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Posts Tagged ‘mutation’


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

 

Gender of a person can affect the kinds of cancer-causing mutations they develop, according to a genomic analysis spanning nearly 2,000 tumours and 28 types of cancer. The results show striking differences in the cancer-causing mutations found in people who are biologically male versus those who are biologically female — not only in the number of mutations lurking in their tumours, but also in the kinds of mutations found there.

 

Liver tumours from women were more likely to carry mutations caused by a faulty system of DNA mending called mismatch repair, for instance. And men with any type of cancer were more likely to exhibit DNA changes thought to be linked to a process that the body uses to repair DNA with two broken strands. These biases could point researchers to key biological differences in how tumours develop and evolve across sexes.

 

The data add to a growing realization that sex is important in cancer, and not only because of lifestyle differences. Lung and liver cancer, for example, are more common in men than in women — even after researchers control for disparities in smoking or alcohol consumption. The source of that bias, however, has remained unclear.

In 2014, the US National Institutes of Health began encouraging researchers to consider sex differences in preclinical research by, for example, including female animals and cell lines from women in their studies. And some studies have since found sex-linked biases in the frequency of mutations in protein-coding genes in certain cancer types, including some brain cancers and advanced melanoma.

 

But the present study is the most comprehensive study of sex differences in tumour genomes so far. It looks at mutations not only in genes that code for proteins, but also in the vast expanses of DNA that have other functions, such as controlling when genes are turned on or off. The study also compares male and female genomes across many different cancers, which can allow researchers to pick up on additional patterns of DNA mutations, in part by increasing the sample sizes.

 

Researchers analysed full genome sequences gathered by the International Cancer Genome Consortium. They looked at differences in the frequency of 174 mutations known to drive cancer, and found that some of these mutations occurred more frequently in men than in women, and vice versa. When they looked more broadly at the loss or duplication of DNA segments in the genome, they found 4,285 sex-biased genes spread across 15 chromosomes.

 

There were also differences found when some mutations seemed to arise during tumour development, suggesting that some cancers follow different evolutionary paths in men and women. Researchers also looked at particular patterns of DNA changes. Such patterns can, in some cases, reflect the source of the mutation. Tobacco smoke, for example, leaves behind a particular signature in the DNA.

 

Taken together, the results highlight the importance of accounting for sex, not only in clinical trials but also in preclinical studies. This could eventually allow researchers to pin down the sources of many of the differences found in this study. Liver cancer is roughly three times as common in men as in women in some populations, and its incidence is increasing in some countries. A better understanding of its aetiology may turn out to be really important for prevention strategies and treatments.

 

References:

 

https://www.nature.com/articles/d41586-019-00562-7?utm_source=Nature+Briefing

 

https://www.nature.com/news/policy-nih-to-balance-sex-in-cell-and-animal-studies-1.15195

 

https://www.ncbi.nlm.nih.gov/pubmed/26296643

 

https://www.biorxiv.org/content/10.1101/507939v1

 

https://www.ncbi.nlm.nih.gov/pubmed/25985759

 

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Multiple Lung Cancer Genomic Projects Suggest New Targets, Research Directions for Non-Small Cell Lung Cancer

Curator, Writer: Stephen J. Williams, Ph.D.

lung cancer

(photo credit: cancer.gov)

A report Lung Cancer Genome Surveys Find Many Potential Drug Targets, in the NCI Bulletin,

http://www.cancer.gov/ncicancerbulletin/091812/page2

summarizes the clinical importance of five new lung cancer genome sequencing projects. These studies have identified genetic and epigenetic alterations in hundreds of lung tumors, of which some alterations could be taken advantage of using currently approved medications.

The reports, all published this month, included genomic information on more than 400 lung tumors. In addition to confirming genetic alterations previously tied to lung cancer, the studies identified other changes that may play a role in the disease.

Collectively, the studies covered the main forms of the disease—lung adenocarcinomas, squamous cell cancers of the lung, and small cell lung cancers.

“All of these studies say that lung cancers are genomically complex and genomically diverse,” said Dr. Matthew Meyerson of Harvard Medical School and the Dana-Farber Cancer Institute, who co-led several of the studies, including a large-scale analysis of squamous cell lung cancer by The Cancer Genome Atlas (TCGA) Research Network.

Some genes, Dr. Meyerson noted, were inactivated through different mechanisms in different tumors. He cautioned that little is known about alterations in DNA sequences that do not encode genes, which is most of the human genome.

Four of the papers are summarized below, with the first described in detail, as the Nature paper used a multi-‘omics strategy to evaluate expression, mutation, and signaling pathway activation in a large cohort of lung tumors. A literature informatics analysis is given for one of the papers.  Please note that links on GENE names usually refer to the GeneCard entry.

Paper 1. Comprehensive genomic characterization of squamous cell lung cancers[1]

The Cancer Genome Atlas Research Network Project just reported, in the journal Nature, the results of their comprehensive profiling of 230 resected lung adenocarcinomas. The multi-center teams employed analyses of

  • microRNA
  • Whole Exome Sequencing including
    • Exome mutation analysis
    • Gene copy number
    • Splicing alteration
  • Methylation
  • Proteomic analysis

Summary:

Some very interesting overall findings came out of this analysis including:

  • High rates of somatic mutations including activating mutations in common oncogenes
  • Newly described loss of function MGA mutations
  • Sex differences in EGFR and RBM10 mutations
  • driver roles for NF1, MET, ERBB2 and RITI identified in certain tumors
  • differential mutational pattern based on smoking history
  • splicing alterations driven by somatic genomic changes
  • MAPK and PI3K pathway activation identified by proteomics not explained by mutational analysis = UNEXPLAINED MECHANISM of PATHWAY ACTIVATION

however, given the plethora of data, and in light of a similar study results recently released, there appears to be a great need for additional mining of this CGAP dataset. Therefore I attempted to curate some of the findings along with some other recent news relevant to the surprising findings with relation to biomarker analysis.

Makeup of tumor samples

230 lung adenocarcinomas specimens were categorized by:

Subtype

33% acinar

25% solid

14% micro-papillary

9% papillary

8% unclassified

5% lepidic

4% invasive mucinous
Gender

Smoking status

81% of patients reported past of present smoking

The authors note that TCGA samples were combined with previous data for analysis purpose.

A detailed description of Methodology and the location of deposited data are given at the following addresses:

Publication TCGA Web Page: https://tcga-data.nci.nih.gov/docs/publications/luad_2014/

Sequence files: https://cghub.ucsc.edu

Results:

Gender and Smoking Habits Show different mutational patterns

 

WES mutational analysis

  1. a) smoking status

– there was a strong correlations of cytosine to adenine nucleotide transversions with past or present smoking. In fact smoking history separated into transversion high (past and previous smokers) and transversion low (never smokers) groups, corroborating previous results.

mutations in groups              Transversion High                   Transversion Low

TP53, KRAS, STK11,                 EGFR, RB1, PI3CA

     KEAP1, SMARCA4 RBM10

 

  1. b) Gender

Although gender differences in mutational profiles have been reported, the study found minimal number of significantly mutated genes correlated with gender. Notably:

  • EGFR mutations enriched in female cohort
  • RBM10 loss of function mutations enriched in male cohort

Although the study did not analyze the gender differences with smoking patterns, it was noted that RBM10 mutations among males were more prevalent in the transversion high group.

Whole exome Sequencing and copy number analysis reveal Unique, Candidate Driver Genes

Whole exome sequencing revealed that 62% of tumors contained mutations (either point or indel) in known cancer driver genes such as:

KRAS, EGFR, BRMF, ERBB2

However, authors looked at the WES data from the oncogene-negative tumors and found unique mutations not seen in the tumors containing canonical oncogenic mutations.

Unique potential driver mutations were found in

TP53, KEAP1, NF1, and RIT1

The genomics and expression data were backed up by a proteomics analysis of three pathways:

  1. MAPK pathway
  2. mTOR
  3. PI3K pathway

…. showing significant activation of all three pathways HOWEVER the analysis suggested that activation of signaling pathways COULD NOT be deduced from DNA sequencing alone. Phospho-proteomic analysis was required to determine the full extent of pathway modification.

For example, many tumors lacked an obvious mutation which could explain mTOR or MAPK activation.

 

Altered cell signaling pathways included:

  • Increased MAPK signaling due to activating KRAS
  • Higher mTOR due to inactivating STK11 leading to increased proliferation, translation

Pathway analysis of mutations revealed alterations in multiple cellular pathways including:

  • Reduced oxidative stress response
  • Nucleosome remodeling
  • RNA splicing
  • Cell cycle progression
  • Histone methylation

Summary:

Authors noted some interesting conclusions including:

  1. MET and ERBB2 amplification and mutations in NF1 and RIT1 may be unique driver events in lung adenocarcinoma
  2. Possible new drug development could be targeted to the RTK/RAS/RAF pathway
  3. MYC pathway as another important target
  4. Cluster analysis using multimodal omics approach identifies tumors based on single-gene driver events while other tumor have multiple driver mutational events (TUMOR HETEROGENEITY)

Paper 2. A Genomics-Based Classification of Human Lung Tumors[2]

The paper can be found at

http://stm.sciencemag.org/content/5/209/209ra153

by The Clinical Lung Cancer Genome Project (CLCGP) and Network Genomic Medicine (NGM),*,

Paper Summary

This sequencing project revealed discrepancies between histologic and genomic classification of lung tumors.

Methodology

– mutational analysis by whole exome sequencing of 1255 lung tumors of histologically

defined subtypes

– immunohistochemistry performed to verify reclassification of subtypes based on sequencing data

Results

  • 55% of all cases had at least one oncogenic alteration amenable to current personalized treatment approaches
  • Marked differences existed between cluster analysis within and between preclassified histo-subtypes
  • Reassignment based on genomic data eliminated large cell carcinomas
  • Prospective classification of 5145 lung cancers allowed for genomic classification in 75% of patients
  • Identification of EGFR and ALK mutations led to improved outcomes

Conclusions:

It is feasible to successfully classify and diagnose lung tumors based on whole exome sequencing data.

Paper 3. Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers[3]

A link to the paper can be found here with Graphic Summary: http://www.cell.com/cell/abstract/S0092-8674%2812%2901022-7?cc=y?cc=y

Methodology

  • Whole genome sequencing and transcriptome sequencing of cancerous and adjacent normal tissues from 17 patients with NSCLC
  • Integrated RNASeq with WES for analysis of
    • Variant analysis
    • Clonality by variant allele frequency anlaysis
    • Fusion genes
  • Bioinformatic analysis

Results

  • 3,726 point mutations and more than 90 indels in the coding sequence
  • Smokers with lung cancer show 10× the number of point mutations than never-smokers
  • Novel lung cancer genes, including DACH1, CFTR, RELN, ABCB5, and HGF were identified
  • Tumor samples from males showed high frequency of MYCBP2 MYCBP2 involved in transcriptional regulation of MYC.
  • Variant allele frequency analysis revealed 10/17 tumors were at least biclonal while 7/17 tumors were monoclonal revealing majority of tumors displayed tumor heterogeneity
  • Novel pathway alterations in lung cancer include cell-cycle and JAK-STAT pathways
  • 14 fusion proteins found, including ROS1-ALK fusion. ROS1-ALK fusions have been frequently found in lung cancer and is indicative of poor prognosis[4].
  • Novel metabolic enzyme fusions
  • Alterations were identified in 54 genes for which targeted drugs are available.           Drug-gable mutant targets include: AURKC, BRAF, HGF, EGFR, ERBB4, FGFR1, MET, JAK2, JAK3, HDAC2, HDAC6, HDAC9, BIRC6, ITGB1, ITGB3, MMP2, PRKCB, PIK3CG, TERT, KRAS, MMP14

Table. Validated Gene-Fusions Obtained from Ref-Seq Data

Note: Gene columns contain links for GeneCard while Gene function links are to the    gene’s GO (Gene Ontology) function.

