-302408  PII: heartjnl-2012-302408
2004  
The anatomical record. Part A, Discoveries in molecular, cellular, and evolutionary biology

  

Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV block has unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with diseasegene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics.
(Benson 2004) – ORIGINAL FIRST PAPER on the Subject
Benson DW (2004). Genetics of atrioventricular conduction disease in humans. Anat Rec A Discov Mol Cell Evol Biol 280 (2): 934-9.
PMID: 15372490  DOI: 10.1002/ar.a.20099
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Other related articles published on this Open Access Online Scientific Journal, include the following:

Aviva Lev-Ari, PhD, RN and Larry H. Bernstein, MD, FCAP

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Reporter: Aviva Lev-Ari, PhD, RN

GWAS Explores Role of Inherited Variants in Childhood ALL

March 20, 2013

NEW YORK (GenomeWeb News) – Inherited genetic variants — including some found at variable frequencies in different human populations — can significantly bump up an individual’s risk of developing acute lymphoblastic leukemia, according to a multi-population genome-wide association study out last night in the Journal of the National Cancer Institute.

“These findings indicate strong associations between inherited genetic variation and ALL susceptibility in children,” senior author Jun Yang, a pharmaceutical sciences researcher with St. Jude Children’s Research Hospital, and colleagues wrote, “and shed new light on ALL molecular etiology in diverse ancestry.”

Through GWAS analyses involving nearly 2,500 children with ALL and almost 11,000 unaffected individuals, Yang and colleagues from St. Jude and elsewhere tracked down ALL-associated loci falling in four genes previously implicated in the disease and in one new chromosome 10 locus.

For those carrying mostly risk versions of the top ALL-associated SNPs in four genes, they found, ALL incidence was far higher than it was in those with no risk alleles or just one risk allele.

Moreover, the team saw examples of risk alleles that occur more often in the Hispanic population than in European or African-American populations — a pattern that study authors said may partly explain the elevated ALL rates described in Hispanic populations in the past.

Previous GWAS support the notion that ALL risk is at least partly inherited, Yang and colleagues explained. But so far variants in just a few genes have been linked to the disease through studies of individuals with European ancestry.

“Although accumulating evidence indicates inherited predisposition to ALL, the genetic basis of ALL susceptibility in diverse ancestry has not been comprehensively examined,” Yang and his co-authors noted.

To begin exploring such questions in individuals from a variety of backgrounds, the group did a GWAS involving cases and controls from diverse ethnic populations, along with analyses focused on individuals with European, African-American, or Hispanic ancestry.

For the discovery stage of the study, the researchers used Affymetrix arrays to genotype 1,605 children from the Children’s Oncology Group study who had been diagnosed with B-cell ALL. Genetic patterns in these patients were compared with those found in 6,661 unaffected control individuals enrolled through the Multi-Ethnic Study of Atherosclerosis.

The analysis uncovered candidate variants that seemed to coincide with ALL risk at one new locus on chromosome 10, along with four loci linked to ALL in the past.

The latter sites are located in and around the ARID5B, IKZF1, CEBPE, and CDKN2A/2B genes, authors of the study explained, while the newly associated locus fell in the vicinity of the BMI1 and PIP4K2A genes.

Following a series of validation studies in another 845 cases and 4,316 controls analyzed by ancestry, the team confirmed that the top SNPs in most of the genes shared ties with ALL regardless of ethnicity. But there was an exception: so far the top SNP in the vicinity of the CEBPE gene seems to have an ALL association that’s specific to Europeans.

In addition, at least some of the ALL-associated variants — particularly those in the ARID5B and PIP4K2A genes — seem to turn up more or less often depending on the population considered.

For instance, the higher risk version of an ALL-linked SNP in PIP4K2A appears to occur with higher-than-usual frequency in the Hispanic population, researchers reported. In contrast, this variant was somewhat less common in the African-American population and intermediate in Europeans.

Such differences may be important, particularly since results of the study suggest that individuals who have inherited predominantly risk alleles at the top SNPs in the ARID5B, IKZF1, CEBPE, and PIP4K2A genes are some nine times more likely to develop ALL than those carrying one or no risk alleles.

“The genetic basis of ALL is most likely to be polygenic,” Yang and colleagues explained. “However, it should be noted that carrying risk variants at merely four SNPs (ARID5B, IKZF1, CEBPE, and PIP4K2A) conferred a nine-fold increase in disease susceptibility.”

Several of these genes, including ARID5B, IKZF1, and CEBPE, have been implicated in processes such as hematopoietic differentiation and development, study authors noted, which are processes that might be expected to be altered in leukemia.

“With these ALL susceptibility genes now on hand (ARID5B, IKZF1, CDKN2A/2B, CEBPE, PIP4K2A), we are armed with novel knowledge of which certain children develop ALL in the first place,” Yang told GenomeWeb Daily News in an email message. “The fact that alterations in these genes lead to ALL raises the question of what would happen if we restore these pathways in ALL and also make them possible exciting therapeutic targets as well.”

Nevertheless, those involved in the study explained that additional work will be needed, both to fine-map causal variants within the ALL-associated regions found already and to uncover additional genetic contributors to ALL risk within and across many different populations.

“The discoveries … are an important step forward in terms of understanding why children develop ALL in the first place, particularly for those with African or Hispanic ethnicity,” Yang said in a statement. “However, this is probably still just a small part of the complete picture.”

 

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Genomics & Genetics of Cardiovascular Disease Diagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013

 

Curators: Aviva Lev-Ari, PhD, RN and Larry H. Bernstein, MD, FCAP

 

348 articles that appeared in AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013 were classified by the curators of this article into the following TEN categories. The first 9, represent DIAGNOSES of cardiovascular diseases, the last, deals with Pharmacogenomics.

The Cardiovascular Diagnoses that were covered in the period of 3/2010 – 3/2013, include the following:

  • Preventative Cardiology
  • MicroRNA in Serum as Bimarker for Cardiovascular Pathologies: acute myocardial infarction, viral myocarditis, diastolic dysfunction, and acute heart failure
  • Genetic Determinants of Potassium Sensitivity and Hypertension
  • Heart and Aging Research in Genomic Epidemiology: 1700 MIs and 2300 coronary heart disease events among about 29 000 eligible patients
  • Genetics of CVD and Hyperlipidemia, Hyper Cholesterolemia, Metabolic Syndrome
  • Genomics and Valvular Disease
  • Pharmacogenomics

Introductions

Larry H. Bernstein, MD, FCAP

 

The curation of this large amount of material in 10 categories begins with a first chapter on preventative cardiology, which has had much public attention for the last decade.  Much of the concern with preventive cardiology has emphasized diet and exercise.  There is much to be said about this in articles not yet written.  However, there are several decades of research on the amino acid composition of foods, and the essential fatty acids, that indicates an essential balance between proinflammatory and antiinflammatory fatty acids in polyunsaturated fatty acids, and of the harmful effects of saturated fats.  There is also much to be said of essential amino acids, and in particular, those essential for methylation processes, and sulfur metabolism.

The next eight chapters are all concerned with genomics in cardiovascular disease.  This is in no small part a follow up on the completion of the genetic code in 2003, a seminal event.  Let us look at these in clusters.

[1]   microRNA in serum is now considered for a biomarker for cardiovascular disease.  It can be measured at very low levels, but we don’t yet know where it fits.   It might be more revealing once we understand the adaptive mechanism in development of congestive heart failure, renal hypertension, and post-genomic events.

[2]  It appears to me that potassium sensitivity and hypertension approached from the genomic side is more complicate.  Why is that?   The kidney excretes a sodium load and in metabolic acidosis, the serum potassium rises with a metabolic acidemia that can’t be compensated by the respiratory loss of CO2 through the carbonic anhydrase mechanism.

[3]  Heart and aging research is a rich area for work on the long term post-genomic changes, and it involves a large population base.

[4][5]  The genomics of cardiac dysrrhytmias and cardiomyopathies will open new doors into our understanding of the mechanisms of these diseases, and perhaps find therapeutic targets.  There has been a large volume of work on lipid synthesis, the role of the liver in generating apolipoproteins, and this has new answers on the way.  The most important feature, not readily accepted is the measurement of particles, which has now been done by a monoclonal antibody.  Metabolic syndrome brings together adipose tissue metabolism, endocrine and changes in CRP and IL-1.

[6]   Vascular pathologies and coagulation, hyperviscosity has had an enormous increase in intensity of research.  The concept of plaque rupture to account for all AMIs is being modified, and the high sensitivity cardio-specific troponins have become the most widely use test.

[7]  The genomics of valvular disease fits with the increased surgical procedures for valvular disease related to atheroschlerosis and advent of minimally invasive surgical procedures for the reapir and replacement of valves, procedure called TAVR vs. Openhealrt surgery for valve replacement.

[8]  Inherited cardiovascular disease is an older family of disorders, going back to Victor McKusik, and also the “Blue Baby” operation, both at Johns Hopkins.

[9] Pharmacogenomics is a vary active field of investigation and has uncovered inter-individual differences in handling Warfarin as a starter.

 

 

Preventative Cardiology

 

Methods in Genetics and Clinical Interpretation Randomized Trial of Personal Genomics for Preventive Cardiology Design and Challenges

Joshua W. Knowles, MD, PhD, Themistocles L. Assimes, MD, PhD, Michaela Kiernan, PhD, Aleksandra Pavlovic, BS, Benjamin A. Goldstein, PhD, Veronica Yank, MD, Michael V. McConnell, MD, Devin Absher, PhD, Carlos Bustamante, PhD, Euan A. Ashley, MD, DPhil and John P.A. Ioannidis, MD, DSc

Author Affiliations

From the Division of Cardiovascular Medicine (J.W.K., T.L.A., A.P., M.V.M., E.A.A.), Stanford Prevention Research Center (M.K., V.Y., J.P.A.I.), Division of General Medical Disciplines (V.Y.), Department of Genetics (C.B.), Department of Health Research and Policy (J.P.A.I.), Stanford University School of Medicine, Stanford, CA; Quantitative Sciences Unit, Stanford University School of Medicine, Palo Alto, CA (B.A.G.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (D.A.); Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA (J.P.A.I.).

Correspondence to Joshua W. Knowles, MD, PhD, Stanford University School of Medicine, Division of Cardiovascular Medicine, Falk CVRC, 300 Pasteur Dr, Stanford, CA 94305. E-mail knowlej@stanford.edu

Background

Genome-wide association studies (GWAS) have identified more than 1500 disease-associated single nucleotide polymorphisms (SNPs), including many related to atherosclerotic cardiovascular disease (CVD). Associations have been found for most traditional risk factors (TRFs), including lipids,1,2 blood pressure/hypertension,3,4 weight/body mass index,5,6 smoking behavior,7 and diabetes.8–13 GWAS have also identified susceptibility variants for coronary heart disease (CHD). The first and, so far, strongest of these signals was found in the 9p21.3 locus, where common variants in this region increase the relative risk of CVD by 15% to 30% per risk allele in most race/ethnic groups.13–20 Subsequent large-scale GWAS meta-analyses and replication studies in largely white/European populations have led to the reliable identification of an additional 26 loci conferring susceptibility to CHD,2,20–23 all with substantially lower effects sizes compared with the 9p21 locus. Many of these CVD susceptibility loci appear to be conferring risk independent of TRFs and thus cannot currently be assessed by surrogate clinical measures (Table 1). Among the 27 independent loci identified in the most recent large meta-analyses of CVD, 21 were reported not to be associated with any of the TRFs.20,21

 SOURCE

Circulation: Cardiovascular Genetics 2012; 5: 368-376

doi: 10.1161/ CIRCGENETICS.112.962746

 

 

MicroRNA in Serum as Bimarker for Cardiovascular Pathologies: acute myocardial infarction, viral myocarditis,  diastolic dysfunction, and acute heart failure

Increased MicroRNA-1 and MicroRNA-133a Levels in Serum of Patients With Cardiovascular Disease Indicate Myocardial Damage

 

Yasuhide Kuwabara, MD, Koh Ono, MD, PhD, Takahiro Horie, MD, PhD, Hitoo Nishi, MD, PhD, Kazuya Nagao, MD, PhD, Minako Kinoshita, MD, PhD, Shin Watanabe, MD, PhD, Osamu Baba, MD, Yoji Kojima, MD, PhD, Satoshi Shizuta, MD, Masao Imai, MD, Toshihiro Tamura, MD, Toru Kita, MD, PhD and Takeshi Kimura, MD, PhD

Author Affiliations

From the Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan (Y. Kuwabara, K.O., T.H., H.N., K.N., M.K., S.W., O.B., Y. Kojima, S.S., M.I., T.T., T. Kimura); and Kobe City Medical Center General Hospital, Kobe, Japan (T. Kita).

Correspondence to Koh Ono, MD, PhD, Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, Japan 606-8507. E-mail kohono@kuhp.kyoto-u.ac.jp

 

Abstract

Background—Recently, elevation of circulating muscle-specific microRNA (miRNA) levels has been reported in patients with acute myocardial infarction. However, it is still unclear from which part of the myocardium or under what conditions miRNAs are released into circulating blood. The purpose of this study was to identify the source of elevated levels of circulating miRNAs and their function in cardiovascular diseases.

Conclusions—These results suggest that elevated levels of circulating miR-133a in patients with cardiovascular diseases originate mainly from the injured myocardium. Circulating miR-133a can be used as a marker for cardiomyocyte death, and it may have functions in cardiovascular diseases.

SOURCE:

Circulation: Cardiovascular Genetics. 2011; 4: 446-454

Published online before print June 2, 2011,

doi: 10.1161/ CIRCGENETICS.110.958975

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Circulating MicroRNA-208b and MicroRNA-499 Reflect Myocardial Damage in Cardiovascular Disease

Maarten F. Corsten, MD, Robert Dennert, MD, Sylvia Jochems, BSc, Tatiana Kuznetsova, MD, PhD, Yvan Devaux, PhD, Leon Hofstra, MD, PhD, Daniel R. Wagner, MD, PhD, Jan A. Staessen, MD, PhD, Stephane Heymans, MD, PhD and Blanche Schroen, PhD

Author Affiliations

From the Center for Heart Failure Research (M.F.C., R.D., S.J., S.H., B.S.), Cardiovascular Research Institute, Maastricht, The Netherlands; the Division of Hypertension and Cardiovascular Rehabilitation (T.K., J.A.S.), Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium and Department of Epidemiology, Maastricht University Medical Center, Maastricht, The Netherlands; Centre de Recherche Public–Santé, Luxembourg (Y.D., D.R.W.), Luxembourg; Maastricht University Medical Center (L.H.), Maastricht, The Netherlands; and Centre Hospitalier Luxembourg (D.R.W.), Luxembourg.

Correspondence to Blanche Schroen, PhD, Center for Heart Failure Research, Cardiovascular Research Institute Maastricht, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands. E-mail b.schroen@cardio.unimaas.nl

Drs Heymans and Schroen contributed equally to this work.

Abstract

Background— Small RNA molecules, called microRNAs, freely circulate in human plasma and correlate with varying pathologies. In this study, we explored their diagnostic potential in a selection of prevalent cardiovascular disorders.

Methods and Results— MicroRNAs were isolated from plasmas from well-characterized patients with varying degrees of cardiac damage:

(1) acute myocardial infarction,

(2) viral myocarditis,

(3) diastolic dysfunction, and

(4) acute heart failure.

Plasma levels of selected microRNAs, including heart-associated (miR-1, -133a, -208b, and -499), fibrosis-associated (miR-21 and miR-29b), and leukocyte-associated (miR-146, -155, and -223) candidates, were subsequently assessed using real-time polymerase chain reaction. Strikingly, in plasma from acute myocardial infarction patients, cardiac myocyte–associated miR-208b and -499 were highly elevated, 1600-fold (P<0.005) and 100-fold (P<0.0005), respectively, as compared with control subjects. Receiver operating characteristic curve analysis revealed an area under the curve of 0.94 (P<1010) for miR-208b and 0.92 (P<109) for miR-499. Both microRNAs correlated with plasma troponin T, indicating release of microRNAs from injured cardiomyocytes. In viral myocarditis, we observed a milder but significant elevation of these microRNAs, 30-fold and 6-fold, respectively. Plasma levels of leukocyte-expressed microRNAs were not significantly increased in acute myocardial infarction or viral myocarditis patients, despite elevated white blood cell counts. In patients with acute heart failure, only miR-499 was significantly elevated (2-fold), whereas no significant changes in microRNAs studied could be observed in diastolic dysfunction. Remarkably, plasma microRNA levels were not affected by a wide range of clinical confounders, including age, sex, body mass index, kidney function, systolic blood pressure, and white blood cell count.

Conclusions— Cardiac damage initiates the detectable release of cardiomyocyte-specific microRNAs-208b and -499 into the circulation.

SOURCE:

Circulation: Cardiovascular Genetics. 2010; 3: 499-506

Published online before print October 4, 2010,

doi: 10.1161/ CIRCGENETICS.110.957415

 

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Genetic Determinants of Potassium Sensitivity and Hypertension

 

Integrated Computational and Experimental Analysis of the Neuroendocrine Transcriptome in Genetic Hypertension Identifies Novel Control Points for the Cardiometabolic Syndrome

Ryan S. Friese, PhD, Chun Ye, PhD, Caroline M. Nievergelt, PhD, Andrew J. Schork, BS, Nitish R. Mahapatra, PhD, Fangwen Rao, MD, Philip S. Napolitan, BS, Jill Waalen, MD, MPH, Georg B. Ehret, MD, Patricia B. Munroe, PhD, Geert W. Schmid-Schönbein, PhD, Eleazar Eskin, PhD and Daniel T. O’Connor, MD

Author Affiliations

From the Departments of Bioengineering (R.S.F., G.W.S.-S.), Medicine (R.S.F., A.J.S., F.R., P.S.N., D.T.O.), Pharmacology (D.T.O.), and Psychiatry (C.M.N.), the Bioinformatics Program (C.Y.), and the Institute for Genomic Medicine (D.T.O.), University of California at San Diego; the VA San Diego Healthcare System, San Diego, CA (D.T.O.); the Departments of Computer Science & Human Genetics, University of California at Los Angeles (E.E.); the Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India (N.R.M.); Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (P.B.M.); Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (G.B.E.); and Scripps Research Institute, La Jolla, CA (J.W.).

Correspondence to Daniel T. O’Connor, MD, Department of Medicine, University of California at San Diego School of Medicine, VASDHS (0838), Skaggs (SSPPS) Room 4256, 9500 Gilman Drive, La Jolla, CA 92093-0838. E-mail doconnor@ucsd.edu

Abstract

Background—Essential hypertension, a common complex disease, displays substantial genetic influence. Contemporary methods to dissect the genetic basis of complex diseases such as the genomewide association study are powerful, yet a large gap exists betweens the fraction of population trait variance explained by such associations and total disease heritability.

Methods and Results—We developed a novel, integrative method (combining animal models, transcriptomics, bioinformatics, molecular biology, and trait-extreme phenotypes) to identify candidate genes for essential hypertension and the metabolic syndrome. We first undertook transcriptome profiling on adrenal glands from blood pressure extreme mouse strains: the hypertensive BPH (blood pressure high) and hypotensive BPL (blood pressure low). Microarray data clustering revealed a striking pattern of global underexpression of intermediary metabolism transcripts in BPH. The MITRA algorithm identified a conserved motif in the transcriptional regulatory regions of the underexpressed metabolic genes, and we then hypothesized that regulation through this motif contributed to the global underexpression. Luciferase reporter assays demonstrated transcriptional activity of the motif through transcription factors HOXA3, SRY, and YY1. We finally hypothesized that genetic variation at HOXA3, SRY, and YY1 might predict blood pressure and other metabolic syndrome traits in humans. Tagging variants for each locus were associated with blood pressure in a human population blood pressure extreme sample with the most extensive associations for YY1 tagging single nucleotide polymorphism rs11625658 on systolic blood pressure, diastolic blood pressure, body mass index, and fasting glucose. Meta-analysis extended the YY1 results into 2 additional large population samples with significant effects preserved on diastolic blood pressure, body mass index, and fasting glucose.

Conclusions—The results outline an innovative, systematic approach to the genetic pathogenesis of complex cardiovascular disease traits and point to transcription factor YY1 as a potential candidate gene involved in essential hypertension and the cardiometabolic syndrome.

 SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 430-440

Published online before print June 5, 2012,

doi: 10.1161/ CIRCGENETICS.111.962415

Genome-Wide Linkage and Positional Candidate Gene Study of Blood Pressure Response to Dietary Potassium Intervention

The Genetic Epidemiology Network of Salt Sensitivity Study

Tanika N. Kelly, PhD, James E. Hixson, PhD, Dabeeru C. Rao, PhD, Hao Mei, MD, PhD, Treva K. Rice, PhD, Cashell E. Jaquish, PhD, Lawrence C. Shimmin, PhD, Karen Schwander, MS, Chung-Shuian Chen, MS, Depei Liu, PhD, Jichun Chen, MD, Concetta Bormans, PhD, Pramila Shukla, MS, Naveed Farhana, MS, Colin Stuart, BS, Paul K. Whelton, MD, MSc, Jiang He, MD, PhD and Dongfeng Gu, MD, PhD

Author Affiliations

From the Department of Epidemiology (T.N.K., H.M., C.-S.C., J.H.), Tulane University School of Public Health and Tropical Medicine, and Department of Medicine (J.H.), Tulane University School of Medicine, New Orleans, La; Department of Epidemiology (J.E.H., L.C.S., C.B., P.S., N.F., C.S.), University of Texas School of Public Health, Houston, Tex; Division of Biostatistics (D.C.R., T.K.R., K.S.), Washington University School of Medicine, St Louis, Mo; Division of Prevention and Population Sciences (C.E.J.), National Heart, Lung, Blood Institute, Bethesda, Md; National Laboratory of Medical Molecular Biology (D.L.), Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Cardiovascular Institute and Fuwai Hospital (J.C., D.G.), Chinese Academy of Medical Sciences and Peking Union Medical College and Chinese National Center for Cardiovascular Disease Control and Research, Beijing, China; and Office of the President (P.K.W.), Loyola University Health System and Medical Center, Maywood, Ill.

Correspondence to Dongfeng Gu, MD, PhD, Division of Population Genetics and Prevention, Cardiovascular Institute and Fuwai Hospital, 167 Beilishi Rd, Beijing 100037, China. E-mail gudongfeng@vip.sina.com

Abstract

Background— Genetic determinants of blood pressure (BP) response to potassium, or potassium sensitivity, are largely unknown. We conducted a genome-wide linkage scan and positional candidate gene analysis to identify genetic determinants of potassium sensitivity.

Conclusions— Genetic regions on chromosomes 3 and 11 may harbor important susceptibility loci for potassium sensitivity. Furthermore, the AGTR1 gene was a significant predictor of BP responses to potassium intake.

