Molecular & Cellular Proteomics最新文献

{"title":"Integrated Analysis of Proteome and Transcriptome Profiling Reveals Pan-Cancer-Associated Pathways and Molecular Biomarkers.","authors":"Guo-Sheng Hu, Zao-Zao Zheng, Yao-Hui He, Du-Chuang Wang, Rui-Chao Nie, Wen Liu","doi":"10.1016/j.mcpro.2025.100919","DOIUrl":"10.1016/j.mcpro.2025.100919","url":null,"abstract":"<p><p>Understanding dysregulated genes and pathways in cancer is critical for precision oncology. Integrating mass spectrometry-based proteomic data with transcriptomic data presents unique opportunities for systematic analyses of dysregulated genes and pathways in pan-cancer. Here, we compiled a comprehensive set of datasets, encompassing proteomic data from 2404 samples and transcriptomic data from 7752 samples across 13 cancer types. Comparisons between normal or adjacent normal tissues and tumor tissues identified several dysregulated pathways including mRNA splicing, interferon pathway, fatty acid metabolism, and complement coagulation cascade in pan-cancer. Additionally, pan-cancer upregulated and downregulated genes (PCUGs and PCDGs) were also identified. Notably, RRM2 and ADH1B, two genes which belong to PCUGs and PCDGs, respectively, were identified as robust pan-cancer diagnostic biomarkers. TNM stage-based comparisons revealed dysregulated genes and biological pathways involved in cancer progression, among which the dysregulation of complement coagulation cascade and epithelial-mesenchymal transition are frequent in multiple types of cancers. A group of pan-cancer continuously upregulated and downregulated proteins in different tumor stages (PCCUPs and PCCDPs) were identified. We further constructed prognostic risk stratification models for corresponding cancer types based on dysregulated genes, which effectively predict the prognosis for patients with these cancers. Drug prediction based on PCUGs and PCDGs as well as PCCUPs and PCCDPs revealed that small molecule inhibitors targeting CDK, HDAC, MEK, JAK, PI3K, and others might be effective treatments for pan-cancer, thereby supporting drug repurposing. We also developed web tools for cancer diagnosis, pathologic stage assessment, and risk evaluation. Overall, this study highlights the power of combining proteomic and transcriptomic data to identify valuable diagnostic and prognostic markers as well as drug targets and treatments for cancer.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100919"},"PeriodicalIF":6.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Analysis of Human Follicular Fluid-Derived Exosomes Reveals That Insufficient Folliculogenesis in Aging Women is Associated With Infertility.","authors":"Zhen Liu, Qilin Zhou, Jun Zan, Jingyan Tian, Yangzhuohan Zhang, Fanggui Wu, Huan Zhao, Qianwen Peng, Shangjie Liu, Qianjun Chen, Endong Liu, Zhengdong Liao, Pengfei Zou, Lin Mei, Wen Wang, Sen Dong, Luo Niu, Shengda Wu, Liangge He, Xiaoyi Zhou, Yanbo Jin, Panpan Li, Sheng Yang","doi":"10.1016/j.mcpro.2025.100930","DOIUrl":"10.1016/j.mcpro.2025.100930","url":null,"abstract":"<p><p>Although the risk of female infertility increases with advancing age, the underlying mechanisms remain unknown. Exosomes in follicular fluid are suggested to regulate folliculogenesis and influence oocyte quality, potentially playing a critical role in age-related infertility. Elucidating their content could enhance the understanding of the molecular mechanisms associated with female aging-induced infertility. In this study, we explored the proteomic profiles of exosomes derived from human follicular fluid to identify protein signatures associated with infertility in both young and aging women. Despite the lack of significant differences in the morphology and particle size of follicular fluid-derived exosomes between the two groups, proteomic analysis revealed a distinct pattern of differentially expressed proteins (DEPs). DEPs associated with B-cell activation, pathogen invasion, and disrupted metabolic processes were significantly more highly expressed in the aging group than in the young group, indicating their involvement in age-related infertility. In vivo experiments demonstrated that the application of exosomes, particularly those derived from young female group, facilitated the successful maturation of follicles. Key exosomal proteins, including ENO1, HSP90B1, fetuin-B, C7, and APOC4, were found to be associated with follicular maturation. Furthermore, the PI3K/AKT signaling pathway, which is known to be related to folliculogenesis, was activated by the application of exosomes in aging female mice. This study provides novel insights into the aging-associated protein signatures of follicular fluid-derived exosomes and their potential role in infertility. These findings suggest that aging-related protein signatures in exosomes could contribute to the treatment of age-related infertility.