{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T14:07:53Z","timestamp":1789567673215,"version":"build-2803163510"},"reference-count":46,"publisher":"American Chemical Society (ACS)","issue":"36","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cultured meat is recognized as a sustainable alternative to animal products, but the gradual stemness loss in seed cells during in vitro culture remains a challenge for industrialization. Here, we isolated chicken embryonic skeletal muscle satellite cells and observed a pronounced decline in stemness following the third passage. Whole-transcriptome and proteome analyses, combined with weighted gene coexpression network analysis (WGCNA) and short time-series expression miner (STEM) trend analysis, identified passage-dependent molecular changes associated with proliferative and differentiation capacities. Five transcriptional and eight protein modules were significantly correlated with stemness, and 31 hub genes were enriched mainly in ECM-receptor interaction and PI3K-Akt pathways. Notably, THBS1 and LAMA5 consistently showed high connectivity and were detected at both RNA and protein levels, thereby being prioritized as core candidate regulators. Our findings offer insights into stemness-associated regulators that could contribute to enhancing stemness maintenance and optimizing long-term cultured meat production.<\/jats:p>","DOI":"10.1021\/acs.jafc.6c09004","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T19:57:46Z","timestamp":1788465466000},"page":"28879-28892","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Transcriptomic-Proteomic\nProfiling Identifies\nCandidate Regulators of Stemness Maintenance in Skeletal Muscle Satellite\nCells"],"prefix":"10.1021","volume":"74","author":[{"given":"Haojie","family":"Ni","sequence":"first","affiliation":[{"name":"Beijing Technology and Business University , , ,","place":["Beijing, P. R. China, 100048"]},{"name":"Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University) , , ,","place":["Beijing, P. R. China, 100048"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youming","family":"Tan","sequence":"additional","affiliation":[{"name":"Beijing Technology and Business University , , ,","place":["Beijing, P. R. China, 100048"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiyu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Sichuan Agricultural University , , , ,","place":["Chengdu, Sichuan, P. R. China, 611130"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1936-1223","authenticated-orcid":true,"given":"Sizhe","family":"Qiu","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, P. R. China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zihao","family":"Liu","sequence":"additional","affiliation":[{"name":"Beijing Technology and Business University , , ,","place":["Beijing, P. R. China, 100048"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Zhu","sequence":"additional","affiliation":[{"name":"Beijing Technology and Business University , , ,","place":["Beijing, P. R. China, 100048"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9598-1432","authenticated-orcid":true,"given":"Yanbo","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Technology and Business University , , ,","place":["Beijing, P. R. China, 100048"]},{"name":"Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University) , , ,","place":["Beijing, P. R. China, 100048"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6617-4466","authenticated-orcid":true,"given":"Hong","family":"Zeng","sequence":"additional","affiliation":[{"name":"Beijing Technology and Business University , , ,","place":["Beijing, P. R. China, 100048"]},{"name":"Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University) , , ,","place":["Beijing, P. R. China, 100048"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"issue":"1","key":"2026091609092555300_cit1","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/s43016-022-00658-w","article-title":"Spontaneous immortalization\nof chicken fibroblasts\ngenerates stable, high-yield cell lines for serum-free production\nof cultured meat","volume":"4","author":"Pasitka","year":"2023","journal-title":"Nat. Food"},{"issue":"18","key":"2026091609092555300_cit2","doi-asserted-by":"publisher","first-page":"14172","DOI":"10.1021\/acs.jafc.6c00869","article-title":"Serum-Free\nMedia in Cellular Agriculture: Current Challenges,\nDesign Strategies, and Future Prospects","volume":"74","author":"He","year":"2026","journal-title":"J.\nAgric. Food Chem."