SOURCE:

Circulation: Cardiovascular Genetics. 2010; 3: 539-547

Published online before print September 22, 2010,

doi: 10.1161/ CIRCGENETICS.110.940635

 

Genome-Wide Association Study of Cardiac Structure and Systolic Function in African Americans

The Candidate Gene Association Resource (CARe) Study

Ervin R. Fox, MD*, Solomon K. Musani, PhD*, Maja Barbalic, PhD*, Honghuang Lin, PhD, Bing Yu, MS, Kofo O. Ogunyankin, MD, Nicholas L. Smith, PhD, Abdullah Kutlar, MD, Nicole L. Glazer, MD, Wendy S. Post, MD, MS, Dina N. Paltoo, PhD, MPH, Daniel L. Dries, MD, MPH, Deborah N. Farlow, PhD, Christine W. Duarte, PhD, Sharon L. Kardia, PhD, Kristin J. Meyers, PhD, Yan V. Sun, PhD, Donna K. Arnett, PhD, Amit A. Patki, MS, Jin Sha, MS, Xiangqui Cui, PhD, Tandaw E. Samdarshi, MD, MPH, Alan D. Penman, PhD, Kirsten Bibbins-Domingo, MD, PhD, Petra Bůžková, PhD, Emelia J. Benjamin, MD, David A. Bluemke, MD, PhD, Alanna C. Morrison, PhD, Gerardo Heiss, MD, J. Jeffrey Carr, MD, MSc, Russell P. Tracy, PhD, Thomas H. Mosley, PhD, Herman A. Taylor, MD, Bruce M. Psaty, MD, PhD, Susan R. Heckbert, MD, PhD, Thomas P. Cappola, MD, ScM and Ramachandran S. Vasan, MD

Author Affiliations

Guest Editor for this article was Barry London, MD, PhD.

Correspondence to Ervin Fox, MD MPH, FAHA, FACC, Professor of Medicine, Department of Medicine, University of Mississippi Medical Center, 2500 North State St, Jackson, MS 39216. E-mail efox@medicine.umsmed.edu

* These authors contributed equally as joint first authors.

Abstract

Background—Using data from 4 community-based cohorts of African Americans, we tested the association between genome-wide markers (single-nucleotide polymorphisms) and cardiac phenotypes in the Candidate-gene Association Resource study.

Methods and Results—Among 6765 African Americans, we related age, sex, height, and weight-adjusted residuals for 9 cardiac phenotypes (assessed by echocardiogram or magnetic resonance imaging) to 2.5 million single-nucleotide polymorphisms genotyped using Genome-wide Affymetrix Human SNP Array 6.0 (Affy6.0) and the remainder imputed. Within the cohort, genome-wide association analysis was conducted, followed by meta-analysis across cohorts using inverse variance weights (genome-wide significance threshold=4.0 ×107). Supplementary pathway analysis was performed. We attempted replication in 3 smaller cohorts of African ancestry and tested lookups in 1 consortium of European ancestry (EchoGEN). Across the 9 phenotypes, variants in 4 genetic loci reached genome-wide significance: rs4552931 in UBE2V2 (P=1.43×107) for left ventricular mass, rs7213314 in WIPI1 (P=1.68×107) for left ventricular internal diastolic diameter, rs1571099 in PPAPDC1A (P=2.57×108) for interventricular septal wall thickness, and rs9530176 in KLF5 (P=4.02×107) for ejection fraction. Associated variants were enriched in 3 signaling pathways involved in cardiac remodeling. None of the 4 loci replicated in cohorts of African ancestry was confirmed in lookups in EchoGEN.

Conclusions—In the largest genome-wide association study of cardiac structure and function to date in African Americans, we identified 4 genetic loci related to left ventricular mass, interventricular septal wall thickness, left ventricular internal diastolic diameter, and ejection fraction, which reached genome-wide significance. Replication results suggest that these loci may be unique to individuals of African ancestry. Additional large-scale studies are warranted for these complex phenotypes.

SOURCE:

Circulation: Cardiovascular Genetics. 2013; 6: 37-46

Published online before print December 28, 2012,

doi: 10.1161/ CIRCGENETICS.111.962365

 

Heart and Aging Research in Genomic Epidemiology: 1700 MIs and 2300 coronary heart disease events among about 29 000 eligible patients

 

Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium

Design of Prospective Meta-Analyses of Genome-Wide Association Studies From 5 Cohorts

Bruce M. Psaty, MD, PhD, Christopher J. O’Donnell, MD, MPH, Vilmundur Gudnason, MD, PhD, Kathryn L. Lunetta, PhD, Aaron R. Folsom, MD, Jerome I. Rotter, MD, André G. Uitterlinden, PhD, Tamara B. Harris, MD, Jacqueline C.M. Witteman, PhD, Eric Boerwinkle, PhD and on Behalf of the CHARGE Consortium

Author Affiliations

From the Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services (B.M.P.), University of Wash; Center for Health Studies, Group Health (B.M.P.), Seattle, Wash; the National Heart, Lung and Blood Institute and the Framingham Heart Study (C.J.O.D.), Framingham, Mass; Icelandic Heart Association and the Department of Cardiovascular Genetics (Y.G.), University of Iceland, Reykjavik, Iceland; Department of Biostatistics (K.L.), Boston University School of Public Health, Mass; Division of Epidemiology and Community Health (A.R.F.), University of Minnesota, Minneapolis; Medical Genetics Institute (J.I.R.), Cedars-Sinai Medical Center, Los Angeles, Calif; Departments of Internal Medicine (A.G.U.) and Epidemiology (A.G.U., J.C.M.W.), Erasmus Medical Center, Rotterdam, The Netherlands; Laboratory of Epidemiology, Demography, and Biometry (T.B.H.), Intramural Research Program, National Institute on Aging, Bethesda, Md; and Human Genetics Center and Division of Epidemiology (E.B.), University of Texas, Houston.

Guest editor for this article was Elizabeth R. Hauser, PhD.

Abstract

Background— The primary aim of genome-wide association studies is to identify novel genetic loci associated with interindividual variation in the levels of risk factors, the degree of subclinical disease, or the risk of clinical disease. The requirement for large sample sizes and the importance of replication have served as powerful incentives for scientific collaboration.

Methods— The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium was formed to facilitate genome-wide association studies meta-analyses and replication opportunities among multiple large population-based cohort studies, which collect data in a standardized fashion and represent the preferred method for estimating disease incidence. The design of the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium includes 5 prospective cohort studies from the United States and Europe: the Age, Gene/Environment Susceptibility—Reykjavik Study, the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study. With genome-wide data on a total of about 38 000 individuals, these cohort studies have a large number of health-related phenotypes measured in similar ways. For each harmonized trait, within-cohort genome-wide association study analyses are combined by meta-analysis. A prospective meta-analysis of data from all 5 cohorts, with a properly selected level of genome-wide statistical significance, is a powerful approach to finding genuine phenotypic associations with novel genetic loci.

Conclusions— The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium and collaborating non-member studies or consortia provide an excellent framework for the identification of the genetic determinants of risk factors, subclinical-disease measures, and clinical events.

Example of Coronary Heart Disease

The cohort-study methods papers provide detail about many of the phenotypes listed in Table 2. For coronary heart disease, investigators knowledgeable about the phenotype in each study decided to focus on fatal and nonfatal myocardial infarction (MI) as the primary outcome because the MI criteria differed in only trivial ways among the studies. There were some minor differences in the definition of the composite outcome of MI, fatal coronary heart disease, and sudden death, which became the secondary outcome. Only subjects at risk for an incident event were included in the analysis. MI survivors whose DNA was drawn after the event were not eligible. The primary analysis was restricted to Europeans or European Americans. Patients entered the analysis at the time of the DNA blood draw, and were followed until an event, death, loss to follow up, or the last visit. The main recommendations of the Analysis Committee were adopted, and a threshold of 5×108 was selected for genome-wide statistical significance. Analyses in progress include about 1700 MIs and 2300 coronary heart disease events among about 29 000 eligible patients. Each cohort conducted its own analysis, and results were uploaded to a secure share site for the fixed-effects meta-analysis. Even with this number of events (Supplemental Figure 2), power is good for only for relatively high minor allele frequencies (>0.25) and large relative risks (>1.3).

The authors had full access to and take full responsibility for the integrity of the data. All authors have read and agree to the manuscript as written.

Discussion

In thousands of published papers, the 5 CHARGE cohort studies and many of the collaborating studies have already characterized the risk factors for and the incidence and prognosis of a variety of aging-related and cardiovascular conditions. The analysis of the incident MI, for instance, is free from the survival bias typically associated with cross-sectional or case-control studies. The methodologic advantages of the prospective population-based cohort design, the similarity of phenotypes across 5 studies, the availability of genome-wide genotyping data in each cohort, and the need for large sample sizes to provide reliable estimates of genotype-phenotype associations have served as the primary incentives for the formation of the CHARGE consortium, which includes GWAS data on about 38 000 individuals. The consortium effort relies on collaborative methods that are similar to those used by the individual contributing cohorts.

Phenotype experts who know the studies and the data well are responsible for phenotype-standardization across cohorts. The coordinated prospectively planned meta-analyses of CHARGE provide results that are virtually identical to a cohort-adjusted pooled analysis of individual level data. This approach–the within-study analysis followed by a between-study meta-analysis–avoids the human subjects issues associated with individual-level data sharing.

Editors, reviewers, and readers expect replication as the standard in science.6 The finding of a genetic association in one population with evidence for replication in multiple independent populations provides moderate assurance against false-positive reports and helps to establish the validity of the original finding. In a single experiment, the discovery-replication structure is traditionally embodied in a 2-stage design. The CHARGE consortium includes up to 5 independent replicate samples as well as additional collaborating studies for some phenotype working groups, so that it would have been possible to set up analysis plans within CHARGE to mimic the traditional 2-stage design for replication. For instance, the 2 largest cohorts could have served as the discovery set and the others as the replication set. However, attaining the extremely small probability values expected in GWAS requires large sample sizes. For any phenotype, a prospective meta-analysis of all participating cohorts, with a properly selected level of genome-wide statistical significance to minimize the chance of false-positives, is the most powerful approach to finding new genuine associations for genetic loci.25 When findings narrowly miss the prespecified significance threshold, genotyping individuals in other independent populations provides additional evidence about the association. For findings that substantially exceed pre-established significance thresholds, the results of a CHARGE meta-analysis effectively provide evidence of a multistudy replication.

The effort to assemble and manage the CHARGE consortium has provided some interesting and unanticipated challenges. Participating cohorts often had relationships with outside study groups that predated the formation of CHARGE. Timelines for genotyping and imputation have shifted. Purchases of new computer systems for the volume of work were sometimes necessary. Each cohort came to the consortium with their own traditions for methods of analysis, organization, and authorship policies that, while appropriate for their own work, were not always optimal for collaboration with multiple external groups. Within each cohort, the investigators had often formed working groups that divided up the large number of available phenotypes in ways that made sense locally but did not necessarily match the configuration that had been adopted by other cohorts. The Research Steering Committee has attempted to create a set of CHARGE working groups that accommodate the needs and the conventions of the various cohorts. Transparency, disclosure, and professional collaborative behavior by all participating investigators have been essential to the process.

Resource limitations are another challenge. Grant applications that funded the original single-study genome-wide genotyping effort typically imagined a much simpler design. The CHS whole-genome study had as its primary aim, for instance, the analysis of data on 3 endpoints, coronary disease, stroke and heart failure. With a score of active phenotype working groups, the CHARGE collaboration broadened the scope of the short-term work well beyond initial expectations for all the participating cohorts.

One of the premier challenges has been communications among scores of investigators at a dozen sites. CHS and ARIC are themselves multi-site studies. To be successful, the CHARGE collaboration has required effective communications: (1) within each cohort; (2) between cohorts; (3) within the CHARGE working groups; and (4) among the major CHARGE committees. In addition to the traditional methods of conference calls and email, the CHARGE “wiki,” set up by Dr J. Bis (Seattle, Wash), has provided a crucial and highly functional user-driven website for calendars, minutes, guidelines, working group analysis plans, manuscript proposals, and other documents. In the end, there is no substitute for face-to-face meetings, especially at the beginning of the collaboration, and this complex meta-organization has benefited from several CHARGE-wide meetings.

The major emerging opportunity is the collaboration with other studies and consortia. Many working groups have already incorporated nonmember studies into their efforts. Several working groups have coordinated submissions of initial manuscripts with the parallel submission of manuscripts from other studies or consortia. Several working groups have embarked on plans for joint meta-analyses between CHARGE and other consortia. CHARGE has tried to acknowledge and reward the efforts of champions, who assume leadership responsibility for moving these large complex projects forward and who are often hard-working young investigators, the key to the future success of population science.

The CHARGE Consortium represents an innovative model of collaborative research conducted by research teams that know well the strengths, the limitations, and the data from 5 prospective population-based cohort studies. By leveraging the dense genotyping, deep phenotyping and the diverse expertise, prospective meta-analyses are underway to identify and replicate the major common genetic determinants of risk factors, measures of subclinical disease, and clinical events for cardiovascular disease and aging.

SOURCE:

Circulation: Cardiovascular Genetics.2009; 2: 73-80

doi: 10.1161/ CIRCGENETICS.108.829747

 

 

Genomics of Ventricular arrhythmias, A-Fib, Right Ventricular Dysplasia, Cardiomyopathy

 

Comprehensive Desmosome Mutation Analysis in North Americans With Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy

A. Dénise den Haan, MD, Boon Yew Tan, MBChB, Michelle N. Zikusoka, MD, Laura Ibañez Lladó, MS, Rahul Jain, MD, Amy Daly, MS, Crystal Tichnell, MGC, Cynthia James, PhD, Nuria Amat-Alarcon, MS, Theodore Abraham, MD, Stuart D. Russell, MD, David A. Bluemke, MD, PhD, Hugh Calkins, MD, Darshan Dalal, MD, PhD and Daniel P. Judge, MD

Author Affiliations

From the Department of Medicine/Cardiology (A.D.d.H., B.Y.T., M.N.Z., L.I.L., R.J., A.D., C.T., C.J., N.A.-A., T.A., S.D.R., H.C., D.D., D.P.J.), Johns Hopkins University School of Medicine, Baltimore, Md; Department of Cardiology, Division of Heart and Lungs (A.D.d.H.), University Medical Center Utrecht, Utrecht, The Netherlands; and National Institutes of Health, Radiology and Imaging Sciences (D.A.B.), Bethesda, Md.

Correspondence to Daniel P. Judge, MD, Johns Hopkins University, Division of Cardiology, Ross 1049; 720 Rutland Avenue, Baltimore, MD 21205. E-mail djudge@jhmi.edu

Abstract

Background— Arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is an inherited disorder typically caused by mutations in components of the cardiac desmosome. The prevalence and significance of desmosome mutations among patients with ARVD/C in North America have not been described previously. We report comprehensive desmosome genetic analysis for 100 North Americans with clinically confirmed or suspected ARVD/C.

Methods and Results— In 82 individuals with ARVD/C and 18 people with suspected ARVD/C, DNA sequence analysis was performed on PKP2, DSG2, DSP, DSC2, and JUP. In those with ARVD/C, 52% harbored a desmosome mutation. A majority of these mutations occurred in PKP2. Notably, 3 of the individuals studied have a mutation in more than 1 gene. Patients with a desmosome mutation were more likely to have experienced ventricular tachycardia (73% versus 44%), and they presented at a younger age (33 versus 41 years) compared with those without a desmosome mutation. Men with ARVD/C were more likely than women to carry a desmosome mutation (63% versus 38%). A mutation was identified in 5 of 18 patients (28%) with suspected ARVD. In this smaller subgroup, there were no significant phenotypic differences identified between individuals with a desmosome mutation compared with those without a mutation.

Conclusions— Our study shows that in 52% of North Americans with ARVD/C a mutation in one of the cardiac desmosome genes can be identified. Compared with those without a desmosome gene mutation, individuals with a desmosome gene mutation had earlier-onset ARVD/C and were more likely to have ventricular tachycardia.

SOURCE:

Circulation: Cardiovascular Genetics.2009; 2: 428-435

Published online before print June 3, 2009,

doi: 10.1161/ CIRCGENETICS.109.858217

 

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Phospholamban R14del mutation in patients diagnosed with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy: evidence supporting the concept of arrhythmogenic cardiomyopathy 
Eur J Heart Fail. 2012;14:1199-1207,

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Assessing the Significance of Pathogenic Mutations and Autopsy Findings in the Light of 2010 Arrhythmogenic Right Ventricular Cardiomyopathy Diagnostic Criteria: A Clinical Challenge 
Circ Cardiovasc Genet. 2012;5:384-386,

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Loss of Cadherin-Binding Proteins {beta}-Catenin and Plakoglobin in the Heart Leads to Gap Junction Remodeling and Arrhythmogenesis 
Mol. Cell. Biol.. 2012;32:1056-1067, 
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J. Cell Sci.. 2012;125:1058-1067,

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General and Disease-Specific Psychosocial Adjustment in Patients With Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy With Implantable Cardioverter Defibrillators: A Large Cohort Study 
Circ Cardiovasc Genet. 2012;5:18-24,

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Hum Mol Genet. 2011;20:4582-4596,

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Mechanistic insights into arrhythmogenic right ventricular cardiomyopathy caused by desmocollin-2 mutations 
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Large-Scale Candidate Gene Analysis in Whites and African Americans Identifies IL6R Polymorphism in Relation to Atrial Fibrillation

The National Heart, Lung, and Blood Institute’s Candidate Gene Association Resource (CARe) Project

Renate B. Schnabel, MD, MSc*, Kathleen F. Kerr, PhD*, Steven A. Lubitz, MD*, Ermeg L. Alkylbekova, MD*, Gregory M. Marcus, MD, MAS, Moritz F. Sinner, MD, Jared W. Magnani, MD, Philip A. Wolf, MD, Rajat Deo, MD, Donald M. Lloyd-Jones, MD, ScM, Kathryn L. Lunetta, PhD, Reena Mehra, MD, MS, Daniel Levy, MD, Ervin R. Fox, MD, MPH, Dan E. Arking, PhD, Thomas H. Mosley, PhD, Martina Müller-Nurasyid, MSc, PhD, Taylor R. Young, MA, H.-Erich Wichmann, MD, PhD, Sudha Seshadri, MD, Deborah N. Farlow, PhD, Jerome I. Rotter, MD, Elsayed Z. Soliman, MD, MSc, MS, Nicole L. Glazer, PhD, James G. Wilson, MD, Monique M.B. Breteler, MD, Nona Sotoodehnia, MD, MPH, Christopher Newton-Cheh, MD, MPH, Stefan Kääb, MD, PhD, Patrick T. Ellinor, MD, PhD*, Alvaro Alonso, MD*, Emelia J. Benjamin, MD, ScM*, Susan R. Heckbert, MD, PhD* and for the Candidate Gene Association Resource (CARe) Atrial Fibrillation/Electrocardiography Working Group

Correspondence to Susan R. Heckbert, MD, PhD, Cardiovascular Health Research Unit, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA 98101. E-mail heckbert@u.washington.edu; Emelia J. Benjamin, MD, ScM, Medicine and Epidemiology, Boston University Schools of Medicine and Public Health, The Framingham Heart Study, 73 Mount Wayte Ave, Framingham, MA 01702–5827. E-mail emelia@bu.edu; Renate B. Schnabel, MD, MSc, Department of Medicine 2, Cardiology, Johannes Gutenberg University, Langenbeckstr 1, 55131 Mainz, Germany. E-mail schnabelr@gmx.de

* These authors contributed equally to the manuscript.

Abstract

Background—The genetic background of atrial fibrillation (AF) in whites and African Americans is largely unknown. Genes in cardiovascular pathways have not been systematically investigated.

Methods and Results—We examined a panel of approximately 50 000 common single-nucleotide polymorphisms (SNPs) in 2095 cardiovascular candidate genes and AF in 3 cohorts with participants of European (n=18 524; 2260 cases) or African American descent (n=3662; 263 cases) in the National Heart, Lung, and Blood Institute’s Candidate Gene Association Resource. Results in whites were followed up in the German Competence Network for AF (n=906, 468 cases). The top result was assessed in relation to incident ischemic stroke in the Cohorts for Heart and Aging Research in Genomic Epidemiology Stroke Consortium (n=19 602 whites, 1544 incident strokes). SNP rs4845625 in the IL6R gene was associated with AF (relative risk [RR] C allele, 0.90; 95% confidence interval [CI], 0.85–0.95; P=0.0005) in whites but did not reach statistical significance in African Americans (RR, 0.86; 95% CI, 0.72–1.03; P=0.09). The results were comparable in the German AF Network replication, (RR, 0.71; 95% CI, 0.57–0.89; P=0.003). No association between rs4845625 and stroke was observed in whites. The known chromosome 4 locus near PITX2 in whites also was associated with AF in African Americans (rs4611994; hazard ratio, 1.40; 95% CI, 1.16–1.69; P=0.0005).

Conclusions—In a community-based cohort meta-analysis, we identified genetic association in IL6R with AF in whites. Additionally, we demonstrated that the chromosome 4 locus known from recent genome-wide association studies in whites is associated with AF in African Americans.

 SOURCE:

Circulation: Cardiovascular Genetics.2011; 4: 557-564

Published online before print August 16, 2011,

doi: 10.1161/ CIRCGENETICS.110.959197

PITX2c Is Expressed in the Adult Left Atrium, and Reducing Pitx2c Expression Promotes Atrial Fibrillation Inducibility and Complex Changes in Gene Expression

Paulus Kirchhof, MD*, Peter C. Kahr*, Sven Kaese, Ilaria Piccini, PhD, Ismail Vokshi, BSc, Hans-Heinrich Scheld, MD, Heinrich Rotering, MD, Lisa Fortmueller, MD (vet), Sandra Laakmann, MD (vet), Sander Verheule, PhD, Ulrich Schotten, MD, PhD, Larissa Fabritz, MD and Nigel A. Brown, PhD

Author Affiliations

From the Department of Cardiology and Angiology (P.K., P.C.K., S.K., I.P., L.F., S.L., L.F.) and the Department of Thoracic and Cardiovascular Surgery (H.-H.S., H.R.), University Hospital Muenster, Germany; Division of Biomedical Sciences (P.C.K., I.V., N.A.B.), St. George’s, University of London, United Kingdom; and the Department of Physiology (S.V., U.S.), Maastricht University, The Netherlands.

Correspondence to Nigel A. Brown, PhD, Division of Biomedical Sciences, St George’s, University of London, Cranmer Terrace, London, SW17 0RE, UK. E-mail nbrown@sgul.ac.uk

* Drs Kirchhof and Kahr contributed equally to this work.

Abstract

Background— Intergenic variations on chromosome 4q25, close to the PITX2 transcription factor gene, are associated with atrial fibrillation (AF). We therefore tested whether adult hearts express PITX2 and whether variation in expression affects cardiac function.

Methods and Results— mRNA for PITX2 isoform c was expressed in left atria of human and mouse, with levels in right atrium and left and right ventricles being 100-fold lower. In mice heterozygous for Pitx2c (Pitx2c+/), left atrial Pitx2c expression was 60% of wild-type and cardiac morphology and function were not altered, except for slightly elevated pulmonary flow velocity. Isolated Pitx2c+/ hearts were susceptible to AF during programmed stimulation. At short paced cycle lengths, atrial action potential durations were shorter in Pitx2c+/ than in wild-type. Perfusion with the β-receptor agonist orciprenaline abolished inducibility of AF and reduced the effect on action potential duration. Spontaneous heart rates, atrial conduction velocities, and activation patterns were not affected in Pitx2c+/ hearts, suggesting that action potential duration shortening caused wave length reduction and inducibility of AF. Expression array analyses comparing Pitx2c+/ with wild-type, for left atrial and right atrial tissue separately, identified genes related to calcium ion binding, gap and tight junctions, ion channels, and melanogenesis as being affected by the reduced expression of Pitx2c.