GeneA (5′) GeneB (3′) GeneA function (link to Gene Ontology) GeneB function (link to Gene Ontology) known function (refs)
GRIP1 TNIP1 glutamate receptor IP transcriptional repressor
SGMS1 STK10 sphingolipid synthesis ser/thr kinase
RASSF3 TTYH2 GTP-binding protein chloride anion channel
KDELR2 ROS1, GOPC ER retention seq. binding proto-oncogenic tyr kinase
ACSL4 DCAF6 fatty acid synthesis ?
MARCH8 PRKG1 ubiquitin ligase cGMP dependent protein kinase
APAF1 UNC13B, TLN1 caspase activation cytoskeletal
EML4 ALK microtubule protein tyrosine kinase
EDR3,PHC3 LOC441601 polycomb pr/DNA binding ?
DKFZp761L1918,RHPN2 ANKRD27 Rhophilin (GTP binding pr ankyrin like
VANGL1 HAO2 tetraspanin family oxidase
CACNA2D3 FLNB VOC Ca++ channel filamin (actin binding)

Author’s Note:

There has been a recent literature on the importance of the EML4-ALK fusion protein in lung cancer. EML4-ALK positive lung tumors were found to be les chemo sensitive to cytotoxic therapy[5] and these tumor cells may exhibit an epitope rendering these tumors amenable to immunotherapy[6]. In addition, inhibition of the PI3K pathway has sensitized EMl4-ALK fusion positive tumors to ALK-targeted therapy[7]. EML4-ALK fusion positive tumors show dependence on the HSP90 chaperone, suggesting this cohort of patients might benefit from the new HSP90 inhibitors recently being developed[8].

Table. Significantly mutated genes (point mutations, insertions/deletions) with associated function.

Gene Function
TP53 tumor suppressor
KRAS oncogene
ZFHX4 zinc finger DNA binding
DACH1 transcription factor
EGFR epidermal growth factor receptor
EPHA3 receptor tyrosine kinase
ENSG00000205044
RELN cell matrix protein
ABCB5 ABC Drug Transporter

Table. Literature Analysis of pathways containing significantly altered genes in NSCLC reveal putative targets and risk factors, linkage between other tumor types, and research areas for further investigation.

Note: Significantly mutated genes, obtained from WES, were subjected to pathway analysis (KEGG Pathway Analysis) in order to see which pathways contained signicantly altered gene networks. This pathway term was then used for PubMed literature search together with terms “lung cancer”, “gene”, and “NOT review” to determine frequency of literature coverage for each pathway in lung cancer. Links are to the PubMEd search results.

KEGG pathway Name # of PUBMed entries containing Pathway Name, Gene ANDLung Cancer
Cell cycle 1237
Cell adhesion molecules (CAMs) 372
Glioma 294
Melanoma 219
Colorectal cancer 207
Calcium signaling pathway 175
Prostate cancer 166
MAPK signaling pathway 162
Pancreatic cancer 88
Bladder cancer 74
Renal cell carcinoma 68
Focal adhesion 63
Regulation of actin cytoskeleton 34
Thyroid cancer 32
Salivary secretion 19
Jak-STAT signaling pathway 16
Natural killer cell mediated cytotoxicity 11
Gap junction 11
Endometrial cancer 11
Long-term depression 9
Axon guidance 8
Cytokine-cytokine receptor interaction 8
Chronic myeloid leukemia 7
ErbB signaling pathway 7
Arginine and proline metabolism 6
Maturity onset diabetes of the young 6
Neuroactive ligand-receptor interaction 4
Aldosterone-regulated sodium reabsorption 2
Systemic lupus erythematosus 2
Olfactory transduction 1
Huntington’s disease 1
Chemokine signaling pathway 1
Cardiac muscle contraction 1
Amyotrophic lateral sclerosis (ALS) 1

A few interesting genetic risk factors and possible additional targets for NSCLC were deduced from analysis of the above table of literature including HIF1-α, mIR-31, UBQLN1, ACE, mIR-193a, SRSF1. In addition, glioma, melanoma, colorectal, and prostate and lung cancer share many validated mutations, and possibly similar tumor driver mutations.

KEGGinliteroanalysislungcancer

 please click on graph for larger view

Paper 4. Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing[9]

For full paper and graphical summary please follow the link: http://www.cell.com/cell/abstract/S0092-8674%2812%2901061-6

Highlights

  • Exome and genome characterization of somatic alterations in 183 lung adenocarcinomas
  • 12 somatic mutations/megabase
  • U2AF1, RBM10, and ARID1A are among newly identified recurrently mutated genes
  • Structural variants include activating in-frame fusion of EGFR
  • Epigenetic and RNA deregulation proposed as a potential lung adenocarcinoma hallmark

Summary

Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

Paper 5. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer[10]

Highlights

  • Whole exome and transcriptome (RNASeq) sequencing 29 small-cell lung carcinomas
  • High mutation rate 7.4 protein-changing mutations/million base pairs
  • Inactivating mutations in TP53 and RB1
  • Functional mutations in CREBBP, EP300, MLL, PTEN, SLIT2, EPHA7, FGFR1 (determined by literature and database mining)
  • The mutational spectrum seen in human data also present in a Tp53-/- Rb1-/- mouse lung tumor model

 

Curator Graphical Summary of Interesting Findings From the Above Studies

DGRAPHICSUMMARYNSLCSEQPOST

The above figure (please click on figure) represents themes and findings resulting from the aforementioned studies including

questions which will be addressed in Future Posts on this site.

References:

  1. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012, 489(7417):519-525.
  2. A genomics-based classification of human lung tumors. Science translational medicine 2013, 5(209):209ra153.
  3. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J et al: Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012, 150(6):1121-1134.
  4. Takeuchi K, Soda M, Togashi Y, Suzuki R, Sakata S, Hatano S, Asaka R, Hamanaka W, Ninomiya H, Uehara H et al: RET, ROS1 and ALK fusions in lung cancer. Nature medicine 2012, 18(3):378-381.
  5. Morodomi Y, Takenoyama M, Inamasu E, Toyozawa R, Kojo M, Toyokawa G, Shiraishi Y, Takenaka T, Hirai F, Yamaguchi M et al: Non-small cell lung cancer patients with EML4-ALK fusion gene are insensitive to cytotoxic chemotherapy. Anticancer research 2014, 34(7):3825-3830.
  6. Yoshimura M, Tada Y, Ofuzi K, Yamamoto M, Nakatsura T: Identification of a novel HLA-A 02:01-restricted cytotoxic T lymphocyte epitope derived from the EML4-ALK fusion gene. Oncology reports 2014, 32(1):33-39.
  7. Yang L, Li G, Zhao L, Pan F, Qiang J, Han S: Blocking the PI3K pathway enhances the efficacy of ALK-targeted therapy in EML4-ALK-positive nonsmall-cell lung cancer. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2014.
  8. Workman P, van Montfort R: EML4-ALK fusions: propelling cancer but creating exploitable chaperone dependence. Cancer discovery 2014, 4(6):642-645.
  9. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A et al: Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012, 150(6):1107-1120.
  10. Peifer M, Fernandez-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, Zander T et al: Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nature genetics 2012, 44(10):1104-1110.

Other posts on this site which refer to Lung Cancer and Cancer Genome Sequencing include:

Multi-drug, Multi-arm, Biomarker-driven Clinical Trial for patients with Squamous Cell Carcinoma called the Lung Cancer Master Protocol, or Lung-MAP launched by NCI, Foundation Medicine, and Five Pharma Firms

US Personalized Cancer Genome Sequencing Market Outlook 2018 –

Comprehensive Genomic Characterization of Squamous Cell Lung Cancers

International Cancer Genome Consortium Website has 71 Committed Cancer Genome Projects Ongoing

Non-small Cell Lung Cancer drugs – where does the Future lie?

Lung cancer breathalyzer trialed in the UK

Diagnosing Lung Cancer in Exhaled Breath using Gold Nanoparticles

Multi-drug, Multi-arm, Biomarker-driven Clinical Trial for patients with Squamous Cell Carcinoma called the Lung Cancer Master Protocol, or Lung-MAP launched by NCI, Foundation Medicine, and Five Pharma Firms

Read Full Post »

USPTO Guidance On Patentable Subject Matter


USPTO Guidance On Patentable Subject Matter

Curator and Reporter: Larry H Bernstein, MD, FCAP

LH Bernstein

LH Bernstein

 

 

 

 

 

 

Revised 4 July, 2014

https://pharmaceuticalintelligence.com/2014/07/03/uspto-guidance-on-patentable-subject-matter

 

I came across a few recent articles on the subject of US Patent Office guidance on patentability as well as on Supreme Court ruling on claims. I filed several patents on clinical laboratory methods early in my career upon the recommendation of my brother-in-law, now deceased.  Years later, after both brother-in-law and patent attorney are no longer alive, I look back and ask what I have learned over $100,000 later, with many trips to the USPTO, opportunities not taken, and a one year provisional patent behind me.

My conclusion is

(1) that patents are for the protection of the innovator, who might realize legal protection, but the cost and the time investment can well exceed the cost of startup and building a small startup enterprize, that would be the next step.

(2) The other thing to consider is the capability of the lawyer or firm that represents you.  A patent that is well done can be expected to take 5-7 years to go through with due diligence.   I would not expect it to be done well by a university with many other competing demands. I might be wrong in this respect, as the climate has changed, and research universities have sprouted engines for change.  Experienced and productive faculty are encouraged or allowed to form their own such entities.

(3) The emergence of Big Data, computational biology, and very large data warehouses for data use and integration has changed the landscape. The resources required for an individual to pursue research along these lines is quite beyond an individuals sole capacity to successfully pursue without outside funding.  In addition, the changed designated requirement of first to publish has muddied the water.

Of course, one can propose without anything published in the public domain. That makes it possible for corporate entities to file thousands of patents, whether there is actual validation or not at the time of filing.  It would be a quite trying experience for anyone to pursue in the USPTO without some litigation over ownership of patent rights. At this stage of of technology development, I have come to realize that the organization of research, peer review, and archiving of data is still at a stage where some of the best systems avalailable for storing and accessing data still comes considerably short of what is needed for the most complex tasks, even though improvements have come at an exponential pace.

I shall not comment on the contested views held by physicists, chemists, biologists, and economists over the completeness of guiding theories strongly held.  Only history will tell.  Beliefs can hold a strong sway, and have many times held us back.

I am not an expert on legal matters, but it is incomprehensible to me that issues concerning technology innovation can be adjudicated in the Supreme Court, as has occurred in recent years. I have postgraduate degrees in  Medicine, Developmental Anatomy, and post-medical training in pathology and laboratory medicine, as well as experience in analytical and research biochemistry.  It is beyond the competencies expected for these type of cases to come before the Supreme Court, or even to the Federal District Courts, as we see with increasing frequency,  as this has occurred with respect to the development and application of the human genome.

I’m not sure that the developments can be resolved for the public good without a more full development of an open-access system of publishing. Now I present some recent publication about, or published by the USPTO.