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100930"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Embryo-Induced Changes in the Protein Profile of Bovine Oviductal Extracellular Vesicles.","authors":"Rosane Mazzarella, José María Sánchez, Beatriz Fernandez-Fuertes, Sandra Guisado Egido, Michael McDonald, Alberto Álvarez-Barrientos, Esperanza González, Juan Manuel Falcón-Pérez, Mikel Azkargorta, Félix Elortza, Maria Encina González, Pat Lonergan, Dimitrios Rizos","doi":"10.1016/j.mcpro.2025.100935","DOIUrl":"10.1016/j.mcpro.2025.100935","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The study of early maternal-embryonic cross-talk remains one of the most challenging topics in reproductive biology. Understanding the physiological mechanisms involved in the interactions between the maternal reproductive tract and the developing embryo is essential for enhancing bovine reproductive efficiency. This complex communication starts within the oviduct, where the modulation of biological processes important for ensuring embryo quality is partially facilitated through extracellular vesicles (EVs). Utilizing a combination of in vivo and in vitro models this study had three main objectives: 1) to examine the protein cargo of EVs isolated from the oviductal fluid (OF) of cyclic and pregnant heifers to understand their role in maternal-embryonic communication in vivo; 2) to characterize the protein profile of EVs in conditioned medium (CM) resulting from the culture of oviductal explants alone (Exp) or in the presence of 8- to 16-cell stage embryos (Exp + Emb); and 3) to compare the protein cargo of EVs from Exp with EVs from cyclic heifers and EVs from Exp + Emb with EVs from pregnant heifers. Proteins were considered \"identified\" if detected in at least three out of five replicates and considered \"exclusive\" if detected in at least three out of five replicates within one group but absent in all samples of other groups. We identified 659 and 1476 proteins in the OF-EVs of cyclic and pregnant heifers, respectively. Among these, 644 proteins were identified in OF-EVs from both cyclic and pregnant heifers, and 40 proteins were exclusive to OF-EVs from the pregnant group. Within the 644 proteins identified in both groups, 31 were identified as differently abundant proteins (DAPs). In pregnant heifers, DAPs were mainly related to genome activation, DNA repair, embryonic cell differentiation, migration, and immune tolerance. In vitro, we identified 841 proteins in the CM-EVs from Exp alone, 613 from Exp + Emb, and 111 in the CM-EVs from Emb alone. In the qualitative analysis between the three in vitro groups, 81 proteins were identified in all groups, 452 were common to Exp and Exp + Emb, 17 were common to Exp and Emb, 5 were common to Exp + Emb and Emb, 4 were unique to Exp, 6 were unique to Exp + Emb, and none were unique to Emb. Proteins identified when there is an interaction between the oviduct and the embryo in vitro, corresponding to the Exp + Emb group, were associated with immune tolerance, structural activity, binding, and cytoskeletal regulation. In vivo and in vitro EVs exhibit distinct qualitative and quantitative protein contents, both when comparing EVs produced in the absence of an embryo (Cyclic and Exp) and those that have undergone embryo-oviduct interaction (Pregnant and Exp + Emb). The observed changes in the protein cargo of EVs due to maternal-embryonic communication in vivo and in vitro suggest that the interaction between the embryo and the maternal milieu initiates within the oviduct and is potentially facilitate","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100935"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What have Data Standards ever done for us?","authors":"S E Orchard","doi":"10.1016/j.mcpro.2025.100933","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100933","url":null,"abstract":"<p><p>The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies for both the field of molecular interaction and that of mass spectrometry for more than 20 years. This review explores some of the ways that the proteomics community has benefitted from the development of community standards and takes a look at some of the tools and resources that have been improved or developed as a result of the work of the HUPO-PSI.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100933"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19.","authors":"Sabarinath Peruvemba Subramanian, Melinda Wojtkiewicz, Fang Yu, Chase Castro, Erin N Schuette, Jocelyn Rodriguez-Paar, Jared Churko, Pranav Renavikar, Daniel Anderson, Claudius Mahr, Rebekah L Gundry","doi":"10.1016/j.mcpro.2025.100929","DOIUrl":"10.1016/j.mcpro.2025.100929","url":null,"abstract":"<p><p>Coronavirus infectious disease of 2019 (COVID-19) can lead to cardiac complications, yet the molecular mechanisms driving these effects remain unclear. Protein glycosylation is crucial for viral replication, immune response, and organ function and has been found to change in the lungs and liver of patients with COVID-19. However, how COVID-19 impacts cardiac protein glycosylation has not been defined. Our study combined single nuclei transcriptomics, mass spectrometry (MS)-based glycomics, and lectin-based tissue imaging to investigate alterations in N-glycosylation in the human heart post-COVID-19. We identified significant expression differences in glycogenes involved in N-glycan biosynthesis and MS analysis revealed a reduction in high mannose and isomers of paucimannose structures post-infection, with changes in paucimannose directly correlating with COVID-19 independent of comorbidities. Our observations suggest that COVID-19 primes cardiac tissues to alter the glycome at all levels, namely, metabolism, nucleotide sugar transport, and glycosyltransferase activity. Given the role of N-glycosylation in cardiac function, this study provides a basis for understanding the molecular events leading to cardiac damage post-COVID-19 and informing future therapeutic strategies to treat cardiac complications resulting from coronavirus infections.