Conclusions— These findings demonstrate a physiological role for PITX2 in the adult heart and support the hypothesis that dysregulation of PITX2 expression can be responsible for susceptibility to AF.

 SOURCE:

Circulation: Cardiovascular Genetics.2011; 4: 123-133

Published online before print January 31, 2011,

doi: 10.1161/ CIRCGENETICS.110.958058

 

Genetics of CVD and Hyperlipidemia, Hyper Cholesterolemia, Metabolic Syndrome

 

Genetic Loci Associated With Plasma Concentration of Low-Density Lipoprotein Cholesterol, High-Density Lipoprotein Cholesterol, Triglycerides, Apolipoprotein A1, and Apolipoprotein B Among 6382 White Women in Genome-Wide Analysis With Replication

Daniel I. Chasman, PhD*, Guillaume Paré, MD, MS*, Robert Y.L. Zee, PhD, MPH, Alex N. Parker, PhD, Nancy R. Cook, ScD, Julie E. Buring, ScD, David J. Kwiatkowski, MD, PhD, Lynda M. Rose, MS, Joshua D. Smith, BS, Paul T. Williams, PhD, Mark J. Rieder, PhD, Jerome I. Rotter, MD, Deborah A. Nickerson, PhD, Ronald M. Krauss, MD, Joseph P. Miletich, MD and Paul M Ridker, MD, MPH

Author Affiliations

From the Center for Cardiovascular Disease Prevention (D.I.C., G.P., R.Y.L.Z., N.R.C., J.E.B., L.M.R., P.M.R.) and Donald W. Reynolds Center for Cardiovascular Research (D.I.C., G.P., R.Y.L.Z., N.R.C., D.J.K., P.M.R.), Brigham and Women’s Hospital, Harvard Medical School, Boston, Mass; Amgen, Inc, Cambridge, Mass (A.N.P., J.M.P.); Department of Genome Sciences, University of Washington, Seattle, Wash (J.D.S., M.J.R., D.A.N.); Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, Calif (P.T.W., R.M.K.); Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, Calif (J.I.R.); and Children’s Hospital Oakland Research Institute, Oakland, Calif (R.M.K.).

Correspondence to Daniel I. Chasman, Center for Cardiovascular Disease Prevention, Brigham and Women’s Hospital, 900 Commonwealth Ave E, Boston, MA 02215. E-mail dchasman@rics.bwh.harvard.edu

Abstract

Background— Genome-wide genetic association analysis represents an opportunity for a comprehensive survey of the genes governing lipid metabolism, potentially revealing new insights or even therapeutic strategies for cardiovascular disease and related metabolic disorders.

Methods and Results— We have performed large-scale, genome-wide genetic analysis among 6382 white women with replication in 2 cohorts of 970 additional white men and women for associations between common single-nucleotide polymorphisms and low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein (Apo) A1, and ApoB. Genome-wide associations (P<5×108) were found at the PCSK9 gene, the APOB gene, the LPL gene, the APOA1-APOA5 locus, the LIPC gene, the CETP gene, the LDLR gene, and the APOE locus. In addition, genome-wide associations with triglycerides at the GCKR gene confirm and extend emerging links between glucose and lipid metabolism. Still other genome-wide associations at the 1p13.3 locus are consistent with emerging biological properties for a region of the genome, possibly related to the SORT1 gene. Below genome-wide significance, our study provides confirmatory evidence for associations at 5 novel loci with low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, or triglycerides reported recently in separate genome-wide association studies. The total proportion of variance explained by common variation at the genome-wide candidate loci ranges from 4.3% for triglycerides to 12.6% for ApoB.

Conclusion— Genome-wide associations at the GCKR gene and near the SORT1 gene, as well as confirmatory associations at 5 additional novel loci, suggest emerging biological pathways for lipid metabolism among white women.

 SOURCE:

Circulation: Cardiovascular Genetics.2008; 1: 21-30

doi: 10.1161/ CIRCGENETICS.108.773168

 

 

Integrated Computational and Experimental Analysis of the Neuroendocrine Transcriptome in Genetic Hypertension Identifies Novel Control Points for the Cardiometabolic Syndrome

Ryan S. Friese, PhD, Chun Ye, PhD, Caroline M. Nievergelt, PhD, Andrew J. Schork, BS, Nitish R. Mahapatra, PhD, Fangwen Rao, MD, Philip S. Napolitan, BS, Jill Waalen, MD, MPH, Georg B. Ehret, MD, Patricia B. Munroe, PhD, Geert W. Schmid-Schönbein, PhD, Eleazar Eskin, PhD and Daniel T. O’Connor, MD

Author Affiliations

From the Departments of Bioengineering (R.S.F., G.W.S.-S.), Medicine (R.S.F., A.J.S., F.R., P.S.N., D.T.O.), Pharmacology (D.T.O.), and Psychiatry (C.M.N.), the Bioinformatics Program (C.Y.), and the Institute for Genomic Medicine (D.T.O.), University of California at San Diego; the VA San Diego Healthcare System, San Diego, CA (D.T.O.); the Departments of Computer Science & Human Genetics, University of California at Los Angeles (E.E.); the Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India (N.R.M.); Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (P.B.M.); Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (G.B.E.); and Scripps Research Institute, La Jolla, CA (J.W.).

Correspondence to Daniel T. O’Connor, MD, Department of Medicine, University of California at San Diego School of Medicine, VASDHS (0838), Skaggs (SSPPS) Room 4256, 9500 Gilman Drive, La Jolla, CA 92093-0838. E-mail doconnor@ucsd.edu

Abstract

Background—Essential hypertension, a common complex disease, displays substantial genetic influence. Contemporary methods to dissect the genetic basis of complex diseases such as the genomewide association study are powerful, yet a large gap exists betweens the fraction of population trait variance explained by such associations and total disease heritability.

Methods and Results—We developed a novel, integrative method (combining animal models, transcriptomics, bioinformatics, molecular biology, and trait-extreme phenotypes) to identify candidate genes for essential hypertension and the metabolic syndrome. We first undertook transcriptome profiling on adrenal glands from blood pressure extreme mouse strains: the hypertensive BPH (blood pressure high) and hypotensive BPL (blood pressure low). Microarray data clustering revealed a striking pattern of global underexpression of intermediary metabolism transcripts in BPH. The MITRA algorithm identified a conserved motif in the transcriptional regulatory regions of the underexpressed metabolic genes, and we then hypothesized that regulation through this motif contributed to the global underexpression. Luciferase reporter assays demonstrated transcriptional activity of the motif through transcription factors HOXA3, SRY, and YY1. We finally hypothesized that genetic variation at HOXA3, SRY, and YY1 might predict blood pressure and other metabolic syndrome traits in humans. Tagging variants for each locus were associated with blood pressure in a human population blood pressure extreme sample with the most extensive associations for YY1 tagging single nucleotide polymorphism rs11625658 on systolic blood pressure, diastolic blood pressure, body mass index, and fasting glucose. Meta-analysis extended the YY1 results into 2 additional large population samples with significant effects preserved on diastolic blood pressure, body mass index, and fasting glucose.

Conclusions—The results outline an innovative, systematic approach to the genetic pathogenesis of complex cardiovascular disease traits and point to transcription factor YY1 as a potential candidate gene involved in essential hypertension and the cardiometabolic syndrome.

 SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 430-440

Published online before print June 5, 2012,

doi: 10.1161/ CIRCGENETICS.111.962415

 

Associations Between Incident Ischemic Stroke Events and Stroke and Cardiovascular Disease-Related Genome-Wide Association Studies Single Nucleotide Polymorphisms in the Population Architecture Using Genomics and Epidemiology Study

Cara L. Carty, PhD, Petra Bůžková, PhD, Myriam Fornage, PhD, Nora Franceschini, MD, Shelley Cole, PhD, Gerardo Heiss, MD, PhD, Lucia A. Hindorff, PhD, MPH, Barbara V. Howard, PhD, Sue Mann, MPH, Lisa W. Martin, MD, Ying Zhang, PhD, Tara C. Matise, PhD, Ross Prentice, PhD, Alexander P. Reiner, MD, MS and Charles Kooperberg, PhD

Author Affiliations

From the Public Health Sciences, Fred Hutchinson Cancer Research Center (C.L.C., S.M., R.P., C.K.); Department of Biostatistics, University of Washington, Seattle, WA (P.B.); Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX (M.F.); Division of Epidemiology, School of Public Health, University of Texas Health Sciences Center, Houston, TX (M.F.); Department of Epidemiology, University of North Carolina, Chapel Hill, NC (N.F., G.H.); Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX (S.C.); Office of Population Genomics, National Human Genome Research Institute, Bethesda, MD (L.A.H.); Medstar Health Research Institute, Washington, DC (B.V.H.); George Washington University School of Medicine, Washington, DC (B.V.H., L.W.M.); University of Oklahoma Health Sciences Center, Oklahoma City, OK (Y.Z.); Department of Genetics, Rutgers University, Piscataway, NJ (T.C.M.); Department of Epidemiology, University of Washington, Seattle, WA (A.P.R.).

Correspondence to Dr Cara L. Carty, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N./M3-A410, Seattle, WA 98109. E-mail ccarty@fhcrc.org

Abstract

Background—Genome-wide association studies (GWAS) have identified loci associated with ischemic stroke (IS) and cardiovascular disease (CVD) in European-descent individuals, but their replication in different populations has been largely unexplored.

Methods and Results—Nine single nucleotide polymorphisms (SNPs) selected from GWAS and meta-analyses of stroke, and 86 SNPs previously associated with myocardial infarction and CVD risk factors, including blood lipids (high density lipoprotein [HDL], low density lipoprotein [LDL], and triglycerides), type 2 diabetes, and body mass index (BMI), were investigated for associations with incident IS in European Americans (EA) N=26 276, African-Americans (AA) N=8970, and American Indians (AI) N=3570 from the Population Architecture using Genomics and Epidemiology Study. Ancestry-specific fixed effects meta-analysis with inverse variance weighting was used to combine study-specific log hazard ratios from Cox proportional hazards models. Two of 9 stroke SNPs (rs783396 and rs1804689) were associated with increased IS hazard in AA; none were significant in this large EA cohort. Of 73 CVD risk factor SNPs tested in EA, 2 (HDL and triglycerides SNPs) were associated with IS. In AA, SNPs associated with LDL, HDL, and BMI were significantly associated with IS (3 of 86 SNPs tested). Out of 58 SNPs tested in AI, 1 LDL SNP was significantly associated with IS.

Conclusions—Our analyses showing lack of replication in spite of reasonable power for many stroke SNPs and differing results by ancestry highlight the need to follow up on GWAS findings and conduct genetic association studies in diverse populations. We found modest IS associations with BMI and lipids SNPs, though these findings require confirmation.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 210-216

Published online before print March 8, 2012,

doi: 10.1161/ CIRCGENETICS.111.962191

 

Common Variation in Fatty Acid Genes and Resuscitation From Sudden Cardiac Arrest

Catherine O. Johnson, PhD, MPH, Rozenn N. Lemaitre, PhD, MPH, Carol E. Fahrenbruch, MSPH, Stephanie Hesselson, PhD, Nona Sotoodehnia, MD, MPH, Barbara McKnight, PhD, Kenneth M. Rice, PhD, Pui-Yan Kwok, MD, PhD, David S. Siscovick, MD, MPH and Thomas D. Rea, MD, MPH

Author Affiliations

From the Departments of Medicine (C.O.J., R.N.L., N.S., D.S.S., T.D.R.), Biostatistics (B.M., K.M.R.), and Epidemiology (D.S.S), University of Washington, Seattle; King County Emergency Medical Services, Seattle, WA (C.E.F.); and Institute of Human Genetics, University of California San Francisco (S.H., P.-Y.K.).

Correspondence to Catherine O. Johnson, PhD, MPH, Department of Medicine, University of Washington, CHRU 1730 Minor Ave, Suite 1360, Seattle, WA 98101. E-mail johnsoco@uw.edu

Abstract

Background—Fatty acids provide energy and structural substrates for the heart and brain and may influence resuscitation from sudden cardiac arrest (SCA). We investigated whether genetic variation in fatty acid metabolism pathways was associated with SCA survival.

Methods and Results—Subjects (mean age, 67 years; 80% male, white) were out-of-hospital SCA patients found in ventricular fibrillation in King County, WA. We compared subjects who survived to hospital admission (n=664) with those who did not (n=689), and subjects who survived to hospital discharge (n=334) with those who did not (n=1019). Associations between survival and genetic variants were assessed using logistic regression adjusting for age, sex, location, time to arrival of paramedics, whether the event was witnessed, and receipt of bystander cardiopulmonary resuscitation. Within-gene permutation tests were used to correct for multiple comparisons. Variants in 5 genes were significantly associated with SCA survival. After correction for multiple comparisons, single-nucleotide polymorphisms in ACSL1 and ACSL3 were significantly associated with survival to hospital admission. Single-nucleotide polymorphisms in ACSL3, AGPAT3, MLYCD, and SLC27A6 were significantly associated with survival to hospital discharge.

Conclusions—Our findings indicate that variants in genes important in fatty acid metabolism are associated with SCA survival in this population.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 422-429

Published online before print June 1, 2012,

doi: 10.1161/ CIRCGENETICS.111.961912

 

Genome-Wide Association Study Pinpoints a New Functional Apolipoprotein B Variant Influencing Oxidized Low-Density Lipoprotein Levels But Not Cardiovascular Events

AtheroRemo Consortium

Kari-Matti Mäkelä, BM, BSc, Ilkka Seppälä, MSc, Jussi A. Hernesniemi, MD, PhD, Leo-Pekka Lyytikäinen, MD, Niku Oksala, MD, PhD, DSc, Marcus E. Kleber, PhD, Hubert Scharnagl, PhD, Tanja B. Grammer, MD, Jens Baumert, PhD, Barbara Thorand, PhD, Antti Jula, MD, PhD, Nina Hutri-Kähönen, MD, PhD, Markus Juonala, MD, PhD, Tomi Laitinen, MD, PhD, Reijo Laaksonen, MD, PhD, Pekka J. Karhunen, MD, PhD, Kjell C. Nikus, MD, PhD, Tuomo Nieminen, MD, PhD, MSc, Jari Laurikka, MD, PhD, Pekka Kuukasjärvi, MD, PhD, Matti Tarkka, MD, PhD, Jari Viik, PhD, Norman Klopp, PhD, Thomas Illig, PhD, Johannes Kettunen, PhD, Markku Ahotupa, PhD, Jorma S.A. Viikari, MD, PhD, Mika Kähönen, MD, PhD, Olli T. Raitakari, MD, PhD, Mahir Karakas, MD, Wolfgang Koenig, MD, PhD, Bernhard O. Boehm, MD, Bernhard R. Winkelmann, MD, Winfried März, MD and Terho Lehtimäki, MD, PhD

Correspondence to Kari-Matti Mäkelä, Department of Clinical Chemistry, Finn-Medi 2, PO Box 2000, FI-33521 Tampere, Finland. E-mail kari-matti.makela@uta.fi

Abstract

Background—Oxidized low-density lipoprotein may be a key factor in the development of atherosclerosis. We performed a genome-wide association study on oxidized low-density lipoprotein and tested the impact of associated single-nucleotide polymorphisms (SNPs) on the risk factors of atherosclerosis and cardiovascular events.

Methods and Results—A discovery genome-wide association study was performed on a population of young healthy white individuals (N=2080), and the SNPs associated with a P<5×10–8 were replicated in 2 independent samples (A: N=2912; B: N=1326). Associations with cardiovascular endpoints were also assessed with 2 additional clinical cohorts (C: N=1118; and D: N=808). We found 328 SNPs associated with oxidized low-density lipoprotein. The genetic variant rs676210 (Pro2739Leu) in apolipoprotein B was the proxy SNP behind all associations (P=4.3×10–136, effect size=13.2 U/L per allele). This association was replicated in the 2 independent samples (A and B, P=2.5×10–47 and 1.1×10–11, effect sizes=10.3 U/L and 7.8 U/L, respectively). In the meta-analyses of cohorts A, C, and D (excluding cohort B without angiographic data), the top SNP did not associate significantly with the age of onset of angiographically verified coronary artery disease (hazard ratio=1.00 [0.94–1.06] per allele), 3-vessel coronary artery disease (hazard ratio=1.03 [0.94–1.13]), or myocardial infarction (hazard ratio=1.04 [0.96–1.12]).

Conclusions—This novel genetic marker is an important factor regulating oxidized low-density lipoprotein levels but not a major genetic factor for the studied cardiovascular endpoints.

 SOURCE:

Circulation: Cardiovascular Genetics.2013; 6: 73-81

Published online before print December 17, 2012,

doi: 10.1161/ CIRCGENETICS.112.964965

Genome-Wide Screen for Metabolic Syndrome Susceptibility Loci Reveals Strong Lipid Gene Contribution But No Evidence for Common Genetic Basis for Clustering of Metabolic Syndrome Traits

Kati Kristiansson, PhD, Markus Perola, MD, PhD, Emmi Tikkanen, MSc, Johannes Kettunen, PhD, Ida Surakka, MSc, Aki S. Havulinna, DSc (Tech.), Alena Stančáková, MD, PhD, Chris Barnes, PhD, Elisabeth Widen, MD, PhD, Eero Kajantie, MD, PhD, Johan G. Eriksson, MD, DMSc, Jorma Viikari, MD, PhD, Mika Kähönen, MD, PhD, Terho Lehtimäki, MD, PhD, Olli T. Raitakari, MD, PhD, Anna-Liisa Hartikainen, MD, PhD, Aimo Ruokonen, MD, PhD, Anneli Pouta, MD, PhD, Antti Jula, MD, PhD, Antti J. Kangas, MSc, Pasi Soininen, PhD, Mika Ala-Korpela, PhD, Satu Männistö, PhD, Pekka Jousilahti, MD, PhD, Lori L. Bonnycastle, PhD, Marjo-Riitta Järvelin, MD, PhD, Johanna Kuusisto, MD, PhD, Francis S. Collins, MD, PhD, Markku Laakso, MD, PhD, Matthew E. Hurles, PhD, Aarno Palotie, MD, PhD, Leena Peltonen, MD, PhD*, Samuli Ripatti, PhD and Veikko Salomaa, MD, PhD

Correspondence to Dr Kati Kristiansson, National Institute for Health and Welfare, University of Helsinki, Biomedicum, PL 104, FI-00251 Helsinki, Finland. E-mail kati.kristiansson@thl.fi

Abstract

Background—Genome-wide association (GWA) studies have identified several susceptibility loci for metabolic syndrome (MetS) component traits, but have had variable success in identifying susceptibility loci to the syndrome as an entity. We conducted a GWA study on MetS and its component traits in 4 Finnish cohorts consisting of 2637 MetS cases and 7927 controls, both free of diabetes, and followed the top loci in an independent sample with transcriptome and nuclear magnetic resonance-based metabonomics data. Furthermore, we tested for loci associated with multiple MetS component traits using factor analysis, and built a genetic risk score for MetS.

Methods and Results—A previously known lipid locus, APOA1/C3/A4/A5 gene cluster region (SNP rs964184), was associated with MetS in all 4 study samples (P=7.23×109 in meta-analysis). The association was further supported by serum metabolite analysis, where rs964184 was associated with various very low density lipoprotein, triglyceride, and high-density lipoprotein metabolites (P=0.024–1.88×105). Twenty-two previously identified susceptibility loci for individual MetS component traits were replicated in our GWA and factor analysis. Most of these were associated with lipid phenotypes, and none with 2 or more uncorrelated MetS components. A genetic risk score, calculated as the number of risk alleles in loci associated with individual MetS traits, was strongly associated with MetS status.

Conclusions—Our findings suggest that genes from lipid metabolism pathways have the key role in the genetic background of MetS. We found little evidence for pleiotropy linking dyslipidemia and obesity to the other MetS component traits, such as hypertension and glucose intolerance.

 SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 242-249

Published online before print March 7, 2012,

doi: 10.1161/ CIRCGENETICS.111.961482

 

Genetics and Vascular Pathologies and Platelet Aggregation, Cardiac Troponin T in Serum

 

 

TGFβRIIb Mutations Trigger Aortic Aneurysm Pathogenesis by Altering Transforming Growth Factor β2 Signal Transduction

Katharine J. Bee, PhD, David C. Wilkes, PhD, Richard B. Devereux, MD, Craig T. Basson, MD, PhD and Cathy J. Hatcher, PhD

Author Affiliations

From the Center for Molecular Cardiology, Greenberg Division of Cardiology, Weill Cornell Medical College, New York, NY.

Correspondence to Cathy J. Hatcher, PhD, Greenberg Division of Cardiology, Weill Cornell Medical College, 525 E. 68th St, New York, NY 10065. E-mail cjhatche@med.cornell.edu

Abstract

Background—Thoracic aortic aneurysm (TAA) is a common progressive disorder involving gradual dilation of the ascending and/or descending thoracic aorta that eventually leads to dissection or rupture. Nonsydromic TAA can occur as a genetically triggered, familial disorder that is usually transmitted in a monogenic autosomal dominant fashion and is known as familial TAA. Genetic analyses of families affected with TAA have identified several chromosomal loci, and further mapping of familial TAA genes has highlighted disease-causing mutations in at least 4 genes: myosin heavy chain 11 (MYH11), α-smooth muscle actin (ACTA2), and transforming growth factor β receptors I and II (TGFβRI and TGFβRII).

Methods and Results—We evaluated 100 probands to determine the mutation frequency in MYH11, ACTA2, TGFβRI, and TGFβRII in an unbiased population of individuals with genetically mediated TAA. In this study, 9% of patients had a mutation in one of the genes analyzed, 3% of patients had mutations in ACTA2, 3% in MYH11, 1% in TGFβRII, and no mutations were found in TGFβRI. Additionally, we identified mutations in a 75 base pair alternatively spliced TGFβRII exon, exon 1a that produces the TGFβRIIb isoform and accounted for 2% of patients with mutations. Our in vitro analyses indicate that the TGFβRIIb activating mutations alter receptor function on TGFβ2 signaling.

Conclusions—We propose that TGFβRIIb expression is a regulatory mechanism for TGFβ2 signal transduction. Dysregulation of the TGFβ2 signaling pathway, as a consequence of TGFβRIIb mutations, results in aortic aneurysm pathogenesis.

SOURCE: 

Circulation: Cardiovascular Genetics.2012; 5: 621-629

Published online before print October 24, 2012,doi: 10.1161/​CIRCGENETICS.112.964064

Matrix Metalloproteinase-9 Genotype as a Potential Genetic Marker for Abdominal Aortic Aneurysm

Tyler Duellman, BS, Christopher L. Warren, PhD, Peggy Peissig, PhD, Martha Wynn, MD and Jay Yang, MD, PhD

Author Affiliations

From the Molecular and Cellular Pharmacology Graduate Program (T.D., J.Y.) and Department of Anesthesiology (M.W., J.Y.), University of Wisconsin School of Medicine and Public Health, Madison; Illumavista Biosciences LLC, Madison, WI (C.L.W.); and Biomedical Informatics Research Center, Marshfield Clinics Research Foundation, Marshfield, WI (P.P.).

