Proteomics in Proximity: Recent Episodes
Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas
Proteomics in Proximity (with co-hosts Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas from Olink Proteomics) discuss the intersection of proteomics with genomics for drug target discovery, the application of proteomics to reveal disease biomarkers, and current trends in using proteomics to unlock biological mechanisms.
Welcome to Olink Proteomics in Proximity Podcast!
Below are some useful resources from this episode:
Highlighted publication:
Girerd N, et al. Protein Biomarkers of New-Onset Heart Failure: Insights From the Heart Omics and Ageing Cohort, the Atherosclerosis Risk in Communities Study, and the Framingham Heart Study. Circ Heart Fail. 2023 May;16(5):e009694. doi: 10.1161/CIRCHEARTFAILURE.122.009694 https://pubmed.ncbi.nlm.nih.gov/37192292/
Large-scale cardiovascular studies:
· Heart “OMics” in AGEing (HOMAGE), a European-based consortium investigating biomarkers to predict heart failure and as drug targets for prevention: https://www.homage-hf.eu/
· Atherosclerosis Risk in Communities (ARIC) consortium, a prospective epidemiologic study to investigate the causes of atherosclerosis and its clinical outcomes: https://sites.cscc.unc.edu/cscc/projects/ARIC
· Framingham Heart Study, a study identifying common factors or characteristics that contribute to cardiovascular disease across three generations: https://www.framinghamheartstudy.org/’
· EMPEROR-Preserved trial, a cohort of patients who had chronic heart failure and a left ventricular ejection fraction of more than 40% : https://www.wikijournalclub.org/wiki/EMPEROR-Preserved
High-throughput platforms mentioned during the podcast or used in this study that measure tens to thousands of proteins simultaneously:
· Olink® Target 96: https://olink.com/products-services/target/
· Olink® Explore 3072: https://olink.com/products-services/explore/
· Olink® Explore HT: https://olink.com/products-services/exploreht/
Podcast mentioned during this podcast:
Cooper, Peter M, host. Easter Island – Where Giants Walked. Fall of Civilizations, Episode 6, July 2019, https://fallofcivilizationspodcast.com/
Books mentioned during the podcast:
· Attia, Peter. Outlive: the science & art of longevity. New York: Harmony, 2023. https://www.goodreads.com/en/book/show/61153739
· Hood, Leroy and Price, Nathan. The Age of Scientific Wellness: Why the Future of Medicine Is Personalized, Predictive, Data-Rich, and in Your Hands. Cambridge, MA and London, England: Harvard University Press, 2023. https://doi.org/10.4159/9780674293465
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In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here: https://bit.ly/3Rt7YiY
For any questions regarding information Olink Proteomics, please email us at info@olink.com or visit our website: https://www.olink.com/
WHAT IS PROTEOMICS IN PROXIMITY?
Proteomics in Proximity discusses the intersection of proteomics with genomics for drug target discovery, the application of proteomics to reveal disease biomarkers, and current trends in using proteomics to unlock biological mechanisms. Co-hosted by Olink's Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas.
Welcome to Olink Proteomics in Proximity Podcast!