DR ANTHONY MELVIN CRASTO

Dr. Melvin Castro - Organic Chemistry and New Drug Development

Dr. Melvin Castro – Organic Chemistry and New Drug Development

 

 

 

 

 

 

 

 

YOU ARE FOLLOWING THIS BLOG You are following this blog, along with 1,014 other amazing people (manage).

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USPTO Guidance On Patentable Subject Matter: Impediment to Biotech Innovation

Joanna T. Brougher, David A. Fazzolare J Commercial Biotechnology 2014 20(3):Brougher

jcbiotech-patents

jcbiotech-patents

 

 

 

 

 

 

 

 

 

 

 

Abstract In June 2013, the U.S. Supreme Court issued a unanimous decision upending more than three decades worth of established patent practice when it ruled that isolated gene sequences are no longer patentable subject matter under 35 U.S.C. Section 101.While many practitioners in the field believed that the USPTO would interpret the decision narrowly, the USPTO actually expanded the scope of the decision when it issued its guidelines for determining whether an invention satisfies Section 101.

The guidelines were met with intense backlash with many arguing that they unnecessarily expanded the scope of the Supreme Court cases in a way that could unduly restrict the scope of patentable subject matter, weaken the U.S. patent system, and create a disincentive to innovation. By undermining patentable subject matter in this way, the guidelines may end up harming not only the companies that patent medical innovations, but also the patients who need medical care.  This article examines the guidelines and their impact on various technologies.

Keywords:   patent, patentable subject matter, Myriad, Mayo, USPTO guidelines

Full Text: PDF

References

35 U.S.C. Section 101 states “Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.

” Prometheus Laboratories, Inc. v. Mayo Collaborative Services, 566 U.S. ___ (2012)

Association for Molecular Pathology et al., v. Myriad Genetics, Inc., 569 U.S. ___ (2013).

Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95, 103 (C.C.S.D.N.Y. 1911)

USPTO. Guidance For Determining Subject Matter Eligibility Of Claims Reciting Or Involving Laws of Nature, Natural Phenomena, & Natural Products.

http://www.uspto.gov/patents/law/exam/myriad-mayo_guidance.pdf

Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 131 (1948)

USPTO. Guidance For Determining Subject Matter Eligibility Of Claims Reciting Or Involving Laws of Nature, Natural Phenomena, & Natural Products.

http://www.uspto.gov/patents/law/exam/myriad-mayo_guidance.pdf

Courtney C. Brinckerhoff, “The New USPTO Patent Eligibility Rejections Under Section 101.” PharmaPatentsBlog, published May 6, 2014, accessed http://www.pharmapatentsblog.com/2014/05/06/the-new-patent-eligibility-rejections-section-101/

Courtney C. Brinckerhoff, “The New USPTO Patent Eligibility Rejections Under Section 101.” PharmaPatentsBlog, published May 6, 2014, accessed http://www.pharmapatentsblog.com/2014/05/06/the-new-patent-eligibility-rejections-section-101/

DOI: http://dx.doi.org/10.5912/jcb664

 

Science 4 July 2014; 345 (6192): pp. 14-15  DOI: http://dx.doi.org/10.1126/science.345.6192.14
  • IN DEPTH

INTELLECTUAL PROPERTY

Biotech feels a chill from changing U.S. patent rules

A 2013 Supreme Court decision that barred human gene patents is scrambling patenting policies.

PHOTO: MLADEN ANTONOV/AFP/GETTY IMAGES

A year after the U.S. Supreme Court issued a landmark ruling that human genes cannot be patented, the biotech industry is struggling to adapt to a landscape in which inventions derived from nature are increasingly hard to patent. It is also pushing back against follow-on policies proposed by the U.S. Patent and Trademark Office (USPTO) to guide examiners deciding whether an invention is too close to a natural product to deserve patent protection. Those policies reach far beyond what the high court intended, biotech representatives say.

“Everything we took for granted a few years ago is now changing, and it’s generating a bit of a scramble,” says patent attorney Damian Kotsis of Harness Dickey in Troy, Michigan, one of more than 15,000 people who gathered here last week for the Biotechnology Industry Organization’s (BIO’s) International Convention.

At the meeting, attorneys and executives fretted over the fate of patent applications for inventions involving naturally occurring products—including chemical compounds, antibodies, seeds, and vaccines—and traded stories of recent, unexpected rejections by USPTO. Industry leaders warned that the uncertainty could chill efforts to commercialize scientific discoveries made at universities and companies. Some plan to appeal the rejections in federal court.

USPTO officials, meanwhile, implored attendees to send them suggestions on how to clarify and improve its new policies on patenting natural products, and even announced that they were extending the deadline for public comment by a month. “Each and every one of you in this room has a moral duty … to provide written comments to the PTO,” patent lawyer and former USPTO Deputy Director Teresa Stanek Rea told one audience.

At the heart of the shake-up are two Supreme Court decisions: the ruling last year in Association for Molecular Pathology v. Myriad Genetics Inc. that human genes cannot be patented because they occur naturally (Science, 21 June 2013, p. 1387); and the 2012 Mayo v. Prometheus decision, which invalidated a patent on a method of measuring blood metabolites to determine drug doses because it relied on a “law of nature” (Science, 12 July 2013, p. 137).

Myriad and Mayo are already having a noticeable impact on patent decisions, according to a study released here. It examined about 1000 patent applications that included claims linked to natural products or laws of nature that USPTO reviewed between April 2011 and March 2014. Overall, examiners rejected about 40%; Myriad was the basis for rejecting about 23% of the applications, and Mayo about 35%, with some overlap, the authors concluded. That rejection rate would have been in the single digits just 5 years ago, asserted Hans Sauer, BIO’s intellectual property counsel, at a press conference. (There are no historical numbers for comparison.) The study was conducted by the news service Bloomberg BNA and the law firm Robins, Kaplan, Miller & Ciseri in Minneapolis, Minnesota.

USPTO is extending the decisions far beyond diagnostics and DNA?

The numbers suggest USPTO is extending the decisions far beyond diagnostics and DNA, attorneys say. Harness Dickey’s Kotsis, for example, says a client recently tried to patent a plant extract with therapeutic properties; it was different from anything in nature, Kotsis argued, because the inventor had altered the relative concentrations of key compounds to enhance its effect. Nope, decided USPTO, too close to nature.

In March, USPTO released draft guidance designed to help its examiners decide such questions, setting out 12 factors for them to weigh. For example, if an examiner deems a product “markedly different in structure” from anything in nature, that counts in its favor. But if it has a “high level of generality,” it gets dinged.

The draft has drawn extensive criticism. “I don’t think I’ve ever seen anything as complicated as this,” says Kevin Bastian, a patent attorney at Kilpatrick Townsend & Stockton in San Francisco, California. “I just can’t believe that this will be the standard.”

USPTO officials appear eager to fine-tune the draft guidance, but patent experts fear the Supreme Court decisions have made it hard to draw clear lines. “The Myriad decision is hopelessly contradictory and completely incoherent,” says Dan Burk, a law professor at the University of California, Irvine. “We know you can’t patent genetic sequences,” he adds, but “we don’t really know why.”

Get creative in using Draft Guidelines!

For now, Kostis says, applicants will have to get creative to reduce the chance of rejection. Rather than claim protection for a plant extract itself, for instance, an inventor could instead patent the steps for using it to treat patients. Other biotech attorneys may try to narrow their patent claims. But there’s a downside to that strategy, they note: Narrower patents can be harder to protect from infringement, making them less attractive to investors. Others plan to wait out the storm, predicting USPTO will ultimately rethink its guidance and ease the way for new patents.

 

Public comment period extended

USPTO has extended the deadline for public comment to 31 July, with no schedule for issuing final language. Regardless of the outcome, however, Stanek Rea warned a crowd of riled-up attorneys that, in the world of biopatents, “the easy days are gone.”

 

United States Patent and Trademark Office

Today we published and made electronically available a new edition of the Manual of Patent Examining Procedure (MPEP). Manual of Patent Examining Procedure uspto.gov http://www.uspto.gov/web/offices/pac/mpep/index.html Summary of Changes

PDF Title Page
PDF Foreword
PDF Introduction
PDF Table of Contents
PDF Chapter 600 –
PDF   Parts, Form, and Content of Application Chapter 700 –
PDF    Examination of Applications Chapter 800 –
PDF   Restriction in Applications Filed Under 35 U.S.C. 111; Double Patenting Chapter 900 –
PDF   Prior Art, Classification, and Search Chapter 1000 –
PDF  Matters Decided by Various U.S. Patent and Trademark Office Officials Chapter 1100 –
PDF   Statutory Invention Registration (SIR); Pre-Grant Publication (PGPub) and Preissuance Submissions Chapter 1200 –
PDF    Appeal Chapter 1300 –
PDF   Allowance and Issue Appendix L –
PDF   Patent Laws Appendix R –
PDF   Patent Rules Appendix P –
PDF   Paris Convention Subject Matter Index 
PDF Zipped version of the MPEP current revision in the PDF format.

Manual of Patent Examining Procedure (MPEP)Ninth Edition, March 2014

The USPTO continues to offer an online discussion tool for commenting on selected chapters of the Manual. To participate in the discussion and to contribute your ideas go to:
http://uspto-mpep.ideascale.com.

Manual of Patent Examining Procedure (MPEP) Ninth Edition, March 2014
The USPTO continues to offer an online discussion tool for commenting on selected chapters of the Manual. To participate in the discussion and to contribute your ideas go to: http://uspto-mpep.ideascale.com.

Note: For current fees, refer to the Current USPTO Fee Schedule.
Consolidated Laws – The patent laws in effect as of May 15, 2014. Consolidated Rules – The patent rules in effect as of May 15, 2014.  MPEP Archives (1948 – 2012)
Current MPEP: Searchable MPEP

The documents updated in the Ninth Edition of the MPEP, dated March 2014, include changes that became effective in November 2013 or earlier.
All of the documents have been updated for the Ninth Edition except Chapters 800, 900, 1000, 1300, 1700, 1800, 1900, 2000, 2300, 2400, 2500, and Appendix P.
More information about the changes and updates is available from the “Blue Page – Introduction” of the Searchable MPEP or from the “Summary of Changes” link to the HTML and PDF versions provided below. Discuss the Manual of Patent Examining Procedure (MPEP) Welcome to the MPEP discussion tool!

We have received many thoughtful ideas on Chapters 100-600 and 1800 of the MPEP as well as on how to improve the discussion site. Each and every idea submitted by you, the participants in this conversation, has been carefully reviewed by the Office, and many of these ideas have been implemented in the August 2012 revision of the MPEP and many will be implemented in future revisions of the MPEP. The August 2012 revision is the first version provided to the public in a web based searchable format. The new search tool is available at http://mpep.uspto.gov. We would like to thank everyone for participating in the discussion of the MPEP.

We have some great news! Chapters 1300, 1500, 1600 and 2400 of the MPEP are now available for discussion. Please submit any ideas and comments you may have on these chapters. Also, don’t forget to vote on ideas and comments submitted by other users. As before, our editorial staff will periodically be posting proposed new material for you to respond to, and in some cases will post responses to some of the submitted ideas and comments.Recently, we have received several comments concerning the Leahy-Smith America Invents Act (AIA). Please note that comments regarding the implementation of the AIA should be submitted to the USPTO via email t aia_implementation@uspto.gov or via postal mail, as indicated at the America Invents Act Web site. Additional information regarding the AIA is available at www.uspto.gov/americainventsact  We have also received several comments suggesting policy changes which have been routed to the appropriate offices for consideration. We really appreciate your thinking and recommendations!