Correspondence to Jay Yang, MD, PhD, Department of Anesthesiology, University of Wisconsin SMPH, SMI 301, 1300 University Ave, Madison, WI 53706. E-mail Jyang75@wisc.edu

Abstract

Background—Degradation of extracellular matrix support in the large abdominal arteries contribute to abnormal dilation of aorta, leading to abdominal aortic aneurysms, and matrix metalloproteinase-9 (MMP-9) is the predominant enzyme targeting elastin and collagen present in the walls of the abdominal aorta. Previous studies have suggested a potential association between MMP-9 genotype and abdominal aortic aneurysm, but these studies have been limited only to the p-1562 and (CA) dinucleotide repeat microsatellite polymorphisms in the promoter region of the MMP-9 gene. We determined the functional alterations caused by 15 MMP-9 single-nucleotide polymorphisms (SNPs) reported to be relatively abundant in the human genome through Western blots, gelatinase, and promoter–reporter assays and incorporated this information to perform a logistic-regression analysis of MMP-9 SNPs in 336 human abdominal aortic aneurysm cases and controls.

Methods and Results—Significant functional alterations were observed for 6 exon SNPs and 4 promoter SNPs. Genotype analysis of frequency-matched (age, sex, history of hypertension, hypercholesterolemia, and smoking) cases and controls revealed significant genetic heterogeneity exceeding 20% observed for 6 SNPs in our population of mostly white subjects from Northern Wisconsin. A step-wise logistic-regression analysis with 6 functional SNPs, where weakly contributing confounds were eliminated using Akaike information criteria, gave a final 2 SNP (D165N and p-2502) model with an overall odds ratio of 2.45 (95% confidence interval, 1.06–5.70).

Conclusions—The combined approach of direct experimental confirmation of the functional alterations of MMP-9 SNPs and logistic-regression analysis revealed significant association between MMP-9 genotype and abdominal aortic aneurysm.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 529-537

Published online before print August 31, 2012,

doi: 10.1161/ CIRCGENETICS.112.963082

Common Genetic Variation in the 3BCL11B Gene Desert Is Associated With Carotid-Femoral Pulse Wave Velocity and Excess Cardiovascular Disease Risk

The AortaGen Consortium

Gary F. Mitchell, MD*, Germaine C. Verwoert, MSc*, Kirill V. Tarasov, MD, PhD*, Aaron Isaacs, PhD, Albert V. Smith, PhD, Yasmin, BSc, MA, PhD, Ernst R. Rietzschel, MD, PhD, Toshiko Tanaka, PhD, Yongmei Liu, MD, PhD, Afshin Parsa, MD, MPH, Samer S. Najjar, MD, Kevin M. O’Shaughnessy, MA, BM, DPhil, FRCP, Sigurdur Sigurdsson, MSc, Marc L. De Buyzere, MSc, Martin G. Larson, ScD, Mark P.S. Sie, MD, PhD, Jeanette S. Andrews, MS, Wendy S. Post, MD, MS, Francesco U.S. Mattace-Raso, MD, PhD, Carmel M. McEniery, BSc, PhD, Gudny Eiriksdottir, MSc, Patrick Segers, PhD, Ramachandran S. Vasan, MD, Marie Josee E. van Rijn, MD, PhD, Timothy D. Howard, PhD, Patrick F. McArdle, PhD, Abbas Dehghan, MD, PhD, Elizabeth S. Jewell, MS, Stephen J. Newhouse, MSc, PhD, Sofie Bekaert, PhD, Naomi M. Hamburg, MD, Anne B. Newman, MD, MPH, Albert Hofman, MD, PhD, Angelo Scuteri, MD, PhD, Dirk De Bacquer, PhD, Mohammad Arfan Ikram, MD, PhD†, Bruce M. Psaty, MD, PhD†, Christian Fuchsberger, PhD‡, Matthias Olden, PhD‡, Louise V. Wain, PhD§, Paul Elliott, MB, PhD§, Nicholas L. Smith, PhD‖, Janine F. Felix, MD, PhD‖, Jeanette Erdmann, PhD¶, Joseph A. Vita, MD, Kim Sutton-Tyrrell, PhD, Eric J.G. Sijbrands, MD, PhD, Serena Sanna, PhD, Lenore J. Launer, MS, PhD, Tim De Meyer, PhD, Andrew D. Johnson, MD, Anna F.C. Schut, MD, PhD, David M. Herrington, MD, MHS, Fernando Rivadeneira, MD, PhD, Manuela Uda, PhD, Ian B. Wilkinson, MA, BM, FRCP, Thor Aspelund, PhD, Thierry C. Gillebert, MD, PhD, Luc Van Bortel, MD, PhD, Emelia J. Benjamin, MD, MSc, Ben A. Oostra, PhD, Jingzhong Ding, MD, PhD, Quince Gibson, MBA, André G. Uitterlinden, PhD, Gonçalo R. Abecasis, PhD, John R. Cockcroft, BSc, MB, ChB, FRCP, Vilmundur Gudnason, MD, PhD, Guy G. De Backer, MD, PhD, Luigi Ferrucci, MD, Tamara B. Harris, MD, MS, Alan R. Shuldiner, MD, Cornelia M. van Duijn, PhD, Daniel Levy, MD*, Edward G. Lakatta, MD* and Jacqueline C.M. Witteman, PhD*

Correspondence to Gary F. Mitchell, MD, Cardiovascular Engineering, Inc, 1 Edgewater Dr, Suite 201A, Norwood, MA 02062. E-mail GaryFMitchell@mindspring.com

* These authors contributed equally.

Abstract

Background—Carotid-femoral pulse wave velocity (CFPWV) is a heritable measure of aortic stiffness that is strongly associated with increased risk for major cardiovascular disease events.

Methods and Results—We conducted a meta-analysis of genome-wide association data in 9 community-based European ancestry cohorts consisting of 20 634 participants. Results were replicated in 2 additional European ancestry cohorts involving 5306 participants. Based on a preliminary analysis of 6 cohorts, we identified a locus on chromosome 14 in the 3′-BCL11B gene desert that is associated with CFPWV (rs7152623, minor allele frequency=0.42, β=−0.075±0.012 SD/allele, P=2.8×1010; replication β=−0.086±0.020 SD/allele, P=1.4×106). Combined results for rs7152623 from 11 cohorts gave β=−0.076±0.010 SD/allele, P=3.1×1015. The association persisted when adjusted for mean arterial pressure (β=−0.060±0.009 SD/allele, P=1.0×1011). Results were consistent in younger (<55 years, 6 cohorts, n=13 914, β=−0.081±0.014 SD/allele, P=2.3×109) and older (9 cohorts, n=12 026, β=−0.061±0.014 SD/allele, P=9.4×106) participants. In separate meta-analyses, the locus was associated with increased risk for coronary artery disease (hazard ratio=1.05; confidence interval=1.02–1.08; P=0.0013) and heart failure (hazard ratio=1.10, CI=1.03–1.16, P=0.004).

Conclusions—Common genetic variation in a locus in the BCL11B gene desert that is thought to harbor 1 or more gene enhancers is associated with higher CFPWV and increased risk for cardiovascular disease. Elucidation of the role this novel locus plays in aortic stiffness may facilitate development of therapeutic interventions that limit aortic stiffening and related cardiovascular disease events.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 81-90

Published online before print November 8, 2011,

doi: 10.1161/ CIRCGENETICS.111.959817

Genetic Variation in PEAR1 is Associated with Platelet Aggregation and Cardiovascular Outcomes

Joshua P. Lewis1, Kathleen Ryan1, Jeffrey R. O’Connell1, Richard B. Horenstein1, Coleen M. Damcott1, Quince Gibson1, Toni I. Pollin1, Braxton D. Mitchell1, Amber L. Beitelshees1, Ruth Pakzy1, Keith Tanner1, Afshin Parsa1, Udaya S. Tantry2, Kevin P. Bliden2, Wendy S. Post3, Nauder Faraday3, William Herzog4, Yan Gong5, Carl J. Pepine6, Julie A. Johnson5, Paul A. Gurbel2 and Alan R. Shuldiner7*

Author Affiliations

1University of Maryland School of Medicine, Baltimore, MD

2Sinai Hospital of Baltimore, Baltimore, MD

3Johns Hopkins University School of Medicine, Baltimore, MD

4Sinai Hospital of Baltimore & Johns Hopkins University School of Medicine, Baltimore, MD

5University of Florida College of Pharmacy, Gainesville, FL

6University of Florida College of Medicine, Gainesville, FL

7University of Maryland School of Medicine & Veterans Administration Medical Center, Baltimore, MD

* University of Maryland School of Medicine & Veterans Administration Medical Center, Baltimore, MD ashuldin@medicine.umaryland.edu

Abstract

Background-Aspirin or dual antiplatelet therapy (DAPT) with aspirin and clopidogrel is standard therapy for patients at increased risk for cardiovascular events. However, the genetic determinants of variable response to aspirin (alone and in combination with clopidogrel) are not known.

Methods and Results-We measured ex-vivo platelet aggregation before and after DAPT in individuals (n=565) from the Pharmacogenomics of Antiplatelet Intervention (PAPI) Study and conducted a genome-wide association study (GWAS) of drug response. Significant findings were extended by examining genotype and cardiovascular outcomes in two independent aspirin-treated cohorts: 227 percutaneous coronary intervention (PCI) patients, and 1,000 patients of the International VErapamil SR/trandolapril Study (INVEST) GENEtic Substudy (INVEST-GENES). GWAS revealed a strong association between single nucleotide polymorphisms on chromosome 1q23 and post-DAPT platelet aggregation. Further genotyping revealed rs12041331 in the platelet endothelial aggregation receptor-1 (PEAR1) gene to be most strongly associated with DAPT response (P=7.66×10-9). In Caucasian and African American patients undergoing PCI, A-allele carriers of rs12041331 were more likely to experience a cardiovascular event or death compared to GG homozygotes (hazard ratio = 2.62, 95%CI 0.96-7.10, P=0.059 and hazard ratio = 3.97, 95%CI 1.10-14.31, P=0.035 respectively). In aspirin-treated INVEST-GENES patients, rs12041331 A-allele carriers had significantly increased risk of myocardial infarction compared to GG homozygotes (OR=2.03, 95%CI 1.01-4.09, P=0.048).

Conclusions-Common genetic variation in PEAR1 may be a determinant of platelet response and cardiovascular events in patients on aspirin, alone and in combination with clopidogrel.

Clinical Trial Registration Information-clinicaltrials.gov; Identifiers: NCT00799396 and NCT00370045

SOURCE:

CIRCGENETICS.112.964627

Published online before print February 7, 2013,

doi: 10.1161/ CIRCGENETICS.111.964627

Association of Genome-Wide Variation With Highly Sensitive Cardiac Troponin-T Levels in European Americans and Blacks

A Meta-Analysis From Atherosclerosis Risk in Communities and Cardiovascular Health Studies

Bing Yu, MD, MSc, Maja Barbalic, PhD, Ariel Brautbar, MD, Vijay Nambi, MD, Ron C. Hoogeveen, PhD, Weihong Tang, PhD, Thomas H. Mosley, PhD, Jerome I. Rotter, MD, Christopher R. deFilippi, MD, Christopher J. O’Donnell, MD, Sekar Kathiresan, MD, Ken Rice, PhD, Susan R. Heckbert, MD, PhD, Christie M. Ballantyne, MD, Bruce M. Psaty, MD, PhD and Eric Boerwinkle, PhD on behalf of the CARDIoGRAM Consortium

Author Affiliations

From the Human Genetic Center, University of Texas Health Science Center at Houston, Houston, TX (B.Y., M.B., E.B.); Deptartment of Medicine (A.B., V.N., R.C.H., C.M.B.), and Human Genome Sequencing Center (E.B.), Baylor College of Medicine, Houston, TX; Department of Epidemiology, University of Minnesota, Minneapolis, MN (W.T.); Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS (T.H.M.); Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA (J.I.R.); School of Medicine, University of Maryland, Baltimore, MD (C.R.D.); National Heart, Lung, and Blood Institute and Framingham Heart Study, National Institutes of Health, Bethesda, MD (C.J.O.D.); Center for Human Genetic Research & Cardiovascular Research Center, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA (S.K.); Department of Biostatistics (K.R.), and Cardiovascular Health Research Unit & Department of Epidemiology (S.R.H.), University of Washington, Seattle, WA; and Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington & Group Health Research Institute, Group Health Cooperative, Seattle, WA (B.M.P.).

Correspondence to Eric Boerwinkle, PhD, Human Genetic Center, University of Texas School of Public Health, 1200 Herman Pressler E-447, Houston, TX 77030. E-mail Eric.Boerwinkle@uth.tmc.edu

Abstract

Background—High levels of cardiac troponin T, measured by a highly sensitive assay (hs-cTnT), are strongly associated with incident coronary heart disease and heart failure. To date, no large-scale genome-wide association study of hs-cTnT has been reported. We sought to identify novel genetic variants that are associated with hs-cTnT levels.

Methods and Results—We performed a genome-wide association in 9491 European Americans and 2053 blacks free of coronary heart disease and heart failure from 2 prospective cohorts: the Atherosclerosis Risk in Communities Study and the Cardiovascular Health Study. Genome-wide association studies were conducted in each study and race stratum. Fixed-effect meta-analyses combined the results of linear regression from 2 cohorts within each race stratum and then across race strata to produce overall estimates and probability values. The meta-analysis identified a significant association at chromosome 8q13 (rs10091374; P=9.06×109) near the nuclear receptor coactivator 2 (NCOA2) gene. Overexpression of NCOA2 can be detected in myoblasts. An additional analysis using logistic regression and the clinically motivated 99th percentile cut point detected a significant association at 1q32 (rs12564445; P=4.73×108) in the gene TNNT2, which encodes the cardiac troponin T protein itself. The hs-cTnT-associated single-nucleotide polymorphisms were not associated with coronary heart disease in a large case-control study, but rs12564445 was significantly associated with incident heart failure in Atherosclerosis Risk in Communities Study European Americans (hazard ratio=1.16; P=0.004).

Conclusions—We identified 2 loci, near NCOA2 and in the TNNT2 gene, at which variation was significantly associated with hs-cTnT levels. Further use of the new assay should enable replication of these results.

 SOURCE:

Circulation: Cardiovascular Genetics.2013; 6: 82-88

Published online before print December 16, 2012,

doi: 10.1161/ CIRCGENETICS.112.963058

 

Genomics and Valvular Disease

 

Supravalvular Aortic Stenosis Elastin Arteriopathy

 

Giuseppe Merla, PhD, Nicola Brunetti-Pierri, MD, Pasquale Piccolo, PhD, Lucia Micale, PhD and Maria Nicla Loviglio, PhD, MSc

Author Affiliations

From the Medical Genetics Unit, IRCCS Casa Sollievo Della Sofferenza Hospital, San Giovanni Rotondo, Italy (G.M., L.M., M.N.L.); Telethon Institute of Genetics and Medicine, Napoli, Italy (N.B-P., P.P.); Department of Pediatrics, Federico II University of Naples, Naples, Italy (N.B-P.); and CIG Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland (M.N.L.).

Correspondence to Giuseppe Merla, PhD, Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, viale Cappuccini, 71013 San Giovanni Rotondo, Italy. E-mail g.merla@operapadrepio.it

Abstract

Supravalvular aortic stenosis is a systemic elastin (ELN) arteriopathy that disproportionately affects the supravalvular aorta. ELN arteriopathy may be present in a nonsyndromic condition or in syndromic conditions such as Williams–Beuren syndrome. The anatomic findings include congenital narrowing of the lumen of the aorta and other arteries, such as branches of pulmonary or coronary arteries. Given the systemic nature of the disease, accurate evaluation is recommended to establish the degree and extent of vascular involvement and to plan appropriate interventions, which are indicated whenever hemodynamically significant stenoses occur. ELN arteriopathy is genetically heterogeneous and occurs as a consequence of haploinsufficiency of the ELN gene on chromosome 7q11.23, owing to either microdeletion of the entire chromosomal region or ELN point mutations. Interestingly, there is a prevalence of premature termination mutations resulting in null alleles among ELN point mutations. The identification of the genetic defect in patients with supravalvular aortic stenosis is essential for a definitive diagnosis, prognosis, and genetic counseling.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 692-696

doi: 10.1161/ CIRCGENETICS.112.962860

Genetic Loci for Coronary Calcification and Serum Lipids Relate to Aortic and Carotid Calcification

Daniel Bos, MD, M. Arfan Ikram, MD, PhD, Aaron Isaacs, PhD, Benjamin F.J. Verhaaren, MD, Albert Hofman, MD, PhD, Cornelia M. van Duijn, PhD, Jacqueline C.M. Witteman, PhD, Aad van der Lugt, MD, PhD and Meike W. Vernooij, MD, PhD

Author Affiliations

From the Departments of Radiology (D.B., M.A.I., B.F.J.V., A.v.d.L., M.W.V), Epidemiology (D.B., M.A.I., A.I., B.F.J.V., A.H., C.M.v.D., J.C.M.W., M.W.V.), and Genetic Epidemiology Unit (A.I., C.M.v.D.), Erasmus MC, Rotterdam, the Netherlands.

Correspondence to Meike W. Vernooij, MD, PhD, Department of Radiology, Erasmus MC, Gravendijkwal 230, PO Box 2040, 3000CA Rotterdam, the Netherlands. E-mail m.vernooij@erasmusmc.nl

Abstract

Background—Atherosclerosis in different vessel beds shares lifestyle and environmental risk factors. It is unclear whether this holds for genetic risk factors. Hence, for the current study genetic loci for coronary artery calcification and serum lipid levels, one of the strongest risk factors for atherosclerosis, were used to assess their relation with atherosclerosis in different vessel beds.

Methods and Results—From 1987 persons of the population-based Rotterdam Study, 3 single-nucleotide polymorphisms (SNPs) for coronary artery calcification and 132 SNPs for total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides were used. To quantify atherosclerotic calcification as a marker of atherosclerosis, all participants underwent nonenhanced computed tomography of the aortic arch and carotid arteries. Associations between genetic risk scores of the joint effect of the SNPs and of all calcification were investigated. The joint effect of coronary artery calcification–SNPs was associated with larger calcification volumes in all vessel beds (difference in calcification volume per SD increase in genetic risk score: 0.15 [95% confidence interval, 0.11–0.20] in aorta, 0.14 [95% confidence interval, 0.10–0.18] in extracranial carotids, and 0.11 [95% confidence interval, 0.07–0.16] in intracranial carotids). The joint effect of total cholesterol SNPs, low-density lipoprotein SNPs, and of all lipid SNPs together was associated with larger calcification volumes in both the aortic arch and the carotid arteries but attenuated after adjusting for the lipid fraction and lipid-lowering medication.

Conclusions—The genetic basis for aortic arch and carotid artery calcification overlaps with the most important loci of coronary artery calcification. Furthermore, serum lipids share a genetic predisposition with both calcification in the aortic arch and the carotid arteries, providing novel insights into the cause of atherosclerosis.

 SOURCE:

Circulation: Cardiovascular Genetics.2013; 6: 47-53

Published online before print December 16, 2012,

doi: 10.1161/ CIRCGENETICS.112.963934

 

Joint Associations of 61 Genetic Variants in the Nicotinic Acetylcholine Receptor Genes with Subclinical Atherosclerosis in American Indians

A Gene-Family Analysis

Jingyun Yang, PhD*, Yun Zhu, MS*, Elisa T. Lee, PhD, Ying Zhang, PhD, Shelley A. Cole, PhD, Karin Haack, PhD, Lyle G. Best, BS MD, Richard B. Devereux, MD, Mary J. Roman, MD, Barbara V. Howard, PhD and Jinying Zhao, MD, PhD

Author Affiliations

From the Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (J.Y., Y. Zhu, J.Z.); Center for American Indian Health Research, University of Oklahoma Health Sciences Center, Oklahoma City, OK (E.T.L., Y. Zhang); Texas Biomedical Research Institute, San Antonio, TX (S.A.C., K.H.); Missouri Breaks Industries Research Inc, Timber Lake, SD (L.G.B.); The New York Hospital-Cornell Medical Center, New York, NY (R.B.D., M.J.R.); MedStar Health Research Institute, Hyattsville, MD (B.V.H.); and Georgetown and Howard Universities Centers for Translational Sciences, Washington, DC (B.V.H.).

Correspondence to Jinying Zhao, MD, PhD, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, SL18, New Orleans, LA 70112. E-mail jzhao5@tulane.edu

* These authors contributed equally to this work.

Abstract

Background—Atherosclerosis is the underlying cause of cardiovascular disease, the leading cause of morbidity and mortality in all American populations, including American Indians. Genetic factors play an important role in the pathogenesis of atherosclerosis. Although a single-nucleotide polymorphism (SNP) may explain only a small portion of variability in disease, the joint effect of multiple variants in a pathway on disease susceptibility could be large.

Methods and Results—Using a gene-family analysis, we investigated the joint associations of 61 tag SNPs in 7 nicotinic acetylcholine receptor genes with subclinical atherosclerosis, as measured by carotid intima-media thickness and plaque score, in 3665 American Indians from 94 families recruited by the Strong Heart Family Study (SHFS). Although multiple SNPs showed marginal association with intima-media thickness and plaque score individually, only a few survived adjustments for multiple testing. However, simultaneously modeling of the joint effect of all 61 SNPs in 7 nicotinic acetylcholine receptor genes revealed significant association of the nicotinic acetylcholine receptor gene family with both intima-media thickness and plaque score independent of known coronary risk factors.

Conclusions—Genetic variants in the nicotinic acetylcholine receptor gene family jointly contribute to subclinical atherosclerosis in American Indians who participated in the SHFS. These variants may influence the susceptibility of atherosclerosis through pathways other than cigarette smoking per se.

SOURCE:

Circulation: Cardiovascular Genetics.2013; 6: 89-96

Published online before print December 22, 2012,

doi: 10.1161/ CIRCGENETICS.112.963967

 

 

Heredity of Cardiovascular Disorders Inheritance

 

A Clinical Approach to Common Cardiovascular Disorders When There Is a Family History

The Implications of Inheritance for Clinical Management

Srijita Sen-Chowdhry, MBBS, MD, FESC, Daniel Jacoby, MD and William J. McKenna, MD, DSc, FESC

Author Affiliations

From the Institute of Cardiovascular Science, University College London, London, United Kingdom (S.S-C., W.J.M.); Department of Epidemiology, Imperial College, London, London, United Kingdom (S.S-C.); Division of Cardiology, Yale School of Medicine, New Haven, CT (D.J., W.J.M.).

