Exploring Proteomic Frontiers: Insights from HUPO 2024

By Justyna Fert-Bober, Ph.D.

This month, I had the privilege of attending the US Human Proteome Organization (HUPO) meeting in the vibrant city of Portland. As a researcher from Cedars-Sinai Medical Center deeply immersed in the world of proteomics, the event never fails to disappoint. HUPO is unique in that it combines both biology and technology in a single conference for the insights needed to fuel proteomic discoveries.  This conference was particularly resonant as I was selected for an oral presentation, invited to present a morning seminar by Quantum-Si, and viewed talks by colleagues at the Cedar-Sinai Precision Biomarker Laboratories.

From the outset of the conference, I found myself immersed in a whirlwind of cutting-edge research and revolutionary technologies. Throughout the meeting, the theme of integrating multi-omics data remained prominent, emphasizing the significance of combining proteomics with genomics, transcriptomics, and metabolomics to gain a comprehensive understanding of biological systems. Dr. Mary Claire-King’s opening plenary session, delivered by the esteemed cancer researcher from the University of Washington, underscored the transformative potential of proteomics in advancing research and therapeutic interventions by bridging the gap between genomics and complex biological systems.

Dr. Neil Kelleher of Northwestern University highlighted the last 20 years of advancements in proteomics and shared the work his team has done to discover proteoforms – myriad versions of distinct molecular proteins.

The sessions on single-cell proteomics captured my attention. The ability to dissect individual cells and unravel the complexities of cellular heterogeneity is not only fascinating but also holds immense promise for advancing our understanding of disease mechanisms and developing targeted therapies. I also enjoyed the Top-Down proteomics sessions. Top-Down techniques allow for analysis of folded proteins and their non-covalent binding partners, which provides a means for studying endogenous protein complexes that may differ between physiological and pathological stages and in each step between them. Here the fragmentation techniques can be used to localize this modification to a single amino acid residue.

I also joined forces with Dr. Kenneth Skinner of Quantum-Si, to demonstrate how Next-Generation Protein Sequencing™ and mass spectrometry (MS) can combine to power post-translational modification (PTM) analysis. I presented the outcome of my lab work, where we revealed that peptidyl arginine deiminases (PAD) signaling facilitates cellular processes, mainly senescence, migration, and invasion, in fibroblasts isolated from dilated cardiomyopathy patients. We seek to prove that PAD inhibition may play an immunoregulatory role in conditions of chronic fibrosis and thus protect from cardiovascular diseases, which are a growing healthcare burden in developed countries.

Also, utilizing a hypercitrullination MS-based platform and next-generation protein sequencing methods, we employed amino acid-specific recognizers to distinguish arginine and citrulline PTM sites on the Platinum® instrument. This groundbreaking technique offers a comprehensive understanding of proteome citrullination, shedding light on its critical role in physiological and pathological processes.

Between the strides made in MS instrumentation and accessible, benchtop protein sequencing platforms like those offered by Quantum-Si, we now have the capability to extract meaningful and deeper insights from vast proteomic datasets like never before.

I attend HUPO, both US and World, every year and served as chair for Early Career Research group (ECR), and now I am Co-Chair of the HUPO Education & Training Committee (ETC).  What truly stands out to me each time is the spirit of collaboration between proteomic researchers. HUPO serves as a melting pot of ideas, bringing together researchers, clinicians, and industry professionals from diverse backgrounds. The exchange of knowledge and expertise fuels innovation, propelling the field of proteomics forward at an accelerated pace.

Looking to the future, I am filled with optimism about the transformative potential of proteomics in healthcare. I envisage diverse proteomic applications that will benefit from MS and single molecule sequencing, such as immunopeptidomics and identifying autoimmune markers. From exploring next-generation protein sequencing to embracing multi-omics integration, the meeting showcased the immense possibilities that lie ahead. By harnessing the power of technology, collaboration, and interdisciplinary approaches, we have the opportunity to unlock new insights into disease mechanisms, develop targeted therapies, and ultimately improve patient outcomes.

Justyna Fert-Bober, Ph.D., Assistant Professor, Department of Cardiology, Smidt Heart Institute, Cedars Sinai

Dr. Justyna Fert-Bober, is an Assistant Professor at Cedars-Sinai Heart Institute, with a broad background of biochemistry, molecular biology, immunology, and proteomics. She received her master’s degree from the Faculty of Biotechnology, the University of Wroclaw, and her Ph.D. from the Wroclaw Medical University in Poland. Fert-Bober received grants from NIH and National Foundation. Her research involves interinstitutional collaborations focused on identifying novel and/or largely understudied protein post-translational modifications (PTMs) called citrullination. Citrulline post-translational modifications of proteins is mediated by protein arginine deiminase (PADI) family members. It plays both a physiological role during apoptosis and epigenetics, and a pathological role in the development of inflammatory diseases and cancer. Fert-Bober’s expertise and strengths in biochemistry and proteomics have allowed her to develop a mass spectrometry (MS) method to identify citrullination at the peptide level, improving the spectrum of citrullinated proteins and allowing for the etiological importance of these citrullinated proteins as a source of neoantigens. In addition to expertise in LC‒MS/MS method development, as well as high-throughput sample analysis in plasma and tissue matrices, her research is pioneering on the role of PAD and citrullinated proteins in heart disease.