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Innovation massively expands view into workings of single cells summary

Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Genomics, cancer-general, Cell Biology, Cell Biology, Signaling & Cell Circuits, Diagnostics and Lab Tests, single cell sequencing, tagged , , , , , , on July 8, 2021| Leave a Comment »

Reporter: Danielle Smolyar, Research Assistant 3 – Text Analysis for 2.0 LPBI Group’s TNS #1 – 2020/2021 Academic Internship in Medical Test Analysis (MTA) 

Reporting on a Study published on July 6, 2021 by  Oregon Health & Science University

Recently, researchers have found many ways to manipulate and alter gene activity in specific cells. As a result of seeing this alteration, it has caused much development and progress in understanding cancer, brain function, and immunity.

IMAGE SOURCE: 3D-model of DNA. Credit: Michael Ströck/Wikimedia/ GNU Free Documentation Lic

Tissues and Organs are composed of cells that look the same but have different roles. For example, single-cell analysis allows us to research and test the cells within an organ or cancerous tumor. However, the single-cell study has its boundaries and limits in trying a more significant number of cells. This result is not an accurate data and analysis of the cells.

Andrew Adey, Ph.D., the senior author of a paper in Nature Biotechnology, https://www.nature.com/articles/s41587-021-00962-z

Mulqueen, R. M., Pokholok, D., O’Connell, B. L., Thornton, C. A., Zhang, F., O’Roak, B. J., Link, J., Yardımcı, G. G., Sears, R. C., Steemers, F. J., & Adey, A. C. (2021, July 5). High-content single-cell combinatorial indexing. Nature News. https://www.nature.com/articles/s41587-021-00962-z

states that the new method gives us the ability to have a ten-fold improvement in the amount of DNA produced from a single DNA sequence. A DNA sequence is composed of units which are called bases. The sequence puts the bases in chronological order for it to code correctly. 

To understand cancer better, single-cell studies are a crucial factor in doing so. Different cells catch on to other mutations in the DNA sequence in a cancerous tumor, which ultimately alters the DNA sequence. This results in tumor cells with new alterations, which could eventually spread to the rest of the body. 

Adey and his team provided evidence that the method they had created can show DNA alterations that have come from cells present in tumor samples from patients with pancreatic cancer. Adey stated,

quote “For example, you can potentially identify rare cell subtypes within a tumor that are resistant to therapy.” 

Abey and his team have been working with OHSU Knight Cancer Institute, and with them, they are testing a single-cell method to see if patients’ tumors have changed by doing chemo or drug therapy. 

This new method allows itself to create DNA libraries and fragments of DNA that helps analyze the different genes and mutations within the sequence. This method uses something called an enzymatic reaction that attaches primers to the end of each DNA fragment.  For the cells to be analyzed, each primer must be present on both ends of the fragment. 

As a result of this new method, all library fragments present must-have primers on both ends of the fragments. At the same time, it improves efficiency by reducing its sequencing  price overall, that these adapters can be used instead of the regular custom workflows. 

SOURCE

Original article:

Mulqueen, R.M., Pokholok, D., O’Connell, B.L. et al. High-content single-cell combinatorial indexing. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-00962-z

Research categories – Cell biology, cancer-general, research, DNA Fragment TAGS- DNA, sequencing, cell fragments, single-cell

Other related articles published on this Open Access Online Scientific Journal include the following: 

Series B: Frontiers in Genomics Research

Series Content Consultant:

Larry H. Bernstein, MD, FCAP, Emeritus CSO, LPBI Group

Volume Content Consultant:

Prof. Marcus W. Feldman

BURNET C. AND MILDRED FINLEY WOHLFORD PROFESSOR IN THE SCHOOL OF HUMANITIES AND SCIENCES

Stanford University, Co-Director, Center for Computational, Evolutionary and Human Genetics (2012 – Present)

Latest in Genomics Methodologies for Therapeutics:

Gene Editing, NGS & BioInformatics,

Simulations and the Genome Ontology

2019

Volume Two

https://www.amazon.com/dp/B08385KF87

 