Correspondence to Professor William J. McKenna, MD, DSc, FESC, Institute of Cardiovascular Science, University College London, The Heart Hospital, 16-18 Westmoreland Street, London, E-mail william.mckenna@uclh.nhs.uk

Introduction

Since the advent of genotyping, recognition of heritable disease has been perceived as an opportunity for genetic diagnosis or new gene identification studies to advance understanding of pathogenesis. Until recently, however, clinical application of DNA-based testing was confined largely to Mendelian disorders. Even within this remit, predictive testing of relatives is cost-effective only in diseases in which the majority of families harbor mutations in known causal genes, such as adult polycystic kidney disease and hypertrophic cardiomyopathy, but not dilated cardiomyopathy. Confirmatory genetic testing of index cases with borderline clinical features may be economic in the still smaller subset of diseases with limited locus heterogeneity, such as Marfan syndrome. Furthermore, Mendelian diseases account for ≈5% of total disease burden.1 Genome-wide association studies have made headway in elucidating the genetic contribution to the more common, complex diseases, and high throughput techniques promise to facilitate integration of genetic analysis into clinical practice. Nevertheless, many genes remain to be identified and implementation of genomic profiling as a population screening tool would not be cost-effective at present. The implications of heredity, however, extend beyond serving as a platform for genetic analysis, influencing diagnosis, prognostication, and treatment of both index cases and relatives, and enabling rational targeting of genotyping resources. This review covers acquisition of a family history, evaluation of heritability and inheritance patterns, and the impact of inheritance on subsequent components of the clinical pathway.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 467-476

doi: 10.1161/ CIRCGENETICS.110.959361

Clinical Considerations of Heritable Factors in Common Heart Failure

Thomas P. Cappola, MD, ScM and Gerald W. Dorn II, MD

Author Affiliations

From the Department of Medicine, University of Pennsylvania, Philadelphia, PA (T.P.C.), and Center for Pharmacogenomics, Washington University School of Medicine, St Louis, MO (G.W.D.II.).

Correspondence to Gerald W. Dorn II, MD, Center for Pharmacogenomics, Washington University, 660 S Euclid Ave, Campus Box 8220, St Louis, MO 63110. E-mail gdorn@dom.wustl.edu

 

Introduction

Heart failure is a common condition responsible for at least 290 000 deaths each year in the United States alone.1 A small minority of heart failure cases are attributed to Mendelian or familial cardiomyopathies. The majority of systolic heart failure cases are not familial but represent the end result of 1 or many conditions that primarily injure the myocardium sufficiently to diminish cardiac output in the absence of compensatory mechanisms. Paradoxically, because they also injure the myocardium, it is the chronic actions of the compensatory mechanisms that in many instances contribute to the progression from simple cardiac injury to dilated cardiomyopathy and overt heart failure. Thus, the epidemiology of common heart failure appears to be just as sporadic as its major antecedent conditions (atherosclerosis, diabetes, hypertension, and viral myocarditis).

Familial trends in preclinical cardiac remodeling2 and risk of developing heart failure3 reveal an important role for genetic modifiers in addition to clinical and environmental factors. Candidate gene studies performed over the past 10 years have identified a few polymorphic gene variants that modify risk or progression of common heart failure.4 Whole-genome sequencing will lead to the discovery of other genetic modifiers that were not candidates.5 The imminent availability of individual whole-genome sequences at a cost competitive with available genetic tests for familial cardiomyopathy will no doubt further expand the list of putative genetic heart failure modifiers. Heart failure risk alleles along with traditional clinical factors will need to be considered by clinical cardiologists in their design of optimal disease surveillance and prevention programs and in individually tailoring heart failure management.

The use of individual genetic make-up is likely to have the earliest and greatest impact on managing patients with heart failure by tailoring available pharmacotherapeutics to optimize patient response and minimize adverse effects (ie, the area of pharmacogenetics). Modern heart failure management has been derived and directed by the results of large, randomized, multicenter clinical trials. When standard therapies are applied according to the selection criteria used in these trials, they prolong average survival across affected populations or decrease the incidence of heart failure in populations at risk.6 For this reason, standardized treatment guidelines prescribe heart failure therapies according to trial designs, aiming for the same target doses and general treatment approaches,7 and largely ignore individual characteristics. In this article, we review established and emerging knowledge of genetic influence on common heart failure and try to anticipate how these genetic factors may be best used to eschew the cookie-cutter approach to heart failure management and move toward implementing a personalized medicine approach for the treatment and prevention of this important and prevalent disease.

The Concept of Genotype-Directed Personal Medical Management in Heart Failure

Variation in clinical heart failure progression and therapeutic response (either benefits or side effects) supports the need for a more individualized approach to disease management. On the basis of clinical stratification (eg, by etiology of heart failure as ischemic versus nonischemic, functional status, comorbid disease), physicians try to match each patient’s specific heart failure syndrome with a therapeutic regime devised to provide the most benefit. Standard heart failure pharmacotherapy currently comprises a minimum of 3 medications (angiotensin-converting enzyme [ACE] inhibitors, β-blockers, and aldosterone antagonists), with consideration of additional medications (hydralazine/isosorbide, angiotensin receptor blockers) and diuretics. The recommended target dosages for these agents, derived from their respective clinical trials, is rarely achieved,8 partly because of untoward clinical side effects such as low blood pressure or renal dysfunction. Accordingly, the published guidelines most often are applied in each individual patient using ad hoc approaches derived from personal experience and the “art of medicine.”

Technological advances in human genomics promise a different approach and are bringing cardiology into an era of clinically applied pharmacogenetics9 (whether we want to or not). As sequencing costs decline, it is not hard to envision that patients will present having had their entire genome already sequenced. The imperative to apply genome information in clinical settings will increase, as demonstrated by recent proof-of-concept studies.10 Our field seems poorly prepared for this type of evolution in care; Roden et al9 identified 3 major barriers: First is the absence of rapidly available genotype information in the clinical workflow. This barrier is being overcome with whole-genome sequencing, which (with proper analysis) promises a permanent and largely immutable genetic roadmap for individual disease risk and drug response at a cost comparable to many other clinical tests.11 Second, we must have the knowledge to properly apply information on genetic variants for the diseases we are managing and the drugs we are using. As we describe, this knowledge is accumulating for heart failure and for other cardiac conditions, and the rate at which we are gaining additional information and developing further expertise appears to be accelerating.

The third and perhaps most formidable barrier is the lack of clinical evidence showing how real-time application of genetic information can best benefit patients. As has been broadly communicated to the medical community and lay public, common functional gene variants in CYP2C19 can impair the transformation of clopidogrel into its active metabolite, leading to increased risk of stent thrombosis after percutaneous coronary intervention.12 The relevant question thus becomes the following: If physicians have this information at the time of clinical care and reacted by adjusting clopidogrel dose or substituting prasugrel, which is unaffected by CYP2C19 genotype,13 would there be any improvement in clinical outcome? It is also important to consider whether any observed benefits justify the additional costs of genetic testing and for the alternate drug. Studies are currently examining these questions, and similar clinical trials will prospectively examine whether a genotype-guided strategy of warfarin dosing will be superior to the standard genotype-blinded approach in reaching target anticoagulation goals. At this time, there are no similar prospective, randomized, blinded trials of genotype-guided care for common heart failure.

Emerging Variants

The variants described here are established, but new ones are emerging. Although findings in heart failure genome-wide association studies have been limited, we can expect additional common heart failure variants to emerge as sample sizes increase.65 The CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) consortium published a genome-wide association study of incident heart failure that tested for associations between >2.4 million HapMap-imputed polymorphisms in >20 000 subjects.7 They identified 2 loci associated with heart failure, rs10519210 (15q22, containing USP3 encoding a ubiquitin-specific protease) in subjects of European ancestry and rs11172782 (12q14, containing LRIG3 encoding a leucine-rich, immunoglobulin-like domain-containing protein of uncertain function) in subjects of African ancestry.66 In a companion study using the same population and genotyping results, mortality analysis of the subgroup of individuals who developed heart failure implicated an intronic SNP in CMTM7 (CKLF-like MARVEL transmembrane domain-containing 7).67 These genetic associations require independent replication and further study to identify the underlying biological mechanisms.

A recently published genome-wide association study by a European consortium on dilated cardiomyopathy identified common variants in BAG3 (BCL2-associated athanogene 3) associated with heart failure57 and identified rare BAG3 missense and truncation mutations that segregate with familial cardiomyopathy. These findings were consistent with an earlier exome-sequencing study that identified BAG3 as a familial dilated cardiomyopathy gene and showed recapitulation of cardiomyopathy with BAG3 morpholino knockdown in zebra fish.68 Together, these studies convincingly support variation in BAG3 as a genetic risk factor of cardiomyopathy and heart failure. It is noteworthy that both common and rare functional variations were identified at this locus. A unifying hypothesis for these findings, which needs to be formally tested, is that common variants in BAG3 serve as proxies for rare functional BAG3 mutations with large effects. In this situation, the underlying genetic lesion is a rare variant with a large functional effect. This has recently been described for common variants in MYH6 that correlated with rare functional MYH6 variants to cause sick sinus syndrome.69 It is premature to speculate on the clinical applications of these newer findings.

Moving Knowledge to Practice

A small number of genomic variants have been identified that modify heart failure by affecting well-understood physiological systems. The principal barrier preventing their adoption in practice may be lack of evidence showing how application of this information can best be used for clinical benefit. Trials testing genotype targeting of antiplatelet therapy and anticoagulation will be completed in the coming years. The findings from these studies will likely determine the level of enthusiasm for conducting genotype-guided trials of β-blockers and RAAS antagonists in heart failure. Given that the lifetime risk of heart failure in the United States is estimated at 1 in 5, even a small favorable effect on heart failure prevention or outcome through use of genome-guided therapy has the potential for a large public health impact. We therefore believe that a near-term goal should be to conduct pharmacogenomic trials in heart failure based on our current understanding of heart failure variants.

Looking ahead, unbiased approaches will continue to reveal a large number heart failure-modifying variants (both common and rare). Based on experience in other complex phenotypes, such has height70 and plasma lipid levels,71 the underlying genetic mechanisms for many new heart failure variants will be completely unknown, and their sheer number will preclude detailed experimentation using murine models to figure them out. Leveraging these variants for clinical application is a challenge that we will be forced to confront.

As our ability to identify rare, disease-causing variants improves through personal genome sequencing, we will be faced with the additional problem of how best to estimate the disease risk conferred by a sequence variant for which there has been no biological validation. In probabilistic terms, because there are 3 billion nucleotides in the human genome and over twice that many humans on the planet, it is likely that a nucleotide substitution for every position is represented in someone. Obviously, it will be impossible to recombinantly express and functionally characterize every DNA variant that is going to be implicated in heart failure. Bioinformatics filters have been used to try and separate functionally significant from insignificant variants based on the likelihood of changing transcript expression or protein function. These tools are limited but will improve if we tailor their results to the known characteristics of each gene product. For example, current approaches to categorize amino acid substitutions as conservative or nonconservative based only on charge or side chains can be improved by molecular modeling that incorporates protein-specific structure-function information. This approach has been used to estimate the pathogenicity of myosin heavy chain (MHC) mutations in an effort to determine which mutations are likely to cause familial cardiomyopathy when linkage analysis is not feasible.72 In concept, this approach can be applied to any protein for which structure-function activities have been finely mapped to distinct domains.

A promising extension of this approach may be to use evolutionary genetics to infer disease causality. Again, using the MHC genes as examples, human genome data show a greater prevalence of nonsynonymous gene variants in MYH6, which encodes the minor cardiac α-MHC isoform, compared with the adjacent MYH7, which encodes the major β-MHC isoform. This disparity suggests a greater tolerance for protein changes in the α-MHC isoform and negative selection against these in β-MHC. We can infer, therefore, that amino acid changes are more likely to have adverse impacts in MYH7-encoded β-MHC. If this paradigm survives prospective testing, then the forthcoming explosion of individual genetic data not only will present a massive problem in interpretation, but also will provide the genetic information by which analyses of rare sequence variants across large unaffected populations can help to differentiate the tolerable variants from those that are more likely to alter disease risk.

Each Reference above is found in:

http://circgenetics.ahajournals.org/content/4/6/701.full

SOURCE: 

Circulation: Cardiovascular Genetics.2011; 4: 701-709

doi: 10.1161/ CIRCGENETICS.110.959379

 

Pharmacogenomics

 

Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives

Results From the Pharmacogenomic Evaluation of Antihypertensive Responses Study

Yan Gong, PhD, Caitrin W. McDonough, PhD, Zhiying Wang, MS, Wei Hou, PhD, Rhonda M. Cooper-DeHoff, PharmD, MS, Taimour Y. Langaee, PhD, Amber L. Beitelshees, PharmD, MPH, Arlene B. Chapman, MD, John G. Gums, PharmD, Kent R. Bailey, PhD, Eric Boerwinkle, PhD, Stephen T. Turner, MD and Julie A. Johnson, PharmD

Author Affiliations

From the Department of Pharmacotherapy and Translational Research (Y.G., C.W.M., R.M.C.-D., T.Y.L., J.G.G., J.A.J.), Department of Biostatistics, College of Medicine (W.H.), Division of Cardiovascular Medicine, College of Medicine (R.M.C.-D., J.A.J.), and Department of Community Health and Family Medicine (J.G.G.), University of Florida, Gainesville, FL; Division of Epidemiology, University of Texas at Houston, Houston, TX (Z.W., E.B.); Division of Endocrinology, Diabetes and Nutrition, University of Maryland, Baltimore, MD (A.L.B.); Renal Division, Emory University, Atlanta, GA (A.B.C.); and Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN (S.T.T.).

Correspondence to Yan Gong, PhD, Department of Pharmacotherapy and Translational Research, University of Florida, PO Box 100486, 1600 SW Archer Rd, Gainesville, FL 32610. E-mail gong@cop.ufl.edu.

Abstract

Background—To date, 39 single nucleotide polymorphisms (SNPs) have been associated with blood pressure (BP) or hypertension in genome-wide association studies in whites. Our hypothesis is that the loci/SNPs associated with BP/hypertension are also associated with BP response to antihypertensive drugs.

Methods and Results—We assessed the association of these loci with BP response to atenolol or hydrochlorothiazide monotherapy in 768 hypertensive participants in the Pharmacogenomics Responses of Antihypertensive Responses study. Linear regression analysis was performed on whites for each SNP in an additive model adjusting for baseline BP, age, sex, and principal components for ancestry. Genetic scores were constructed to include SNPs with nominal associations, and empirical P values were determined by permutation test. Genotypes of 37 loci were obtained from Illumina 50K cardiovascular or Omni1M genome-wide association study chips. In whites, no SNPs reached Bonferroni-corrected α of 0.0014, 6 reached nominal significance (P<0.05), and 3 were associated with atenolol BP response at P<0.01. The genetic score of the atenolol BP-lowering alleles was associated with response to atenolol (P=3.3×10–6 for systolic BP; P=1.6×10–6 for diastolic BP). The genetic score of the hydrochlorothiazide BP-lowering alleles was associated with response to hydrochlorothiazide (P=0.0006 for systolic BP; P=0.0003 for diastolic BP). Both risk score P values were <0.01 based on the empirical distribution from the permutation test.

Conclusions—These findings suggest that selected signals from hypertension genome-wide association studies may predict BP response to atenolol and hydrochlorothiazide when assessed through risk scoring.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 686-691

Published online before print October 19, 2012,

doi: 10.1161/ CIRCGENETICS.112.964080

 

Genetic Determinants of Statin-Induced Low-Density Lipoprotein Cholesterol Reduction

The Justification for the Use of Statins in Prevention: An Intervention Trial Evaluating Rosuvastatin (JUPITER) Trial

Daniel I. Chasman, PhD, Franco Giulianini, PhD, Jean MacFadyen, BA, Bryan J. Barratt, PhD, Fredrik Nyberg, MD, PhD, MPH and Paul M Ridker, MD, MPH

Author Affiliations

From the Center for Cardiovascular Disease Prevention (D.I.C., F.G., J.M., P.M.R.), JUPITER Trial Coordinating Center (D.I.C., F.G., J.M., P.M.R.), Brigham and Women’s Hospital and Harvard Medical School (D.I.C., P.M.R.), Boston, MA; Personalised Healthcare and Biomarkers, AstraZeneca Research and Development, Alderley Park, United Kingdom (B.J.B.); AstraZeneca Research and Development, Mölndal, Sweden (F.N.); and Unit of Occupational and Environmental Medicine, Department of Public Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden (F.N.).

Correspondence to Daniel I. Chasman, PhD, Center for Cardiovascular Disease Prevention, Brigham and Women’s Hospital, 900 Commonwealth Ave E, Boston, MA 02215. E-mail dchasman@rics.bwh.harvard.edu

Abstract

Background—In statin trials, each 20 mg/dL reduction in cholesterol results in a 10–15% reduction of annual incidence rates for vascular events. However, interindividual variation in low-density lipoprotein cholesterol (LDL-C) response to statins is wide and may partially be determined on a genetic basis.

Methods and Results—A genome-wide association study of LDL-C response was performed among a total of 6989 men and women of European ancestry who were randomly allocated to either rosuvastatin 20 mg daily or placebo. Single nucleotide polymorphisms (SNPs) for genome-wide association (P<5×108) with LDL-C reduction on rosuvastatin were identified at ABCG2, LPA, and APOE, and a further association at PCSK9 was genome-wide significant for baseline LDL-C and locus-wide significant for LDL-C reduction. Median LDL-C reductions on rosuvastatin were 40, 48, 51, 55, 60, and 64 mg/dL, respectively, among those inheriting increasing numbers of LDL-lowering alleles for SNPs at these 4 loci (P trend=6.2×1020), such that each allele approximately doubled the odds of percent LDL-C reduction greater than the trial median (odds ratio, 1.9; 95% confidence interval, 1.8–2.1; P=5.0×1041). An intriguing additional association with sub–genome-wide significance (P<1×10-6) was identified for statin related LDL-C reduction at IDOL, which mediates posttranscriptional regulation of the LDL receptor in response to intracellular cholesterol levels. In candidate analysis, SNPs in SLCO1B1 and LDLR were confirmed as associated with LDL-C lowering, and a significant interaction was observed between SNPs in PCSK9 and LDLR.

Conclusions—Inherited polymorphisms that predominantly relate to statin pharmacokinetics and endocytosis of LDL particles by the LDL receptor are common in the general population and influence individual patient response to statin therapy.

SOURCE:

Circulation: Cardiovascular Genetics.2012; 5: 257-264

Published online before print February 13, 2012,

doi: 10.1161/ CIRCGENETICS.111.961144

Genetic Variation in the β2 Subunit of the Voltage-Gated Calcium Channel and Pharmacogenetic Association With Adverse Cardiovascular Outcomes in the INternational VErapamil SR-Trandolapril STudy GENEtic Substudy (INVEST-GENES)

Yuxin Niu, PhD*, Yan Gong, PhD*, Taimour Y. Langaee, PhD, Heather M. Davis, PharmD, Hazem Elewa, PhD, Amber L. Beitelshees, PharmD, MPH, James I. Moss, PhD, Rhonda M. Cooper-DeHoff, PharmD, Carl J. Pepine, MD and Julie A. Johnson, PharmD

Author Affiliations

From the Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics (Y.N., Y.G., T.Y.L., H.M.D., H.E., J.I.M., R.M.C.-D., J.A.J.), College of Pharmacy, University of Florida, Gainesville, Fla; Division of Endocrinology, Diabetes and Nutrition (A.L.B.), University of Maryland School of Medicine, Baltimore, Md; and Division of Cardiovascular Medicine (R.M.C.-D., C.J.P., J.A.J.), University of Florida College of Medicine, Gainesville, Fla.

Correspondence to Julie A. Johnson, PharmD, Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, PO Box 100486, Gainesville, FL 32610. E-mail Johnson@cop.ufl.edu

* Drs Niu and Gong contributed equally to this work.

Abstract

Background— Single-nucleotide polymorphisms (SNPs) within the regulatory β2 subunit of the voltage-gated calcium channel (CACNB2) may contribute to variable treatment response to antihypertensive drugs and adverse cardiovascular outcomes.

Methods and Results— SNPs in CACNB2 from 60 ethnically diverse individuals were identified and characterized. Three common SNPs (rs2357928, rs7069292, and rs61839258) and a genome-wide association study-identified intronic SNP (rs11014166) were genotyped for a clinical association study in 5598 hypertensive patients with coronary artery disease randomized to a β-blocker (BB) or a calcium channel blocker (CCB) treatment strategy in the INternational VErapamil SR-Trandolapril STudy GENEtic Substudy (INVEST-GENES). Reporter gene assays were conducted on the promoter SNP, showing association with clinical outcomes. Twenty-one novel SNPs were identified. A promoter A>G SNP (rs2357928) was found to have significant interaction with treatment strategy for adverse cardiovascular outcomes (P for interaction, 0.002). In whites, rs2357928 GG patients randomized to CCB were more likely to experience an adverse outcome than those randomized to BB treatment strategy, with adjusted hazard ratio (HR) (CCB versus BB) of 2.35 (95% CI, 1.19 to 4.66; P=0.014). There was no evidence for such treatment difference in AG (HR, 1.16; 95% CI, 0.75 to 1.79; P=0.69) and AA (HR, 0.63; 95% CI, 0.36 to 1.11; P=0.11) patients. This finding was consistent in Hispanics and blacks. CACNB2 rs11014166 showed similar pharmacogenetic effect in Hispanics, but not in whites or blacks. Reporter assay analysis of rs2357928 showed a significant increase in promoter activity for the G allele compared to the A allele.

Conclusions— These data suggest that genetic variation within CACNB2 may influence treatment-related outcomes in high-risk patients with hypertension.

Clinical Trial Registration— URL: http://www.clinicaltrials.gov. Unique identifier: NCT00133692.

SOURCE:

Circulation: Cardiovascular Genetics.2010; 3: 548-555

doi: 10.1161/ CIRCGENETICS.110.957654

 

Hepatic Metabolism and Transporter Gene Variants Enhance Response to Rosuvastatin in Patients With Acute Myocardial Infarction

The GEOSTAT-1 Study

Kristian M. Bailey, MBChB, Simon P.R. Romaine, BSc, Beryl M. Jackson, RGN, Amanda J. Farrin, MSc, Maria Efthymiou, MSc, Julian H. Barth, MD, Joanne Copeland, BSc, Terry McCormack, MBBS, Andrew Whitehead, MSc, Marcus D. Flather, MBBS, Nilesh J. Samani, MD, FMedSci, Jane Nixon, PhD, Alistair S. Hall, MD, PhD, Anthony J. Balmforth, PhD and on behalf of the SPACE ROCKET Trial Group

Author Affiliations

From the Division of Cardiovascular and Diabetes Research (K.M.B., S.P.R.R., B.M.J., A.J.B.), and Division of Cardiovascular and Neuronal Remodelling (A.S.H.), Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, United Kingdom; Clinical Trials Research Unit (A.J.F., M.E., J.C., J.N.), University of Leeds, Leeds, United Kingdom; Clinical Biochemistry (J.H.B.), Leeds General Infirmary, Leeds, United Kingdom; Whitby Group Practice (T.M.), Spring Vale Medical Centre, Whitby, North Yorkshire, United Kingdom; Pharmacy Department (A.W.), Leeds General Infirmary, Leeds, United Kingdom; Clinical Trials and Evaluation Unit (M.D.F.), Royal Brompton and Harefield NHS Trust and Imperial College, London, United Kingdom; and Department of Cardiovascular Sciences (N.J.S.), University of Leicester, Leicester, United Kingdom.

