The Human Genome Project brought with it the promise of personalised medicine and revolutionary treatments for many diseases. Whilst this has been partially fulfilled, over the next two decades it became evident that genomics alone may not be enough.
Enter proteomics; the study of all proteins in the human body. Proteins make up the majority of drug targets, and their dynamic nature allows for real-time monitoring of disease states. Ultimately, proteomics can reveal mechanisms that genomics alone cannot, making it an exciting avenue for clinical research.
At The Festival of Genomics and Biodata, Chris Whelan (Director, Johnson & Johnson) gave an exciting talk on the topic, entitled ‘What’s next for Next Generation proteomics?’. Here, we summarise some of his key takeaways.
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The Pharma Proteomics Project
In the wake of the ‘proteomics revolution’, several large-scale projects are ramping up. Principally among these is the Pharma Proteomics Project. The PPP is a consortium of 13 major pharmaceutical companies that came together to conduct a large-scale proteomic study using UK Biobank data. The initial pilot project measured around 3,000 proteins across 55,000 UK Biobank participants using the Olink Explore 3072 platform between 2021 and 2023.
This pilot project identified over 14,000 protein quantitative trait loci (pQTLs) – genetic associations with protein levels. These pQTLs are being used to identify new drug targets for diseases such as Parkinson’s, as they can provide more precise mechanistic insights compared to traditional GWAS approaches.
What’s next?
Given the success of the pilot study, the project has now expanded. The goal is to analyse proteomic data across the full 600,000 UK Biobank samples using the Olink Explore HT platform. The first 300,000 samples worth of data is expected by December 2025, and should be released to UK Biobank users in 2026.
The expanded project should enable longitudinal tracking of protein changes over time within the same individuals. This will provide valuable insights into how proteins dynamically change in relation to disease onset and progression.
In addition, this large-scale dataset could enable the development of foundational models using generative AI. Current work shows that disease states can already be differentiated using the smaller pilot study cohort, implying that the larger cohort holds significant promise.
Clinical impacts
In the short-term, Chris predicts that proteomics will be applied more regularly in clinical trials. Integration in current Phase III trials has revealed pharmacodynamic networks, showing which proteins change during a treatment course. Some changes are related to the drug targets themselves, whilst others relate to side effects and other biological indications. This could point towards drug repurposing opportunities.
In the long-term, Chris is hopeful that proteomics could make its way into primary care.
With thanks to Chris Whelan, speaker at The Festival of Genomics and Biodata 2025.
