Proteomics in Proximity

Welcome to the Olink® Proteomics in Proximity podcast! Below are some useful resources mentioned in this episode: UK Biobank Pharma Proteomics Project (UKB-PPP), 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 UKB-PPP online resources developed by Nick Lehner and Maria Wörheide https://metabolomips.org/ukbbpgwas/ Metabolomics and Proteomics Core in Munich: https://www.helmholtz-munich.de/en/core-facility-overview/metabolomics-and-proteomics https://www.helmholtz-munich.de/core-facilities Stefanie.hauck@helmholtz-munich.de ClinspectM (https://clinspect-m.mscoresys.de/) consortium in the Munich area dedicated to move proteomics forward to clinical application More joint initiatives towards Germany-wide benchmarking and standardized processes are in the making, follow the news on https://www.mscoresys.de/ Research articles Sun, B.B., Chiou, J., Traylor, M. et al. Plasma proteomic associations with genetics and health in the UK Biobank. 2023 Nature, DOI: 10.1038/s41586-023-06592-6 https://www.nature.com/articles/s41586-023-06592-6 Petrera A, von Toerne C, Behlr J, et al. Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling. (2020) Journal of Proteome Research https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.0c00641 Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens. Kardell O, von Toerne C, Merl-Pham J, König AC, Blindert M, Barth TK, Mergner J, Ludwig C, Tüshaus J, Eckert S, Müller SA, Breimann S, Giesbertz P, Bernhardt AM, Schweizer L, Albrecht V, Teupser D, Imhof A, Kuster B, Lichtenthaler SF, Mann M, Cox J, Hauck SM. J Proteome Res. 2024 Jan 5;23(1):117-129. doi: 10.1021/acs.jproteome.3c00473. Epub 2023 Nov 28. PMID: 38015820 https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00473 Olink tools and software Olink® Explore 3072, the platform utilized by the UK Biobank to measure ~3000 proteins in plasma: https://olink.com/products-services/explore/ Olink® Explore HT, Olink’s most advanced solution for high-throughput biomarker discovery, measuring 5400+ proteins simultaneously with a streamlined workflow and industry-leading specificity: https://olink.com/products-services/exploreht/ Subscribe to the podcast on your favorite player or app: Apple Podcasts: https://apple.co/3T0YbSm Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music:

Welcome to the Olink® Proteomics in Proximity podcast! Below are some useful resources mentioned in this episode: Olink tools and software • Olink® Explore 3072, the platform utilized by the UK Biobank to measure ~3000 proteins in plasma: https://olink.com/products-services/explore/ • Olink® Explore HT, Olink’s most advanced solution for high-throughput biomarker discovery, measuring 5400+ proteins simultaneously with a streamlined workflow and industry-leading specificity: https://olink.com/products-services/exploreht/ UK Biobank Pharma Proteomics Project (UKB-PPP), 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 Research articles • Dhindsa, R.S., Burren, O.S., Sun, B.B. et al. Rare variant associations with plasma protein levels in the UK Biobank. 2023 Nature, DOI: 10.1038/s41586-023-06547-x https://www.nature.com/articles/s41586-023-06547-x • Sun, B.B., Chiou, J., Traylor, M. et al. Plasma proteomic associations with genetics and health in the UK Biobank. 2023 Nature, DOI: 10.1038/s41586-023-06592-6 https://www.nature.com/articles/s41586-023-06592-6 • Ticau S, Sridharan G, Tsour S, et al. Neurofilament Light Chain as a Biomarker of Hereditary Transthyretin-Mediated Amyloidosis 2021 Neurology, DOI: 10.1212/WNL.0000000000011090 https://n.neurology.org/content/96/3/e412.long • Zannad F, Ferreira JP, Butler J, et al. Effect of Empagliflozin on Circulating Proteomics in Heart Failure: Mechanistic Insights from the EMPEROR Program. 2022 European Heart Journal, DOI: 10.1093/eurheartj/ehac495 https://academic.oup.com/eurheartj/advance-article/doi/10.1093/eurheartj/ehac495/6676779 • Eldjarn GH, et al. Large-scale plasma proteomics comparisons through genetics and disease associations. Nature. 2023 Oct;622(7982):348-358. doi: 10.1038/s41586-023-06563-x https://www.nature.com/articles/s41586-023-06563-x#Sec44 • [PREPRINT] Carrasco-Zanini et al 2023 Proteomic prediction of common and rare diseases MedRxiv https://www.medrxiv.org/content/10.1101/2023.07.18.23292811v1 • Michaëlsson E, Lund LH, Hage C, et al. Myeloperoxidase Inhibition Reverses Biomarker Profiles Associated With Clinical Outcomes in HFpEF. 2023 JACC. Heart Failure, DOI: 10.1016/j.jchf.2023.03.002 https://www.sciencedirect.com/science/article/pii/S2213177923001257 • Girerd N, Levy D, Duarte K, 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. 2023 Circulation Heart Failure, DOI: 10.1161/CIRCHEARTFAILURE.122.009694 https://www.ahajournals.org/doi/abs/10.1161/CIRCHEARTFAILURE.122.009694 Subscribe to the podcast on your favorite player or app: Apple Podcasts: https://apple.co/3T0YbSm Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... Podcast Addict: https://podcastaddict.com/podcast/409... Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598 In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink technology called the Proximity Extension Assay (PEA). More information about the assay and how it works can be found here: https://bit.ly/3Rt7YiY For any questions regarding information about Olink Proteomics, please email us at info@olink.com or visit our website: https://www.olink.com/ Interested in a specific podcast topic or guest? Reach out to us at PIP@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 Cindy...