Correspondence to Alistair S. Hall, Clinical Cardiology, Multidisciplinary Cardiovascular Research Centre (MCRC), G Floor, Jubilee Building, Leeds General Infirmary, Leeds, LS1 3EX, United Kingdom. E-mail A.S.Hall@leeds.ac.uk

* Dr Bailey, Mr Romaine, Dr Hall, and Dr Balmforth contributed equally to this study.

Abstract

Background— Pharmacogenetics aims to maximize benefits and minimize risks of drug treatment. Our objectives were to examine the influence of common variants of hepatic metabolism and transporter genes on the lipid-lowering response to statin therapy.

Methods and Results— The Genetic Effects On STATins (GEOSTAT-1) Study was a genetic substudy of Secondary Prevention of Acute Coronary Events—Reduction of Cholesterol to Key European Targets (SPACE ROCKET) (a randomized, controlled trial comparing 40 mg of simvastatin and 10 mg of rosuvastatin) that recruited 601 patients after myocardial infarction. We genotyped the following functional single nucleotide polymorphisms in the genes coding for the cytochrome P450 (CYP) metabolic enzymes, CYP2C9*2 (430C>T), CYP2C9*3 (1075A>C), CYP2C19*2 (681G>A), CYP3A5*1 (6986A>G), and hepatic influx and efflux transporters SLCO1B1 (521T>C) and breast cancer resistance protein (BCRP; 421C>A). We assessed 3-month LDL cholesterol levels and the proportion of patients reaching the current LDL cholesterol target of <70 mg/dL (<1.81 mmol/L). An enhanced response to rosuvastatin was seen for patients with variant genotypes of either CYP3A5 (P=0.006) or BCRP (P=0.010). Furthermore, multivariate logistic-regression analysis revealed that patients with at least 1 variant CYP3A5 and/or BCRP allele (n=186) were more likely to achieve the LDL cholesterol target (odds ratio: 2.289; 95% CI: 1.157, 4.527; P=0.017; rosuvastatin 54.0% to target vs simvastatin 33.7%). There were no differences for patients with variants of CYP2C9, CYP2C19, or SLCO1B1 in comparison with their respective wild types, nor were differential effects on statin response seen for patients with the most common genotypes for CYP3A5 and BCRP (n=415; odds ratio: 1.207; 95% CI: 0.768, 1.899; P=0.415).

Conclusion— The LDL cholesterol target was achieved more frequently for the 1 in 3 patients with CYP3A5 and/or BCRP variant genotypes when prescribed rosuvastatin 10 mg, compared with simvastatin 40 mg.

Clinical Trial Registration— URL: http://isrctn.org. Unique identifier: ISRCTN 89508434.

SOURCE:

Circulation: Cardiovascular Genetics.2010; 3: 276-285

Published online before print March 5, 2010,

doi: 10.1161/ CIRCGENETICS.109.898502

 

Comprehensive Whole-Genome and Candidate Gene Analysis for Response to Statin Therapy in the Treating to New Targets (TNT) Cohort

John F. Thompson, PhD, Craig L. Hyde, PhD, Linda S. Wood, MS, Sara A. Paciga, MA, David A. Hinds, PhD, David R. Cox, MD, PhD, G. Kees Hovingh, MD, PhD and John J.P. Kastelein, MD, PhD

Author Affiliations

From the Helicos BioSciences (J.F.T.), Cambridge, Mass; Molecular Medicine (J.F.T., L.S.W., S.A.P.) and Statistical Applications (C.L.H.), Pfizer Global Research and Development, Groton, Conn; Perlegen Sciences (D.A.H., D.R.C.), Mountain View, Calif; and Department of Vascular Medicine (G.K.H., J.J.P.K.), Academic Medical Center, Amsterdam, The Netherlands.

Correspondence to John J.P. Kastelein, MD, PhD, Department of Vascular Medicine, Academic Medical Center, Meibergdreef 9, Room F4-159.2, 1105 AZ Amsterdam, The Netherlands. E-mail j.j.kastelein@amc.uva.nl or j.s.jansen@amc.uva.nl

Abstract

Background— Statins are effective at lowering low-density lipoprotein cholesterol and reducing risk of cardiovascular disease, but variability in response is not well understood. To address this, 5745 individuals from the Treating to New Targets (TNT) trial were genotyped in a combination of a whole-genome and candidate gene approach to identify associations with response to atorvastatin treatment.

Methods and Results— A total of 291 988 single-nucleotide polymorphisms (SNPs) from 1984 individuals were analyzed for association with statin response, followed by genotyping top hits in 3761 additional individuals. None was significant at the whole-genome level in either the initial or follow-up test sets for association with low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, or triglyceride response. In addition to the whole-genome platform, 23 candidate genes previously associated with statin response were analyzed in these 5745 individuals. Three SNPs in apoE were most highly associated with low-density lipoprotein cholesterol response, followed by 1 in PCSK9 with a similar effect size. At the candidate gene level, SNPs in HMGCR were also significant though the effect was less than with those in apoE and PCSK9. rs7412/apoE had the most significant association (P=6×1030), and its high significance in the whole-genome study (P=4×109) confirmed the suitability of this population for detecting effects. Age and gender were found to influence low-density lipoprotein cholesterol response to a similar extent as the most pronounced genetic effects.

Conclusions— Among SNPs tested with an allele frequency of at least 5%, only SNPs in apoE are found to influence statin response significantly. Less frequent variants in PCSK9 and smaller effect sizes in SNPs in HMGCR were also revealed.

SOURCE:

Circulation: Cardiovascular Genetics.2009; 2: 173-181

Published online before print February 12, 2009,

doi: 10.1161/ CIRCGENETICS.108.818062

Summary

Larry H. Bernstein, MD, FCAP

This review has examined a compendium of well regarded documents drawn from 248 articles in Circulation Cardiovascular Genetics from March 2010 to March 2013. The large amount of evidence obtained from large population studies identifying Genome Wide Analysis Studies (GWAS) examines a host of cardiac and vascular diseases in which there is association between specific single nucleotide peptides (SNPs), and gene loci, that may play or have no significant role in developing heart disease. It certainly is evidence of the role that the American Heart Association has is in supporting the leading research today for tomorrow’s patients.   It is too early to sort them out, but it speaks to a large volume of discovery in this area.

It raises another issue that we have been confronted with mostly since the second half of the 20th century.  What is that issue?  The issue, it appears to me, is the vast improvements in analytical technology so that “imprecision” is far less likely to be a confounder in biological measurements and this lends access to far better accuracy?  But from that question arises another! Accuracy only refers to what is measured, but does it give us better ability to explain a complex and dynamic process?  In other words, what is what we are looking at representative of in manageable events?   I think that this is the most important idea that should come out of the recent criticism of the trajectory that molecular genetics been on in the last 5 years.

It was still in an era that “BIG’ science was not the normal.  One could spend an enormous effort at stepwise purification of a protein or enzyme, or other biomolecule starting with a slurry made from 100 lbs of “chicken heart”, for example.  These separations were based on negative charges on the molecules and positive charges on the column, and the molecules of no interest were eluted by gradient elution.  Much was learned about large scale preparation from small scale trials.  But this work was not undertaken without the intent to carry out a number of investigations to understand the “functionality” of a link in a metabolic pathway.  The studies that followed the purification required kinetic investigation with a coenzyme, or with a synthetically modified coenzyme, amino acid sequencing, NMR studies, etc.  You could not put together a “mechanism” without having the minimum amount of necessary information for a reliable account.  It is probably this requirement that led to today’s “BIG” science, that is founded upon multiple methods, now large data bases, and teams of investigators across institutions and continents.  The acquisition of knowledge has been astounding, but the integration of knowledge has not caught up.

However, let’s see if we can sort out the most meaningful signals from what I too am beginning to call the “noisy channel”.  As often happens, important areas of research are opened up that are followed by significant discovery and, in the long run, many other dead end publications that have no lasting significance.  In order to do justice to the work, I’ll pick through documents I find interesting, keeping in mind there is a hidden layer of complexity of which only sufficient information leads to a better understanding.  As much literature calls attention to, much of what ails us has nothing to do with classical Mendelian genetics, and has a postgenomic component.

The most fascinating aspect of this is the withering “dark matter” of the genome. While that component may be silent or expressed, the understanding comes at a higher observed order.  The dark became light! The expression became subtle, like weak bond interactions. The underlying organization is a component of the adaptive ability of an organism or individual in an environment with plants and animals in a changing climate, at particular altitudes, with given water supplies, with disease vectors, and with endogenous sources of essential nutrients.  This brings into focus the regulatory role of the genome as just as important a factor as transmission of the genetic code, especially in somatic cell populations.

The remainder of this discussion deals specifically with my observations on cardiovascular genomics. The following conclusion is appropriate, if incomplete, at this time on circulating miRNAs, particularly miR-133a:

  • elevated levels of circulating miR-133a in patients with cardiovascular diseases originate mainly from the injured myocardium.
  • Circulating miR-133a can be used as a marker for cardiomyocyte death, and

A number of articles that cite this article suggest that it may be useful for following disease progression:
Plasma microRNAs serve as biomarkers of therapeutic efficacy and disease progression in hypertension-induced heart failure  Eur J Heart Fail  2013

MicroRNAs Within the Continuum of Postgenomics Biomarker Discovery Arterio. Thromb. Vasc. Bio. 2013;33:206-214

“Need for Rigor in Design, Reporting, and Interpretation of Transcriptomic Biomarker Studies”  J. Clin. Microbiol.. 2012;50:4192-4193

Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases. Am. J. Physiol. Heart Circ. Physiol.. 2012;303:H1085-H1095,

Circulating MicroRNAs: Novel Biomarkers and Extracellular Communicators in Cardiovascular Disease? Circ. Res.. 2012;110:483-495

Circulating MicroRNAs: Biomarkers or Mediators of Cardiovascular Diseases?  Arterioscler. Thromb. Vasc. Bio. 2011;31:2383-2390,

Circulating MicroRNA-208b and MicroRNA-499 Reflect Myocardial Damage in Cardiovascular Disease MF Corsten, R Dennert, S Jochem, T Kuznetsova,  et al.

The finding refers to an association that is related to the appearance of a miRNA in the circulation of patients with acute cardiac ischemia, and particular released into the circulation of patients from injured myocardium.  This finding has to be distinguished from a finding of another miRNA released with acute injury.  In the case of miR499 (and miR208b), there is a comparison with plasma cTnT, and an ROC curve is produced.

The List of this follows:

Circulation: Cardiovascular Genetics 2010; 3: 499-506

Strikingly, in plasma from

  • acute myocardial infarction patients, cardiac myocyte–associated miR-208b and -499 were highly elevated, 1600-fold (P<0.005) and 100-fold (P<0.0005), respectively, as compared with control subjects. Receiver operating characteristic curve analysis revealed an area under the curve of 0.94 (P<10−10) for miR-208b and 0.92 (P<10−9) for miR-499. Both microRNAs correlated with plasma troponin T, indicating release of microRNAs from injured cardiomyocytes.
  • In patients with acute heart failure, only miR-499 was significantly elevated (2-fold), whereas
  • no significant changes in microRNAs studied could be observed in diastolic dysfunction.

Remarkably, plasma microRNA levels were not affected by a wide range of clinical confounders, including

  • age,
  • sex,
  • body mass index,
  • kidney function,
  • systolic blood pressure, and
  • white blood cell count.

This is miRNA with a different twist.  It appears that there are 3 types found in AMI (133a, 208b, 409).  But type 499 alone is increased with acute heart failure (no mention of chronic cardiomyopathy and no effect of estimated GFR, or of age).

If the problem was just of AMI, then we have to know what this brings to the table.  As it is the hs-troponins have yet to be shown to effectively not only increase the high sensitivity of the tests, but to decrease the confusion generated by the elevation.  The enormous improvement of a test that may be superior to the hs-ctn’s is for the patient with very indeterminiate shortness of breath, a nondefinitive ECG, and in a prodromal phase of AMI.  This happened in the past, and it may happen now, and it may account for many cases of silent MI that were found at autopsy.

Cited by
Plasma microRNAs serve as biomarkers of therapeutic efficacy and disease progression in hypertension-induced heart failure Eur J Heart Fail. 2013;0:hft018v1-hft018,
Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases Am. J. Physiol. Heart Circ. Physiol.. 2012;303:H1085-H1095,

Circulation Editors’ Picks: Most Read Articles in Cardiovascular Genetics Circulation. 2012;126:e163-e169,
MicroRNAs in Patients on Chronic Hemodialysis (MINOS Study) CJASN. 2012;7:619-623,

Novel techniques and targets in cardiovascular microRNA research Cardiovasc Res. 2012;93:545-554,

Microparticles: major transport vehicles for distinct microRNAs in circulation Cardiovasc Res. 2012;93:633-644,

Profiling of circulating microRNAs: from single biomarkers to re-wired networks Cardiovasc Res. 2012;93:555-562,

Small but smart–microRNAs in the centre of inflammatory processes during cardiovascular diseases, the metabolic syndrome, and ageing   Cardiovasc Res. 2012;93:605-613,

Circulation: Heart Failure Editors’ Picks: Most Important Papers in Pathophysiology and Genetics Circ Heart Fail. 2012;5:e32-e49

Use of Circulating MicroRNAs to Diagnose Acute Myocardial Infarction   Clin. Chem. 2012;58:559-567,

Circulating microRNAs to identify human heart failure   Eur J Heart Fail. 2012;14:118-119,

Next Steps in Cardiovascular Disease Genomic Research–Sequencing, Epigenetics, and Transcriptomics  Clin. Chem. 2012;58:113-126,

Most Read in Cardiovascular Genetics on Biomarkers, Inherited Cardiomyopathies and Arrhythmias, Metabolomics, and Genomics Circ Cardiovasc Genet. 2011;4:e24-e30,

MicroRNA-126 modulates endothelial SDF-1 expression and mobilization of Sca-1+/Lin- progenitor cells in ischaemia  Cardiovasc Res. 2011;92:449-455,

The use of genomics for treatment is another matter, and has several factors, e.g., age, residual function after AMI, comorbidities

This is a lot of interesting work that opens as many questions as it answers. The observations are real, and they lead to questions relating to the heart and the circulation.  Maybe it will generate answers to very tough issues concerning hypertension, renal disease and the heart.  It is far too early to tell.  It appears that we are about to hear a cacophony of miR’s in a symphony on cardiac and circulatory diseases not be be pieced together soon. But we have many more tools at our disposal than we did when Karmen discovered and made a distinction between

  • Aspartate and Alanine aminotransferases in the late 1950s, followed in the 1960s by
  • Creatine phosphokinase, the
  • MB-isoenzyme of CK by Sobel, Shell and Kjeckshus,
  • isoenzyme-1 of lactate dehydrogenase, and later the
  • Troponins,

leading to the programs to “reduce the extent of infarct damage”.  Then came the

  • a- and b-type natriuretic peptides,

which are still not fully understood in their role in congestive heart failure and in renal disease.

One item strikes the imagination as a fruitful area of further study.   Genetic Determinants of Potassium Sensitivity and Hypertension.    Integrated Computational and Experimental Analysis of the Neuroendocrine Transcriptome in Genetic Hypertension Identifies Novel Control Points for the Cardiometabolic Syndrome

Essential hypertension, a common complex disease, displays substantial genetic influence. Contemporary methods to dissect the genetic basis of complex diseases such as the genomewide association study are powerful, yet a large gap exists betweens the fraction of population trait variance explained by such associations and total disease heritability.

The researchers

  • developed a novel, integrative method (combining animal models, transcriptomics, bioinformatics, molecular biology, and trait-extreme phenotypes)
  • to identify candidate genes for essential hypertension and the metabolic syndrome.

Method  …  transcriptome profiling on adrenal glands from blood pressure extreme mouse strains:

  1. the hypertensive BPH (blood pressure high) and
  2. hypotensive BPL (blood pressure low).

Results….   Microarray data clustering revealed

  • underexpression of intermediary metabolism transcripts in HIGH BLOOD PRESSURE.
  • The MITRA algorithm identified a conserved motif in the transcriptional regulatory regions of the underexpressed metabolic genes,
  • They decide that regulation through this motif contributed to the global underexpression.
  • Luciferase reporter assays demonstrated transcriptional activity of the motif through transcription factors
    • HOXA3,
    • SRY, and
    •  YY1.

They finally hypothesized that genetic variation at HOXA3, SRY, and YY1 might predict blood pressure and other metabolic syndrome traits in humans. Tagging variants for each locus were associated with

  • blood pressure in a human population blood pressure extreme sample with
  • the most extensive associations for YY1 tagging single nucleotide polymorphism rs11625658 on
  1. systolic blood pressure,
  2. diastolic blood pressure,
  3. body mass index, and
  4. fasting glucose.

Meta-analysis extended the YY1 results into 2 additional large population samples with significant effects preserved on diastolic blood pressure, body mass index, and fasting glucose.

It will take much more of this beautiful integrative work to open up our imagination as to what physiological processes are occurring.

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Lp(a) Gene Variant Association

Reporter: Larry H Bernstein, MD, FCAP

Lp(a) Gene Variant Associated With Aortic Stenosis

Reported by Lisa Nainggolan Feb 06, 2013; GThanassoulis et al. NEJM http://www.theheart.org/article/1503525.do

People carrying this single nucleotide polymorphism (SNP) had a doubling of the risk of valve calcification on computer tomography (CT) compared with those without the variation. The same SNP has previously been identified as a risk factor for increased Lp(a) levels and coronary artery disease (CAD). Findings Could Reawaken Interest in Therapies Targeting Lp(a)

A Single Nucleotide Polymorphism is a change o...

A Single Nucleotide Polymorphism is a change of a nucleotide at a single base-pair location on DNA. Created using Inkscape v0.45.1. (Photo credit: Wikipedia)

 

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Genomic Promise for Neurodegenerative Diseases, Dementias, Autism Spectrum, Schizophrenia, and Serious Depression

Reporter and writer: Larry H Bernstein, MD, FCAP

There has been an considerable success in the current state of expanding our knowledge in genomics and therapeutic targets in cancer (although clinical remission targets and relapse are a concern), cardiovascular disease, and infectious disease.  Our knowledge of  prenatal and perinatal events is still at an early stage.  The neurology front is by no means unattended.  Here there are two prominent drivers of progress –

  • genomic control of cellular apoptosis by ubiquitin pathways, and
  • epigenetic investigations,

among a complex sea of sequence-changes.  I indicate some of the current status in this.  However, as much as we have know, there is an incredible barrier to formulate working models because:

  1. ligand binding between DNA short-sequences is not predictable over time
  2. binding between proteins and DNA is still largely unknown
  3. specific regulatory roles between nucleotide-sequences and histone proeins are still unclear
  4. the relationship between intracellular as well as extracellular cations and the equilibria between cations and anions in intertitial fluid that bathes the cell and between organelles is virgin territory

Consequently, it is quite an accomplishment to have come as far as we have come, and yet, even with the huge compuational power at our disposal, there is insuficient data to unravel the complexity.  This may be especially true in the pathway to understanding of neurological and behavioral disorders.

Broad Map of Brain

John Markoff reports in the Feb 18 front-page of New York Times (Project would construct a broad map of the brain) that the Obama administration envisions a decade-long effort to examine the workings of the human brain and construct a map, comparable to what the Human Genome Project did for genetics.  It will be a collaboration between universities, the federal government, private foundations, and teams of scientists (neuro-, nano- and whoever else).  The goal is to break through the barrier to understanding the brain’s billions of neurons and gain greater insight into

  • perception
  • actions
  • and consciousness.

Essentially, it holds great promise for understanding

Alzheimer’s disease and Parkinson’s, as well as finding therapies for a variety of mental illnesses.  An open-ended question is whether it will also advance artificial intelligence research.  It is termed the Brain Activity Map project.
http://NYTimes/broad-map-of-brain/

Schizophrenia Genomics

Scientists Reveal Genomic Explanation for Schizophrenia

July 11, 2011 

http://GenWeb.com/Exome Sequences Reveal Role for De Novo Mutations in Schizophrenia/
h
ttp://NatureGenetics.com/Exome Sequences Reveal Role for De Novo Mutations in Schizophrenia/
http://SchizophreniaResearch.com/INFS integrates diverse neurological signals that control the development of embryonic stem cell and neural progenitor cells/

Buffalo, NY (Scicast) (GenomeWeb News) –

Two new studies, published in Schizophrenia Research and in Nature Genetics, propose hypotheses in a new mouse model of schizophrenia that demonstrates how gestational brain changes cause behavioural problems later in life.  

The first study implicates

A fibroblast growth factor receptor protein, (FGFR1), targets diverse genes implicated in schizophrenia.  The research demonstrates how defects in an important neurological pathway in early development

  • may be responsible for the onset of schizophrenia later in life.

Individuals with sporadic schizophrenia tend to carry more deleterious genetic changes than found in the general population, according to an exome sequencing study  that appeared online in Nature Genetics yesterday.  “The occurrence of de novo mutations may in part explain the high worldwide incidence of schizophrenia,”  according to co-senior author Guy Rouleau, CHU Sainte-Justine Research Center of University of Montreal.
Researchers from Canada and France did exome sequencing on individuals from 14 parent-child trios, each comprised of an individual with schizophrenia and his or her unaffected parents. In the process, they found

  • 15 de novo mutations in coding sequences from eight individuals with the psychiatric condition, including
  • four nonsense mutations predicted to abbreviate protein sequences.

“They surmise that [de novo mutations] may account for some of the heritability reported for schizophrenia.  Recent exome sequencing studies involving parent-child trios have implicated de novo mutations in other brain-related conditions, including

  • autism spectrum disorder and
  • mental retardation.

To detect de novo genetic changes specific to schizophrenia, the team compared coding sequences from affected individuals with

  • the human reference genome, with
  • both of his or her parents, and
  • with 26 unrelated control individuals.

Of the 15 de-novo mutations verified by Sager sequencing,

  • 11 were missense mutations predicted to alter the amino acid sequence of the resulting protein and
  • four were nonsense mutations predicted to truncate it.

Among the genes containing nonsense mutations were the zinc finger protein-coding gene ZNF480, the karyopherin alpha 1 gene KPNA1, the low-density lipoprotein receptor-related gene LRP1, and the ALS-like protein-coding gene ALS2CL.

The 15 mutations were found in coding sequences from eight of the individuals with schizophrenia,

  • hinting at a higher de novo mutation rate in individuals with sporadic schizophrenia than is predicted in the population overall.

This difference seems to be specific to exomes, and the researchers noted that

  • de novo mutation rates across the entire genome are likely comparable in those with or without schizophrenia.

They conclude that the enrichment of [de novo mutations] within the coding sequence of individuals with schizophrenia may underlie the pathogenesis of many of these individual.  Most of the genes identified in this study have not been previously linked to schizophrenia, thereby providing new potential therapeutic targets.

The second study

  • identifies the Integrative Nuclear FGFR 1 Signaling (INFS) as a central intersection point for multiple pathways of
  • as many as 160 different genes believed to be involved in the disorder.

