Celebrating Women in Proteomics and Metabolomics
2024; American Chemical Society; Volume: 23; Issue: 8 Linguagem: Inglês
10.1021/acs.jproteome.4c00613
ISSN1535-3907
AutoresIleana M. Cristea, Claire E. Eyers,
Tópico(s)Health and Medical Research Impacts
ResumoInfoMetricsFiguresRef. Journal of Proteome ResearchVol 23/Issue 8Article This publication is free to access through this site. Learn More CiteCitationCitation and abstractCitation and referencesMore citation options ShareShare onFacebookX (Twitter)WeChatLinkedInRedditEmailJump toExpandCollapse EditorialAugust 2, 2024Celebrating Women in Proteomics and MetabolomicsClick to copy article linkArticle link copied!Ileana M. CristeaIleana M. CristeaMore by Ileana M. Cristeahttps://orcid.org/0000-0002-6533-2458Claire E. EyersClaire E. EyersMore by Claire E. Eyershttps://orcid.org/0000-0002-3223-5926Open PDFJournal of Proteome ResearchCite this: J. Proteome Res. 2024, 23, 8, 2675–2679Click to copy citationCitation copied!https://pubs.acs.org/doi/10.1021/acs.jproteome.4c00613https://doi.org/10.1021/acs.jproteome.4c00613Published August 2, 2024 Publication History Received 18 July 2024Published online 2 August 2024Published in issue 2 August 2024editorialCopyright © Published 2024 by American Chemical Society. This publication is available under these Terms of Use. Request reuse permissionsThis publication is licensed for personal use by The American Chemical Society. ACS PublicationsCopyright © Published 2024 by American Chemical SocietySubjectswhat are subjectsArticle subjects are automatically applied from the ACS Subject Taxonomy and describe the scientific concepts and themes of the article.CancerLipidomicsMetabolomicsPeptides and proteinsProteomicsSPECIAL ISSUEThis article is part of the Women in Proteomics and Metabolomics special issue.It has been such a great privilege organizing this JPR Special Issue to celebrate the essential contributions that women scientists have made and are making in the fields of Proteomics and Metabolomics. In these rich and fast-moving fields of scientific research, women have been core contributors to both technological developments and biological or clinical discoveries. They have continuously pushed the boundaries of research and have opened new scientific directions. This is perhaps not surprising, as some of the fundamental knowledge that has promoted the founding of these fields of research has been supported by women scientists. Among these have been Dorothy Crowfoot Hodkin, Gerty Theresa Cori, Kamala Sohonie, Mildred Cohn, Ada Yonath, and Marie Mayard Daly, to name just a few, who have provided extraordinary insights into protein structure–function relationships, protein synthesis, subcellular composition, and cellular metabolism, transforming directions of research and means for therapeutic interventions. (1−6) This tradition of scientific excellence has been continued by many distinguished women scientists who inspire us and empower the next generation of researchers. Examples include the work of Catherine Fenselau in proteomics, metabolomics, and lipidomics, of Carol Robinson in analyzing intact proteins and complexes, of Carolyn Bertozzi, Catherine Costello, and Nicolle Packer in glycobiology, of Natalie Ahn in kinase-mediated signaling, of Anne-Claude Gingras and Alice Ting in protein interactions, of Emma Lundberg and Kathryn Lilley in spatial protein regulation, of Lisa Jones and Paola Picotti in structural proteomics, of Erin Baker in metabolomics, of Yu-Ju Chen in proteogenomics, of Olga Vitek and Olga Troyanskaya in computational biology, of Jennifer van Eyk, Peipei Ping, and Ying Ge in cardiovascular research, Lingjun Li in neurobiology, and of Michal Bassani-Sternberg and Nicola Ternette in immunopeptidomics. These names provide just few examples and are joined by many other extraordinary women scientists, some of which are highlighted in this Special Issue, who have made substantial discoveries and have paved the way for research in proteomics and metabolomics.Despite these numerous and far-reaching accomplishments, women remain a historically underrepresented and sometimes underappreciated cohort in science, including in proteomics and metabolomics. The ACS 2022 Diversity Data Report (7) has shown that women account for less than 25% of all submitting authors, having more frequently the role of a contributing rather than a corresponding author. Women also frequently represent a minority among Editors, Editorial Advisory Board members, and reviewers. Acknowledging that, as JPR editors, we can seek to accelerate the path forward to gender parity, we have launched this Special Issue dedicated to women in proteomics and metabolomics. Mindful to represent current and future women leaders in these fields of science, we have invited submissions from women scientists as first or corresponding