Jul 2026· Frontiers in Bioscience· Vol 31 7, pp.
52436
· 0 citations· 25 references
Medicine
TL;DR
This study investigated how LINC00673-V4 drives CRC proliferation by modulating the Hippo-Yes-associated protein (Hippo-YAP) signaling pathway and identified LINC00673-V4 as an isoform-specific oncogenic lncRNA in CRC.
Abstract
Background
Colorectal cancer (CRC) is a leading cause of cancer-related morbidity and mortality worldwide; thus, understanding its molecular mechanisms is critical for developing novel therapeutic targets. Long non-coding RNAs (lncRNAs) play crucial isoform-specific roles in cancer. While oncogenic lncRNA LINC00673 is known to be involved in multiple malignancies and possesses five distinct transcript variants, the functional role of LINC00673-V4-a highly expressed transcript variant in CRC-remains largely unexplored. This study investigated how LINC00673-V4 drives CRC proliferation by modulating the Hippo-Yes-associated protein (Hippo-YAP) signaling pathway.
Methods
Survival analysis was performed using the GSE39582 dataset to assess the prognostic value of LINC00673 in patients with CRC. The expression of LINC00673 transcript variants in CRC cell lines was detected by quantitative PCR. Cell Counting Kit-8 and 5-ethynyl-2'-deoxyuridine (EdU) incorporation assays were used to assess cell proliferation upon LINC00673-V4 knockdown or overexpression. Western blotting and immunofluorescence staining were utilized to analyze the expression of Hippo-YAP target genes. To confirm the interaction between LINC00673-V4 and fused in sarcoma (FUS), RNA immunoprecipitation (RIP) was performed, while co-IP was used to investigate potential protein-protein interactions.
Results
High LINC00673 expression was observed in CRC cell lines and was associated with a poor prognosis in patients with CRC. Among the five LINC00673 transcript variants, LINC00673-V3 and LINC00673-V4 were the predominantly expressed isoforms; however, only LINC00673-V4 significantly promoted CRC cell proliferation. LINC00673-V4 inhibited YAP phosphorylation at Ser127, promoted YAP nuclear translocation, and upregulated the expression of Hippo-YAP target genes (connective tissue growth factor, cysteine-rich angiogenic inducer 61, survivin). RIP assays confirmed an association between LINC00673-V4 and FUS, while co-immunoprecipitation (co-IP) assays revealed that FUS interacted with both YAP and large tumor suppressor 1 (LATS1), suggesting FUS may facilitate LATS1-mediated YAP phosphorylation. FUS was found to promote LATS1-mediated YAP Ser127 phosphorylation, induce YAP cytoplasmic retention, and down-regulate Hippo-YAP target gene expression. Rescue experiments showed that LINC00673-V4 reversed the FUS-induced suppression of Hippo-YAP target gene expression.
Conclusions
Our study identified LINC00673-V4 as an isoform-specific oncogenic lncRNA in CRC. By associating with FUS, LINC00673-V4 sequesters FUS away from the LATS1/YAP complex; thereby inhibiting FUS-mediated YAP phosphorylation and enhancing Hippo-YAP target gene expression. These findings expand the landscape of lncRNA isoform-specific regulation in cancer, highlighting LINC00673-V4 as a potential prognostic biomarker and therapeutic target for CRC.
In terms of cancer-related death, non-small cell lung cancer (NSCLC), the world’s leading cause, highlights the need for continued research into the genetic factors that influence tumor growth. Long non-coding RNAs (lncRNAs) are now well recognized as essential regulators of oncogenic signaling cascades; nevertheless, the specific role and molecular basis of the SOX2 overlapping transcript (SOX2OT) in NSCLC are not entirely understood. This study examined the functional importance of SOX2OT and its regulatory interactions with tumor-suppressive microRNAs in NSCLC cells. In A549 and Calu-3 cells, RNA interference-mediated SOX2OT silencing dramatically reduced cellular proliferation, migration, and invasiveness. Moreover, SOX2OT knockdown was associated with inhibition of epithelial–mesenchymal transition (EMT), alongside induction of cell cycle arrest and activation of apoptotic pathways. Integrated transcriptomic profiling and bioinformatic prediction analyses identified miR-143 as a putative downstream effector of SOX2OT activity. Consistently, depletion of SOX2OT resulted in marked elevation of miR-143 expression, which corresponded with downregulation of oncogenic mediators, including STAT3, EZH2, and CXCL13. As a result of SOX2OT suppression, both the transcript and the protein levels of PTEN were restored. Further functional characterization demonstrated that SOX2OT knockdown inhibits EMT progression by decreasing mesenchymal markers and EMT-related transcription factors (TFs) while concomitantly enhancing epithelial marker expression. Collectively, these findings suggest that SOX2OT contributes to NSCLC pathogenesis through regulation of a miR-143-centered signaling network that influences oncogenic signaling, cellular survival, and metastatic potential. Targeting the SOX2OT/miR-143 regulatory axis may therefore represent a promising therapeutic approach for NSCLC, while also underscoring the broader importance of lncRNA-mediated post-transcriptional regulation in lung cancer biology.