FDA Guidance for Industry:Electronic Source Data in Clinical Investigations

Electronic Source Data

Electronic Source Data

 

 

 

 

 

 

 

The FDA published its new Guidance for Industry (GfI) – “Electronic Source Data in Clinical Investigations” in September 2013.
The Guidance defines the expectations of the FDA concerning electronic source data generated in the context of clinical trials. Find out more about this Guidance.
http://www.gmp-compliance.org/enews_4288_FDA%20Guidance%20for%20Industry%3A%20Electronic%20Source%20Data%20in%20Clinical%20Investigations
_8534,8457,8366,8308,Z-COVM_n.html

After more than 5 years and two draft versions, the final version of the Guidance for
Industry (GfI) – “Electronic Source Data in Clinical Investigations” was published in
September 2013. This new FDA Guidance defines the FDA’s expectations for sponsors,
CROs, investigators and other persons involved in the capture, review and retention of
electronic source data generated in the context of FDA-regulated clinical trials.In an
effort to encourage the modernization and increased efficiency of processes in clinical
trials, the FDA clearly supports the capture of electronic source data and emphasizes
the agency’s intention to support activities aimed at ensuring the reliability, quality,
integrity and traceability of this source data, from its electronic source to the electronic
submission of the data in the context of an authorization procedure. The Guidance
addresses aspects as data capture, data review and record retention. When the
computerized systems used in clinical trials are described, the FDA recommends
that the description not only focus on the intended use of the system, but also on
data protection measures and the flow of data across system components and
interfaces. In practice, the pharmaceutical industry needs to meet significant
requirements regarding organisation, planning, specification and verification of
computerized systems in the field of clinical trials. The FDA also mentions in the
Guidance that it does not intend to apply 21 CFR Part 11 to electronic health records
(EHR). Author: Oliver Herrmann Q-Infiity Source: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/
Guidances/UCM328691.pdf
Webinar: https://collaboration.fda.gov/p89r92dh8wc

 

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Atrioventricular (AV) Conduction Disease (block): Human Mutations affecting the Voltage Clock

Reporter: Aviva Lev-Ari, PhD, RN

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 Block Conduction block can occur at any level of the cardiac conduction system (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

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.

REFERENCES

http://circ.ahajournals.org/content/123/8/904 [Circulation.2011; 123: 904-915 doi: 10.1161/​CIRCULATIONAHA.110.942284]

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

 

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

Reporter-Curator: Stephen J. Williams, Ph.D.

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

Word Cloud by Daniel Menzin

There has been a causal link between alterations in cellular metabolism and the cancer phenotype.  Reorganization of cellular metabolism, marked by a shift from oxidative phosphorylation to aerobic glycolysis for cellular energy requirements (Warburg effect), is considered a hallmark of the transformed cell.  In addition, if tumors are to survive and grow, cancer cells need to adapt to environments high in metabolic stress and to avoid programmed cell death (apoptosis). Recently, a link between cancer growth and metabolism has been supported by the discovery that the LKB1/AMPK signaling pathway as a tumor suppressor axis[1].

LKB1/AMPK/mTOR Signaling Pathway

The Liver Kinase B1 (LKB1)/AMPK  AMP-activated protein kinase/mammalian Target of Rapamycin Complex 1 (mTORC1) signaling pathway links cellular metabolism and energy status to pathways involved in cell growth, proliferation, adaption to energy stress, and autophagy.  LKB1 is a master control for 14 other kinases including AMPK, a serine-threonine kinase which senses cellular AMP/ATP ratios.  In response to cellular starvation, AMPK is allosterically activated by AMP, leading to activation of ATP-generating pathways like fatty acid oxidation and blocking anabolic pathways, like lipid and cholesterol synthesis (which consume ATP).  In addition, AMPK regulates cell growth, proliferation, and autophagy by regulating the mTOR pathway.  AMPK activates the tuberous sclerosis complex 1/2, which ultimately inhibits mTORC1 activity and inhibits protein translation.  This mTOR activity is dis-regulated in many cancers.

LKB1AMPK pathway

LKB1/AMPK in Cancer

  • Somatic mutations of the STK11 gene encoding LKB1 are detected in lung and cervical cancers
  • Therefore LKB1 may be a strong tumor suppressor
  • Pharmacologic activation of LKB1/AMPK with metformin can suppress cancer cell growth

In a recent Cell Metabolism paper[2], Brandon Faubert and colleagues describe how AMPK activity reduces aerobic glycolysis and tumor proliferation while loss of AMPK activity promotes tumor proliferation by shifting cells to aerobic glycolysis and increasing anabolic pathways in a HIF1-dependent manner.

The paper’s major findings were as follows:

  • Loss of AMPKα1 cooperates with the Myc oncogene to accelerate lymphomagenesis
  • AMPKα dysfunction enhances aerobic glycolysis (Warburg effect)
  • Inhibiting HIF-1α reverses the metabolic effects of AMPKα loss
  • HIF-1α mediates the growth advantage of tumors with reduced AMPK signaling

Summary

AMPK is a metabolic sensor that helps maintain cellular energy homeostasis. Despite evidence linking AMPK with tumor suppressor functions, the role of AMPK in tumorigenesis and tumor metabolism is unknown. Here we show that AMPK negatively regulates aerobic glycolysis (the Warburg effect) in cancer cells and suppresses tumor growth in vivo. Genetic ablation of the α1 catalytic subunit of AMPK accelerates Myc-induced lymphomagenesis. Inactivation of AMPKα in both transformed and nontransformed cells promotes a metabolic shift to aerobic glycolysis, increased allocation of glucose carbon into lipids, and biomass accumulation. These metabolic effects require normoxic stabilization of the hypoxia-inducible factor-1α (HIF-1α), as silencing HIF-1α reverses the shift to aerobic glycolysis and the biosynthetic and proliferative advantages conferred by reduced AMPKα signaling. Together our findings suggest that AMPK activity opposes tumor development and that its loss fosters tumor progression in part by regulating cellular metabolic pathways that support cell growth and proliferation.

Below is the graphical abstract of this paper.

Graphical Abstract FINAL.pptx

(Photo credit reference(2; Faubert et. al) permission from Elsevier)

However, this regulation of tumor promotion by AMPK may be more complicated and dependent on the cellular environment.

Nissam Hay from the University of Illinois College of Medicine, Chicago, Illinois, USA and his co-workers Sang-Min Jeon and Navdeep Chandel were investigating the mechanism through which LKB1/AMPK regulate the balance between cancer cell growth and apoptosis under energy stress[3]. In their system, the loss of function of either of these proteins makes cells more sensitive to apoptosis in low glucose environments, and cells deficient in either AMPK or LKB1 were shown to be resistant to oncogenic transformation.  Whereas previous studies showed (as above) AMPK opposes tumor proliferation in a HIF1-dependent manner, their results showed AMPK could promote tumor cell survival during periods of low glucose or altered redox status.

The researchers incubated LKB1-deficient cancer cells in the presence of either glucose or one of the non-metabolizable glucose analogues 2-deoxyglucose (2DG) and 5-thioglucose (5TG), and found that 2DG, but not 5TG, induced the activation of AMPK and protected the cells from apoptosis, even in cells that were deficient in LKB1.

The authors demonstrated that glucose deprivation depleted NADPH levels, increased H2O2 levels and increased cell death, and that this was accelerated in cells deficient in the enzyme glucose-6-phosphate dehydrogenase. Anti-oxidants were also found to inhibit cell death in cells deficient in either AMPK or LKB1.

Knockdown or knockout of either LKB1 or AMPK in cancer cells significantly increased levels of H2O2 but not of peroxide (O2) during glucose depletion. The glucose analogue 2DG was able to activate AMPK and maintain high levels of NADPH and low levels of H2O2 in these cells.

The nucleotide coenzyme NADPH is generated in the pentose phosphate pathway and mitochondrial metabolism, and consumed in H2O2 elimination and fatty acid synthesis. If glucose is limited mitochondrial metabolism becomes the major source of NADPH, supported by fatty acid oxidation. AMPK is known to be a regulator of fatty acid metabolism through inhibition of two acetyl-CoA carboxylases, ACC1 and ACC2.

Short interfering RNAs (siRNAs) to knock down levels of both ACC1 and ACC2 in A549 cancer cells and found that only ACC2 knockdown significantly increased peroxide accumulation and apoptosis, while over-expression of mutant ACC1 and ACC2 in LKB1-proficient cells increased H2O2 and apoptosis.

Therefore, it was concluded AMPK acts to promote early tumor growth and prevent apoptosis in conditions of energy stress through inhibiting acetyl-CoA carboxylase activity, thus maintaining NADPH levels and preventing the build-up of peroxide in glucose-deficient conditions.

This may appear to be conflicting with the previous report in this post however, it is possible that these reports reflect differences in the way cells respond to various cellular stresses, be it hypoxia, glucose deprivation, or changes in redox status.  Therefore a complex situation may arise:

  • AMPK promotes tumor progression under glucose starvation
  • AMPK can oppose tumor proliferation under a normoxic, HIF1-dependent manner
  • Could AMPK regulation be different in cancer stem cells vs. non-stem cell?

References:

1.            Green AS, Chapuis N, Lacombe C, Mayeux P, Bouscary D, Tamburini J: LKB1/AMPK/mTOR signaling pathway in hematological malignancies: from metabolism to cancer cell biology. Cell Cycle 2011, 10(13):2115-2120.

2.            Faubert B, Boily G, Izreig S, Griss T, Samborska B, Dong Z, Dupuy F, Chambers C, Fuerth BJ, Viollet B et al: AMPK is a negative regulator of the Warburg effect and suppresses tumor growth in vivo. Cell metabolism 2013, 17(1):113-124.

3.            Jeon SM, Chandel NS, Hay N: AMPK regulates NADPH homeostasis to promote tumour cell survival during energy stress. Nature 2012, 485(7400):661-665.

 Other posts on this site related to Warburg Effect and Cancer include:

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Unraveling Retrograde Signaling Pathways

Reporter: Larry H. Bernstein, MD, FCAP

Unraveling Retrograde Signaling

Image Source: Created by Noam Steiner Tomer 8/10/2020

Unraveling retrograde signaling pathways: finding candidate signaling molecules via metabolomics and systems biology driven approaches
C Caldana, AR Fernie, L Willmitzer and D Steinhauser
Front. Plant Sci. 2012; 3:267.                    http://dx.doi.org/10.3389/fpls.2012.00267

http://fpls.com/Unraveling retrograde signaling pathways: finding candidate signaling molecules via
metabolomics and systems biology driven approaches

signals can be generated within organelles, such as chloroplasts and mitochondria,

  • modulating the nuclear gene expression in a process called
    • retrograde signaling.

Recently, integrative genomics approaches, in which correlation analysis has been applied on transcript and metabolite profiling data
of Arabidopsis thaliana, revealed the identification of metabolites which are

  • putatively acting as mediators of nuclear gene expression.

http://fpls.com/unraveling_retrograde_signaling_pathways:_finding_candidate_signaling_molecules_
via_metabolomics_and_systems_biology_driven_approaches

English: Plant Pathology in Arabidopsis thaliana

English: Plant Pathology in Arabidopsis thaliana (Photo credit: Wikipedia)

B0004313 Gene expression in normal and cancer ...

