{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T12:28:15Z","timestamp":1786969695501,"version":"build-2736575974"},"reference-count":53,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T00:00:00Z","timestamp":1786752000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Long non-coding RNAs (lncRNAs) are emerging as important regulators of cellular adaptation to environmental and molecular stress, but the extent to which their responses remain reproducible and stress-type-dependent across human stress conditions remains unclear. Here, we performed an integrative transcriptomic meta-analysis of human stress-response datasets from ASTRA and GEO, focusing on normal, non-cancerous, wild-type human cell lines exposed to oxidative stress (H2O2), hypoxia, heat stress, or UV-induced DNA damage. Gene Ontology (GO) enrichment analysis of differentially expressed (DE) protein-coding mRNAs confirmed that the resulting stress-stratified comparison captured biologically coherent transcriptional programmes to oxidative stress signaling, hypoxic and metabolic adaptation, heat-induced proteostasis, UV-induced DNA damage signaling, apoptosis, and cell-cycle regulation. Differential expression analysis was subsequently integrated with Weighted Gene Co-expression Network Analysis (WGCNA) -based module\u2013treatment associations to rank network-supported lncRNA candidates. By prioritizing candidates for recurrence across at least two different stress studies, we identified lncRNAs with increased recurrence and consistent stress-type-dependent expression regulation, embedded within coordinated stress-associated mRNA programs.<\/jats:p>","DOI":"10.3390\/ijms27167288","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T12:01:26Z","timestamp":1786968086000},"page":"7288","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative RNA-Seq Analysis Reveals Stress Type-Dependent lncRNA-Centered Co-Expression Networks Across Human Cellular Stress Contexts"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-0095-1908","authenticated-orcid":false,"given":"Christina","family":"Anastasiadi","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aggeliki","family":"Kasapi","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ioannis","family":"Sentementes","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1218-9109","authenticated-orcid":false,"given":"Vasileios","family":"Gouzouasis","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8603-3767","authenticated-orcid":false,"given":"Margaritis","family":"Tsifintaris","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19017, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2975-0326","authenticated-orcid":false,"given":"Antonis","family":"Giannakakis","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece"},{"name":"University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","article-title":"Long Non-Coding RNAs: Definitions, Functions, Challenges and Recommendations","volume":"24","author":"Mattick","year":"2023","journal-title":"Nat. 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