{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T05:20:45Z","timestamp":1787808045410,"version":"build-2784847793"},"reference-count":32,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":25,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82274269"],"award-info":[{"award-number":["82274269"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Cell Biochemistry &amp;amp; Function"],"published-print":{"date-parts":[[2026,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Breast cancer (BC) is a highly heterogeneous malignancy with complex molecular mechanisms, highlighting the need for effective biomarkers and therapeutic targets. The Fritillariae Thunbergii Bulbus\u2013Bolbostemmatis Rhizoma (ZBM\u2013TBM) herb pair has been used in the treatment of BC, although its potential molecular mechanisms remain incompletely understood. In this study, an integrated strategy combining transcriptomic analysis, machine learning, liquid chromatography\u2013tandem mass spectrometry (LC\u2013MS\/MS), network pharmacology, molecular docking, molecular dynamics (MD) simulations, and single\u2010cell virtual knockout analysis was employed to identify BC\u2010associated molecular biomarkers and explore the potential mechanisms underlying the effects of ZBM\u2013TBM. Integration of weighted gene co\u2010expression network analysis with least absolute shrinkage and selection operator regression, random forest, and support vector machine\u2013recursive feature elimination identified EPCAM as the only common core gene. EPCAM was significantly upregulated in BC tissues and showed favorable diagnostic performance (AUC = 0.903), while high EPCAM expression was associated with shorter overall survival (log\u2010rank P = 0.032). Functional analyses indicated that EPCAM was associated with tumor\u2010related and immune\u2010related biological processes, including cell cycle regulation, DNA replication, and immune regulation. LC\u2013MS\/MS analysis identified 32 major active constituents of ZBM\u2013TBM, and subsequent network pharmacology analysis identified 33 overlapping targets and 10 hub genes enriched in multiple tumor\u2010 and immune\u2010related signaling pathways, including the Notch, IL\u201017, HIF\u20101, and TGF\u2010\u03b2 signaling pathways. Although ZBM\u2013TBM did not directly target EPCAM in the predicted target network, computational analyses indicated functional associations between EPCAM and hub gene\u2010associated regulatory networks. Molecular docking and MD simulations further suggested that peiminine may represent a potential active constituent, exhibiting favorable predicted binding characteristics with multiple candidate targets, particularly AURKA. Single\u2010cell virtual knockout analysis showed that computational perturbation of AURKA was associated with alterations in cell cycle\u2010, extracellular matrix\u2010, and cell adhesion\u2010related processes, supporting its potential functional relevance at the cellular level.<\/jats:p>","DOI":"10.1002\/cbf.70285","type":"journal-article","created":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T04:17:21Z","timestamp":1787804241000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated RNA Sequencing and Multi\u2010Bioinformatics Analyses Reveal the Molecular Mechanisms Underlying the Anti\u2010Breast Cancer Effects of the Fritillariae Thunbergii Bulbus\u2013Bolbostemmatis Rhizoma Herb Pair"],"prefix":"10.1002","volume":"44","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-9413-2701","authenticated-orcid":false,"given":"Quan","family":"Tang","sequence":"first","affiliation":[{"name":"Department of Oncology Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1488-4161","authenticated-orcid":false,"given":"Dong","family":"Niu","sequence":"additional","affiliation":[{"name":"Department of Oncology Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"He","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Oncology Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-0142-0759","authenticated-orcid":false,"given":"Heng Zhou","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Oncology Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8795-9542","authenticated-orcid":false,"given":"Chun Hui","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Oncology Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo Qing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Office of Academic Research, Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao Dan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Oncology Nanjing University of Chinese Medicine Wuxi Affiliated Hospital: Wuxi Hospital of Traditional Chinese Medicine Wuxi P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"issue":"3","key":"e_1_2_13_2_1","first-page":"229","article-title":"Global Cancer Statistics 2022: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"74","author":"Bray F.","year":"2024","journal-title":"CA: A Cancer Journal for Clinicians"},{"issue":"1","key":"e_1_2_13_3_1","doi-asserted-by":"crossref","DOI":"10.1038\/s41392-024-02108-4","article-title":"Breast Cancer: Pathogenesis and Treatments","volume":"10","author":"Xiong X.","year":"2025","journal-title":"Signal Transduction and Targeted