The Promise of Next-Generation Proteomics in Revolutionizing Cancer Research and Treatment

Artificial intelligence (AI) is undoubtedly a big deal in the pharmaceutical industry, bringing the unprecedented abilities of modeling biology at a scale of not just separate biological processes, but whole cells and even tissues and organs (e.g. “network biology”, multi omics modeling, etc).?

In previous issues of this newsletter we have discussed not once various drug design companies that created sophisticated AI-drive platforms for novel target discovery, lead generation, NLP-supported drug repurposing, biomarker discovery, and clinical trial improvement (e.g. better patient stratification, predicting drug responders vs. non-responders based on unique molecular markers, etc).??

However, let’s face it, at the heart of the modern “AI revolution” are oftentimes deep neural networks and those are extremely data-greedy. Besides, “garbage-in garbage-out” is a known thing. An AI drug discovery platform will only be as good as the data used for training systems.?

Naturally, in the era of AI-driven drug discovery, quality biological data is becoming new gold. This brings us to another interesting topic, which I will be covering occasionally in this newsletter series: advanced technologies for generating biological data.?

Today, let’s talk about Next Generation Proteomics (NGP).?

Recently, I came across this article on GenomeWeb: “Next-Generation Proteomics Delivers Insights Across the Oncology Pipeline: Highlights from the AACR 2022 Annual Meeting”, which triggered my interest in this area, as I was quite interested in some of the mass spectrometry methods during my MSc research work long time ago (although, I was not involved in proteomics field per se, we used to apply mass spec to studying coordination compounds as models of some metal-containing enzyme active sites…).?

Nowadays, proteomics technologies such as mass spectrometry are coming into prominence as powerful tools to deliver insights across every stage of the oncology drug discovery pipeline, for instance, helping uncover and validate novel drug targets, helping to understand drug mechanisms of action, and helping identify novel diagnostic, prognostic, or predictive biomarkers, and so on.

The authors of the above article, Biognosys, is a notable company active in development of new technologies and methods in mass spectrometry proteomics across the oncology pipeline, they presented their quite promising next-generation proteomics approach at the recent American Association for Cancer Research (AACR) Annual Meeting.

As Dr. Basem Goueli, a key opinion leader in Hematology and Oncology, expanded on this topic in his comment for BiopharmaTrend channel:?

“With that said, Biognosys is by no means alone here. Somalogic and Quantum-Si both IPOd relatively recently. 908 Devices will have something to say about this once they realize the true opportunity with their table top mass spec machines. Seer, Inc, Nautilus Biotechnology, etc., are also in this space. Precision proteomics companies, once we can figure out the cost issues, will become as ubiquitous as genomics. To this end, consider that we started largely with FoundationOne. Now, off the top of my head, we have: Tempus, Caris, Neogenomics, Guardant Health, OmniSeq, Invitae, SEMA4.?

Exact Science is moving into this space, Protean Biodiagnostics is a new entrant in this space.?

And a bunch of others I'm missing at this moment. Indeed, many institutions have their own genomics and proteomics facilities, including some outside of academia (e.g. Intermountain Health). This same phenomenon is coming to oncology, but it will be much more complicated. After all, there are numerous protein posttranslational modifications that are going to be very difficult to fully account for with proteomics.”

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On a side note, we at BiopharmaTrend are happy to announce the start of a bi-monthly editorial series by Dr. Basem Goueli: “The Insider's Guide to Translational Medicine”.?

This is meant to be an exploration of the future of clinical hematology and oncology through precision medicine, drug development, and artificial intelligence. The series will provide unique insights about how multiomics integrates into clinical practice and will help understand present and future trends in this context, key players, and notable developments.

Read the first article in the series: “Playing Chess Against Cancer: A Pharmaceutical, Biotechnological, and Clinical Guide to Modern Day Oncologic Treatment Cartography”

Subscribe to BiopharmaTrend newsletter to stay tuned for the upcoming articles.?

See you at "Where Technology Meets Biology" next week!

-- Andrii