Part 4: Single Cell Genomics

Introduction to Part 4: Single Cell Genomics – Voice of Aviva Lev-Ari & Stephen Williams


4.1 The Science

4.1.1   Single-cell biology

Special | 05 July 2017

https://www.nature.com/collections/gbljnzchgg

4.1.2   The race to map the human body — one cell at a time, A host of detailed cell atlases could revolutionize understanding of cancer and other diseases

https://www.nature.com/news/the-race-to-map-the-human-body-one-cell-at-a-time-1.21508

4.1.3   Single-cell Genomics: Directions in Computational and Systems Biology – Contributions of Prof. Aviv Regev @Broad Institute of MIT and Harvard, Cochair, the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute

Curator: Aviva Lev-Ari, PhD, RN

Single-cell Genomics: Directions in Computational and Systems Biology – Contributions of Prof. Aviv Regev @Broad Institute of MIT and Harvard, Cochair, the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute

4.1.4   Cellular Genetics

https://www.sanger.ac.uk/science/programmes/cellular-genetics

4.1.5   Cellular Genomics

https://www.garvan.org.au/research/cellular-genomics

4.1.6   SINGLE CELL GENOMICS 2019 – sometimes the sum of the parts is greater than the whole, September 24-26, 2019, Djurönäset, Stockholm, Sweden http://www.weizmann.ac.il/conferences/SCG2019/single-cell-genomics-2019

Reporter: Aviva Lev-Ari, PhD, RN

SINGLE CELL GENOMICS 2019, September 24-26, 2019, Djurönäset, Stockholm, Sweden

4.1.7   Norwich Single-Cell Symposium 2019, Earlham Institute, single-cell genomics technologies and their application in microbial, plant, animal and human health and disease, October 16-17, 2019, 10AM-5PM

Reporter: Aviva Lev-Ari, PhD, RN

Norwich Single-Cell Symposium 2019, Earlham Institute, single-cell genomics technologies and their application in microbial, plant, animal and human health and disease, October 16-17, 2019, 10AM-5PM

4.1.8   Newly Found Functions of B Cell

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

Newly Found Functions of B Cell

4.1.9 RESEARCH HIGHLIGHTS: HUMAN CELL ATLAS

https://www.broadinstitute.org/research-highlights-human-cell-atlas

4.2 Technologies and Methodologies

4.2.1   How to build a human cell atlas – Aviv Regev is a maven of hard-core biological analyses. Now she is part of an effort to map every cell in the human body.

Anna Nowogrodzki, 05 July 2017, Article tools

https://www.nature.com/news/how-to-build-a-human-cell-atlas-1.22239

4.2.2   Featuring Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute (SKI), The Dana Pe’er Lab

Reporter: Aviva Lev-Ari, PhD, RN

Featuring Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute (SKI), The Dana Pe’er Lab

4.2.3   Genomic Diagnostics: Three Techniques to Perform Single Cell Gene Expression and Genome Sequencing Single Molecule DNA Sequencing

Curator: Aviva Lev-Ari, PhD, RN

Genomic Diagnostics: Three Techniques to Perform Single Cell Gene Expression and Genome Sequencing Single Molecule DNA Sequencing

4.2.4   Three Technology Leaders in Single Cell Sequencing: 10X Genomics, Illumina and MissionBio

Reporter: Aviva Lev-Ari, PhD, RN

Three Technology Leaders in Single Cell Sequencing: 10X Genomics, Illumina and MissionBio

4.2.5   scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments

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

scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments

4.2.6   Nano-guided cell networks: new methods to detect intracellular signaling and implications

Curator: Stephen J. Williams, PhD

Nano-guided cell networks: new methods to detect intracellular signaling and implications

4.3 Clinical Aspects

4.3.1 Using single cell sequencing data to model the evolutionary history of a tumor.

Kim KI, Simon R.

BMC Bioinformatics. 2014 Jan 24;15:27. doi: 10.1186/1471-2105-15-27.