Below are some useful resources from this episode:
Highlighted article from the UK Biobank Pharma Proteomics Project (UKB-PPP): Styrkarsdottir U, Lund SH, Thorleifsson G, Saevarsdottir S, Gudbjartsson DF, Thorsteinsdottir U, Stefansson K. Cartilage Acidic Protein 1 in Plasma Associates With Prevalent Osteoarthritis and Predicts Future Risk as Well as Progression to Joint Replacements: Results From the UK Biobank Resource. Arthritis Rheumatol. 2023 Apr;75(4):544-552. doi: 10.1002/art.42376. Epub 2022 Dec 28. PMID: 36239377. https://pubmed.ncbi.nlm.nih.gov/36239377/
Highlighted platform that was used to measure proteins in this study with a next-generation sequencing (NGS) readout (Olink® Explore 3072): https://olink.com/products-services/explore/
UKB-PPP consortium, one of the world’s largest scientific studies of blood protein biomarkers conducted to date: https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies
ENIGMA consortium, an international effort to understand brain structure and function based on imaging and genetic data: https://enigma.ini.usc.edu/about-2/
SCALLOP consortium, a collaborative framework for discovery and follow-up of genetic associations with proteins on the Olink Proteomics platform: https://olink.com/our-community/scallop/
ClinVar, a public archive of supporting evidence of human variations and phenotypes from the National Center for Biotechnology Information (NCBI): https://www.ncbi.nlm.nih.gov/clinvar/intro/
GWAS (genome-wide association studies): https://www.genome.gov/genetics-glossary/Genome-Wide-Association-Studies
Learn more about some of the scientists mentioned in the podcast who are performing cutting-edge research:
Dr. Kári Stefánsson, Founder and CEO of deCODE genetics: https://www.decode.com/management/
Dr. Claudia Langenberg, Director of Queen Mary’s Precision Health University Research Institute (PHURI): https://www.bihealth.org/en/research/research-group/computational-medicine
Dr. Jochen Schwenk, Professor of Translational Proteomics at SciLife Lab: https://www.scilifelab.se/researchers/jochen-schwenk/
Dr. Karsten Suhre, Professor of Physiology and Biophysics at Weill Cornell Medicine-Qatar: https://physiology.med.cornell.edu/people/karsten-suhre-ph-d/
Dr. Paul Thompson: Director at ENIGMA Center for Worldwide Medicine, Imaging, & Genomics; Professor in the Keck School of Medicine at USC: https://keck.usc.edu/faculty-search/paul-m-thompson/
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In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here: https://bit.ly/3Rt7YiY
For any questions regarding information Olink Proteomics, please email us at info@olink.com or visit our website: https://www.olink.com/
WHAT IS PROTEOMICS IN PROXIMITY?
Proteomics in Proximity discusses the intersection of proteomics with genomics for drug target discovery, the application of proteomics to reveal disease biomarkers, and current trends in using proteomics to unlock biological mechanisms. Co-hosted by Olink's Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas.
To access Olink Insight free of charge, visit https://insight.olink.com
The first two data stories, with Normal Range data and COVID-19 data, has been recently updated with the first Disease Atlas, with data characterizing 15 cancer types. This is available on Olink Insight here: https://insight.olink.com/data-stories/disease-atlas-cancer
To access the COVID-19 Data Story dataset itself, information about the study and how to access the data is available on our website here: https://olink.com/application/mgh-covid-19-study/
If you would like to contact Dale, Cindy or Sarantis feel free to email us at info@olink.com.
In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.
List of names and affiliations mentioned in the UK Biobank context: Mark McCarthy (Genentech), Slavé Petrovski (AstraZeneca), Chris Whelan (Johnson and Johnson), Erin Smith (Takeda Pharmaceuticals), Melissa Miller (Pfizer), Ben Sun (Biogen).
The ASHG announcement, honoring Sir Peter Donnelly, CEO of Genomics plc and Emeritus Professor of Statistical Science at the University of Oxford with the William Allan Award.
A list of the many abstracts and plenary presentations at ASHG 2022 that mention Olink can be found here (PDF).
The Ben Sun et al. preprint mentioned is titled “Genetic regulation of the human plasma proteome in 54,306 UK Biobank participants” and is available on BioRxiv here.
An overview published in 2013 of the STUCTURE software (one of the “most widely used population analysis tools”) is available here.
To join the All of Us research program, visit https://www.joinallofus.org/ and information about the Francis Collins asking for an African Moonshot on GenomeWeb is here.
If you would like to contact Dale, Cindy or Sarantis feel free to email us at info@olink.com.
In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.