Therapy"},{"key":"e_1_2_13_4_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.drup.2025.101288","article-title":"Drug Resistance in Breast Cancer: Mechanisms and Strategies for Management","volume":"83","author":"Wu G. Y.","year":"2025","journal-title":"Drug Resistance Updates"},{"issue":"28","key":"e_1_2_13_5_1","doi-asserted-by":"crossref","first-page":"3347","DOI":"10.2174\/1381612824666180607124038","article-title":"Machine Learning\u2010Based Virtual Screening and Its Applications to Alzheimer's Drug Discovery: A Review","volume":"24","author":"Carpenter K. A.","year":"2018","journal-title":"Current Pharmaceutical Design"},{"issue":"1","key":"e_1_2_13_6_1","doi-asserted-by":"crossref","DOI":"10.1186\/s13020-023-00719-7","article-title":"Traditional Chinese Medicine for Colorectal Cancer Treatment: Potential Targets and Mechanisms of Action","volume":"18","author":"Chen J. F.","year":"2023","journal-title":"Chinese Medicine"},{"key":"e_1_2_13_7_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.jep.2020.113249","article-title":"The Signaling Pathways and Targets of Traditional Chinese Medicine and Natural Medicine in Triple\u2010Negative Breast Cancer","volume":"264","author":"Yang Z.","year":"2021","journal-title":"Journal of Ethnopharmacology"},{"issue":"03","key":"e_1_2_13_8_1","first-page":"559","article-title":"Experience of Couplet Medicinals \u201cBolbostemma Paniculatum\u2010Peimine\u201d on Breast Cancer","volume":"36","author":"Xi Z.","year":"2018","journal-title":"Chinese Archives of Traditional Chinese Medicine"},{"issue":"7","key":"e_1_2_13_9_1","doi-asserted-by":"crossref","DOI":"10.3390\/ijms20071667","article-title":"Fritillariae Thunbergii Bulbus: Traditional Uses, Phytochemistry, Pharmacodynamics, Pharmacokinetics and Toxicity","volume":"20","author":"Li H.","year":"2019","journal-title":"International Journal of Molecular Sciences"},{"issue":"17","key":"e_1_2_13_10_1","first-page":"4314","article-title":"Research Progress on Chemical Constituents, Pharmacological Activities and Clinical Application of Bolbostemma paniculatum","volume":"46","author":"Ha L.","year":"2021","journal-title":"China Journal of Chinese Materia Medica"},{"key":"e_1_2_13_11_1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.ejmech.2018.11.001","article-title":"The Potential Role of Tubeimosides in Cancer Prevention and Treatment","volume":"162","author":"Islam M. S.","year":"2019","journal-title":"European Journal of Medicinal Chemistry"},{"key":"e_1_2_13_12_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.fct.2021.112289","article-title":"Fritillaria thunbergii Miq. (Zhe Beimu): A Review on Its Traditional Uses, Phytochemical Profile and Pharmacological Properties","volume":"153","author":"Nile S. H.","year":"2021","journal-title":"Food and Chemical Toxicology"},{"issue":"05","key":"e_1_2_13_13_1","first-page":"1508","article-title":"Study on the Combined Function of Bolbostemma Paniculatum Saponins and Peimine In Vitro of Human Breast Cancer Cell","volume":"30","author":"Xi Z.","year":"2015","journal-title":"Chinese Archives of Traditional Chinese Medicine"},{"key":"e_1_2_13_14_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.jep.2022.115058","article-title":"Methodology Improvement for Network Pharmacology to Correct the Deviation of Deduced Medicinal Constituents and Mechanism: Xian\u2010Ling\u2010Gu\u2010Bao as an Example","volume":"289","author":"Li Z.","year":"2022","journal-title":"Journal of Ethnopharmacology"},{"key":"e_1_2_13_15_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.canlet.2022.215828","article-title":"Predictive Biomarkers for Personalized Medicine in Breast Cancer","volume":"545","author":"Rodrigues\u2010ferreira S.","year":"2022","journal-title":"Cancer Letters"},{"issue":"7","key":"e_1_2_13_16_1","first-page":"2509","article-title":"Real\u2010Time Imaging of Apoptosis Induction of Human Breast Cancer Cells by the Traditional Chinese Medicinal Herb Tubeimu","volume":"32","author":"Hu M.","year":"2012","journal-title":"Anticancer Research"},{"issue":"1","key":"e_1_2_13_17_1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.3892\/ijmm.2024.5447","article-title":"Advances in Predicting Breast Cancer Driver Mutations: Tools for Precision Oncology (Review)","volume":"55","author":"Hao W.","year":"2025","journal-title":"International Journal of Molecular Medicine"},{"issue":"8","key":"e_1_2_13_18_1","doi-asserted-by":"crossref","first-page":"12569","DOI":"10.1002\/jcp.28132","article-title":"Shedding Light on the EpCAM: An Overview","volume":"234","author":"YAHYAZADEH Mashhadi S. M.","year":"2019","journal-title":"Journal of Cellular Physiology"},{"issue":"4","key":"e_1_2_13_19_1","doi-asserted-by":"crossref","first-page":"3626","DOI":"10.1002\/jcp.29252","article-title":"Hypoxia Modulates Stem Cell Properties and Induces EMT through N\u2010Glycosylation of EpCAM in Breast Cancer Cells","volume":"235","author":"Zhang D.","year":"2020","journal-title":"Journal of Cellular Physiology"},{"issue":"22","key":"e_1_2_13_20_1","doi-asserted-by":"crossref","first-page":"5035","DOI":"10.1158\/0008-5472.CAN-20-1264","article-title":"EpCAM Signaling Promotes Tumor Progression and Protein Stability of PD\u2010L1 Through the EGFR Pathway","volume":"80","author":"Chen H. 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