Proteomics in Proximity – Details, episodes & analysis

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

[email protected] 

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 [email protected] or visit our website: https://www.olink.com/

Interested in a specific podcast topic or guest? Reach out to us at [email protected]

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 Lawley and Sarantis Chlamydas.

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 [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
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 [email protected].

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 [email protected].

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 [email protected].

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.