Welcome to the Olink® Proteomics in Proximity podcast! Below are some useful resources from this episode: Published study of primary focus Koprulu M, Carrasco-Zanini J, Wheeler E, Lockhart S, Kerrison ND, Wareham NJ, Pietzner M, Langenberg C. Proteogenomic links to human metabolic diseases. Nat Metab. 2023 Mar;5(3):516-528. doi: 10.1038/s42255-023-00753-7. Epub 2023 Feb 23. Erratum in: Nat Metab. 2023 Mar 19;: PMID: 36823471; PMCID: PMC7614946. https://pubmed.ncbi.nlm.nih.gov/36823471/ Laboratory, first author, and corresponding author of the study · Public Health University Research Institute (PHURI), a multidisciplinary research center to drive personalized healthcare: https://www.qmul.ac.uk/phuri/about/ · Mine Koprulu (first author), PhD student, University of Cambridge: https://www.linkedin.com/in/mine-koprulu-497659b9/ · Dr. Claudia Langenberg (corresponding author); Director of PHURI, Queen Mary, University of London; Professor of Computational Medicine, Berlin Institute of Health at Charité: https://www.qmul.ac.uk/phuri/our-people/professor-claudia-langenberg/ Olink tools and software · Olink® Explore 3072, the platform that measured proteins in this study with a next-generation sequencing (NGS) readout: https://olink.com/products-services/explore/ UK Biobank Pharma Proteomics Project (UKB-PPP), 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 Genotype-Tissue Expression (GTEx) project, a biobank and open-access database to study tissue-specific gene expression and regulation: https://www.gtexportal.org/home/ European Prospective Investigation into Cancer (EPIC)-Norfolk study, a prospective cohort of middle-aged individuals from Eastern England: https://www.epic-norfolk.org.uk/ Genome Aggregation Database (gnomAD), the largest publicly available collection of population variation from harmonized exome and genome sequencing data: https://gnomad.broadinstitute.org/ 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/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... Podcast Addict: https://podcastaddict.com/podcast/409... Deezer:

Welcome to the Olink® Proteomics in Proximity podcast! Below are some useful resources from this episode: Published study of primary focus Álvez MB, Edfors F, von Feilitzen K, Zwahlen M, Mardinoglu A, Edqvist PH, Sjöblom T, Lundin E, Rameika N, Enblad G, Lindman H, Höglund M, Hesselager G, Stålberg K, Enblad M, Simonson OE, Häggman M, Axelsson T, Åberg M, Nordlund J, Zhong W, Karlsson M, Gyllensten U, Ponten F, Fagerberg L, Uhlén M. Next generation pan-cancer blood proteome profiling using proximity extension assay. Nat Commun. 2023 Jul 18;14(1):4308. doi: 10.1038/s41467-023-39765-y. PMID: 37463882; PMCID: PMC10354027. https://pubmed.ncbi.nlm.nih.gov/37463882/ Laboratory, first author, and corresponding author of the study · SciLifeLab, a collaborative resource for life scientists located in Sweden: https://www.scilifelab.se/ · María Bueno Álvez (first author), PhD student, Science for Life Laboratory (SciLifeLab): https://www.linkedin.com/in/mar%C3%ADa-bueno-%C3%A1lvez-33395b192/ · Dr. Mathias Uhlén (corresponding author), Professor of Microbiology, Royal Institute of Technology (KTH), Leader of the Human Protein Atlas, Founding director of the Science for Life Laboratory (SciLifeLab): https://www.kth.se/pro/sysbio/uhlen-group/researchers/mathias-uhlen-1.67763 Olink tools and software · Olink® Explore 1536, the platform that measured proteins in this study with a next-generation sequencing (NGS) readout: https://olink.com/products-services/explore/ · Olink® Explore HT, Olink’s newest solution for high-throughput biomarker discovery that measures 5300+ proteins simultaneously with minimal sample consumption: https://olink.com/products-services/exploreht/ · Olink® Insight, an open-access resource to accelerate protein biomarker discovery: https://insight.olink.com/ UK Biobank Pharma Proteomics Project (UKB-PPP), one of the world’s largest scientific studies of blood protein biomarkers conducted to date · Published article: 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/ · UKB-PPP website: https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies Analysis of UK Biobank proteomics data from cancer patients, with co-authors including Ruth C. Travis, Karl Smith-Byrne, and Joshua R. Atkins Preprint article: Papier K, Atkins JR, Tong TYN, Gaitskell K, Desai T, Ogamba CF, Parsaeian M, Reeves GK, Mills IG, Key TJ, Smith-Byrne K, Travis RC. Identifying proteomic risk factors for cancer using prospective and exome analyses: 1,463 circulating proteins and risk of 19 cancers in the UK Biobank. medRxiv 2023.07.28.23293330; doi: https://doi.org/10.1101/2023.07.28.23293330. https://www.medrxiv.org/content/10.1101/2023.07.28.23293330v1 U-CAN Biobank, a prospective biobank of cancer patient biomaterial in Sweden Glimelius B, Melin B, Enblad G, Alafuzoff I, Beskow A, Ahlström H, Bill-Axelson A, Birgisson H, Björ O, Edqvist PH, Hansson T, Helleday T, Hellman P, Henriksson K, Hesselager G, Hultdin M, Häggman M, Höglund M, Jonsson H, Larsson C, Lindman H, Ljuslinder I, Mindus S, Nygren P, Pontén F, Riklund K, Rosenquist R, Sandin F, Schwenk JM, Stenling R, Stålberg K, Stålberg P, Sundström C, Thellenberg Karlsson C, Westermark B, Bergh A, Claesson-Welsh L, Palmqvist R, Sjöblom T. U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden. Acta Oncol. 2018 Feb;57(2):187-194. doi: 10.1080/0284186X.2017.1337926. Epub 2017 Jun 20. PMID: 28631533. https://pubmed.ncbi.nlm.nih.gov/28631533/ Galleri GRAIL test, a...

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 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/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... Podcast Addict: https://podcastaddict.com/podcast/409... 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/ 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/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... 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/ 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/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... Podcast Addict: https://podcastaddict.com/podcast/409... 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 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:

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 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/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... Podcast Addict: https://podcastaddict.com/podcast/409... Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598 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.

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. 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 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

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 Spotify Podcasts: https://open.spotify.com/show/2sZ2wxOqI4b4vSngkajLs8?si=d957d55c8db046f7 Google Podcasts: https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy50cmFuc2lzdG9yLmZtL3Byb3Rlb21pY3MtaW4tcHJveGltaXR5 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

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: Apple Podcasts: https://apple.co/3T0YbSm Spotify Podcasts: https://open.spotify.com/show/2sZ2wxOqI4b4vSngkajLs8?si=d957d55c8db046f7 Google Podcasts: https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy50cmFuc2lzdG9yLmZtL3Byb3Rlb21pY3MtaW4tcHJveGltaXR5 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

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 Spotify Podcasts: https://open.spotify.com/show/2sZ2wxOqI4b4vSngkajLs8?si=d957d55c8db046f7 Google Podcasts: https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy50cmFuc2lzdG9yLmZtL3Byb3Rlb21pY3MtaW4tcHJveGltaXR5 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

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 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 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 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

Primary reference: Suhre K, Sarwath H, Engelke R, Sohail MU, Cho SJ, Whalen W, Alvarez-Mulett S, Krumsiek J, Choi AMK, Schmidt F. Identification of Robust Protein Associations With COVID-19 Disease Based on Five Clinical Studies. Front Immunol. 2022 12:781100. doi:10.3389/fimmu.2021.781100 Dr. Karsten Suhre’s Weill Cornell Medicine laboratory page: https://vivo.weill.cornell.edu/display/cwid-kas2049 Leukemia Inhibitory Factor reference: Loriot Y, Marabelle A, Guégan JP, 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 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 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

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 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.

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 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 Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840 Podcast Addict: https://podcastaddict.com/podcast/4098296 Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598

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 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.