PMID:

4.3.2   eProceedings 2019 Koch Institute Symposium – 18th Annual Cancer Research Symposium – Machine Learning and Cancer, June 14, 2019, 8:00 AM-5:00 PM ET MIT Kresge Auditorium, 48 Massachusetts Ave, Cambridge, MA

Real Time Press Coverage: Aviva Lev-Ari, PhD, RN

eProceeding 2019 Koch Institute Symposium – 18th Annual Cancer Research Symposium – Machine Learning and Cancer, June 14, 2019, 8:00 AM-5:00 PMET MIT Kresge Auditorium, 48 Massachusetts Ave, Cambridge, MA

4.3.3   The Impact of Heterogeneity on Single-Cell Sequencing

Samantha L. Goldman1,2, Matthew MacKay1,2, Ebrahim Afshinnekoo1,2,3, Ari M. Melnick4, Shuxiu Wu5,6 and Christopher E. Mason1,2,3,7*

https://www.frontiersin.org/articles/10.3389/fgene.2019.00008/full

4.3.4   Single-cell approaches to immune profiling

https://www.nature.com/articles/d41586-018-05214-w

4.3.5   Single-cell sequencing made simple. Data from thousands of single cells can be tricky to analyse, but software advances are making it easier.

by Jeffrey M. Perkel

https://www.nature.com/news/single-cell-sequencing-made-simple-1.22233

4.3.6  Single-cell RNA-seq helps in finding intra-tumoral heterogeneity in pancreatic cancer

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

Single-cell RNA-seq helps in finding intra-tumoral heterogeneity in pancreatic cancer

4.3.7 Cancer Genomics: Multiomic Analysis of Single Cells and Tumor Heterogeneity

Curator: Stephen J. Williams, PhD

Cancer Genomics: Multiomic Analysis of Single Cells and Tumor Heterogeneity

4.4 Business and Legal

4.4.1   iBioChips integrate diagnostic assays and cellular engineering into miniaturized chips that achieve cutting-edge sensitivity and high-throughput. We have resolved traditional biotech challenges with innovative biochip approaches

https://ibiochips.com/?gclid=Cj0KCQjwuLPnBRDjARIsACDzGL0wb6u79VHHkftodfApMYs-oxI-5cOZIBUaELdmd2wDOIk3W0OQg2caAqMyEALw_wcB

4.4.2   Targeted Single-Cell Solutions for High Impact Applications – Mission Bio’s Tapestri® Platform is the only technology that provides single-cell targeted DNA sequencing at single-base resolution.

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Part 4: Summary – Single Cell Genomics – Voice of Stephen Williams

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Nitric Oxide and Platelet Aggregation

Posted in Biomarkers & Medical Diagnostics, Cardiovascular Pharmacogenomics, Cell Biology, Signaling & Cell Circuits, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Human Immune System in Health and in Disease, Infectious Disease & New Antibiotic Targets, Innovations in Neurophysiology & Neuropsychology, Nitric Oxide in Health and Disease, Pharmacotherapy of Cardiovascular Disease, tagged , , , , , , , , , , , , , on August 16, 2012| 13 Comments »

Author: Dr. Venkat S. Karra, Ph.D.

Platelets are a natural source of growth factors and they circulate in the blood. They are involved in hemostasis, leading to the formation of blood clots. Platelets, otherwise known as thrombocytes, are small, irregularly shaped clear cell fragments derived from fragmentation of precursor megakaryocytes. The average lifespan of a platelet is 5 to 9 days. An abnormality or disease of the platelets leads to a condition called thrombocytopathy.

For example:
1. If the number of platelets is too low (called thrombocytopenia), excessive bleeding can occur.

Disorders leading to a reduced platelet count are:
Thrombocytopenia
Idiopathic thrombocytopenic purpura – also known as immune thrombocytopenic purpura (ITP)
Thrombotic thrombocytopenic purpura
Drug-induced thrombocytopenic purpura (for example heparin-induced thrombocytopenia (HIT))
Gaucher’s disease
Aplastic anemia
Onyalai
Alloimmune disorders
Fetomaternal alloimmune thrombocytopenia

2. If the number of platelets is too high (called thrombocytosis), blood clots (thrombosis) can form. Such clots in the blood may obstruct blood vessels and result in events like stroke, myocardial infarction, pulmonary embolism or the blockage of blood vessels to other parts of the body (e.g., arms, legs).

