Proteomics in Proximity Olink Proteomics

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/ 
 
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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-xhttps://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.0000000000011090https://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-xhttps://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.2023.03.002https://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.122.009694https://www.ahajournals.org/doi/abs/10.1161/CIRCHEARTFAILURE.122.009694
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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 O

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/ 
 
 
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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)

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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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/ 
 
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