authors at different career stages. The need for this Special Issue and the recognition that it brings to women in science was highlighted by the extraordinary response from the scientific community and the large number of manuscripts submitted. We are delighted to present to our readers 47 manuscripts published by scientists from different parts of the world, including (in alphabetical author) from research groups in Argentina, Australia, Austria, Brazil, China, Czech Republic, Germany, India, Korea, Poland, Portugal, Spain, United Kingdom, and United States.In line with the remarkable versatility of proteomics and metabolomics, the manuscripts included in this Special Issue present both method developments and applications to a broad range of biological and clinical investigations. Among the method development papers is the study led by Tian Zhang from the Paulo group, which showed that a peptide fractionation workflow that sequentially combines strong anion-exchange and basic pH reversed-phase fractionation improves the achieved depth of proteome characterization. (8) Hanna Budayeva and colleagues report the increased throughput of sample analyses for activity-based proteome profiling by introducing a real-time database search method and designing PairQuant, a method that pairs protein isotope labeling with peptide TMT labeling. (9) A collaborative effort from the group of Ying Ge and colleagues showed the value of coupling the use of a photocleavable surfactant with trapped ion mobility MS with diaPASEF analyses for characterizing the human pulmonary extracellular matrix proteome. (10) Aiming to enhance the ability to separate and characterize specific cell populations, research from the group of Sonja Hess demonstrated the improved performance of microfluidic chip-based, when compared to droplet-based, sorting for minimizing the effect on metabolism and the phosphoproteomic profile. (11) Sample preparation workflows have been also advanced for proteomic analyses in different species, as shown by Elizabeth Mojica and Dietmar Kultz for the analysis of histone posttranslational modifications in different tissues from fish. (12) A focus on histone PTM regulation also comes from Ming-Ming Zhang from the Xin-Qing Zhao group in a study examining the role of the histone H4 methyltransferase Set5p in acetic acid stress. (13) In a creative study from the group of Heather Desaire, a noninvasive method is described as a possible means for future biomarker studies by combining sample collection from fingerprints with lipidomic MS analyses. (14) Seeking to optimize workflows for metabolomics studies, a report from Andrea Bileck emphasizes the preferred use of plasma rather than serum samples for clinical metabolomics studies, (15) and a paper from Jennifer Kirwan compares extraction protocols for the analysis of polar and nonpolar compounds in mouse plasma. (16)As the continuous developments in sample preparation and mass spectrometry instrumentation have afforded the acquisition of proteomics and metabolomics data sets with improved depth and quality, effort has been also placed on the development of computational platforms and software required for the analysis of these increasingly complex data sets. This is well represented in this Special Issue, with papers introducing software for assessing the quality of cross-linking mass spectrometry data (RawVegetable 2.0 by Louise Ulrich Kurt and colleagues from the Costa Carvalho group), (17) an open-source R package for relative quantification of positional isomers (IsoForma from the Aivett Bilbao group), (18) and a computational platform for improving peptide identification from the rescoring of peptide-spectrum matches (MS2 Rescore 3.0 by Louie Buur and colleagues). (19) The Special issue also presents web-based tools for analyzing N-glycocapture data (Veneer from the Rebekah Gundry group) (20) and for analyzing proteomics, metabolomics, lipidomics, and transcriptomics data (PMart by Kelly Stratton from Lisa Bramer's group). (21) For MS-based metabolomics data, an open-source pipeline (Tidy-Direct-to-MS from the group of Maria Eugenia Monge) (22) is described, as well as an ensemble learning-based spatial segmentation strategy for analyzing MS imaging data and characterizing metabolic heterogeneity in different tissue subregions (eLIMS from Jingjing Xu and colleagues). (23)Papers published in this Special Issue also highlight the application of proteomics and metabolomics methods to a broad range biological and clinical investigations. The use of diaPASEF proteomics by Kamila Říhová from the group of Petr Beneš led to the identification of a possible role for caspase-9 in osteoplastic cell migration. (24) Protein interaction studies performed by Hui-Su Kim and Yong-In Kim from the group of Je-Yoel Cho uncovered the regulation of ARID3C