Disorders featuring an elevated count are:
Thrombocytosis, including essential thrombocytosis (elevated counts, either reactive or as an expression of myeloproliferative disease).

3. Thrombasthenia is a condition in which a decrease in function of platelets is observed.

Disorders leading to platelet dysfunction or reduced count are:
HELLP syndrome
Hemolytic-uremic syndrome
Chemotherapy
Dengue

Platelets play a significant role in the repair and regeneration of connective tissues. They release a multitude of growth factors, which have been used as an adjunct to wound healing, include:

Platelet-derived growth factor (PDGF), a potent chemotactic agent,
TGF beta, which stimulates the deposition of extracellular matrix.
Fibroblast growth factor,
Insulin-like growth factor 1,
Platelet-derived epidermal growth factor,
Vascular endothelial growth factor.

As said earlier, the function of platelets is the maintenance of hemostasis (the opposite of hemostasis is hemorrhage). This is achieved primarily by the formation of thrombi. When a damage to the endothelium of blood vessels occurs, the endothelial cells stop secretion of coagulation and aggregation inhibitors and instead secrete von Willebrand factor which initiate the maintenance of hemostasis after injury.

Hemostasis has three major steps: 1) vasoconstriction, 2) temporary blockage of a break by a platelet plug, and 3) blood coagulation, or formation of a clot that seals the hole until tissues are repaired.

The platelets get activated when a damage occurs to the blood vessel and the platelets clump at the site of blood vessel injury as a protective mechanism – a process that precedes the formation of a blood clot. This is the case if there is a damage to the endothelium otherwise thrombus formation should be considered seriously and must be inhibited immediately.

Vascular spasm is the first response as the blood vessels constrict to allow less blood to be lost during the injury to the blood vessel. In the second step – platelet plug formation – platelets stick together to form a temporary seal to cover the break in the vessel wall. The third and last step is called coagulation or blood clotting. Coagulation reinforces the platelet plug with fibrin threads that act as a “molecular glue”

Disorders of platelet adhesion or aggregation are:
Bernard-Soulier syndrome
Glanzmann’s thrombasthenia
Scott’s syndrome
von Willebrand disease
Hermansky-Pudlak Syndrome
Gray platelet syndrome

In normal hemostasis a thin layer of endothelial cells, that are lined with the inner surface of blood vessels, act to inhibit platelet activation by producing nitric oxide, endothelial-ADPase (which clears away the platelet activator, ADP – this activator otherwise can be blocked by the famous blockbuster clopidogrel), and PGI2 (also known as prostacyclin or eicosanoids, like PGD2, PGI2 is an inflammatory product that inhibits the aggregation of platelets). Intact blood vessels are central to moderating blood’s tendency to clot because the endothelial cells of intact vessels prevent blood clotting with a heparin-like molecule and thrombomodulin and prevent platelet aggregation with
1. Nitric oxide (NO), and
2. Prostacyclin (PGI2) – a member of eicosanoids family.

In this post, nitric oxide role in inhibiting platelet aggregation will be presented. Similarly Interaction of NO and prostacyclin (PGI2) in vascular endothelium will be presented as a separate post.

Nitric oxide (NO) and its role in inhibiting platelet aggregation:

Nitric oxide (NO) is known as the ‘endothelium-derived relaxing factor’, or ‘EDRF’. The endothelium (inner lining) of blood vessels uses NO to signal the surrounding smooth muscle to relax, thus resulting in vasodilation and increasing blood flow. NO is biosynthesized endogenously from L-arginine, oxygen and NADPH by various nitric oxide synthase (NOS) enzymes. Nitric oxide is highly reactive and yet diffuses freely across membranes that makes it ideal for a transient paracrine (between adjacent cells) and autocrine (within a single cell) signaling molecule.

