Proteomics in Proximity

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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Deezer:

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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Podcast Addict:

Welcome to Olink Proteomics in Proximity Podcast! 
 

Below are some useful resources from this episode: 
 

Highlighted pre-print article: Malarstig A, Grassman F, Dahl L, et al. Evaluation of Circulating Plasma Proteins in Breast Cancer: A Mendelian Randomization Analysis. ResearchSquare 2023.04.04. DOI: https://doi.org/10.21203/rs.3.rs-2749047/v1

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/

Learn more about the consortiums or cohorts mentioned in the podcast:

UK Biobank Pharma Proteomics Project (UKB-PPP) is currently performing 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 

Human Proteome Atlas (HPA) aims to map all human proteins using various omics technologies: https://www.proteinatlas.org/ 

SCALLOP consortium is a collaborative framework for discovery and follow-up of genetic associations with proteins on the Olink Proteomics platform: https://olink.com/our-community/scallop/ 

KARMA cohort is a prospective screening cohort for breast cancer in Sweden: https://karmastudy.org/ongoing-research/the-karma-cohort/ 

Swedish Twin Registry (referred as “Twin Gene cohort” in the podcast) is the largest of its kind, containing genetic information about ~87,000 twin pairs: https://ki.se/en/research/the-swedish-twin-registry 

Additional published articles and books mentioned during the podcast:

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

Suhre K, McCarthy MI, Schwenk JM. Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet. 2021 Jan;22(1):19-37. doi: 10.1038/s41576-020-0268-2. Epub 2020 Aug 28. PMID: 32860016. https://pubmed.ncbi.nlm.nih.gov/32860016/

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Deezer:

Welcome to Olink Proteomics in Proximity Podcast! 

Below are some useful resources from this episode: 

Highlighted publication: Grasberger H, Magis AT, Sheng E, Conomos MP, Zhang M, Garzotto LS, Hou G, Bishu S, Nagao-Kitamoto H, El-Zaatari M, Kitamoto S, Kamada N, Stidham RW, Akiba Y, Kaunitz J, Haberman Y, Kugathasan S, Denson LA, Omenn GS, Kao JY. DUOX2 variants associate with preclinical disturbances in microbiota-immune homeostasis and increased inflammatory bowel disease risk. J Clin Invest. 2021 May 3;131(9):e141676. doi: 10.1172/JCI141676. PMID: 33651715; PMCID: PMC8087203. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8087203/

Highlighted platform that was used to measure proteins in this study with a qPCR readout (Olink® Target 96): https://olink.com/products-services/target/ 

Learn more about the Crohn’s & Colitis Foundation, which is non-profit, volunteer-fueled organization dedicated to finding cures for Crohn's disease and ulcerative colitis: https://www.crohnscolitisfoundation.org/about

In the fall of 2021, Dr. Andrés Hurtado-Lorenzo spoke at a Boston Olink event, and his 25-minute presentation is available here where he discusses the discovery and follow-up work with both RNA and protein biomarkers for Crohn's Disease: https://7074596.fs1.hubspotuserconten...

Olink® Insight is an open-access resource, which aims to support the user throughout the Olink user journey, starting from product selection and study setup to post-run analysis and visualization of data output. Features include a pathway browser to reveal and understand connections between proteins and human biology, a publication browser, automatic annotations, and access to exclusive data sets. Sign up for free: https://insight.olink.com/

Here is general information about inflammatory bowel disease (IBD) from the U.S. Centers for Disease Control and Prevention (CDC): https://www.cdc.gov/ibd/what-is-IBD.htm#:~:text=Inflammatory%20bowel%20disease%20(IBD)%20is,damage%20to%20the%20GI%20tract.

Here is general information from GeneCards about DUOX2, one of the protein biomarkers identified in this study: https://www.genecards.org/cgi-bin/carddisp.pl?gene=DUOX2

Here is general information from GeneCards about IL-17C, one of the protein biomarkers identified in this study: https://www.genecards.org/cgi-bin/carddisp.pl?gene=IL17C&keywords=il17c

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Spotify Podcasts:

Welcome to Olink Proteomics in Proximity Podcast! 