},{"key":"2026091609092555300_cit3","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1146\/annurev-animal-021022-055132","article-title":"Advances and Challenges in Cell Biology\nfor Cultured Meat","volume":"12","author":"Martins","year":"2024","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"2026091609092555300_cit4","unstructured":"Fao, O.\n          ,  OECD-FAO agricultural\noutlook 2025\u20132034. OECD; FAO: Paris, France ; Rome, Italy, 2025. (DOI: 10.1787\/601276cd-en) (Accessed January 6, 2026)."},{"issue":"6392","key":"2026091609092555300_cit5","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1126\/science.aaq0216","article-title":"Reducing food\u2019s environmental impacts through\nproducers and consumers","volume":"360","author":"Poore","year":"2018","journal-title":"Science"},{"issue":"3","key":"2026091609092555300_cit6","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1007\/s10021-011-9517-8","article-title":"A Global Assessment\nof the Water Footprint of Farm\nAnimal Products","volume":"15","author":"Mekonnen","year":"2012","journal-title":"Ecosystems"},{"issue":"1","key":"2026091609092555300_cit7","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s41538-025-00605-6","article-title":"Chick embryo extract-driven culture\nsystem enhances chicken muscle satellite cell differentiation and\n3D myotube formation","volume":"9","author":"Kang","year":"2025","journal-title":"npj Science of Food"},{"issue":"10","key":"2026091609092555300_cit8","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1038\/s43016-023-00857-z","article-title":"Stem cell-based\nstrategies and challenges\nfor production of cultivated meat","volume":"4","author":"Jara","year":"2023","journal-title":"Nat. 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Physiol., Part D:Genomics\nProteomics"},{"issue":"1","key":"2026091609092555300_cit16","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/s41538-026-00706-w","article-title":"Optimizing\nmuscle satellite cell\nsources for cultured meat: anatomical origin influences cellular properties\nand quality attributes","volume":"10","author":"Lee","year":"2026","journal-title":"npj Science of Food"},{"issue":"12","key":"2026091609092555300_cit17","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.3390\/cells13121031","article-title":"Integrated\nATAC-seq and RNA-seq Analysis of In Vitro Cultured Skeletal Muscle\nSatellite Cells to Understand Changes in Cell Proliferation","volume":"13","author":"Ren","year":"2024","journal-title":"Cells"},{"issue":"1","key":"2026091609092555300_cit18","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1038\/s41467-022-28612-1","article-title":"CPEB1 directs\nmuscle stem cell activation by reprogramming\nthe translational landscape","volume":"13","author":"Zeng","year":"2022","journal-title":"Nat. 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Biotechnol."},{"issue":"17","key":"2026091609092555300_cit26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt646","article-title":"Utilizing sequence intrinsic composition\nto classify protein-coding and long non-coding transcripts","volume":"41","author":"Sun","year":"2013","journal-title":"Nucleic Acids Res."},{"issue":"suppl_2","key":"2026091609092555300_cit27","doi-asserted-by":"publisher","first-page":"W345","DOI":"10.1093\/nar\/gkm391","article-title":"CPC: assess the protein-coding potential of transcripts\nusing sequence features and support vector machine","volume":"35","author":"Kong","year":"2007","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"2026091609092555300_cit28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1306","article-title":"FEELnc: a tool for long non-coding\nRNA annotation and its application to the dog transcriptome","volume":"45","author":"Wucher","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2026091609092555300_cit29","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq\ndata with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC\nBioinf."},{"issue":"1","key":"2026091609092555300_cit30","doi-asserted-by":"publisher","first-page":"12.10.1","DOI":"10.1002\/0471250953.bi1210s36","article-title":"Identification\nof Novel and Known miRNAs in Deep-Sequencing Data with miRDeep2","volume":"36","author":"Mackowiak","year":"2011","journal-title":"Curr. Protoc. Bioinform."},{"issue":"D1","key":"2026091609092555300_cit31","doi-asserted-by":"publisher","first-page":"D447","DOI":"10.1093\/nar\/gku1003","article-title":"STRING v10:\nprotein-protein interaction networks, integrated\nover the tree of life","volume":"43","author":"Szklarczyk","year":"2015","journal-title":"Nucleic Acids Res."