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100929"},"PeriodicalIF":6.1,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How to deal with internal fragment ions?","authors":"Arthur Grimaud, Masa Babovic, Frederik Haugaard Holck, Ole N Jensen, Veit Schwämmle","doi":"10.1016/j.mcpro.2024.100896","DOIUrl":"https://doi.org/10.1016/j.mcpro.2024.100896","url":null,"abstract":"<p><p>Tandem mass spectrometry of peptides and proteins generates mass spectra of their gas-phase fragmentation product ions, including N-terminal, C-terminal, and internal fragment ions. Whereas N- and C-terminal ions are routinely assigned and identified using computational methods, internal fragment ions are often difficult to annotate correctly. They become particularly relevant for long peptides and full proteoforms where the peptide backbone is more likely to be fragmented multiple times. Internal fragment ions potentially offer tremendous information regarding amino acid sequences and positions of post-translational modifications of peptides and intact proteins. However, their practical application is challenged by the vast number of theoretical internal fragments that exist for long amino acid sequences, leading to a high risk of false-positive annotations. We analyze the mass spectral contributions of internal fragment ions in spectra from middle-down and top-down experiments and introduce a novel graph-based annotation approach designed to manage the complexity of internal fragments. Our graph-based representation allows us to compare multiple candidate proteoforms in a single graph, and to assess different candidate annotations in a fragment ion spectrum. We demonstrate cases from middle-down and top-down data where internal ions enhance amino acid sequence coverage of polypeptides and proteins and accurate localization of post-translational modifications. We conclude that our graph-based method provides a general approach to process complex tandem mass spectra, enhance annotation of internal fragment ions, and improve proteoform sequencing and characterization by mass spectrometry.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100896"},"PeriodicalIF":6.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Region and cell-type resolved multi-omic altas of the heart.","authors":"Fan Zhang, Yunzhi Wang, Jiajun Zhu, Jinxi Wang, Qiang Li, Jinwen Feng, Mingwei Liu, Kai Li, Jiliang Tan, Rongkui Luo, Huangtian Yang, Yingyong Hou, Fuchu He, Jun Qin, Chen Ding, Wenjun Yang","doi":"10.1016/j.mcpro.2025.100922","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100922","url":null,"abstract":"<p><p>The heart is a vital muscular organ in vertebrate animals, responsible for maintaining blood circulation through rhythmic contraction. Although previous studies have investigated the heart proteome, the full hierarchical molecular network at cell-type and region resolved level, illustrating the specialized roles and crosstalk among different cell types and regions, remains unclear. Here, we presented an atlas of cell-type resolved proteome for mouse heart and region resolved proteome for both mouse and human hearts. In-depth proteomic analysis identified 11,794 proteins across four cell types and 11,995 proteins across six regions of the mouse heart. To further illustrate protein expression patterns in both physiological and pathological conditions, we conducted proteomic analysis on human heart samples from four regions with dilated cardiomyopathy (DCM). We quantified 8,201 proteins in DCM tissue and 8,316 proteins in adjacent unaffected myocardium (AUM) tissue across the four human heart regions. Notably, we found that the retinoic acid synthesis pathway was significantly enriched in the DCM-affected left ventricle, and functional experiments demonstrated that all-trans retinoic acid (atRA) efficiently rescued Ang II-induced myocardial hypertrophy and transverse aorta constriction (TAC)- induced heart failure. In conclusion, our datasets uncovered the functional features of different cell types and their synergistic cooperation centered by cell-type specific transcription factors (ctsTF) in different regions, while these TF-TG (target gene) axes were significantly altered in DCM. Additionally, atRA was demonstrated to be an efficient treatment for heart failure. This work presented a panoramic heart proteome map, offering a valuable resource for future cardiovascular research.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100922"},"PeriodicalIF":6.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteogenomic Profiling Reveals Small ORFs and Functional Microproteins in Activated T Cells.","authors":"Yang Yang, Chuangmiao Chen, Kecheng Li, Yuanliang Zhang, Lei Chen, Jue Shi, Quanhua Mu, Yang Xu, Qian Zhao","doi":"10.1016/j.mcpro.2025.100914","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100914","url":null,"abstract":"<p><p>Noncanonical micropeptides or called novel microproteins, i.e., polypeptides mostly under 10 kDa, are encoded by genomic sequences that have been previously annotated as noncoding but now known as small open reading frames (sORFs). The recent identification of microproteins encoded by sORFs has provided evidence that many sORFs encode functional microproteins that play crucial roles in various biological processes. T cell activation is a critical biological process for adaptive immune response. Understanding key players in this process will allow us to decipher the complex mechanisms as well as develop immunotherapy for treating a wide range of