The lead author Dr. Michal Stachowiakthis (UB School of Medicine and Biomedical Sciences) suggests this  is the first model that explains schizophrenia

  1. from genes
  2. to development
  3. to brain structure and
  4. finally to behaviour .

A key challenge has been that patients with schizophrenia exhibit mutations in different genes. It is  possible to have 100 patients with schizophrenia and each one has a different genetic mutation that causes the disorder. The explanation is possibly because INFS integrates diverse neurological signals that control the development of embryonic stem cell and neural progenitor cells, and

  • links pathways involving schizophrenia-linked genes.

“INFS functions like the conductor of an orchestra,” explains Stachowiak. “It doesn’t matter which musician is playing the wrong note,

  • it brings down the conductor and the whole orchestra.

With INFS, we propose that

  • when there is an alteration or mutation in a single schizophrenia-linked gene,
  • the INFS system that controls development of the whole brain becomes untuned.

Using embryonic stem cells, Stachowiak and colleagues at UB and other institutions found that

  • some of the genes implicated in schizophrenia bind the FGFR1 (fibroblast growth factor receptor) protein,
  • which in turn, has a cascading effect on the entire INFS.

“We believe that FGFR1 is the conductor that physically interacts with all genes that affect schizophrenia,” he says. “We think that schizophrenia occurs

  • when there is a malfunction in the transition from stem cell to neuron, particularly with dopamine neurons.”

The researchers tested their hypothesis by creating an FGFR1 mutation in mice, which produced the hallmarks of the human disease: altered brain anatomy,

  • behavioural impacts and
  • overloaded sensory processes.

The researchers would like to devise ways to arrest development of the disease before it presents fully in adolescence or adulthood. The UB work adds to existing evidence that nicotinic agonists, might  help improve cognitive function in schizophrenics by acting on the INFS.

childhood-schizophrenia-symptoms

childhood-schizophrenia-symptoms (Photo credit: Life Mental Health)

English: Types of point mutations. With examples.

English: Types of point mutations. With examples. (Photo credit: Wikipedia)

Parkinson’s Disease

http:// CMEcorner.com/file:///G:/neurodegenerative_disease/Parkinson’s_disease.htm

PINK1 and Parkin and Parkinson’s Disease

Studies of the familial Parkinson disease-related proteins PINK1 and Parkin have demonstrated that these factors promote the fragmentation and turnover of mitochondria following treatment of cultured cells with mitochondrial depolarizing agents. Whether PINK1 or Parkin influence mitochondrial quality control under normal physiological conditions in dopaminergic neurons, a principal cell type that degenerates in Parkinson disease, remains unclear. To address this matter, we developed a method to purify and characterize neural subtypes of interest from the adult Drosophila brain.

Using this method, we find that dopaminergic neurons from Drosophila parkin mutants accumulate enlarged, depolarized mitochondria, and that genetic perturbations that promote mitochondrial fragmentation and turnover rescue the mitochondrial depolarization and neurodegenerative phenotypes of parkin mutants. In contrast, cholinergic neurons from parkin mutants accumulate enlarged depolarized mitochondria to a lesser extent than dopaminergic neurons, suggesting that a higher rate of mitochondrial damage, or a deficiency in alternative mechanisms to repair or eliminate damaged mitochondria explains the selective vulnerability of dopaminergic neurons in Parkinson disease.

Our study validates key tenets of the model that PINK1 and Parkin promote the fragmentation and turnover of depolarized mitochondria in dopaminergic neurons. Moreover, our neural purification method provides a foundation to further explore the pathogenesis of Parkinson disease, and to address other neurobiological questions requiring the analysis of defined neural cell types.

Burmana JL, Yua S, Poole AC, Decala RB , Pallanck L. Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants.

http://Burmana JL, Yua S, Poole AC, Decala RB , Pallanck L. Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants./

Autophagy in Parkinson’s Disease.

Parkinson’s disease is a common neurodegenerative disease in the elderly. To explore the specific role of autophagy and the ubiquitin-proteasome pathway in apoptosis,

  • a specific proteasome inhibitor and macroautophagy inhibitor and stimulator were selected to investigate
  1. pheochromocytoma (PC12) cell lines
  2. transfected with human mutant (A30P) and wildtype (WT) -synuclein.
  • The apoptosis ratio was assessed by flow cytometry.
  • LC3heat shock protein 70 (hsp70) and caspase-3 expression in cell culture were determined by Western blot.
  • The hallmarks of apoptosis and autophagy were assessed with transmission electron microscopy.

Compared to the control group or the rapamycin (autophagy stimulator) group, the apoptosis ratio in A30P and WT cells was significantly higher after treatment with inhibitors of the proteasome and macroautophagy.

  1. The results of Western blots for caspase-3 expression were similar to those of flow cytometry;
  2. hsp70 protein was significantly higher in the proteasome inhibitor group than in control, but
  3. in the autophagy inhibitor and stimulator groups, hsp70 was similar to control.

These findings show that

  1. inhibition of the proteasome and autophagy promotes apoptosis, and
  2. the macroautophagy stimulator rapamycin reduces the apoptosis ratio.
  3. And inhibiting or stimulating autophagy has less impact on hsp70 than the proteasome pathway.

In conclusion,

  • either stimulation or inhibition of macroautophagy, has less impact on hsp70 than on the proteasome pathway.
  • rapamycin decreased apoptotic cells in A30P cells independent of caspase-3 activity.

Although several lines of evidence recently demonstrated crosstalk between autophagy and caspase-independent apoptosis, we could not confirm that

  • autophagy activation protects cells from caspase-independent cell death.

Undoubtedly, there are multiple connections between the apoptotic and autophagic processes. Inhibition of autophagy may

  • subvert the capacity of cells to remove
  • damaged organelles or to remove misfolded proteins, which
  • would favor apoptosis.

However, proteasome inhibition activated macroautophagy and accelerated apoptosis. A likely explanation is inhibition of the proteasome favors oxidative reactions that trigger apoptosis, presumably through

  • a direct effect on mitochondria, and
  • the absence of NADPH2 and ATP which may
  • deinhibit the activation of caspase-2 or MOMP.

Another possibility is that aggregated proteins induced by proteasome inhibition increase apoptosis.

Yang F, Yanga YP, Maoa CJ, Caoa BY, et al. Role of autophagy and proteasome degradation pathways in apoptosis of PC12 cells overexpressing human -synuclein. Neuroscience Letters 2009; 454:203–208. doi:10.1016/j.neulet.2009.03.027. www.elsevier.com/locate/neulet   http://neurosciletters.com/ Role_of_autophagy_and_proteasome_degradation_pathways_in_apoptosis_of_PC12_cells_overexpressing_human –synuclein/

Parkin-dependent Ubiquitination of Endogenous Bax

Autosomal recessive loss-of-function mutations within the PARK2 gene functionally inactivate the E3 ubiquitin ligase parkin, resulting

  • in neurodegeneration of catecholaminergic neurons and a familial form of Parkinson disease.

Current evidence suggests both

  • a mitochondrial function for parkin and
  • a neuroprotective role, which may in fact be interrelated.

The antiapoptotic effects of Parkin have been widely reported, and may involve

fundamental changes in the threshold for apoptotic cytochrome c release, but the substrate(s) involved in Parkin dependent protection had not been identified. This study demonstrates

  • the Parkin-dependent ubiquitination of endogenous Bax
  • comparing primary cultured neurons from WT and Parkin KO mice and
  • using multiple Parkin-overexpressing cell culture systems.

The direct ubiquitination of purified Bax was also observed in vitro following incubation with recombinant parkin.

  1. Parkin prevented basal and apoptotic stress induced translocation of Bax to the mitochondria.
  2. an engineered ubiquitination-resistant form of Bax retained its apoptotic function,
  3. but Bax KO cells complemented with lysine-mutant Bax
  • did not manifest the antiapoptotic effects of Parkin that were observed in cells expressing WT Bax.

The conclusion is that Bax is the primary substrate responsible for the antiapoptotic effects of Parkin, and provides mechanistic insight into at least a subset of the mitochondrial effects of Parkin.

Johnson BN, Berger AK, Cortese GP, and LaVoie MJ. The ubiquitin E3 ligase Parkin regulates the proapoptotic function of Bax. PNAS 2012, pp 6. www.pnas.org/cgi/doi/10.1073/pnas.1113248109
http://
PNAS.org/ The_ubiquitin_E3_ligase_Parkin_regulates_the_proapoptotic_function_of_Bax

                                                                                                                           nature10774-f3.2   ubiquitin structures  Rn1  Rn2

Ubiquitin is a small, compact protein characterized by a b-grasp fold.

Parkin Promotes Mitochondrial Loss in Autophagy

Parkin, an E3 ubiquitin ligase implicated in Parkinson’s disease,

  • promotes degradation of dysfunctional mitochondria by autophagy.

upon translocation to mitochondria, Parkin activates the ubiquitin–proteasome system (UPS) for

  • widespread degradation of outer membrane proteins.

We observe

  1. an increase in K48-linked polyubiquitin on mitochondria,
  2. recruitment of the 26S proteasome and
  3. rapid degradation of multiple outer membrane proteins.

The degradation of proteins by the UPS occurs independently of the autophagy pathway, and

  • inhibition of the 26S proteasome completely abrogates Parkin-mediated mitophagy in HeLa, SH-SY5Y and mouse cells.

Although the mitofusins Mfn1 and Mfn2 are rapid degradation targets of Parkin, degradation of additional targets is essential for mitophagy.

It appears that remodeling of the mitochondrial outer membrane proteome is important for mitophagy, and reveal

  • a causal link between the UPS and autophagy, the major pathways for degradation of intracellular substrates.

Chan NC, Salazar AM, Pham AH, Sweredoski MJ, et al. Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy. Human Molecular Genetics 2011; 20(9): 1726–1737. doi:10.1093/hmg/ddr048.  http://HumMolecGenetics.com/ Broad_activation_of_the_ubiquitin–proteasome_system_by_Parkin_is_critical_for_mitophagy/

Autophagy impairment: a crossroad

Nassif M and Hetz C.  Autophagy impairment: a crossroad between neurodegeneration and tauopathies.  BMC Biology 2012; 10:78. http://www.biomedcentral.com/1741-7007/10/78

http://BMC.com/Biology/Autophagy impairment: a crossroad between neurodegeneration and tauopathies/
http://
Molecular Neurodegeneration/Nassif M and Hetz C/

Impairment of protein degradation pathways such as autophagy is emerging as

  • a consistent and transversal pathological phenomenon in neurodegenerative diseases, including Alzheimer´s, Huntington´s, and Parkinson´s disease.

Genetic inactivation of autophagy in mice has demonstrated a key role of the pathway in maintaining protein homeostasis in the brain,

  • triggering massive neuronal loss and
  • the accumulation of abnormal protein inclusions.

This paper in Molecular Neurodegeneration from Abeliovich´s group now suggests a role for

  • phosphorylation of Tau and
  • the activation of glycogen synthase kinase 3β (GSK3β)
  • in driving neurodegeneration in autophagy-deficient neurons.

This study illuminatess the factors driving neurofibrillary tangle formation in Alzheimer´s disease and tauopathies.

autophagy & apoptosis          stem cell reprogramming     lysosomes.jpeg   exosomes.jpeg   Epigenetics

images: autophagy, stem cell remodeling, lysosome, exosome, epigenetics,

Alzheimer’s Disease

Alzheimer’s Linked To Rare Gene Mutation That Affects Immune System

Article Date: 15 Nov 2012 –
Two international studies published this week point to a link between Alzheimer’s disease and a rare gene mutation that affects the immune system’s inflammation response. The discovery supports an emerging theory about the role of the immune system in the development of Alzheimer’s disease.  Both studies were published online this week in the New England Journal of Medicine, one led by John Hardy of University College London, and the other led by the Iceland-based global company deCode Genetics.
Alzheimer’s is a form of distressing brain-wasting disease that gradually robs people of their memories and their ability to lead independent lives. Its main characteristic is the build up of
  • protein tangles and
  • plaques inside and between brain cells, which eventually
  • disrupts their ability to communicate with each other.
Both teams conclude that a rare mutation in a gene called TREM2, which helps trigger immune system responses, raises the risk for developing Alzheimer’s disease. One study suggests it raises it three-fold, the other, four-fold.  The UCL-led study included researchers from 44 institutions around the world and data on a total of 25,000 people.
After homing in on the TREM2 gene using new sequencing techniques, they carried out further sequencing that identified a set of
  • rare mutations that occurred more often in 1,092 Alzheimer’s disease patients than in a group of 1,107 healthy controls.
They evaluated the most common mutation, R47H, and confirmed that this variant of TREM2 substantially increases the risk for Alzheimer’s disease.  R47H mutation was present in 1.9 percent of the Alzheimer’s patients and in only 0.37 percent of the controls.  The researchers on the study led by deCode Genetics indicate that this strong effect is on a par with that of the well-established gene variant known as APOE4. Not all people who have  the R47H variant will develop Alzheimer’s and in those who do, other genes and environmental factors will also play a role — but like APOE 4 it does substantially increase risk,” Carrasquillo explains.
The study led by deCode Genetics involved collaborators from Iceland, Holland, Germany and the US, not only found a strong link between the R47H variant and Alzheimer’s disease, but the variant also

  • predicts poorer cognitive function in older people without Alzheimer’s.
 In a statement, lead author Kari Stefánsson, CEO and co-founder of deCODE Genetics says:
The discovery of variant TREM2 is important because
  • it confers high risk for Alzheimer’s and
  • because the gene’s normal biological function has been shown to reduce immune response
 He surmises that the  combined factors make TREM2 an attractive target for drug development.
Using deCode’s genome sequencing and genotyping technology, Stefánsson and colleagues identified
  • approximately 41 million markers, including 191,777 functional variants, from
  • 2,261 Icelandic samples.
They further analyzed these variants against the genomes of
  • 3,550 people with Alzheimer’s disease and
  • a control group of over-85s who did not have a diagnosis of Alzheimer’s.
This led to them finding the TREM2 variant, and to make sure this was not just a feature of Icelandic people,
  • they replicated the findings against other control populations in the United States, Germany, the Netherlands and Norway.
Stefánsson says that the results were enabled by having
  • sophisticated research tools,
  • access to expanded and high quality genomic data sets, and
  • investigators with profound analytic skills,
Researching into genetic causes of disease can, thereby,  be carried out using an approach that combines sequence data and biological knowledge to find new drug targets.

R47H Variant of TREM2 and Immune Response

 Preclinical studies have found that
  • TREM2 is important for clearing away cell debris and amyloid protein, the protein that is associated with the brain plaques
  • that are characteristic of Alzheimer’s disease.
 The gene helps control the
  • inflammation response associated with Alzheimer’s and cognitive decline.
Rosa Rademakers, a co-author in the UCL-led study, runs a lab at the Mayo Clinic in Florida that helped to pinpoint the R47H variant of TREM2.  Other studies also link the immune system to Alzheimer’s disease, but
  • studies are needed to establish that R47H  acts by altering immune function.

EPIGENETICS, HISTONE PROTEINS, AND ALZHEIMER’S DISEASE

12/10/12 · Emily Humphreys
Epigenetic effects were first described by Conrad Waddington in 1942 as phenotypic changes resulting from an organism interacting with its environment.1 Today, epigenetics is
  • heritable effects in gene expression that are
  • not based on the genetic sequence.
One known epigenetic mechanism includes posttranslational modifications of histones that are
  • found in the nuclei of nearly all eukaryotes and
  • function to package DNA into nucleosomes.
Histone proteins can be heavily decorated with posttranslational modifications (PTMs), such as
  • acetyl-,
  • methyl-, and
  • phosphoryl- groups at distinct amino acid residues.
These modifications are mainly
  • located in the N-terminal tails of the histone and
  • protrude from the core nucleosome structure.
Gene regulation, and the downstream epigenetic effects, can also
  • depend on the cis or trans orientation of the PTMs.2
One PTM, acetylation, is an important determinant of cell replication, differentiation, and death.3  Zhang, et al. investigated the acetylation of histone proteins in Alzheimer’s disease (AD) pathology found in postmortem human brain tissue compared to neurological controls. To study histone acetylation,
  • histones were isolated from frozen temporal lobe samples of patients with advanced AD.
Histones were quantified using Selected-reaction-monitoring (SRM)-based targeted proteomics, an LC-MS/MS-based technique demonstrated by the Zhang lab.4  Histones were also analyzed using western blot analysis and LC-MS/MS-TMT (tandem-mass-tagging) quantitative proteomics. The results of these three experimental strategies agreed, further validating the specificity and sensitivity of the targeted proteomics methods. Histone acetylation was  reduced throughout in the AD temporal lobe compared to matched controls.
  • the histone H3 K18/K23 acetylation was significantly reduced.
Alzheimer’s disease and aging have also been associated with loss of histone acetylation in mouse model studies.5 In addition, Francis et al. found
  • cognitively impaired mice had a 50% reduced H4 acetylation in APP/PS1 mice than wild-type littermates.6
In mice, histone deacetylase inhibitors heve restored histone acetylation and improved memory in mice with age-related impairments or in models for other neurodegenerative diseases.7
Further studies of histone acetylation in AD could lead to target therapies in the disease pathology of neurodegenerative diseases, and
  • increase our understanding of how epigenetic mechanisms, such as histone acetylation, alter gene regulation.
References
1. Waddington, C.H., (1942). ‘The epigenotype‘, Endeavour, 1942 (1), (pp. 18-20)
2. Sidoli, S., Cheng, L., and Jensen O.N. (2012) ‘Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry‘, Journal of Proteomics, 75 (12), (pp. 3419-3433)
3. Zhang. K., et al. (2012) ‘Targeted proteomics for quantification of histone acetylation in Alzheimer’s disease‘, Proteomics, 12 (8), (pp. 1261-1268)
4. Darwanto, A., et al., (2010) ‘A modified “cross-talk” between histone H2B Lys-120 ubiquitination and H3 Lys-K79 methylation‘, The Journal of Biological Chemistry, 285 (28), (pp. 21868-21876)
5. Govindarajan, N., et al. (2011) ‘Sodium butyrate improves memory function in an Alzheimer’s disease model when administered at an advanced stage of disease progression‘, Journal of Alzheimer’s Disease, 26 (1), (pp.187-197)
6. Francis, Y.I., et al., (2009) ‘Dysregulation of histone acetylation in the APP/PS1 mouse model of Alzheimer’s disease‘, Journal of Alzheimer’s Disease, 18 (1), (pp. 131-139)
7. Kilgore, M., et al., (2010) ‘Inhibitors of class 1 histone deacetylases reverse contextual memory deficits in a mouse model of Alzheimer’s disease‘, Neuropsychopharmacology, 35 (4), (pp. 870-880)
Tags: acetylation, alzheimers disease, epigenetics, histone, targeted proteomics

Tau amyloid

An Outcast Among Peers Gains Traction on Alzheimer’s Cure

By JEANNE WHALEN   jeanne.whalen@wsj.com
Gareth Phillips for The Wall Street Journal
 November 10, 2012, on page A1 in the U.S. edition of The Wall Street Journal
After years of effort, researcher Dr. Claude Wischik is awaiting the results of new clinical trials that will test his theory on the cause of Alzheimer’s.
Dr. Wischik, an Australian in his early 30s in the 1980s, was attempting to answer a riddle: What causes Alzheimer’s disease? He needed to examine brain tissue from Alzheimer’s patients soon after death, which required getting family approvals and enlisting mortuary technicians to extract the brains. He collected more than 300 over about a dozen years.
Alzheimer’s researcher Claude Wischik had a view that a brain protein called tau-not plaque is largely responsible. WSJ’s Shirley Wang spoke with Dr. Wischik about his work on a new drug to treat the devastating disease.
The 63-year-old researcher believes that a protein called tau
  • forms twisted fibers known as tangles inside the brain cells of Alzheimer’s patients and is largely responsible for driving the disease.
For 20 years, billions of dollars of pharmaceutical investment has placed chief blame on a different protein, beta amyloid, which
  • forms sticky plaques in the brains of sufferers.
A string of experimental drugs designed to attack beta amyloid have failed recently in clinical trials.

Wherefore Tau thy go?

Dr. Wischik, who now lives in Scotland, sees this as tau’s big moment. The company he co-founded 10 years ago, TauRx Pharmaceuticals Ltd., has developed an experimental Alzheimer’s drug that it will begin testing in the coming weeks in two large clinical trials. Other companies are also investing in tau research. Roche Holding bought the rights to a type of experimental tau drug from Switzerland’s closely held AC Immune SA.

Wischik is a scientist who has struggled against a prevailing orthodoxy. In 1854, British doctor John Snow traced a cholera outbreak in London to a contaminated water supply, but his discovery was rejected. A very infamous example is the discovery of the cause of child-bed fever in Rokitanski’s University of Vienna by Ignaz Semmelweis. In 1982, two Australian scientists declared that bacteria (H. pylori) caused peptic ulcers, later to be awarded the 2005 Nobel Prize in medicine for their discovery.
Dr. Wischik says he and other tau-focused scientists have been shouted down over the years by what he calls the “amyloid orthodoxy.”  But Dr. Wischik has been hampered by inconclusive research. A small clinical trial of TauRx’s drug in 2008 produced  mixed, results. Of course, influential scientists still think that beta amyloid plays a central role. Although Roche is investing in tau, Richard Scheller, head of drug research at Roche’s biotech unit, Genentech, says the company still has a strong interest in beta amyloid (hedging the bet).  He thinks amyloid drugs may have better results if  testing on Alzheimer’s patients occurs much earlier in the disease to prove effective; Roche recently announced plans to conduct such a trial.  Simply put -“Drugs tied to conventional theories on Alzheimer’s causes haven’t so far been effective.” Scientists Dr. Wischik accuses of wrongly fixating on beta amyloid argue that the evidence for pursuing amyloid is strong. One view expressed is that drugs to attack both beta amyloid and tau will be necessary.
Alzheimer’s disease is the leading cause of dementia in the elderly, and according to the World Health Organization, the cost of caring for dementia sufferers totals about $600 billion each year world-wide. The disease was first identified in 1906 by German physician Alois Alzheimer, who found in the brain of a deceased woman who had suffered from dementia the plaques and tangles that riddled the tissue. In the 1960s, Dr. Martin Roth and colleagues showed that
  • the degree of clinical dementia was worse for patients with more tangles in the brain.
In the 1980s, Dr. Wischik joined Dr. Roth’s research group at Cambridge University as a Ph.D student, and was quickly assigned the task of
  • determining what tangles were made of, which launched his brain-collecting mission, and years of examining tissue.
Finally, in 1988, he and colleagues at Cambridge published a paper demonstrating for the first time that
  • the tangles first observed by Alzheimer were made at least in part of the protein tau, which was supported by later research.
Like all of the body’s proteins, tau has a normal, helpful function—working inside neurons to help
  • stabilize the fibers that connect nerve cells.
When it misfires, tau clumps together to form harmful tangles that kill brain cells.
Dr. Wischik’s discovery was important news in the Alzheimer’s field:
  • identifying the makeup of tangles made it possible to start developing ways to stop their formation. But by the early 1990s, tau was overtaken by another protein: beta amyloid.

