{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T21:46:36Z","timestamp":1770327996893,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"vor","delay-in-days":61,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM138192"],"award-info":[{"award-number":["R35GM138192"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HL161389"],"award-info":[{"award-number":["R01HL161389"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R00CA207865"],"award-info":[{"award-number":["R00CA207865"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Predoctoral Training Program in Biomedical Data Driven Discovery","award":["T32LM012203"],"award-info":[{"award-number":["T32LM012203"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA259388"],"award-info":[{"award-number":["R01CA259388"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Studies have identified genes and molecular pathways regulating cancer metastasis. However, it remains largely unknown whether metastatic potentials of cancer cells from different lineage types are driven by the same or different gene networks. Here, we aim to address this question through integrative analyses of 493 human cancer cells\u2019 transcriptomic profiles and their metastatic potentials in vivo. Using an unsupervised approach and considering both gene coexpression and protein\u2013protein interaction networks, we identify different gene networks associated with various biological pathways (i.e. inflammation, cell cycle, and RNA translation), the expression of which are correlated with metastatic potentials across subsets of lineage types. By developing a regularized random forest regression model, we show that the combination of the gene module features expressed in the native cancer cells can predict their metastatic potentials with an overall Pearson correlation coefficient of 0.90. By analyzing transcriptomic profile data from cancer patients, we show that these networks are conserved in vivo and contribute to cancer aggressiveness. The intrinsic expression levels of these networks are correlated with drug sensitivity. Altogether, our study provides novel comparative insights into cancer cells\u2019 intrinsic gene networks mediating metastatic potentials across different lineage types, and our results can potentially be useful for designing personalized treatments for metastatic cancers.<\/jats:p>","DOI":"10.1093\/bib\/bbae357","type":"journal-article","created":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T01:20:37Z","timestamp":1721697637000},"source":"Crossref","is-referenced-by-count":2,"title":["Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types"],"prefix":"10.1093","volume":"25","author":[{"given":"Sheng","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering , McCormick School of Engineering, , 2145 Sheridan Road, Evanston, IL 60628 , United States"},{"name":"Northwestern University , McCormick School of Engineering, , 2145 Sheridan Road, Evanston, IL 60628 , United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily K","family":"Stroup","sequence":"additional","affiliation":[{"name":"Department of Pharmacology , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"},{"name":"Northwestern University , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4354-3198","authenticated-orcid":false,"given":"Ting-You","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Urology , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"},{"name":"Northwestern University , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rendong","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Urology , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"},{"name":"Northwestern University , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1809-8099","authenticated-orcid":false,"given":"Zhe","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering , McCormick School of Engineering, , 2145 Sheridan Road, Evanston, IL 60628 , United States"},{"name":"Northwestern University , McCormick School of Engineering, , 2145 Sheridan Road, Evanston, IL 60628 , United States"},{"name":"Department of Pharmacology , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United States"},{"name":"Northwestern University , Feinberg School of Medicine, , 303 E Superior Street, Chicago, IL 60611 , United 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