Below are some useful resources from this episode: 

Highlighted publication: Diaz-Canestro C, Chen J, Liu Y, Han H, Wang Y, Honoré E, Lee CH, Lam KSL, Tse MA, Xu A. A machine-learning algorithm integrating baseline serum proteomic signatures predicts exercise responsiveness in overweight males with prediabetes. Cell Rep Med. 2023 Feb 21;4(2):100944. doi: 10.1016/j.xcrm.2023.100944. Epub 2023 Feb 13: https://www.cell.com/cell-reports-medicine/pdf/S2666-3791(23)00036-8.pdf PMID: 36787735; PMCID: PMC9975321: https://pubmed.ncbi.nlm.nih.gov/36787735/ 

Highlighted platform that was used to measure proteins in this study with a next-generation sequencing (NGS) readout (Olink® Explore): https://olink.com/products-services/explore/ 

Here is general information from Wikipedia about IL-6, one of the protein biomarkers identified in this study: https://en.wikipedia.org/wiki/Interleukin_6 

Here is general information from Wikipedia about TFF-2, one of the protein biomarkers identified in this study: https://en.wikipedia.org/wiki/Trefoil_factor_2 

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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 [email protected] 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.

Highlighted publication: Zannad F, Ferreira JP, Butler J, Filippatos G, Januzzi JL, Sumin M, Zwick M, Saadati M, Pocock SJ, Sattar N, Anker SD, Packer M. Effect of empagliflozin on circulating proteomics in heart failure: mechanistic insights into the EMPEROR programme. Eur Heart J. (2022) 43(48):4991-5002. doi:10.1093/eurheartj/ehac495. PMID: 36017745; PMCID: PMC9769969.

Review paper of research by Voltar Longo and David Sinclair on longevity and aging, mentioning sirtuins and mTOR. Longo VD, Antebi A, Bartke A, Barzilai N, Brown-Borg HM, Caruso C, Curiel TJ, de Cabo R, Franceschi C, Gems D, Ingram DK, Johnson TE, Kennedy BK, Kenyon C, Klein S, Kopchick JJ, Lepperdinger G, Madeo F, Mirisola MG, Mitchell JR, Passarino G, Rudolph KL, Sedivy JM, Shadel GS, Sinclair DA, Spindler SR, Suh Y, Vijg J, Vinciguerra M, Fontana L. Interventions to Slow Aging in Humans: Are We Ready? Aging Cell. 2015 Aug;14(4):497-510. doi: 10.1111/acel.12338. Epub 2015 Apr 22. PMID: 25902704; PMCID: PMC4531065.

General information about Empaglifozin (Jardiance) on Wikipedia is here. 

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.

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All about Olink Flex: https://olink.com/flex

Olink Insight (where you can build a 21-plex Olink Flex panel from 200 proteins): https://insight.olink.com 

Sweden’s Science for Life laboratory website: https://www.scilifelab.se/about-us/

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.

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
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Primary reference: 

Loriot Y and Italiano A et al. Plasma proteomics identifies leukemia inhibitory factor (LIF) as a novel predictive biomarker of immune-checkpoint blockade resistance. Ann Oncol. (2021) 32(11):1381-1390. doi:10.1016/j.annonc.2021.08.1748

Olink Insight Knowledge Platform with Hilda Andersson, Episode 6, Proteomics in Proximity. 

Description of the MATCH-R clinical trial, “A Prospective Trial to Study the Evolution of Clonal Architecture of Tumors From Patients Treated With Molecular Targeted Agents (MATCH-R)”, NCT02517892

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.

Would you like to subscribe to the podcast on your favorite player or app? You can do so here: 

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Primary reference: 

Ticau S and Nioi P et al. (2021) Neurofilament Light Chain as a Biomarker of Hereditary Transthyretin-Mediated Amyloidosis. Neurology. 96(3):e412-e422. doi:10.1212/WNL.0000000000011090

Information about the APOLLO clinical trial: “APOLLO: The Study of an Investigational Drug, Patisiran (ALN-TTR02), for the Treatment of Transthyretin (TTR)-Mediated Amyloidosis” Link to NCT01960348 at the US National Library of Medicine’s Clinical Trials database https://clinicaltrials.gov/ct2/show/NCT01960348

Epstein Barr Virus research presenting a stronger link between EBV and Multiple Sclerosis.

Bjornevik K and Ascherio A et al. (2022) Longitudinal analysis reveals high prevalence of Epstein-Barr virus associated with multiple sclerosis. Science. 375(6578):296-301. doi:10.1126/science.abj8222

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.

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
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The 2019 Cell Reports paper, “Chromatin Remodeling in Response to BRCA2-Crisis” by J Gruber and M Snyder et al. is available online here.

Dr. Michael Snyder’s Stanford laboratory home page is here.

A 1998 Oncogene paper, “The BRCA2 is a histone acetyltransferase” by S Habibur and E S P Reddy et al. is located online here. A 2014 Cancer Discovery paper, “R-loop Processing by BRCA2 is Required for Genomic Stability” is located here. And more about TIP60 can be found in this recent 2022 Oncogenesis reference, “The TIP60-ATM axis regulates replication fork stability in BRCA-deficient cells” located online here. 

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected] 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 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.

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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