{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T13:02:01Z","timestamp":1770814921176,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,2]],"date-time":"2024-11-02T00:00:00Z","timestamp":1730505600000},"content-version":"vor","delay-in-days":40,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Cisplatin is one of the most commonly used chemotherapy drugs for treating solid tumors. As a genotoxic agent, cisplatin binds to DNA and forms platinum-DNA adducts that cause DNA damage and activate a series of signaling pathways mediated by various DNA-binding proteins (DBPs), ultimately leading to cell death. Therefore, DBPs play crucial roles in the cellular response to cisplatin and in determining cell fate. However, systematic studies of DBPs responding to cisplatin damage and their temporal dynamics are still lacking. To address this, we developed a novel and user-friendly stand-alone software, DEWNA, designed for dynamic entropy weight network analysis to reveal the dynamic changes of DBPs and their functions. DEWNA utilizes the entropy weight method, multiscale embedded gene co-expression network analysis and generalized reporter score-based analysis to process time-course proteome expression data, helping scientists identify protein hubs and pathway entropy profiles during disease progression. We applied DEWNA to a dataset of DBPs from A549 cells responding to cisplatin-induced damage across 8 time points, with data generated by data-independent acquisition mass spectrometry (DIA-MS). The results demonstrate that DEWNA can effectively identify protein hubs and associated pathways that are significantly altered in response to cisplatin-induced DNA damage, and offer a comprehensive view of how different pathways interact and respond dynamically over time to cisplatin treatment. Notably, we observed the dynamic activation of distinct DNA repair pathways and cell death mechanisms during the drug treatment time course, providing new insights into the molecular mechanisms underlying the cellular response to DNA damage.<\/jats:p>","DOI":"10.1093\/bib\/bbae564","type":"journal-article","created":{"date-parts":[[2024,11,2]],"date-time":"2024-11-02T02:37:21Z","timestamp":1730515041000},"source":"Crossref","is-referenced-by-count":1,"title":["DEWNA: dynamic entropy weight network analysis and its application to the DNA-binding proteome in A549 cells with cisplatin-induced damage"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5812-3941","authenticated-orcid":false,"given":"Shisheng","family":"Wang","sequence":"first","affiliation":[{"name":"Department of General Surgery and Liver Transplant Center , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Institutes for Systems Genetics , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application , West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , West China Hospital, , Chengdu ,","place":["China"]}]},{"given":"Wenjuan","family":"Zeng","sequence":"additional","affiliation":[{"name":"Department of General Surgery and Liver Transplant Center , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Institutes for Systems Genetics , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application , West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , West China Hospital, , Chengdu ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0162-5611","authenticated-orcid":false,"given":"Yin","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of General Surgery and Liver Transplant Center , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Institutes for Systems Genetics , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]}]},{"given":"Jingqiu","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of General Surgery and Liver Transplant Center , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Institutes for Systems Genetics , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]}]},{"given":"Dan","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine , West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , West China Hospital, , Chengdu ,","place":["China"]},{"name":"State Key Laboratory of Respiratory Health and Multimorbidity , West China Hospital, , Chengdu, Sichuan ,","place":["China"]},{"name":"Sichuan University , West China Hospital, , Chengdu, Sichuan ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2214-9474","authenticated-orcid":false,"given":"Hao","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of General Surgery and Liver Transplant Center , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Proteomics-Metabolomics Analysis Platform, NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Institutes for Systems Genetics , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application , West China Hospital, , Chengdu ,","place":["China"]},{"name":"Sichuan University , West China Hospital, , Chengdu ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,1]]},"reference":[{"key":"2024110202365503800_ref1","doi-asserted-by":"publisher","first-page":"115323","DOI":"10.1016\/j.bcp.2022.115323","article-title":"Cisplatin in cancer treatment","volume":"206","author":"Romani","year":"2022","journal-title":"Biochem Pharmacol"},{"key":"2024110202365503800_ref2","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1016\/j.ejphar.2014.07.025","article-title":"Cisplatin in cancer therapy: molecular mechanisms of action","volume":"740","author":"Dasari","year":"2014","journal-title":"Eur J Pharmacol"},{"key":"2024110202365503800_ref3","doi-asserted-by":"publisher","first-page":"102925","DOI":"10.1016\/j.bioorg.2019.102925","article-title":"Cisplatin: the first metal based anticancer drug","volume":"88","author":"Ghosh","year":"2019","journal-title":"Bioorg 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