subcellular localization via its interaction with NPM1, which controls the function of ARID3C in immune response by promoting gene expression for monocyte-to-macrophage differentiation. (25) Another application to characterizing mechanisms underlying innate immune responses comes from the group of Aleksandra Nita-Lazar through the use of RNA sequencing and proteome analyses for the identification of the RNA-bound proteome in immortalized mouse macrophages upon exposure to lipopolysaccharide stimulation. (26) Investigating immune signaling in response to type I and II interferons and virus infections, Krystal Lum from the Cristea group demonstrated the induction of distinct protein complexes and ISG profiles that coordinate antiviral defenses. (27) Looking at another critical aspect of host response to viral infection, Sara Martinez from Coral Barbas group defined the metabolomic and lipidomic profiles of plasma samples from patients experiencing Long COVID symptoms, providing support for the notion of altered mitochondrial function in these patients. (28) Studies presented in this Special Issue have also delved into understanding pathogen infections and antimicrobial activities in different hosts and systems. Quantitative proteomics of serum samples led by Alejandra Isabel Navarro Leon from the Rosa Casais group pointed to the regulation of certain proteins in pathological forms of bovine paratuberculosis. (29) A study from the group of Leslie Hicks characterized the still understudied antimicrobial peptides expressed in plants, pointing to a new subfamily of α-hairpinins. (30) Rachel Lombardi from the group of Caroln Slupsky focused on the fatal citrus disease, huanglongbing, derived from inoculation with Candidatus Liberibacter asiaticus, performing transcriptomic and proteomics analyses to characterize vector-transmitted plat pathogen interactions. (31) From the group of Subhra Chakraborty, the integration of proteomics and metabolomics pointed to the contribution of wall-degrading enzymes and calcium signaling to stem rot response of jute to Macrophomina phaseolina infection. (32) The combined use of proteomics and metabolomics in plant research also comes from the group of Sophie Alvarez via a study of phosphorus utilization in popcorn. (33)With a goal to understand the development of human diseases, several contributions to this Special Issue have performed proteomics and metabolomics investigations in the context of cancer, cardiac disease, and neurobiology studies. The group of Lan Huang employed a DSBSO-based in vivo cross-linking MS analysis of endogenous protein–protein interactions from breast cancer patient-derived xenograft models, uncovering interactions enriched in certain cancer subtypes. (34) Using a mouse syngeneic model to also study breast cancer, Rita Araújo from the group of Ana Gil used nuclear magnetic resonance metabolomics to define lipid signatures associated with tumor growth and the acquisition of resistance to endocrine therapy. (35) Lipidomic characterization was also employed by the group of Amanda Hummon to define the effects of different fatty acid synthase (FAS) inhibitors on colorectal cancer spheroids. (36) The relevance of developing adequate 3D cell culture systems, such as spheroids, for cancer studies was further emphasized by another report from the same group, in which proteomic analyses demonstrated that cocultures spheroids have similar protein abundance landscapes to patient samples. (37) A different perspective of the ability to capture the molecular composition of clinical samples was investigated by the group of Andréa Rodrigues Chaves by performing mRNA, lipid extraction, and MS imaging in gingiva tissue from healthy individuals or patients with oral squamous cell carcinoma. (38) With a focus on cardiac research, a study from the group of Maggie Lam provides evidence for the presence of protein variants derived from alternative splicing in different human heart chambers. (39) A study led by Ariadna Martin-Blazquez from the group of Gloria Alvarez-Llamas established that patients with a bicuspid aortic valve exhibit an enhanced DNA damage response and cell cycle arrest in aortic vascular smooth muscle cells, suggesting possible markers for determining the effectiveness of a therapy. (40) Markers for cardiac disease were also investigated in the context of pulmonary arterial hypertension in a study led by Renata Wawrzyniak and Alicja Da Browska-Kugacka by profiling patient plasma and urine metabolomes. (41) Looking more broadly at several chronic metabolic diseases, including hypertension, hypercholesterolemia, and obesity, Yuqing Zhang from the Guowang Xu group defined the serum metabolomic and lipidomic profiles. (42) With a goal to improve the ability to quantify proteins in clinical samples, a study led by Geraldine Williams from