Special review series: provocative questions in platelet omics studies

The first efforts to catalog the complete protein repertoire, or proteome, of platelets emerged at the end of the last century.^1–4 At that time, it was difficult to foresee how the platelet proteomics field would grow – now with more than 1,900 publications indexed in PubMed, including over 900 studies published since 2018. Initial studies of platelet proteomes were mostly explorative. These “shotgun” style experiments, driven by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS), noted that platelets contain abundant cytoskeletal, metabolic, signaling, and yet-to-be characterized proteins that likely contribute to platelet phenotype and function.^5,6 As protein capture, separation and MS tools evolved, platelet proteomics studies began to unravel protein:protein interactions and site-specific post-translational modifications (PTMs) – especially reversible phosphorylation – with roles in platelet signaling and agonist responses.^7–9 For example, proteomics tools fueled the discovery of the C-type lectin-like type II (CLEC-2) receptor in platelets,¹⁰ and the dissection of its signaling pathways.^11,12

In addition to discovering and elucidating molecular mechanisms of platelet function, proteomics tools also hold tremendous promise in identifying platelet-associated biomarkers and therapeutic targets in wellness and disease.^13,14 Over the past decade, platelet proteomics groups have increasingly turned their attention to acute pathologies and diseases, where platelets play fundamental roles – especially cardiovascular, metabolic, hemorrhagic, thrombotic, immunologic, and degenerative conditions.^14–18 To this end, basic as well as translational and clinical studies of platelets have all benefited from ongoing advances in mass spectrometry, computational biology, and other systems biology tools.¹⁹ As the platelet proteomics field continues to mature, other omics platforms also advance in parallel, including genomics, transcriptomics, metabolomics, and lipidomics.^20–23 Proteomics and each of these other omics modalities all have their own strengths and weaknesses but together are poised to provide a full picture of platelet biology in ways not imaginable just a few years ago.

In this issue of Platelets, we present a Special Review Series on Provocative Questions in Platelet Omics Studies to highlight key achievements of omics approaches in platelet research and to discuss what is expected and possible in the near future. Through a combination of mini-review and commentary articles, these topics are approached by posing and answering key questions raised by the authors from their past and current experiences within the platelet omics community. While proteomics is a central theme of this series, other omics modalities, including transcriptomics, metabolomics, and lipidomics, are also highlighted.

Methodological, logistical, and conceptual challenges have long impacted omics studies, especially of platelets.^24,25 In this context, Aslan discusses how platelets have historically been examined with omics experiments, and, considers how community efforts to standardize the design, interpretation, and communication of platelet omics studies can ideally move platelet research forward.²⁶ Although proteomics methods have already led to many basic and translational discoveries in platelets, expectations for progress have always been high, and many obstacles remain in translating omics data to the clinic. Indeed, while many potential biomarkers and drug targets have been uncovered, to date, only a few have progressed to more promising stages.²⁷ Technical issues related to inter-lab reproducibility affecting sample processing and proteomics platforms, together with the inherent biological variability of clinical samples, make the application of proteomics to platelet clinical studies complex and challenging. A discussion of guidelines and standards to overcome these issues represents an important step forward.

Focusing on clinical applications, Zellner addresses how proteomics tools may be used to interrogate platelets in disease. Taking Alzheimer´s disease as a driving example, Zellner discusses advantages and disadvantages of top-down and bottom-up proteomics methods to analyze the platelet proteome and post-translational modifications (PTMs), focusing on technical differences and methodological barriers.²⁸ These challenges are not wholly unique to proteomics studies of platelets and have been encountered and approached by colleagues in studies of plasma and other blood components.^24,29 Accordingly, Bruzek and colleagues review what the plasma and platelet proteomes can tell us from each other.³⁰ There is a clear interconnection between the proteome of plasma and platelets and the ideal situation should be, especially in clinical scenarios, to consider both proteomes as part of the same studies, rather than as distinct entities.^31,32 The translation of proteomics data to the clinic often requires studies with animal models, especially mice. In this respect, Martínez-Botía and colleagues analyze similarities and differences in mouse and human platelet phenotypes from a proteomics perspective.³³ They compare databases of mouse and human platelet proteomes and secretomes and conclude that both species share a highly conserved proteome in terms of identified proteins and their abundance.

This review series also provides three articles on platelet proteomics from a multi-omics perspective, with discussions around the platelet lipidome and transcriptome in health and disease. Huang et al. compare the classified platelet transcriptome (17.6k transcripts) with the identified platelet proteome (5.2k proteins).³⁴ They discuss procedures to obtain a complete human platelet proteome based on the quantitative comparisons of genome-wide platelet and megakaryocyte transcriptomes. They emphasize methodological challenges and conclude that the availability of a reference transcriptome and proteome for human platelets will be important in deciphering intra- and inter-subject differences in platelet proteomes in health and disease. In another article of the present series, Allan and colleagues review transcriptomic and proteomic research on platelets as they age over their 5–10 days in circulation. They highlight that aged or, “senescent” platelets have reduced RNA and protein content and an associated loss of structural integrity and reduced hemostatic capabilities.³⁵ Finally, in the last article of this series, Chicanne et al. introduce the emerging field of platelet lipidomics.³⁶ In addition to proteins, lipids also represent an important, dynamic class of molecules modulating platelet function in response to stimuli as well as pathology. Platelet lipidomics also has its own methodological challenges, and the application of lipidomics in a clinical setting is still in its early days. Nevertheless, the authors summarize the advances in the field and highlight the potential of lipidomics to provide platelet biomarkers that may have major implications in diagnostic/prognostic follow-up and treatment of diseases.

Altogether, the present Special Review Series on Provocative Questions in Platelet Omics Studies brings together seven complementary perspectives to review and further advance omics approaches to platelet research. These articles each highlight methodological challenges, as well as the strong promise for present and future applications of omics tools to studies of platelets in health and disease. A common message throughout these articles is that guidelines for sample processing and omics analysis will ensure more robust data and inter-lab reproducibility. The analytical development of mass spectrometers in recent years, together with big data analysis and systems biology tools, will also continue to help to integrate the enormous amounts of data that combined omics studies produce. It is clear that proteomics and complementary omics studies have already made valuable contributions to the platelet biology field; nonetheless, these omics studies are still likely in their early stages and are poised to synergize and expand our understanding of platelets in health and disease going forward.

Acknowledgments

AG is supported by grants from the Spanish Ministry of Science and Innovation [grants No. PID2019-108727RB-I00 and PDC2022-133743-I00], co-funded by the European Regional Development Fund (ERDF) and the Sociedad Española de Trombosis y Hemostasia (SETH-FETH). JEA is supported by the National Institutes of Health [R01HL146549].

Disclosure statement

No potential conflict of interest was reported by the authors.

Correction Statement

This article has been republished with minor changes. These changes do not impact the academic content of the article.