This is an important cellular signaling molecule involved in many physiological and pathological processes. It is a powerful vasodilator with a short half-life of a few seconds in the blood. Low levels of nitric oxide production are important in protecting organs such as the liver from ischemic damage. Nitric oxide is considered an antianginal drug as it causes vasodilation, which can help with ischemic pain, known as angina, by decreasing the cardiac workload. By dilating the veins, nitric oxide lowers arterial pressure and left ventricular filling pressure. This vasodilation does not decrease the volume of blood the heart pumps, but rather it decreases the force the heart muscle must exert to pump the same volume of blood.

Chronic expression of NO is associated with various carcinomas and inflammatory conditions including Type-1 diabetes, multiple sclerosis, arthritis and ulcerative colitis.

Endothelium-derived relaxing factor (EDRF), the best-characterized is nitric oxide (NO), is produced and released by the endothelium to promote smooth muscle relaxation. EDRF was discovered and characterized by Robert F. Furchgott, a winner of the Nobel Prize in Medicine in 1998 with his co-researchers Louis J. Ignarro and Ferid Murad.

According to Furchgott’s website at SUNY Downstate Medical Center, “…we are investigating whether the endothelium-derived relaxing factor (EDRF) is simply nitric oxide or a mixture of substances”.

Although there is strong evidence that nitric oxide elicits vasodilation, there is some evidence tying this effect to neuronal rather than endothelial reactions. http://www.nature.com/jhh/journal/v15/n4/abs/1001165a.html.

The article says that “The possibility that neuronal rather than endothelial production of NO might play a significant role in the aetiology of essential hypertension is a promising area for future human research”.

Mechanism of Platelet Aggregation:

Platelets aggregate, or clump together, using fibrinogen and von Willebrand factor (vWF) as a connecting agent. The most abundant platelet aggregation receptor is glycoprotein IIb/IIIa (gpIIb/IIIa) which is a calcium-dependent receptor for fibrinogen, fibronectin, vitronectin, thrombospondin, and vWF. Other receptors include GPIb-V-IX complex (vWF) and GPVI (collagen).

Activated platelets will adhere, via glycoprotein (GP) Ia, to the collagen that is exposed by endothelial damage. Aggregation and adhesion act together to form the platelet plug. Myosin and actin filaments in platelets are stimulated to contract during aggregation, further reinforcing the plug. Platelet aggregation is stimulated by ADP, thromboxane, and α2 receptor-activation, and further enhanced by exogenous administration of anabolic steroids.

In an injury to the blood vessel, once the blood clot takes control of the bleeding, the aggregated platelets help the healing process by secreting chemicals that promote the invasion of fibroblasts from surrounding connective tissue into the wounded area to completely heal the wound or form a scar. The obstructing clot is slowly dissolved by the fibrinolytic enzyme, plasmin, and the platelets are cleared by phagocytosis.

Possible usefulness of measuring GP IIb-IIIa content as a marker of increased platelet reactivity is discussed in the following very recent (2011) reveiw article: “Glycoprotein IIb-IIIa content and platelet aggregation in healthy volunteers and patients with acute coronary syndrome”. http://www.ncbi.nlm.nih.gov/pubmed/21329420

Further readings:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134593/?tool=pubmed

http://www.ncbi.nlm.nih.gov/pubmed/2620689

http://pharmaceuticalintelligence.com/2012/07/25/nitric-oxide-production-in-systemic-sclerosis/

http://pharmaceuticalintelligence.com/2012/08/10/nitric-oxide-chemistry-and-function/

http://pharmaceuticalintelligence.com/2012/08/05/nitric-oxide-a-short-historic-perspective-7/

http://pharmaceuticalintelligence.com/2012/07/19/cardiovascular-disease-cvd-and-the-role-of-agent-alternatives-in-endothelial-nitric-oxide-synthase-enos-activation-and-nitric-oxide-production/

http://pharmaceuticalintelligence.com/2012/07/16/nitric-oxide-in-bone-metabolism/

http://pharmaceuticalintelligence.com/2012/06/22/bone-remodelling-in-a-nutshell/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717403/?tool=pubmed

http://www.ncbi.nlm.nih.gov/pubmed/7605019

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