B0004313 Gene expression in normal and cancer cells (Photo credit: wellcome images)

Related articles

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Reporter: Aviva Lev-Ari, PhD, RN

Somatic mutations in ATP1A1 and ATP2B3 lead to aldosterone-producing adenomas and secondary hypertension

Nature Genetics

Published online 17 February 2013
Mutations affecting a pair of related enzyme-coding genes can contribute to the 

risk of benign glandular tumors 

called adenomas and secondary hypertension, a new 

Nature Genetics

 study suggests. An international team led by investigators in Germany performed

exome sequencing

on matched tumor and normal samples from nine individuals with forms of adenoma that enhance aldosterone hormone production. This leads to a type of so-called aldosteronism that can bump up blood pressure and cause other adverse symptoms.

When researchers sorted through the exome sequence data, they saw ties between aldosterone-producing adenoma and mutations in two ATPase genes — ATP1A1 and ATP2B3 — that participate in sodium/potassium and calcium signaling, respectively. Somatic ATP1A1 mutations turned up in more than 5 percent of 308 aldosterone-producing adenoma samples screened subsequently, the team noted, while 1.6 percent of those tumors contained ATP2B3 alterations.

“[T]hese findings expand the spectrum of somatic alterations leading to [aldosterone-producing adenomas] to two members of the P-type ATPase pump family, extend knowledge of the molecular mechanism leading to [aldosterone-producing adenoma],” the Ludwig Maximilian University of Munich researcher Martin Reincke, the study’s corresponding author, and colleagues wrote, “and indicate new potential therapeutic targets for the most frequent secondary form of arterial hypertension.”

SOURCE:

http://www.genomeweb.com//node/1194476?hq_e=el&hq_m=1505701&hq_l=6&hq_v=6fcaf1aef4

Somatic mutations in ATP1A1 and ATP2B3 lead to aldosterone-producing adenomas and secondary hypertension

Primary aldosteronism is the most prevalent form of secondary hypertension. To explore molecular mechanisms of autonomous aldosterone secretion, we performed exome sequencing of aldosterone-producing adenomas (APAs). We identified somatic hotspot mutations in the ATP1A1 (encoding an Na+/K+ ATPase α subunit) and ATP2B3 (encoding a Ca2+ ATPase) genes in three and two of the nine APAs, respectively. These ATPases are expressed in adrenal cells and control sodium, potassium and calcium ion homeostasis. Functional in vitro studies of ATP1A1 mutants showed loss of pump activity and strongly reduced affinity for potassium. Electrophysiological ex vivo studies on primary adrenal adenoma cells provided further evidence for inappropriate depolarization of cells with ATPase alterations. In a collection of 308 APAs, we found 16 (5.2%) somatic mutations in ATP1A1 and 5 (1.6%) in ATP2B3.

Mutation-positive cases showed

  • male dominance,
  • increased plasma aldosterone concentrations and
  • lower potassium concentrations compared with mutation-negative cases.

In summary, dominant somatic alterations in two members of the ATPase gene family result in autonomous aldosterone secretion.

Author information

Primary authors

  1. These authors contributed equally to this work.

    • Maria-Christina Zennaro &
    • Tim M Strom

Affiliations

  1. Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-Universität München, Munich, Germany.

    • Felix Beuschlein,
    • Andrea Osswald,
    • Urs D Lichtenauer,
    • Evelyn Fischer &
    • Martin Reincke
  2. Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche Scientifique (UMRS) 970, Paris Cardiovascular Research Center, Paris, France.

    • Sheerazed Boulkroun,
    • Laurence Amar,
    • Benoit Samson-Couterie,
    • Pierre-Francois Plouin,
    • Xavier Jeunemaitre &
    • Maria-Christina Zennaro
  3. Université Paris Descartes, Sorbonne Paris Cité, Paris, France.

    • Sheerazed Boulkroun,
    • Laurence Amar,
    • Benoit Samson-Couterie,
    • Pierre-Francois Plouin,
    • Xavier Jeunemaitre &
    • Maria-Christina Zennaro
  4. Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.

    • Thomas Wieland,
    • Anett Walther,
    • Thomas Schwarzmayr,
    • Susanne Diener,
    • Elisabeth Graf,
    • Thomas Meitinger &
    • Tim M Strom
  5. Department of Biomedicine, Aarhus University, Aarhus, Denmark.

    • Hang N Nielsen,
    • Vivien R Schack &
    • Bente Vilsen
  6. Medizinische Zellbiologie, Universität Regensburg, Regensburg, Germany.

    • David Penton,
    • Philipp Tauber &
    • Richard Warth
  7. Assistance Publique–Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France.

    • Laurence Amar,
    • Pierre-Francois Plouin,
    • Xavier Jeunemaitre &
    • Maria-Christina Zennaro
  8. Department of Medicine I, Endocrine and Diabetes Unit, University Hospital Würzburg, Würzburg, Germany.

    • Bruno Allolio
  9. Centre National de la Recherche Scientifique (CNRS), Institut des Hautes Etudes Scientifiques, Bures sur Yvette, France.

    • Arndt Benecke
  10. Clinical Endocrinology, Campus Mitte, University Hospital Charité, Berlin, Germany.

    • Marcus Quinkler
  11. Department of Medicine, University of Padova, Padova, Italy.

    • Francesco Fallo
  12. Endocrine Unit, Department of Medicine, University of Padova, Padova, Italy.

    • Franco Mantero
  13. Institute of Human Genetics, Technische Universität München, Munich, Germany.

    • Thomas Meitinger &
    • Tim M Strom
  14. DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.

    • Thomas Meitinger
  15. Department of Medical Sciences, Division of Internal Medicine and Hypertension, University of Torino, Turin, Italy.

    • Paolo Mulatero

Contributions

S.B., H.N.N., U.D.L., D.P., V.R.S., A.W., P.T., S.D. and B.S.-C. performed the experiments. A.O., T.W., L.A., E.F., T.S., T.M.S., E.G. and A.B. performed statistical analysis and analyzed the data. B.A., M.Q., F.F., P.-F.P., F.M. and P.M. contributed materials. F.B., T.M., X.J., R.W., B.V., M.-C.Z., T.M.S. and M.R. jointly supervised research, conceived and designed the experiments, analyzed the data, contributed reagents, materials and/or analysis tools and wrote the manuscript.

SOURCE:

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2550.html

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Rewriting the Mathematics of Tumor Growth[1]; Teams Use Math Models to Sort Drivers from Passengers[2]:  Two JNCI Reviews by Mike Martin Regarding Genomics, Cancer, and Mutation

Curator: Stephen J. Williams, Ph.D.

Recently, there has been extensive interest in the cancer research and oncology community on detecting those mutations responsible for the initiation and propagation of a neoplastic cell (driver mutations) versus those mutations that are randomly (or by selective pressures) acquired due to the genetic instability of the transformed cell.  The impact of either type of mutation has been a topic for debate, with a recent article showing that some passenger mutations may actually be responsible for tumor survival.  In addition many articles, highlighted on this site (and referenced below) in recent years have described the importance of classifying driver and passenger mutations for the purposes of more effective personalized medicine strategies directed against tumors. Two review articles by Mike Martin in the Journal of the National Cancer Institute (JCNI) shed light on the current efforts and successes to discriminate between these passenger and driver mutations and determine impact of each type of mutation to tumor growth.  However, as described in the associated article, the picture is not as clear cut as previously thought and highlights some revolutionary findings. In Rewriting the Mathematics of Tumor Growth, researchers discovered that driver mutations may confer such a small growth advantage that, multiple mutations, including the so called passenger mutations are necessary in order to sustain tumor growth. In fact, much experimental evidence has suggested at least six defined genetic events may be necessary for the in-vitro transformation of human cells.  The following table shows some of the genetic events required for in-vitro transformation in cell culture systems.

Genetic events required for transformation

 Species  Cell type  # of genes required for tumor formation*  Genes used  Reference Events required for priming
Human FibroblastsEmbryonic kidney 3 hTERTH-rasLarge T (a)Hahn(Weinberg) 2LT+hTERT
Mammary epithelialMyoblastsEmbryonic kidney 6 hTERTH-rasP53DDc-myc

cyclin D1CDK4

(b)Kendall(Counter) Hras required for tumorigenesis so probably 5 events needed
Fibroblasts 4 Large TSmall TH-rashTERT (c)Sun(Hornsby) 2Large T + H-ras
Fibroblasts 4 Large TSmall ThTERTRas (d)Rangarajan(Weinberg) 3hTERT, Ras and either small or largeT
Keratinocytes 4 CyclinD1

dnp53

EGFR

c-myc

(e)Goessel(Opitz) 3 for anchorage independence (cyclin D1, dnp53, EGFR),Cyclin D1+dnp53 for immortalization
HOSE 6 CDK4, cyclin D, hTERT plus combination of either P53DD, myrAkt, and H-ras or P53DD, H-ras, c-myc Bcl2 (f)Sasaki(Kiyono) 5
HOSE 3 hTERTSV40 earlyH-ras orK-ras (g)Liu(Bast) 2hTERT+ SV40 early
HOSE 3 Large ThTERTH-ras orc-erB-2 (h)Kusakari(Fujii) 2hTERT+large T
Rat Fibroblasts 2 Large TH-ras (i)Hirakawa Did not analyze
Fibroblasts 2 Large TH-ras (d)Rangarajan(Weinberg) Large T
Mouse MOSEIn p53-/- background 3 c-mycK-rasAkt (j)Orsulic
Pig Fibroblasts 6 p53DDhTERT

CDK4H-ras c-myc

cyclin D1

(k)Adam(Counter) 5 need all butp53DD

Note: priming means events required to immortalize but not fully transform.  * Note that both ability to form colonies in soft agarose and subsequently tested for tumor formation in immunocompromised mice.

a.         Hahn, W. C., Counter, C. M., Lundberg, A. S., Beijersbergen, R. L., Brooks, M. W., and Weinberg, R. A. (1999) Creation of human tumour cells with defined genetic elements, Nature 400, 464-468.

b.         Kendall, S. D., Linardic, C. M., Adam, S. J., and Counter, C. M. (2005) A network of genetic events sufficient to convert normal human cells to a tumorigenic state, Cancer Res 65, 9824-9828.

c.         Sun, B., Chen, M., Hawks, C. L., Pereira-Smith, O. M., and Hornsby, P. J. (2005) The minimal set of genetic alterations required for conversion of primary human fibroblasts to cancer cells in the subrenal capsule assay, Neoplasia 7, 585-593.

d.         Rangarajan, A., Hong, S. J., Gifford, A., and Weinberg, R. A. (2004) Species- and cell type-specific requirements for cellular transformation, Cancer Cell 6, 171-183.

e.         Goessel, G., Quante, M., Hahn, W. C., Harada, H., Heeg, S., Suliman, Y., Doebele, M., von Werder, A., Fulda, C., Nakagawa, H., Rustgi, A. K., Blum, H. E., and Opitz, O. G. (2005) Creating oral squamous cancer cells: a cellular model of oral-esophageal carcinogenesis, Proc Natl Acad Sci U S A 102, 15599-15604.

f.          Sasaki, R., Narisawa-Saito, M., Yugawa, T., Fujita, M., Tashiro, H., Katabuchi, H., and Kiyono, T. (2009) Oncogenic transformation of human ovarian surface epithelial cells with defined cellular oncogenes, Carcinogenesis 30, 423-431.

g.         Liu, J., Yang, G., Thompson-Lanza, J. A., Glassman, A., Hayes, K., Patterson, A., Marquez, R. T., Auersperg, N., Yu, Y., Hahn, W. C., Mills, G. B., and Bast, R. C., Jr. (2004) A genetically defined model for human ovarian cancer, Cancer Res 64, 1655-1663.

h.         Kusakari, T., Kariya, M., Mandai, M., Tsuruta, Y., Hamid, A. A., Fukuhara, K., Nanbu, K., Takakura, K., and Fujii, S. (2003) C-erbB-2 or mutant Ha-ras induced malignant transformation of immortalized human ovarian surface epithelial cells in vitro, Br J Cancer 89, 2293-2298.

i.          Hirakawa, T., and Ruley, H. E. (1988) Rescue of cells from ras oncogene-induced growth arrest by a second, complementing, oncogene, Proc Natl Acad Sci U S A 85, 1519-1523.

j.          Orsulic, S., Li, Y., Soslow, R. A., Vitale-Cross, L. A., Gutkind, J. S., and Varmus, H. E. (2002) Induction of ovarian cancer by defined multiple genetic changes in a mouse model system, Cancer Cell 1, 53-62.

k.         Adam, S. J., Rund, L. A., Kuzmuk, K. N., Zachary, J. F., Schook, L. B., and Counter, C. M. (2007) Genetic induction of tumorigenesis in swine, Oncogene 26, 1038-1045.

