{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T06:04:11Z","timestamp":1783749851834,"version":"3.55.0"},"reference-count":66,"publisher":"Baishideng Publishing Group Inc.","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["World J Gastroenterol"],"abstract":"<jats:p>BACKGROUND<\/jats:p>\n          <jats:p>Hepatocellular carcinoma (HCC) is the most common subtype of primary liver cancer with varied incidence and epidemiology worldwide. Sorafenib is still a recommended treatment for a large proportion of patients with advanced HCC. Different patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 cells.<\/jats:p>\n          <jats:p>AIM<\/jats:p>\n          <jats:p>To define the long non-codingRNA-microRNA-mRNA (lncRNA-miRNA-mRNA) predicted signatures related to selected hallmarks of cancer (apoptosis, autophagy, cell stress, cell dedifferentiation and invasiveness) in RNAseq studies using Sorafenib-treated HepG2 and SNU449 cells. Various available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 cells.<\/jats:p>\n          <jats:p>METHODS<\/jats:p>\n          <jats:p>HepG2 and SNU449 cells were treated with Sorafenib (10 \u03bcmol\/L) for 24 hours. Total RNA, including small and long RNA, was extracted with a commercial miRNeasy kit. RNAseq was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory axes.<\/jats:p>\n          <jats:p>RESULTS<\/jats:p>\n          <jats:p>MALAT, THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7 , TIRARP , TFAP4  and FAXDC2  in HepG2 cells. SNHG12, EPB41 L4A-AS1, LINC01578, SNHG12 and GAS5 interacted with let-7b-3p, miR-195-5p and VEGFA  in SNU449 cells. The axes MALAT1\/hsa-mir-374b-3p\/SMAD7  and MALAT1\/hsa-mir-769-5p\/TFAP4  were of high relevance for Sorafenib response in HepG2 cells, whereas PVT1 \/hsa-miR-195-5p\/VEGFA  was responsible for the differential response of SNU449 cells to Sorafenib treatment.<\/jats:p>\n          <jats:p>CONCLUSION<\/jats:p>\n          <jats:p>Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression, whose proteins mainly increased the antitumor effectiveness of the treatment (SMAD7 , TIRARP , TFAP4 , FAXDC2  and ADRB2 ). However, the broad regulatory axis leading to increased VEGFA  expression may be related to the side effect of Sorafenib in SNU449 cells.<\/jats:p>","DOI":"10.3748\/wjg.v31.i3.95207","type":"journal-article","created":{"date-parts":[[2024,12,17]],"date-time":"2024-12-17T08:18:05Z","timestamp":1734423485000},"source":"Crossref","is-referenced-by-count":3,"title":["<i>In silico<\/i> analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells"],"prefix":"10.3748","volume":"31","author":[{"given":"Patricia","family":"de la Cruz-Ojeda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ester","family":"Parras-Mart\u00ednez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raquel","family":"Rey-P\u00e9rez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordi","family":"Muntan\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2060","published-online":{"date-parts":[[2025,1,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3322\/caac.21660"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2018.03.024"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2021.11.018"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03362-0"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0708857"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(08)70285-7"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.26855"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.22843"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1038\/aps.2014.122"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1158\/1535-7163.MCT-13-1043"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-309501"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/s41419-020-2558-1"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2010.12.043"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-020-0187-x"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1038\/nrgastro.2017.169"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.2147\/OTT.S232453"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines9070813"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3390\/cells11172673"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2011.08.018"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.649619"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2009.97"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506580102"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1038\/ng1180"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz353"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1210s36"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2008.211"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa1074"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx247"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz1036"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06046-y"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00462"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky967"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra1713263"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.32543"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-16-1464"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-19-0472"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.3892\/ol.2020.11696"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.27567"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1007\/s13577-021-00587-z"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.27095"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1186\/s13046-019-1177-0"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.12659\/MSM.915541"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2021.04.016"},{"key":"B45","unstructured":"Liu C, Tang L, Xu M, Lin Y, Shen J, Zhou L, Ho L, Lu J, Ai X. 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