AUTHOR=Kołat Damian , Kałuzińska-Kołat Żaneta , Kośla Katarzyna , Orzechowska Magdalena , Płuciennik Elżbieta , Bednarek Andrzej K. 

TITLE=LINC01137/miR-186-5p/WWOX: a novel axis identified from WWOX-related RNA interactome in bladder cancer

JOURNAL=Frontiers in Genetics

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1214968

DOI=10.3389/fgene.2023.1214968

ISSN=1664-8021

ABSTRACT=<p><bold>Introduction:</bold> The discovery of non-coding RNA (ncRNA) dates back to the pre-genomics era, but the progress in this field is still dynamic and leverages current post-genomics solutions. WWOX is a global gene expression modulator that is scarcely investigated for its role in regulating cancer-related ncRNAs. In bladder cancer (BLCA), the link between WWOX and ncRNA remains unexplored. The description of AP-2α and AP-2γ transcription factors, known as WWOX-interacting proteins, is more commonplace regarding ncRNA but still merits investigation. Therefore, this <italic>in vitro</italic> and <italic>in silico</italic> study aimed to construct an ncRNA-containing network with WWOX/AP-2 and to investigate the most relevant observation in the context of BLCA cell lines and patients.</p><p><bold>Methods:</bold> RT-112, HT-1376, and CAL-29 cell lines were subjected to two stable lentiviral transductions. High-throughput sequencing of cellular variants (deposited in the Gene Expression Omnibus database under the GSE193659 record) enabled the investigation of WWOX/AP-2-dependent differences using various bioinformatics tools (e.g., limma-voom, FactoMineR, multiple Support Vector Machine Recursive Feature Elimination (mSVM-RFE), miRDB, Arena-Idb, ncFANs, RNAhybrid, TargetScan, Protein Annotation Through Evolutionary Relationships (PANTHER), Gene Transcription Regulation Database (GTRD), or Evaluate Cutpoints) and repositories such as The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia. The most relevant observations from cap analysis gene expression sequencing (CAGE-seq) were confirmed using real-time PCR, whereas TCGA data were validated using the GSE31684 cohort.</p><p><bold>Results:</bold> The first stage of the whole study justified focusing solely on WWOX rather than on WWOX combined with AP-2α/γ. The most relevant observation of the developed ncRNA-containing network was LINC01137, i.e., long non-coding RNAs (lncRNAs) that unraveled the core network containing UPF1, ZC3H12A, LINC01137, WWOX, and miR-186-5p, the last three being a novel lncRNA/miRNA/mRNA axis. Patients’ data confirmed the LINC01137/miR-186-5p/WWOX relationship and provided a set of dependent genes (i.e., <italic>KRT18</italic>, <italic>HES1</italic>, <italic>VCP</italic>, <italic>FTH1</italic>, <italic>IFITM3</italic>, <italic>RAB34</italic>, and <italic>CLU</italic>). Together with the core network, the gene set was subjected to survival analysis for both TCGA-BLCA and GSE31684 patients, which indicated that the increased expression of <italic>WWOX</italic> or <italic>LINC01137</italic> is favorable, similar to their combination with each other (<italic>WWOX</italic>↑ and <italic>LINC01137</italic>↑) or with <italic>MIR186</italic> (<italic>WWOX</italic>↑/<italic>LINC01137</italic>↑ but <italic>MIR186</italic>↓).</p><p><bold>Conclusion:</bold> WWOX is implicated in the positive feedback loop with LINC01137 that sponges WWOX-targeting miR-186-5p. This novel WWOX-containing lncRNA/miRNA/mRNA axis should be further investigated to depict its relationships in a broader context, which could contribute to BLCA research and treatment.</p>