However it may be argued that the aforementioned experimental examples were produced in cell lines with a more stable genome than that which is seen in most tumors and had used traditional assays of transformation, such as growth in soft agarose and tumorigenicity in immunocompromised mice, as endpoints of transformation, and not representative of the tumor growth seen in the clinical setting.

Therefore Bert Vogelstein, M.D., along with collaborators around the world developed a model they termed the “sequential driver mutation theory”, in which they describe that driver mutations multiply over time with each mutation “slightly increasing the tumor growth rate through a process that depends on three factors”:

  1. Driver mutation rate
  2. The 0.4% selective growth advantage
  3. Cell division time

This model was based on a combination of experimental data and computer simulations of gliobastoma multiforme and pancreatic adenocarcinoma.  Most tumor models follow a Gompertz kinetics, which show how tumor growth is exponential but eventually levels off over time.

This new theory shows though that a tumor cell with only one driver mutation can only grow so much, until a second driver mutation is required.  Using data for the COSMIC database (Catalog of Somatic Mutations in Cancer) together with analysis software CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) the researchers analyzed 713 mutations sequenced from 14 glioma patients and 562 mutations in nine pancreatic adenocarcinomas, revealing at least 100 tumor suppressor genes and 100 oncogenes altered.  Therefore, the authors suggested these may be possible driver mutations, or at least mutations required for the sustained growth of these tumors.  Applying this new model to data obtained from Dr. Giardiello’s publication concerning familial adenopolypsis in New England Journal of medicine in 19993 and 2000, the sequential driver mutation model predicted age distribution of FAP patients, number and size of polyps, and polyp growth rate than previous models.  This surprising number of required driver mutations for full transformation was also verified in a study led by University of Texas Southwestern Medical Center biologist Jerry Shay, Ph.D., who noted “this team’s surprise nearly 45% of all colorectal candidate oncogenes (65 mutations) drove malignant proliferation”[3].

However, some investigators do not believe the model is complex enough to account for other factors involved in oncogenesis, such as epigenetic factors like methylation and acetylation.  In addition the review also discusses host and tissue factors which may complicate the models, such as location where a tumor develops.  However, most of the investigators interviewed for this review agreed that focusing on this long-term progression of the disease may give us clues to other potential druggable targets.

Teams Use Math Models to Sort Drivers From Passengers

A related review from Mike Martin in JNCI [2] describes a statistical method, published in 2009 Cancer Informatics[4], which distinguishes chromosomal abnormalities that can drive oncogenesis from passenger abnormalities.  Chromosomal abnormalities, such as deletions, additions, and translocations are common in cancer.  For instance, the well-known Philadelphia chromosome, a translocation between chromosome 9 and 22 which results in the BCR-ABL tyrosine kinase fusion protein is the molecular basis of chronic myelogenous leukemia.

In the report, Eytan Domany, Ph.D., from Weizmann Institute and several colleagues from University of Lausanne, University of Haifa and the Broad Institute were analyzing chromosomal aberrations in a subset of medulloblastoma, which had more gain and losses in chromosomes than had been attributed to the disease.  Using a statistical method they termed a “volumetric sieve”, the investigators were able to identify driver versus passenger aberrations based on three filters:

  • Fraction of patients with the abnormality
  • Length of DNA involved in the aberrant chromosome
  • Abnormality’s copy number

Another method to sort the most “important” chromosomal aberrations from less relevant alterations is termed GISTIC[5], as the website describes is: a tool to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth (at the Broad Institute website http://www.broadinstitute.org/software/cprg/?q=node/31).  The method allows for comparison across multiple tumors so noise is eliminated and improves consistency of analysis.  This method had been successfully used to determine driver aberrations is mesotheliomas, leukemias, and identify new oncogenes in adenocarcinomas of the lung and squamous cell carcinoma of the esophagus.

Main references for the two Mike Martin articles are as follows:

1.         Martin M: Rewriting the mathematics of tumor growth. Journal of the National Cancer Institute 2011, 103(21):1564-1565.

2.         Martin M: Aberrant chromosomes: teams use math models to sort drivers from passengers. Journal of the National Cancer Institute 2010, 102(6):369-371.

3.         Eskiocak U, Kim SB, Ly P, Roig AI, Biglione S, Komurov K, Cornelius C, Wright WE, White MA, Shay JW: Functional parsing of driver mutations in the colorectal cancer genome reveals numerous suppressors of anchorage-independent growth. Cancer research 2011, 71(13):4359-4365.

4.         Shay T, Lambiv WL, Reiner-Benaim A, Hegi ME, Domany E: Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes. Cancer informatics 2009, 7:91-104.

5.         Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S et al: Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(50):20007-20012.

Further posts on CANCER and GENOMICS and Sequencing published on the site include:

The Initiation and Growth of Molecular Biology and Genomics

Inaugural Genomics in Medicine – The Conference Program, 2/11-12/2013, San Francisco, CA

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

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

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

Computational Genomics Center: New Unification of Computational Technologies at Stanford

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”

arrayMap: Genomic Feature Mining of Cancer Entities of Copy Number Abnormalities (CNAs) Data

Comprehensive Genomic Characterization of Squamous Cell Lung Cancers

Mosaicism’ is Associated with Aging and Chronic Diseases like Cancer: detection of genetic mosaicism could be an early marker for detecting cancer.

http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2011.00905.x/full

https://pharmaceuticalintelligence.com/2013/02/05/winning-over-cancer-progression-new-oncology-drugs-to-suppress-driver-mutations-vs-passengers-mutations/

Additional references:

[1] Michor F, Iwasa Y, and Nowak MA (2004) Dynamics of cancer

progression. Nature Reviews Cancer 4, 197-205.

[2] Crespi B and Summers K (2005) Evolutionary biology of cancer.

Trends in Ecology and Evolution 20, 545-552.

[3] Merlo LMF, et al. (2006) Cancer as an evolutionary and ecological

process. Nature Reviews Cancer 6, 924-935.

[4] McFarland C, et al. “Accumulation of deleterious passenger mutations

in cancer,” in preparation.

[5] Birkbak NJ, et al. (2011) Paradoxical relationship between

chromosomal instability and survival outcome in cancer. Cancer

Research 71,3447-3452.

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Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell(1)

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

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell

Word Cloud by Zach Day

Most tumors exhibit a level of diversity, at the cellular, histologic, and even genetic level (2).  This genetic heterogeneity within a tumor has been a focus of recent research efforts to analyze the characteristics, expression patterns, and genetic differences between individual tumor cells.  This genetic diversity is usually manifested as single nucleotide variations (SNV) and copy number variations (CNV), both of which provide selection pressures in both cancer and evolution.

As cancer research and personalized medicine is focused on analyzing this tumor heterogeneity it has become pertinent view the tumor as a heterogeneous population of cells instead of as a homogenous mass.  In, fact, studies have suggested that cancer cell lines growing on plastic in culture, even though thought of as clonogenic, can actually display a varied degree of expression differences between neighboring cells growing on the same dish.  Indeed, cancer stem cells show an asynchronous cell division, for example a parent CD133-positive cell will divide into a CD133-positive and a CD133-negative cell(3). In addition, the discovery that circulating tumor cells (a rare population of circulating cells in the blood) can be prognostic of outcome in cancer such as inflammatory breast cancer(4), it is ever more important to develop methods to analyze single cell populations.

Harvard University researchers, Dr. Chenghang Zong, Sijia Lu, Alec Chapman and Sunney Xie developed a new amplification method utilizing multiple annealing and looping-based amplification cycles (MALBAC)(1).   A quasilinear preamplification process is used on pictograms of DNA genomic fragments (form 10 to 100 kb) isolated from a single cell.   This is performed to reduce the bias associated with nonlinear DNA amplification.  A series of random primers (which the authors termed MALBAC primers, constructed with a common sequence tags) are annealed at low temperature (0 °C). PCR rounds produce semiamplicons.  Further rounds of amplification, after a step of looping the amplicons, result in full amplicons with complementary ends.  When the two ends hybridize to form the looped DNA, this prevents use of this loop structure as a template, therefore leading to a close-to–linear amplification.    The process allows for a higher fidelity of DNA replication and the ability to amplify a whole genome.  The amplicons are then sequenced either by whole-genome sequencing methods using Sanger-sequencing to verify any single nucleotide polymorphisms.  This procedure of MALBAC-amplification resulted in coverage of 85-93% of the genome of a single cell.

As proof of principle, the authors used MALBAC to amplify the DNA of single SW480 cancer cells (picked from a clonally expanded population of a heterogeneous population (the bulk DNA).  Comparison of the MALBAC method versus the MDA method revealed copy number variations (CNV) between three individual cells, which had been picked from the clonally expanded pool. Their results were in agreement with karyotyping studies on the SW480 cell line.  Meticulous quality controls were performed to limit contamination, high false positive rates of SNV detection due to amplification bias, and false positives due to amplification or sequencing errors.

Interestingly, the authors found 35 unique single nucleotide variations which h had occurred from 20 cell divisions from a single SW480 cancer cell.  This resulted in an estimated 49 mutations which occurred in 20 generations, yielding a mutation rate of 2.5 nucleotides per generation.  In addition, the authors were able to map some of these mutations on various chromosomes and perform next-gen sequencing (deep sequencing) to verify the nucleotide mutations and found an unusually high purine-pyrimidine exchange rate.

In a subsequent paper, investigators from the same group at Harvard used this technology to sequence 99 sperm cells from a single individual to study genetic diversity created during meiotic recombination, a mechanism involved in evolution and development(5).