One of the first publications using Olink technology came out by Enroth S and Gyllensten U et al. Nature Communications 2014 “Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs”. Link to the paper is here: DOI:10.1038/ncomms5684
To access the Olink Insight platform for protein biomarker data discovery free-of-charge with an email address, click here: https://insight.olink.com And be sure to check out the Publication Explorer!
A recent publication by the same group from the University of Uppsala is by Gyllensten U and Enroth S et al. Cancers 2022 “Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer”. Link to the paper is here: DOI:10.3390/cancers14071757
For the main Olink webpage that has over 900 publications as a single list (also classified by disease area and application type) you can access it here.
If you would like to contact Dale, Cindy or Sarantis feel free to email us at info@olink.com.
In case you were wondering, Proteomics in Promixity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.
The 2022 Science Advances paper, “Proteomic profiling platforms head to head: Leveraging genetics and clinical traits to compare aptamer- and antibody-based methods” by Daniel H Katz and Rob Gerszten et al. is available online here.
A highly informative Twitter thread by the first author Dr. Daniel Katz reviewing the figures of the paper is available here.
If you are interested in learning more about the use of proteomics in multiomic strategies, here’s link to the Olink website where examples of combinations of omics methods are combined.
If you would like to contact Dale, Cindy or Sarantis feel free to email us at info@olink.com.
In case you were wondering, Proteomics in Promixity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.
Would you like to subscribe to the podcast on your favorite player or app? You can do so here:
Apple Podcasts: https://apple.co/3T0YbSm
Spotify Podcasts: https://open.spotify.com/show/2sZ2wxOqI4b4vSngkajLs8?si=d957d55c8db046f7 Google Podcasts: https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy50cmFuc2lzdG9yLmZtL3Byb3Rlb21pY3MtaW4tcHJveGltaXR5
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Show Notes for PiP Ep 02 “Empower Genomics with Proteomics”
For more information about the UK Biobank, an Olink to Science blog post called “Genetic Regulation of the Human Plasma Proteome in the UK Biobank” is available here. The preprint publication itself is available here on bioRxiv.
If you’d like to see a great 15 minute presentation on what the goals are for the UK Biobank Pharma Proteomics Project, Dr. Chris Whelan (Biogen) presented this YouTube video at one of the UK Biobank’s scientific meetings that is worth watching.
A paper discussed by Folkersen et al., “Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals” was published in Nature Metabolism in late 2020, and is available here.
If you would like to contact Dale, Cindy or Sarantis feel free to email us at info@olink.com and if you would like to learn more about our backgrounds, Cindy’s LinkedIn is here, Sarantis’ is here, and Dale’s is here.
In case you were wondering, Proteomics in Promixity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.
In case you would like to learn more about our backgrounds, Cindy’s LinkedIn is here, Sarantis’ is here, and Dale’s is here.
For more information about the UK Biobank, an Olink to Science blog post called “Genetic Regulation of the Human Plasma Proteome in the UK Biobank” is available here. The preprint publication itself is available here on bioRxiv. If you’d like to see a great 15 minute presentation on what the goals are for the UK Biobank Pharma Proteomics Project, Dr. Chris Whelan (Biogen) presented this YouTube video at one of the UK Biobank’s scientific meetings that is worth watching.
If you would like to contact Dale, Cindy or Sarantis feel free to email us at info@olink.com
In case you were wondering, Proteomics in Promixity refers to the principal underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.
Co-hosts Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas from Olink Proteomics talk about the intersection of proteomics with genomics for drug target discovery, the application of proteomics to reveal disease biomarkers, and current trends in using proteomics to unlock biological mechanisms.
In case you were wondering, "in Proximity" refers to Olink's underpinning technology called the Proximity Extension Assay, to allow highly multiplexed protein analysis from small sample volumes for pharmaceutical, clinical translation and academic research. More information about PEA can be found here on Olink's website.
If you have any questions or comments, feel free to email us at info@olink.com. Thank you for listening!