},{"issue":"21","key":"2026091609092555300_cit32","doi-asserted-by":"publisher","first-page":"6531","DOI":"10.1111\/febs.16552","article-title":"Ca(2+) as a coordinator of skeletal\nmuscle differentiation, fusion and contraction","volume":"289","author":"Sinha","year":"2022","journal-title":"FEBS J."},{"key":"2026091609092555300_cit33","doi-asserted-by":"publisher","first-page":"668600","DOI":"10.3389\/fphys.2021.668600","article-title":"The Role of\nEmbryonic Chick Muscle\nCell Culture in the Study of Skeletal Myogenesis","volume":"12","author":"Costa","year":"2021","journal-title":"Front. Physiol."},{"key":"2026091609092555300_cit34","doi-asserted-by":"publisher","first-page":"17003","DOI":"10.1038\/cddiscovery.2017.3","article-title":"Characterization and isolation of\nhighly purified porcine satellite\ncells","volume":"3","author":"Ding","year":"2017","journal-title":"Cell Death Discov"},{"issue":"2","key":"2026091609092555300_cit35","doi-asserted-by":"publisher","first-page":"vvaf220","DOI":"10.1093\/ijfood\/vvaf220","article-title":"Cultured\nmeat: advances in stem cell biology, tissue engineering, and bioprocess\noptimization for scalable and sustainable production\u2500a review","volume":"60","author":"Kim","year":"2025","journal-title":"Int. J. Food Sci. Technol."},{"issue":"3\u20134","key":"2026091609092555300_cit36","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1007\/s12079-009-0074-2","article-title":"The interaction of Thrombospondins with extracellular\nmatrix proteins","volume":"3","author":"Tan","year":"2009","journal-title":"J. Cell Commun. 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Sci."},{"issue":"7\u20139","key":"2026091609092555300_cit40","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1387\/ijdb.150211jp","article-title":"Calcium signals regulated\nby NAADP\nand two-pore channels--their role in development, differentiation\nand cancer","volume":"59","author":"Parrington","year":"2015","journal-title":"Int. J. Dev. Biol."},{"issue":"10","key":"2026091609092555300_cit41","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/s41580-021-00386-2","article-title":"Translational control\nof stem cell function","volume":"22","author":"Saba","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"7742","key":"2026091609092555300_cit42","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41586-019-0888-x","article-title":"Onset of differentiation\nis post-transcriptionally controlled in adult neural stem cells","volume":"566","author":"Baser","year":"2019","journal-title":"Nature"},{"issue":"1","key":"2026091609092555300_cit43","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1038\/s41467-020-15449-9","article-title":"The translational landscape of ground\nstate pluripotency","volume":"11","author":"Atlasi","year":"2020","journal-title":"Nat. Commun."},{"issue":"2","key":"2026091609092555300_cit44","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1016\/j.stem.2020.01.005","article-title":"Post-Transcriptional\nRegulation of Homeostatic, Stressed, and Malignant Stem Cells","volume":"26","author":"Chua","year":"2020","journal-title":"Cell Stem Cell"},{"issue":"1","key":"2026091609092555300_cit45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3109\/03008207.2014.947369","article-title":"Extracellular matrix\nregulation in\nthe muscle satellite cell niche","volume":"56","author":"Thomas","year":"2015","journal-title":"Connect. Tissue\nRes."},{"issue":"5","key":"2026091609092555300_cit46","doi-asserted-by":"publisher","first-page":"114149","DOI":"10.1016\/j.celrep.2024.114149","article-title":"Thbs1 regulates\nskeletal muscle mass\nin a TGF\u03b2-Smad2\/3-ATF4-dependent manner","volume":"43","author":"Vanhoutte","year":"2024","journal-title":"Cell Rep."}],"container-title":["Journal of Agricultural\nand Food Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jafc.6c09004","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/36\/28879\/68275587\/acs.jafc.6c09004.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/36\/28879\/68275587\/acs.jafc.6c09004.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T13:32:12Z","timestamp":1789565532000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jafcau\/article\/74\/36\/28879\/5412232\/Integrated-Transcriptomic-Proteomic-Profiling"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,3]]},"references-count":46,"journal-issue":{"issue":"36","published-online":{"date-parts":[[2026,9,3]]},"published-print":{"date-parts":[[2026,9,16]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jafc.6c09004","relation":{},"ISSN":["0021-8561","1520-5118"],"issn-type":[{"value":"0021-8561","type":"print"},{"value":"1520-5118","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,3]]}}}