Reference:

1.            Zong, C., Lu, S., Chapman, A. R., and Xie, X. S. (2012) Science 338, 1622-1626

2.            Cooke, S. L., Temple, J., Macarthur, S., Zahra, M. A., Tan, L. T., Crawford, R. A., Ng, C. K., Jimenez-Linan, M., Sala, E., and Brenton, J. D. (2011) British journal of cancer 104, 361-368

3.            Guo, R., Wu, Q., Liu, F., and Wang, Y. (2011) Oncology reports 25, 141-146

4.            Giuliano, M., Giordano, A., Jackson, S., Hess, K. R., De Giorgi, U., Mego, M., Handy, B. C., Ueno, N. T., Alvarez, R. H., De Laurentiis, M., De Placido, S., Valero, V., Hortobagyi, G. N., Reuben, J. M., and Cristofanilli, M. (2011) Breast cancer research : BCR 13, R67

5.            Lu, S., Zong, C., Fan, W., Yang, M., Li, J., Chapman, A. R., Zhu, P., Hu, X., Xu, L., Yan, L., Bai, F., Qiao, J., Tang, F., Li, R., and Xie, X. S. (2012) Science 338, 1627-1630

Other related posts on this website regarding Cancer and Genomics include:

Cancer Genomics – Leading the Way by Cancer Genomics Program at UC Santa Cruz

Identifying Aggressive Breast Cancers by Interpreting the Mathematical Patterns in the Cancer Genome

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Consumer Market for Personal DNA Sequencing: Part 4

Reporter: Aviva Lev-Ari, PhD RN

FDA Warning for the Leader of Consumer Market for Personal DNA Sequencing Part 4

Word Cloud by Daniel Menzin

This Part 4 of the series on Present and Future Frontier of Research in Genomics has been 

UPDATED on 12/6/2013

23andMe Suspends Health Interpretations

December 06, 2013

Direct-to-consumer genetic testing company 23andMe hasstopped offering its health-related test to new customers, bringing it in line with a request from the US Food and Drug Administration.

In letter sent on Nov. 22, FDA said that 23andMe had not adequately responded to its concerns regarding the validity of their Personal Genome Service. The letter instructed 23andMe to “immediately discontinue marketing” the service until it receives authorization from the agency.

According to a post at the company’s blog from CEO Anne Wojcicki, 23andMe customers who purchased their kits on or after Nov. 22 “will not have access to health-related results.” They will, though, have access to ancestry information and their raw genetic data. Wojcicki notes that the customers may have access to the health interpretations in the future depending on FDA marketing authorization. Those customers are also being offered a refund.

Customers who purchased their kits before Nov. 22 will have access to all reports.

“We remain firmly committed to fulfilling our long-term mission to help people everywhere have access to their own genetic data and have the ability to use that information to improve their lives,” a notice at the 23andMe site says.

In a letter appearing in the Wall Street Journal earlier this week, FDA Commissioner Margaret Hamburg wrote that the agency “supports the development of innovative tests.” As an example, she pointed to its recent clearance of sequencing-based testsfrom Illumina.

She added that the agency also understands that some consumers do want to know more about their genomes and their genetic risk of disease, and that a DTC model would let consumers take an active role in their health.

“The agency’s desire to review these particular tests is solely to ensure that they are safe, do what they claim to do and that the results are communicated in a way that a consumer can understand,” Hamburg said.

In a statement, 23andMe’s Wojcicki says that the company remains committed to its ethos of allowing people access to their genetic information. “Our goal is to work cooperatively with the FDA to provide that opportunity in a way that clearly demonstrates the benefit to people and the validity of the science that underlies the test,” Wojcicki adds.

SOURCE

UPDATED on 11/27/2013

FDA Tells Google-Backed 23andMe to Halt DNA Test Service

VIEW VIDEO

http://www.bloomberg.com/news/2013-11-25/fda-tells-google-backed-23andme-to-halt-dna-test-service.html

FDA Letter to 23andME

Department of Health and Human Services logoDepartment of Health and Human Services

Public Health Service
Food and Drug Administration
10903 New Hampshire Avenue
Silver Spring, MD 20993

Nov 22, 2013

Ann Wojcicki
CEO
23andMe, Inc.
1390 Shoreline Way
Mountain View, CA 94043
Document Number: GEN1300666
Re: Personal Genome Service (PGS)
WARNING LETTER
Dear Ms. Wojcicki,
The Food and Drug Administration (FDA) is sending you this letter because you are marketing the 23andMe Saliva Collection Kit and Personal Genome Service (PGS) without marketing clearance or approval in violation of the Federal Food, Drug and Cosmetic Act (the FD&C Act).
This product is a device within the meaning of section 201(h) of the FD&C Act, 21 U.S.C. 321(h), because it is intended for use in the diagnosis of disease or other conditions or in the cure, mitigation, treatment, or prevention of disease, or is intended to affect the structure or function of the body. For example, your company’s website at http://www.23andme.com/health (most recently viewed on November 6, 2013) markets the PGS for providing “health reports on 254 diseases and conditions,” including categories such as “carrier status,” “health risks,” and “drug response,” and specifically as a “first step in prevention” that enables users to “take steps toward mitigating serious diseases” such as diabetes, coronary heart disease, and breast cancer. Most of the intended uses for PGS listed on your website, a list that has grown over time, are medical device uses under section 201(h) of the FD&C Act. Most of these uses have not been classified and thus require premarket approval or de novo classification, as FDA has explained to you on numerous occasions.
Some of the uses for which PGS is intended are particularly concerning, such as assessments for BRCA-related genetic risk and drug responses (e.g., warfarin sensitivity, clopidogrel response, and 5-fluorouracil toxicity) because of the potential health consequences that could result from false positive or false negative assessments for high-risk indications such as these. For instance, if the BRCA-related risk assessment for breast or ovarian cancer reports a false positive, it could lead a patient to undergo prophylactic surgery, chemoprevention, intensive screening, or other morbidity-inducing actions, while a false negative could result in a failure to recognize an actual risk that may exist. Assessments for drug responses carry the risks that patients relying on such tests may begin to self-manage their treatments through dose changes or even abandon certain therapies depending on the outcome of the assessment. For example, false genotype results for your warfarin drug response test could have significant unreasonable risk of illness, injury, or death to the patient due to thrombosis or bleeding events that occur from treatment with a drug at a dose that does not provide the appropriately calibrated anticoagulant effect. These risks are typically mitigated by International Normalized Ratio (INR) management under a physician’s care. The risk of serious injury or death is known to be high when patients are either non-compliant or not properly dosed; combined with the risk that a direct-to-consumer test result may be used by a patient to self-manage, serious concerns are raised if test results are not adequately understood by patients or if incorrect test results are reported.
Your company submitted 510(k)s for PGS on July 2, 2012 and September 4, 2012, for several of these indications for use. However, to date, your company has failed to address the issues described during previous interactions with the Agency or provide the additional information identified in our September 13, 2012 letter for(b)(4) and in our November 20, 2012 letter for (b)(4), as required under 21 CFR 807.87(1). Consequently, the 510(k)s are considered withdrawn, see 21 C.F.R. 807.87(1), as we explained in our letters to you on March 12, 2013 and May 21, 2013.  To date, 23andMe has failed to provide adequate information to support a determination that the PGS is substantially equivalent to a legally marketed predicate for any of the uses for which you are marketing it; no other submission for the PGS device that you are marketing has been provided under section 510(k) of the Act, 21 U.S.C. § 360(k).
The Office of In Vitro Diagnostics and Radiological Health (OIR) has a long history of working with companies to help them come into compliance with the FD&C Act. Since July of 2009, we have been diligently working to help you comply with regulatory requirements regarding safety and effectiveness and obtain marketing authorization for your PGS device. FDA has spent significant time evaluating the intended uses of the PGS to determine whether certain uses might be appropriately classified into class II, thus requiring only 510(k) clearance or de novo classification and not PMA approval, and we have proposed modifications to the device’s labeling that could mitigate risks and render certain intended uses appropriate for de novo classification. Further, we provided ample detailed feedback to 23andMe regarding the types of data it needs to submit for the intended uses of the PGS.  As part of our interactions with you, including more than 14 face-to-face and teleconference meetings, hundreds of email exchanges, and dozens of written communications, we provided you with specific feedback on study protocols and clinical and analytical validation requirements, discussed potential classifications and regulatory pathways (including reasonable submission timelines), provided statistical advice, and discussed potential risk mitigation strategies. As discussed above, FDA is concerned about the public health consequences of inaccurate results from the PGS device; the main purpose of compliance with FDA’s regulatory requirements is to ensure that the tests work.
However, even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions. In your letter dated January 9, 2013, you stated that the firm is “completing the additional analytical and clinical validations for the tests that have been submitted” and is “planning extensive labeling studies that will take several months to complete.” Thus, months after you submitted your 510(k)s and more than 5 years after you began marketing, you still had not completed some of the studies and had not even started other studies necessary to support a marketing submission for the PGS. It is now eleven months later, and you have yet to provide FDA with any new information about these tests.  You have not worked with us toward de novo classification, did not provide the additional information we requested necessary to complete review of your 510(k)s, and FDA has not received any communication from 23andMe since May. Instead, we have become aware that you have initiated new marketing campaigns, including television commercials that, together with an increasing list of indications, show that you plan to expand the PGS’s uses and consumer base without obtaining marketing authorization from FDA.
Therefore, 23andMe must immediately discontinue marketing the PGS until such time as it receives FDA marketing authorization for the device. The PGS is in class III under section 513(f) of the FD&C Act, 21 U.S.C. 360c(f). Because there is no approved application for premarket approval in effect pursuant to section 515(a) of the FD&C Act, 21 U.S.C. 360e(a), or an approved application for an investigational device exemption (IDE) under section 520(g) of the FD&C Act, 21 U.S.C. 360j(g), the PGS is adulterated under section 501(f)(1)(B) of the FD&C Act, 21 U.S.C. 351(f)(1)(B).  Additionally, the PGS is misbranded under section 502(o) of the Act, 21 U.S.C. § 352(o), because notice or other information respecting the device was not provided to FDA as required by section 510(k) of the Act, 21 U.S.C. § 360(k).
Please notify this office in writing within fifteen (15) working days from the date you receive this letter of the specific actions you have taken to address all issues noted above. Include documentation of the corrective actions you have taken. If your actions will occur over time, please include a timetable for implementation of those actions. If corrective actions cannot be completed within 15 working days, state the reason for the delay and the time within which the actions will be completed. Failure to take adequate corrective action may result in regulatory action being initiated by the Food and Drug Administration without further notice. These actions include, but are not limited to, seizure, injunction, and civil money penalties.
We have assigned a unique document number that is cited above. The requested information should reference this document number and should be submitted to:
James L. Woods, WO66-5688
Deputy Director
Patient Safety and Product Quality
Office of In vitro Diagnostics and Radiological Health
10903 New Hampshire Avenue
Silver Spring, MD 20993
If you have questions relating to this matter, please feel free to call Courtney Lias, Ph.D. at 301-796-5458, or log onto our web site at www.fda.gov for general information relating to FDA device requirements.
Sincerely yours,
/S/
Alberto Gutierrez
Director
Office of In vitro Diagnostics
and Radiological Health
 Center for Devices and Radiological Health

SOURCE

http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm

Cancer Diagnostics by Genomic Sequencing: ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

Symposia

http://aaas.confex.com/aaas/2013/webprogram/start.html

Personal Genetics: An Intersection Between Science, Society, and Policy

Saturday, February 16, 2013: 8:30 AM-11:30 AM

Room 203 (Hynes Convention Center)

On 26 June 2000, scientists announced the completion of a rough draft of the human genome, the result of the $3 billion publicly funded Human Genome Project. In the decade since, the cost of genome sequencing has plummeted, coinciding with the development of deep sequencing technologies and allowing, for the first time, personalized genetic medicine. The advent of personal genetics has profound implications for society that are only beginning to be discussed, even as the technologies are rapidly maturing and entering the market. This symposium will focus on how the genomic revolution may affect our society in coming years and how best to reach out to the general public on these important issues. How has the promise of genomics, as stated early in the last decade, matched the reality we observe today? What are the new promises — and pitfalls — of genomics and personal genetics as of 2013? What are the ethical implications of easy and inexpensive human genome sequencing, particularly with regard to ownership and control of genomic datasets, and what stakeholder interests must be addressed? How can the scientific community engage with the public at large to improve understanding of the science behind these powerful new technologies? The symposium will comprise three 15-minute talks from representatives of relevant sectors (academia/education, journalism, and industry), followed by a 45-minute panel discussion with the speakers.