the group of Colleen Maxwell shows the effectiveness of using nonhuman sera as an economical alternative to stable isotope-labeled internal standards, providing proof of concept analysis in the context of cardiovascular disease. (43)A series of papers included in this Special Issue present studies in the field of neurobiology. Led by Melanie Odenkirk from the group of Erin Baker comes a comprehensive study of the impact of apolipoprotein E disparities in patients with Alzheimer's disease on the proteome and lipidome of distinct brain regions from post-mortem patients, suggesting mitochondrial dysfunction and cell proteostasis as tightly linked to pathology. (44) The group of Stephanie Cologna contributed a study of the NPC intracellular cholesterol transporter 1 (NPC1) endogenous protein–protein interactions in the mouse cortex and human iPSCs neuronal models of disease. (45) A characterization of human iPSCs and iPSC-derived neurons was also performed by Gwang Bin Lee in the group of Ling Hao via a multiomic integration of proteomics, lipidomics, and metabolomics analyses. (46) Lipidomic profiles were characterized by the group of Meredith Hartley in the brain, spinal cord, and serum of a mouse model of demyelination, leading to the discovery of elevated plasmalogen levels early in demyelination. (47) To further facilitate neurobiological studies, from the group of Lingjun Li comes a report led by Lauren Fields that presents a database searching strategy, EndoGenius, for improving neuropeptide identification. (48)Offering another valuable example of an integrative proteomic and metabolomic study, a paper led by Melissa Pergande from the group of Ying Ge presents a characterization of molecular signatures associated with age-related loss of skeletal muscle mass in rhesus monkeys, identifying metabolic signatures of sarcopenia. (49) A longitudinal study was also conducted by Monique Ryan from the group of Nicola Gray to understand nonsevere burn injury in adults, discovering metabolic signatures plasma samples reflective of chronic inflammatory states. (50)This Special Issue is further enriched by the inclusion of several review articles that touch on different areas of these fields of study. Vanya Bhushan and Aleksandra Nita-Lazar present an overview of advances in subcellular proteomics, (51) while Chase Skawinski and Priya Shah highlight important considerations when performing protein–protein interaction studies. (52) Liya Popova, Rachel Carr, and Valerie Carabetta provide an update view of the importance of post-translational modifications in bacteria, with an emphasis on lysine acetylation and its mechanisms of regulation. (53) Finally, a review manuscript from the Neelam Atri group presents the contribution of proteomics in understanding the diversity and dynamics of cyanobacteria, with a focus on characterizing post-translational modifications and dynamic proteome changes. (54)We are grateful to all the contributors for making this Special Issue possible and for their support and enthusiasm in highlighting research performed by women scientists. We wish for this Special Issue to empower women scientists to continue to make important discoveries and to provide the knowledge that their voices are heard and appreciated in our scientific communities. As our work on this Special Issue adds to many other past and current efforts to recognize the substantial contributions made by women scientists, we also hope that this issue will encourage other publication platforms and scientific organizations to devise means to promote gender parity and to celebrate women in science.Author InformationClick to copy section linkSection link copied!Corresponding AuthorIleana M. Cristea, Associate Editor, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA, https://orcid.org/0000-0002-6533-2458AuthorClaire E. Eyers, Associate Editor, Center for Proteome Research and Department of Biochemistry, University of Liverpool, Liverpool, UK, https://orcid.org/0000-0002-3223-5926NotesViews expressed in this editorial are those of the authors and not necessarily the views of the ACS.ReferencesClick to copy section linkSection link copied! This article references 54 other publications. 1Daly, M. M.; Mirsky, A. E. Chromatography of purines and pyrimidines on starch columns. J. Biol. Chem. 1949, 179 (2), 981, DOI: 10.1016/S0021-9258(19)51291-1 Google ScholarThere is no corresponding record for this reference.2Daly, M. M.; Mirsky, A. E.; Ris, H. The amino acid composition and some properties of histones. J. Gen Physiol 1951, 34 (4), 439– 450, DOI: 10.1085/jgp.34.4.439 Google Scholar2Amino acid composition and some properties of histonesDaly, Marie M.; Mirsky, A. E.; Ris, HansJournal of General Physiology (1951), 34 (), 439-50CODEN: JGPLAD; ISSN:0022-1295. 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