diseases. Although there have been extensive studies on canonical proteins in T cell activation, the novel microproteins in T cells and their roles have been uncharted water to date. Nascent proteins are defined as newly synthesized polypeptides emerged during the translation of mRNA. In this study, we combined nascent proteomics and quantitative proteomics to identify 411 novel microproteins in primary human T cells, including 83 nascent microproteins. We activated the T cell function with either PMA/Ionomycin (distal activation) or CD3/CD28 activating antibodies (proximal activation), and obtained a comprehensive canonical protein and microprotein profiles to pinpoint common and distinct differentially expressed proteins under these two activation conditions. After experimental testing, three microproteins numbered T1, T2 and T3 were found to be functional in regulating T cell activation. Bioinformatic and proteomic analyses suggested that T1 was functional related to immune as negative feedback to T cell activation. Our study not only established an integrated approach to uncover and elucidate novel microproteins but also highlight the significant role of microproteins in regulating T cell activation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100914"},"PeriodicalIF":6.1,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143365507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics.","authors":"Jarne Pauwels, Tessa Van de Steene, Jana Van de Velde, Freya De Muyer, Danaë De Pauw, Femke Baeke, Sven Eyckerman, Kris Gevaert","doi":"10.1016/j.mcpro.2025.100907","DOIUrl":"10.1016/j.mcpro.2025.100907","url":null,"abstract":"<p><p>Extracellular vesicles (EVs), membrane-delimited nanovesicles that are secreted by cells into the extracellular environment, are gaining substantial interest due to their involvement in cellular homeostasis and their contribution to disease pathology. The latter in particular has led to an exponential increase in interest in EVs as they are considered to be circulating packages containing potential biomarkers and are also a possible biological means to deliver drugs in a cell-specific manner. However, several challenges hamper straightforward proteome analysis of EVs as they are generally low abundant and reside in complex biological matrices. These matrices typically contain abundant proteins at concentrations that vastly exceed the concentrations of proteins found in the EV proteome. Therefore, extensive EV isolation and purification protocols are imperative and many have been developed, including (density) ultracentrifugation, size-exclusion, and precipitation methods. Here, we describe filter-aided extracellular vesicle enrichment (FAEVEr) as an approach based on 300 kDa molecular weight cutoff filtration that allows the processing of multiple samples in parallel within a reasonable time frame and at moderate cost. We demonstrate that FAEVEr is capable of quantitatively retaining EV particles on filters, while allowing extensive washing with the mild detergent Tween-20 to remove interfering non-EV proteins. The retained particles are directly lysed on the filter for a complete recovery of the EV protein cargo toward proteome analysis. Here, we validate and optimize FAEVEr on recombinant EV material and apply it on conditioned medium as well as on complex bovine serum, human plasma, and urine. Our results indicate that EVs isolated from MCF7 cells cultured with or without serum have a drastic different proteome because of nutrient deprivation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100907"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides.","authors":"Meng-Hsuan Hsiao, Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Daphne Chun-Che Chien, Wayne Denis Monteiro, Lee-Shin Chu, William Morgenlander, Sahana Jayaraman, Sung-Eun Jang, Jeffrey J Gray, Heng Zhu, Xinzhong Dong, Martin Steinegger, H Benjamin Larman","doi":"10.1016/j.mcpro.2024.100901","DOIUrl":"10.1016/j.mcpro.2024.100901","url":null,"abstract":"<p><p>Animal venoms, distinguished by their unique structural features and potent bioactivities, represent a vast and relatively untapped reservoir of therapeutic molecules. However, limitations associated with comprehensively constructing and expressing highly complex venom and venom-like molecule libraries have precluded their therapeutic evaluation via high-throughput screening. Here, we developed an innovative computational approach to design a highly diverse library of animal venoms and \"metavenoms\". We used programmable M13 hyperphage display to preserve critical disulfide-bonded structures for highly parallelized single-round biopanning with quantitation via high-throughput DNA sequencing. Our approach led to the discovery of Kunitz-type domain containing proteins that target the human itch receptor Mas-related G-protein coupled receptor member X4, which plays a crucial role in itch perception. Deep learning-based structural homology mining identified two endogenous human homologs, tissue factor pathway inhibitor (TFPI), and serine peptidase inhibitor, Kunitz type 2 (SPINT2), which exhibit agonist-dependent potentiation of Mas-related G-protein coupled receptor member X4. Highly multiplexed screening of animal venoms and metavenoms is therefore a promising approach to uncover new drug candidates.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100901"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11833617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}