Signs of Decline

Several pieces of evidence convinced an influential group of scientists that beta amyloid was the primary cause of Alzheimer’s.
  •  the discovery of several genetic mutations that all but guaranteed a person would develop a hereditary type of the disease.
  • these appeared to increase the production or accumulation of beta amyloid in the brain,
  • which led scientists to believe that amyloid deposits were the main cause of the disease.
 Athena Neurosciences, a biotech company whose founders included Harvard’s Dr. Selkoe, focused in earnest on developing drugs to attack amyloid. Meanwhile, tau researchers say they found it hard to get research funding or to publish papers in medical journals. It became difficult to have a good publication on tau, because the amyloid cascade was like a dogma. It became the case that if you were not working in the amyloid field you were not working on Alzheimer’s disease. Dr. Wischik and his colleagues fought to keep funding from the UK’s Medical Research Council for the repository of brain tissue they maintained at Cambridge, he says. The brain bank became an important tool. In the early 1990s, Dr. Wischik and his colleagues compared the postmortem brains of Alzheimer’s sufferers against those of people who had died without dementia, to see how their levels of amyloid and tau differed. They found that both healthy brains and Alzheimer’s brains could be filled with amyloid plaque, but only Alzheimer’s brains contained aggregated tau.
  • as the levels of aggregated tau in a brain increased, so did the severity of dementia.
In the mid-1990s, Dr. Wischik discovered that
  • a drug sometimes used to treat psychosis dissolved tangles
Nevertheless, American and British venture capitalists wanted to invest in amyloid projects, not tau.
By 2002, Dr. Wischik scraped together about $5 million from Asian investors with the help of a Singaporean physician who was the father of a classmate of Dr. Wischik’s son in Cambridge. TauRx is based in Singapore but conducts most of its research in Aberdeen, Scotland. As his tau effort launched, early tests of drugs designed to attack amyloid plaques were disappointing. To better understand these results, a team of British scientists largely unaffiliated with Athena or the failed clinical trial decided to examine the brains of patients who had participated in the study. They waited for the patients to die, and then, after probing the brains, concluded that
  • the vaccine had indeed cleared amyloid plaque but hadn’t prevented further neurodegeneration.

Peter Davies, an Alzheimer’s researcher at the Feinstein Institute for Medical Research in Manhasset, NY, recalls hearing a researcher at a conference in the early 2000s concede that his amyloid research results “don’t fit the hypothesis, but we’ll continue until they do! “I just sat there with my mouth open,” he recalls.

In 2004, TauRx began a clinical trial of its drug, called methylene blue, in 332 Alzheimer’s patients. Around the same time, a drug maker called Elan Corp., which had bought Athena Neurosciences, began a trial of an amyloid-targeted drug called bapineuzumab in 234 patients. A key moment came in 2008, when Dr. Wischik and Elan presented results of their studies at an Alzheimer’s conference in Chicago. The Elan drug
  • failed to improve cognition any better than a placebo pill, causing Elan shares to plummet by more than 60% over the next few days.
The TauRx results Dr. Wischik presented were more positive, though not unequivocal. The study showed that,
  • after 50 weeks of treatment, Alzheimer’s patients taking a placebo had fallen 7.8 points on a test of cognitive function,
  • while people taking 60 mg of TauRx’s drug three times a day had fallen one point—
  • translating into an 87% reduction in the rate of decline for people taking the TauRx drug.
But TauRx didn’t publish a full set of data from the trial, causing some skepticism among researchers. (Dr. Wischik says it didn’t to protect the company’s commercial interests). What’s more,
  • a higher, 100-mg dose of the drug didn’t produce the same positive effects in patients;
Dr. Wischik blames this on the way the 100-mg dose was formulated, and says the company is testing a tweaked version of the drug in its new clinical trials, which will begin enrolling patients late this year.
This summer, a trio of companies that now own the rights to bapineuzumab—Elan, Pfizer and Johnson & Johnson—
  • scrapped development of the drug after it failed to work in two large clinical trials.
Then in August, Eli Lilly & Co. said its experimental medicine targeting beta amyloid,
  • solanezumab, failed to slow the loss of memory or basic skills like bathing and dressing in two trials
  • involving 2,050 patients with mild or moderate Alzheimer’s.
Lilly has disclosed that in one of the trials, when moderate patients were stripped away,
  • the drug slowed cognitive decline only in patients with mild forms of the disease.
Still fervent believers assert that beta amyloid needs to be attacked very early in the disease cycle—
  • perhaps before symptoms begin.
This spring, the U.S. government said it would help fund a $100 million trial of Roche’s amyloid-targeted drug, crenezumab, in 300 people
  • who are genetically predisposed to develop early-onset Alzheimer’s but who don’t yet have symptoms.
This trial should help provide a “definitive” answer about the theory.
Scientists and investors are giving more attention to tau. Roche this year said it would pay Switzerland’s AC Immune an undisclosed upfront fee for the rights to a new type of tau-targeted drug, and up to CHF400 million in additional payments if any drugs make it to market.
Dr. Buee, the longtime tau researcher in France, says Johnson & Johnson asked him to provide advice on tau last year, and that he’s currently discussing a tau research contract with a big pharmaceutical company. (A Johnson & Johnson spokeswoman says the company invited Dr. Buee and other scientists to a meeting to discuss a range of approaches to fighting Alzheimer’s.)
With its new clinical trial program under way, TauRx is the first company to test a tau-targeted drug against Alzheimer’s in a large human study, known in the industry as a phase 3 trial.  Dr. Wischik

  • In the end…it’s down to the phase 3 trial.

Protein Degradation in Neurodegenerative Diseases

Cebollero E , Reggiori F  and Kraft C.  Ribophagy: Regulated Degradation of Protein Production Factories. Int J Cell Biol. 2012; 2012: 182834. doi:  10.1155/2012/182834 (online).

During autophagy, cytosol, protein aggregates, and organelles

  • are sequestered into double-membrane vesicles called autophagosomes and delivered to the lysosome/vacuole for breakdown and recycling of their basic components.

In all eukaryotes this pathway is important for

  • adaptation to stress conditions such as nutrient deprivation, as well as
  • to regulate intracellular homeostasis by adjusting organelle number and clearing damaged structures.

Starvation-induced autophagy has been viewed as a nonselective transport pathway; but recent studies have revealed that

  • autophagy is able to selectively engulf specific structures, ranging from proteins to entire organelles.

In this paper, we discuss recent findings on the mechanisms and physiological implications of two selective types of autophagy:

  • ribophagy, the specific degradation of ribosomes, and
  • reticulophagy, the selective elimination of portions of the ER.

Lee JH, Yu WH,…, Nixon RA.  Lysosomal Proteolysis and Autophagy Require Presenilin 1 and Are Disrupted by Alzheimer-Related PS1 Mutations. Cell 2010; 141, 1146–1158. DOI 10.1016/j.cell.2010.05.008.

Macroautophagy is a lysosomal degradative pathway essential for neuron survival. Here, we show

  • that macroautophagy requires the Alzheimer’s disease (AD)-related protein presenilin-1 (PS1).

In PS1 null blastocysts, neurons from mice hypomorphic for PS1 or conditionally depleted of PS1,

  • substrate proteolysis and autophagosome clearance during macroautophagy are prevented
  • as a result of a selective impairment of autolysosome acidification and cathepsin activation.

These deficits are caused by failed PS1-dependent targeting of the v-ATPase V0a1 subunit to lysosomes. N-glycosylation of the V0a1 subunit,

  • essential for its efficient ER-to-lysosome delivery,
  • requires the selective binding of PS1 holoprotein to the unglycosylated subunit and the  sec61alpha/ oligosaccharyltransferase complex.

PS1 mutations causing early-onset AD produce a similar lysosomal/autophagy phenotype in fibroblasts from AD patients. PS1 is therefore essential for v-ATPase targeting to lysosomes, lysosome acidification, and proteolysis during autophagy. Defective lysosomal proteolysis represents a basis for pathogenic protein accumulations and neuronal cell death in AD and suggests previously unidentified therapeutic targets.

Hanai JI, Cao P, Tanksale P, Imamura S, et al. The muscle-specific ubiquitin ligase atrogin-1/MAFbx mediates statin-induced muscle toxicity. The Journal of Clinical Investigation  2007; 117(12):3930-3951.    http://www.jci.org

Gene Wars Span Eons

Transposons have been barging into genomes and crossing species boundaries throughout evolution. Rapidly evolving bacterial species often use them to transmit antibiotic resistance to one another.  Nearly half of the DNA in the human genome consists of transposons, and the percentage can potentially creep upward with every generation. That’s because nearly 20 percent of transposons are capable of replicating in a way that is unconstrained by the normal rules of DNA replication during cell division ― although through generations over time, most have become inactivated and no longer pose a threat.

While humans are riddled with transposons, compared to some organisms, they’ve gotten off easy, according to Madhani, a professor of biochemistry and biophysics at UCSF. The water lily’s genome is 99 percent derived from transposons. The lowly salamander has about the same number of genes as humans, but in some species the genome is nearly 40 times bigger, due to all the inserted, replicating transposons.

The scientists’ discovery of SCANR and how it targets transposons in the yeast Cryptococcus neoformans builds upon the Nobel-Prize-winning discovery of jumping genes by maize geneticist Barbara McClintock, and the Nobel-prize-winning discovery by molecular biologists Richard Roberts and Phillip Sharp that parts of a single gene may be separated along chromosomes by intervening bits of DNA, called introns. Introns are transcribed into RNA from DNA but then are spliced out of the instructions for building proteins.

In the current study, the researchers discovered that the cell’s splicing machinery stalls when it gets to transposon introns. SCANR recognizes this glitch and

  • prevents transposon replication by
  • triggering the production of “small interfering RNA” molecules, which
  • neutralize the transposon RNA.

The earlier discovery by biologists Andrew Fire and Craig Mello of the phenomenon of RNA interference, a feature of this newly identified transposon targeting, also led to a Nobel Prize. “Scientists might find that many of the peculiar ways in which genes are expressed differently in higher organisms are, like

  • intron splicing in the case of SCANR, useful
  • in distinguishing and defending ‘self’ genes from ‘non-self’ genes,” Madhani said.

Researchers  at UCSF ( Phillip Dumesic, an MD/PhD student and first author of the study, graduate students Prashanthi Natarajan and Benjamin Schiller, and postdoctoral fellow Changbin Chen, PhD.) and collaborators at the Whitehead Institute of Medical Research in Cambridge, Mass., and from the Scripps Research Institute in La Jolla, Calif., contributed to the research.

Researchers Discover Gene Invaders Are Stymied by a Cell’s Genome Defense

If unrestrained, transposons replicate and insert themselves randomly throughout the genome.

San Francisco, CA  (Scicasts) – Gene wars rage inside our cells, with invading DNA regularly threatening to subvert our human blueprint. Now, building on Nobel-Prize-winning findings, UC San Francisco researchers have discovered a molecular machine that helps protect a cell’s genes against these DNA interlopers.

The machine, named SCANR, recognizes and targets foreign DNA. The UCSF team identified it in yeast, but comparable mechanisms might also be found in humans. The targets of SCANR are

  • small stretches of DNA called transposons, a name that conjures images of alien scourges.

But transposons are real, and to some newborns, life threatening. Found inside the genomes

  • of organisms as simple as bacteria and
  • as complex as humans,

they are in a way alien ― at some point,

  • each was imported into its host’s genome from another species.

Unlike an organism’s native genes, which are reproduced a single time during cell division, transposons ― also called jumping genes ― replicate multiple times, and

  • insert themselves at random places within the DNA of the host cell.

When transposons insert themselves in the middle of an important gene, they may cause malfunction, disease or birth defects.

But just as the immune system has ways of distinguishing what is part of the body and what is foreign and does not belong, researchers led by UCSF’s Dr. Hiten Madhani, discovered in

  • SCANR a novel way through which the genetic machinery within a cell’s nucleus recognizes and targets transposons.

“We’ve known that only a fraction of human-inherited diseases are caused by these mobile genetic elements,” Madhani said. “Now we’ve found that cells use a step in gene expression to distinguish ‘self’ from ‘non-self’ and to halt the spread of transposons.” The study was published online Feb. 13 in the journal Cell (http://www.cell.com/abstract/S0092-8674%2813%2900138-4).

Epigenetics of brain and brawn

Study Shows Epigenetics Shapes Fate of Brain vs. Brawn Castes in Carpenter Ants

Philadelphia, PA (Scicasts) – The recently published genome sequences of seven well-studied ant species are opening up new vistas for biology and medicine.  A detailed look at molecular mechanisms that underlie the complex behavioural differences in two worker castes in the Florida carpenter ant, Camponotus floridanus, has revealed a link to epigenetics. This is the study of how the expression or suppression of particular genes by chemical modifications affects an organism’s

  • physical characteristics,
  • development, and
  • behaviour.

Epigenetic processes not only play a significant role in many diseases, but are also involved in longevity and aging. Interdisciplinary research teams led by Dr. Shelley Berger, from the Perelman School of Medicine at the University of Pennsylvania, in collaboration with teams led by Danny Reinberg from New York University and Juergen Liebig from Arizona State University, describe their work in Genome Research. The group found that epigenetic regulation is key to

  • distinguishing one caste, the “majors”, as brawny Amazons of the carpenter ant colony,
  • compared to the “minors”, their smaller, brainier sisters.

These two castes have the same genes, but strikingly distinct behaviours and shape.

Ants, as well as termites and some bees and wasps, are eusocial species that organize themselves into rigid caste-based societies, or colonies, in which only one queen and a small contingent of male ants are usually fertile and reproduce. The rest of a colony is composed of functionally sterile females that are divided into worker castes that perform specialized roles such as

  • foragers,
  • soldiers, and
  • caretakers.

In Camponotus floridanus, there are two worker castes that are physically and behaviourally different, yet genetically very similar.  “For all intents and purposes, those two castes are identical when it comes to their gene sequences,” notes senior author Berger, professor of Cell and Developmental Biology. “The two castes are a perfect situation to understand

  • how epigenetics,
  • how regulation ‘above’ genes,

plays a role in establishing these dramatic differences in a whole organism.”

To understand how caste differences arise, the team examined the role of modifications of histones throughout the genome. They produced the first genome-wide epigenetic maps of genome structure in a social insect. Histones can be altered by the addition of small chemical groups, which affect the expression of genes. Therefore, specific histone modifications can create dramatic differences between genetically similar individuals, such as the physical and behavioural differences between ant castes. “These chemical modifications of histones alter how compact the genome is in a certain region,” Simola explains. “Certain modifications allow DNA to open up more, and some of them to close DNA more. This, in turn, affects how genes get expressed, or turned on, to make proteins.

In examining several different histone modifications, the team found a number of distinct differences between the major and minor castes. Simola states that the most notable modification,

  • discriminates the two castes from each other and
  • correlates well with the expression levels of different genes between the castes.

And if you look at which genes are being expressed between these two castes, these genes correspond very nicely to the brainy versus brawny idea. In the majors we find that genes that are involved in muscle development are expressed at a higher level, whereas in the minors, many genes involved in brain development and neurotransmission are expressed at a higher level.”

These changes in histone modifications between ant castes are likely caused by a regulator gene, called CBP, that has “already been implicated in aspects of learning and behaviour by genetic studies in mice and in certain human diseases,” Berger says. “The idea is that the same CBP regulator and histone modification are involved in a learned behaviour in ants – foraging – mainly in the brainy minor caste, to establish a pattern of gene regulation that leads to neuronal patterning for figuring out where food is and being able to bring the food back to the nest.”  Simola notes that “we know from mouse studies that if you inactivate or delete the CBP regulator, it actually leads to significant learning deficits in addition to craniofacial muscular malformations.  So from mammalian studies, it’s clear this is an important protein involved in learning and memory.”

The research team is looking ahead to expand the work by manipulating the expression of the CBP regulator in ants to observe effects on caste development and behaviour. Berger observes that all of the genes known to be major epigenetic regulators in mammals are conserved in ants, which makes them a  good model for studying behaviour and longevity.

Research Reveals Mechanism of Epigenetic Reprogramming

Cambridge, UK (Scicasts) – New research reveals a potential way for how parents’ experiences could be passed to their offspring’s genes.

Epigenetics is a system that turns our genes on and off. The process works by chemical tags, known as epigenetic marks, attaching to DNA and telling a cell to either use or ignore a particular gene. The most common epigenetic mark is a methyl group.

  • When these groups fasten to DNA through a process called methylation
  • they block the attachment of proteins which normally turn the genes on.

As a result, the gene is turned off.

Scientists have witnessed epigenetic inheritance, the observation that offspring may inherit altered traits due to their parents’ past experiences. For example, historical incidences of famine have resulted in health effects on the children and grandchildren of individuals who had restricted diets,

  • possibly because of inheritance of altered epigenetic marks caused by a restricted diet.

However, it is thought that between each generation

  • the epigenetic marks are erased in cells called primordial gene cells (PGC), the precursors to sperm and eggs.

This ‘reprogramming’ allows all genes to be read afresh for each new person – leaving scientists to question how epigenetic inheritance could occur.

The new Cambridge study initially discovered how the DNA methylation marks are erased in PGCs. The methylation marks are converted to hydroxymethylation which is then

  • progressively diluted out as the cells divide.

This process turns out to be remarkably efficient and seems to reset the genes for each new generation.

The researchers,  also found that some rare methylation can ‘escape’ the reprogramming process and can thus be passed on to offspring – revealing how epigenetic inheritance could occur. This is important because aberrant methylation could accumulate at genes during a lifetime in response to environmental factors, such as chemical exposure or nutrition, and can cause abnormal use of genes, leading to disease. If these marks are then inherited by offspring, their genes could also be affected. The  research demonstrates how genes could retain some memory of their past experiences, indicating that the idea that epigenetic information is erased between generations – should be reassessed.  The precursors to sperm and eggs are very effective in erasing most methylation marks, but they are fallible and at a low frequency may allow some epigenetic information to be transmitted to subsequent generations.

Professor Azim Surani from the University of Cambridge, principal investigator of the research, said: “The new study has the potential to be exploited in two distinct ways.

  1. how to erase aberrant epigenetic marks that may underlie some diseases in adults.
  2. address whether germ cells can acquire new epigenetic marks through environmental or dietary influences on parents that may evade erasure and be transmitted to subsequent generations

The research was published 25 January, in the journal Science. Story adapted from the University of Cambridge.

Study Suggests Expanding the Genetic Alphabet May Be Easier than Previously Thought

Featured In: Academia News | Genomics

Monday, June 4, 2012

A new study led by scientists at The Scripps Research Institute suggests that the replication process for DNA—the genetic instructions for living organisms that is composed of four bases (C, G, A and T)—is more open to unnatural letters than had previously been thought. An expanded “DNA alphabet” could carry more information than natural DNA, potentially coding for a much wider range of molecules and enabling a variety of powerful applications, from precise molecular probes and nanomachines to useful new life forms.

The new study, which appears in the June 3, 2012 issue of Nature Chemical Biology, solves the mystery of how a previously identified pair of artificial DNA bases can go through the DNA replication process almost as efficiently as the four natural bases.

“We now know that the efficient replication of our unnatural base pair isn’t a fluke, and also that the replication process is more flexible than had been assumed,” said Floyd E. Romesberg, associate professor at Scripps Research, principal developer of the new DNA bases, and a senior author of the new study. The Romesberg laboratory collaborated on the new study with the laboratory of co-senior author Andreas Marx at the University of Konstanz in Germany, and the laboratory of Tammy J. Dwyer at the University of San Diego.

Adding to the DNA Alphabet

Romesberg and his lab have been trying to find a way to extend the DNA alphabet since the late 1990s. In 2008, they developed the efficiently replicating bases NaM and 5SICS, which come together as a complementary base pair within the DNA helix, much as, in normal DNA, the base adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).

The following year, Romesberg and colleagues showed that NaM and 5SICS could be efficiently transcribed into RNA in the lab dish. But these bases’ success in mimicking the functionality of natural bases was a bit mysterious. They had been found simply by screening thousands of synthetic nucleotide-like molecules for the ones that were replicated most efficiently. And it had been clear immediately that their chemical structures lack the ability to form the hydrogen bonds that join natural base pairs in DNA. Such bonds had been thought to be an absolute requirement for successful DNA replication‑—a process in which a large enzyme, DNA polymerase, moves along a single, unwrapped DNA strand and stitches together the opposing strand, one complementary base at a time.

An early structural study of a very similar base pair in double-helix DNA added to Romesberg’s concerns. The data strongly suggested that NaM and 5SICS do not even approximate the edge-to-edge geometry of natural base pairs—termed the Watson-Crick geometry, after the co-discoverers of the DNA double-helix. Instead, they join in a looser, overlapping, “intercalated” fashion. “Their pairing resembles a ‘mispair,’ such as two identical bases together, which normally wouldn’t be recognized as a valid base pair by the DNA polymerase,” said Denis Malyshev, a graduate student in Romesberg’s lab who was lead author along with Karin Betz of Marx’s lab.

Yet in test after test, the NaM-5SICS pair was efficiently replicable. “We wondered whether we were somehow tricking the DNA polymerase into recognizing it,” said Romesberg. “I didn’t want to pursue the development of applications until we had a clearer picture of what was going on during replication.”

Edge to Edge

To get that clearer picture, Romesberg and his lab turned to Dwyer’s and Marx’s laboratories, which have expertise in finding the atomic structures of DNA in complex with DNA polymerase. Their structural data showed plainly that the NaM-5SICS pair maintain an abnormal, intercalated structure within double-helix DNA—but remarkably adopt the normal, edge-to-edge, “Watson-Crick” positioning when gripped by the polymerase during the crucial moments of DNA replication.

“The DNA polymerase apparently induces this unnatural base pair to form a structure that’s virtually indistinguishable from that of a natural base pair,” said Malyshev.

NaM and 5SICS, lacking hydrogen bonds, are held together in the DNA double-helix by “hydrophobic” forces, which cause certain molecular structures (like those found in oil) to be repelled by water molecules, and thus to cling together in a watery medium. “It’s very possible that these hydrophobic forces have characteristics that enable the flexibility and thus the replicability of the NaM-5SICS base pair,” said Romesberg. “Certainly if their aberrant structure in the double helix were held together by more rigid covalent bonds, they wouldn’t have been able to pop into the correct structure during DNA replication.”

An Arbitrary Choice?

The finding suggests that NaM-5SICS and potentially other, hydrophobically bound base pairs could some day be used to extend the DNA alphabet. It also hints that Evolution’s choice of the existing four-letter DNA alphabet—on this planet—may have been somewhat arbitrary. “It seems that life could have been based on many other genetic systems,” said Romesberg.

He and his laboratory colleagues are now trying to optimize the basic functionality of NaM and 5SICS, and to show that these new bases can work alongside natural bases in the DNA of a living cell.

“If we can get this new base pair to replicate with high efficiency and fidelity in vivo, we’ll have a semi-synthetic organism,” Romesberg said. “The things that one could do with that are pretty mind blowing.”

The other contributors to the paper, “KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry,” are Thomas Lavergne of the Romesberg lab, Wolfram Welte and Kay Diederichs of the Marx lab, and Phillip Ordoukhanian of the Center for Protein and Nucleic Acid Research at The Scripps Research Institute.

Source: The Scripps Research Institute

 

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