Organizer:

Peter Yang, Harvard University

Co-organizers:

Brenna Krieger, Harvard University

and Kevin Bonham, Harvard University

Discussant:

James Thornton, Harvard University

Speakers:

 

Ting Wu, Harvard University

Personal Genetics and Education

Mary Carmichael, Boston Globe

The Media and the Personal Genetics Revolution

Brian Naughton, 23andMe Inc.

Commercialization of Personal Genomics: Promise and Potential Pitfalls

Mira Irons, Children’s Hospital Boston

Personal Genomic Medicine: How Physicians Can Adapt to a Genomic World

Sheila Jasanoff, Harvard University

Citizenship and the Personal Genomics

Jonathan Gitlin, National Human Genome Research Institute

Personal Genomics and Science Policy

THIS IS A SERIES OF FOUR POINTS OF VIEW IN SUPPORT OF the Paradigm Shift in Human Genomics

How to Tailor Cancer Therapy to the particular Genetics of a patient’s Cancer

‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities PRESENTED in the following FOUR PARTS. Recommended to be read in its entirety for completeness and arrival to the End Point of Present and Future Frontier of Research in Genomics

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine

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

Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment

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

Part 3:

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

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

Part 4:

The Consumer Market for Personal DNA Sequencing

 

Part 4:

The Consumer Market for Personal DNA Sequencing

How does 23andMe genotype my DNA?

Technology and Standards

23andMe is a DNA analysis service providing information and tools for individuals to learn about and explore their DNA. We use the Illumina OmniExpress Plus Genotyping BeadChip (shown here). In addition to the variants already included on the chip by Illumina, we’ve included our own, customized set of variants relating to conditions and traits that are interesting. Technical information on the performance of the chip can be found on Illumina’s website.

All of the laboratory testing for 23andMe is done in a CLIA-certified laboratory.

Once our lab receives your sample, DNA is extracted from cheek cells preserved in your saliva. The lab then copies the DNA many times — a process called “amplification” — growing the tiny amount extracted from your saliva until there is enough to be genotyped.

In order to be genotyped, the amplified DNA is “cut” into smaller pieces, which are then applied to our DNA chip, a small glass slide with millions of microscopic “beads” on its surface (read more about this technology). Each bead is attached to a “probe”, a bit of DNA that matches one of the approximately one million genetic variants that we test. The cut pieces of your DNA stick to the matching DNA probes. A fluorescent signal on each probe provides information that can tell us which version of that genetic variant your DNA corresponds to.

Although the human genome is estimated to contain about 10-30 million genetic variants, many of them are correlated due to their proximity to each other. Thus, one genetic variant is often representative of many nearby variants, and the approximately one million variants on our genotyping chip provide very good coverage of common variation across the entire genome.

Our research team has also hand-picked tens of thousands of additional genetic variants linked to various conditions and traits in the scientific literature to analyze on our genotyping chip. As a result we can provide you with personal genetic information available only through 23andMe.

Genetics service 23andMe announced some new cash in the bank today with a $50 million raise from Yuri Milner, 23andMe CEO Anne Wojcicki, Google’s Sergey Brin (who also happens to be Wojcicki’s husband), New Enterprise Associates, MPM Capital, and Google Ventures.

With today’s new funding also comes the reduction of the price of its genome analysis service to $99. This isn’t special holiday pricing (as 23andMe has run repeatedly in the past) the company tells me, but rather what its normal pricing will be from now on.

This move is overdue, at least as far as 23andMe’s business model is concerned. Just yesterday TechCrunch Conference Chair Susan Hobbs told me she was waiting for another $99 pricing deal to buy the Personal Genome Analysis product. Sure 23andMe has experimented with various pricing models, including subscription, since its founding in 2007, but had been at an official and prohibitive $299 price point until today. It’s also apparently been rigorously beta-testing various price points in the past couple of weeks, at some point experimenting with some lower than $99.

For comparison, the company’s original pricing began at $999 and offered subscribers just 14 health and trait reports versus today’s 244 reports, as well as genetic ancestry information. Natera, Counsyl and Pathway Genomics are also in the genomics space, but they work by offering their services through doctors rather than direct to consumer.

Since the company’s launch five years ago, it’s had 180K civilians profile their DNA, and representative Catherine Afarian tells us that, post-price drop and funding, its goal is to reach a million customers in 2013. This is a supremely ambitious goal considering it wants to turn an average user acquisition rate of 36K per year into one of 820K in one year alone.

But Afarian isn’t fazed and brings up how the company once sold out 20k in $99 account inventory on something called “DNA Day.” “Once we can offer the service at $99 it means the average American will buy in,” she said.

That $299 was too pricey, according to Hobbs, but $99 might be just right. She said the $99 price point, which yes, is less than an iPhone, was the main factor in her decision to buy in. “23andMe is more ‘nice-to-know’ information rather than ‘need-to-know’ information. It’s nice to know your ancestry. It’s more of a need to know that you are predisposed genetically for a type of cancer, so that you may take precautionary measures,” she said, implying that the data given by 23andMe isn’t necessarily vital medical information, or actionable when it is. While 23andMe can give you indicators about certain disease risks, it doesn’t close the loop, as in tell you what to do to prevent these diseases.

“Its [utility] depends on your genetic data,” said Afarian when I asked her about the usefulness of the product. “If you’ve got a Factor 5 that puts you at risk for clotting, you might want to invest in anti-clotting socks. [And] there’s always something about themselves that people didn’t know.”

Hobbs said eventually that she wouldn’t buy it, but only because she was looking into more exact lineage information for her little girl, and you need a Y chromosome in all DNA tests to show paternal lineage. Afarian also countered this hesitation, saying that what makes 23andMe unique is that it’s not only looking at just your Y or your mitochondrial DNA, but also your autosomal DNA, which does show some patrilineal information for females who lack that precious Y.

While still sort of a novelty, the potential for 23andMe goes beyond lineage and hopefully that extra $50 million will go further than keeping the price low and into research. The company hopes that a million users will result in a giant database of 23andWe genetic info that can be used to spot trends, like which genes mean a higher risk of diabetes/cancer, etc. Which is great if it happens but for now remains a pipe dream for 23andMe/We.

http://techcrunch.com/2012/12/11/23andnotme/

12/13/2012 @ 5:23PM |6,471 views

What Is 23andMe Really Selling: The Moral Quandary At The Center Of The Personalized Genomics Revolution

This week, 23andme, the personalized genomics company founded by Anne Wojcicki, wife of Google co-founder Sergey Brin, got an influx of investment cash ($50 million). According to their press release, they are using the money to bring the cost of their genetic test down to $99 (it was previously $299) which, they hope, will inspire the masses to get tested.

So should the masses indulge?

I prefer a quantified self approach to this question. At the heart of the quantified self-movement lies a very simple idea: metrics make us better. For devotees, this means “self-tracking,” using everything from the Nike fuel band to the Narcissism Personality Index to gather large quantities of personal data and—the bigger idea—use that data to improve performance.

If you consider that performance suffers when health suffers then a genetic test can been seen as a kind of metric used to improve performance. This strikes me as the best way to evaluate this idea and leads us to ask the same question about personalized genomics that the quantified self movement asks about every other metric: will it improve performance.

Arguments rage all over the place on this one, but the short answer is that SNP tests—which is the kind of DNA scan 23andme relies upon— don’t tell us all that much (yet).  They analyze a million genes out of three billion total and the impact those million play in long term-health outcomes is still in dispute. For example, the nature/nurture split is normally viewed at 30/70—meaning environmental factors play a far more significant role in long-term health outcomes than genetics.

Moreover, all of the performance metrics used by the quantified self movement are used to for behavior modification—to drive self-improvement. Personalized genomics isn’t there yet. As Stanford University’s Nobel Prize-winning RNA researcher Andy Fire once told me, “if someone off the street is looking for pointers on how to live a healthier life, there’s nothing these tests will tell you besides basic physician advice like ‘eat right, don’t smoke and get plenty of exercise.’”

And even with more well-regarded SNP tests, like the ones that examine the BRCA 1 and 2 markers for breast cancer—which  . NYU Langone Medical Center bioethicist Arthur Caplan explains it like this, “Say you test positive for a breast cancer disposition—then what are you going to do? The only preventative step you can take is to chop off your breasts.”

So if prevention is not available the only thing left is fear and anxiety. Unfortunately, in the past few decades, there have been hundreds of studies linking stress to everything from immunological disorders to heart disease to periodonitic troubles. So while finding out you may be at risk for Parkinson’s may make you feel informed, that knowledge isn’t going to stop you from developing the disease—but the resulting stress may contribute to a host of other complications.

This brings up a different question: if personalized genomics can’t yet help us much and could possibly hurt us—where’s the upside?

Turns out there’s a big upside: Citizen science. SNP tests are not yet viable because we need more info. 23andme talks about the “power of one million people,” meaning, if one million take these tests then the resulting genetic database could lead to big research breakthroughs and these could lead to all sorts of health/performance improvements.

This is what 23andme is really selling for $99 bucks a pop—a crowdsourced shot at unraveling a few more DNA mysteries.

And this also means that the question at the heart of the personalized genomics industry is not about metrics at all—it’s about morals: Should I risk my health for the greater good?

http://www.forbes.com/sites/stevenkotler/2012/12/13/what-is-23andme-really-selling-the-moral-quandary-at-the-center-of-the-personalized-genomics-revolution/

You can browse your data for all of the variants we test using the Browse Raw Data feature, or download your data here.

before you buy (59) »

What unexpected things might I learn?

How does 23andMe genotype my DNA?

Can I use the saliva collection kit for infants and toddlers?

getting started (20) »

When and how do I get my data?

How do I collect saliva samples?

How long will it take for my sample to reach the lab?

account/profile settings (20) »

Which Ancestry setting in My Profile should I choose?

How do I use Browse Raw Data?

What do the options under the “Account” link in the upper right-hand corner control?

product features (145) »

I know that a particular person is my relative. What’s the probability that we share a sufficient amount of DNA to be detected by Relative Finder?

What is the average percent DNA shared for different types of cousins?

How does Relative Finder estimate the Predicted Relationship?

research initiatives (8) »

What do I get in return for taking surveys?

What is your research goal?

What is 23andMe Research?

https://customercare.23andme.com/categories/20021003-faqs

https://customercare.23andme.com/home

REFERENCES

http://www.foundationmedicine.com/diagnostics-publications.php

http://www.coriell.org/media-center/publications

Http://www.coriell.org/assets/pdfs/gronowski_etal_coriellinstitute_clinicalchemistry2011_humantissuesinresearch.pdf

http://scholar.google.com/scholar?start=10&q=Gene+Mutation+Aberration+%26+Analysis+of+Gene+Abnormalities&hl=en&as_sdt=0,22&as_vis=1

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