M. Zarei, Elahe Asadollahi, Babak Jahangiri et al.· bioRxiv· 0 citations
This study found that LINC02257 and LINC00659 are upregulated in BC and are associated with malignancy-related genes and patient survival, suggesting their potential as therapeutic targets and prognostic biomarkers.
Fatemeh Badzohre, Azin Azadfekr, Farnoosh Akbari et al.· Current Genetic Medicine Rep...· 0 citations
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of tumor initiation and progression through transcriptional and posttranscriptional mechanisms. UPK1A antisense RNA 1 (UPK1A-AS1), a cancer‐associated lncRNA, has been reported to participate in oncogenic processes; however, its overall landscape across human malignancies and its biological role in therapy resistance remain poorly understood. Given the increasing importance of identifying functional lncRNAs with prognostic and therapeutic potential, this study presents a comprehensive multiomics characterization of UPK1A-AS1 and its experimental validation in hepatocellular carcinoma (HCC). We integrated datasets from The Cancer Genome Atlas (TCGA), the Genotype‐Tissue Expression Project (GTEx), the cancer immunology data engine (CIDE), and the cBioPortal for cancer genomics (cBioPortal) to systematically assess its expression pattern, genomic alterations, clinical significance, and immunological associations. Our analyses revealed that UPK1A-AS1 is significantly upregulated in multiple tumor types, with copy‐number amplification as the predominant genomic alteration driving its overexpression. Elevated UPK1A-AS1 expression was correlated with advanced disease stage, poor differentiation, immune exclusion, and unfavorable prognosis, supporting its potential as a cancer type‐dependent biomarker. In parallel, functional studies demonstrated that hypoxia transcriptionally induces UPK1A-AS1 in HCC, where it promotes sorafenib resistance by suppressing apoptosis. Silencing UPK1A-AS1 restored apoptotic and enhanced sorafenib efficacy both in vitro and in vivo. Collectively, our findings suggest that UPK1A-AS1 is a hypoxia‐inducible oncogenic lncRNA that plays dual roles in cancer, with cancer type‐dependent associations with progression and immune modulation across malignancies and mechanistically mediating hypoxia‐associated drug resistance in HCC.
Ze-Kai Li, Min Luo, Shu-Sen Fang et al.· Analytical Cellular Patholog...· 0 citations
INTRODUCTION
Colorectal cancer (CRC) remains a significant global health burden; therefore, a better understanding of its molecular underpinnings is needed to develop more effective therapeutic methods. Traf2 and Nck-interacting kinase (TNIK) have emerged as key regulators in various malignancies, including CRC, but their exact roles and regulatory mechanisms remain only partially understood. The present study aimed to characterize TNIK expression in colorectal cancer through integrative analysis of two independent GEO microarray datasets (GSE9348 and GSE21510) comprising a total of 193 CRC and 37 normal tissue samples.
METHODS
Differential gene expression (DEG) analysis was conducted using GEO2R with the limma package, and protein-protein interaction network analysis was performed using STRING v12.0 and visualized in Cytoscape v3.8.2 to identify TNIK's functional partners within the Wnt signaling pathway. This work highlights genes that are up- and downregulated in CRC using a significance threshold of p < 0.05 and log FC > 1. Additionally, to investigate the epigenetic regulation of TNIK, an exploratory differential methylation analysis was performed on a murine CRC RRBS dataset (PRJNA589067) that models Wnt hyperactivation in APC-mutant CRC organoids. The data were processed through Bismark v0.24.2 for alignment and the Bioconductor package edgeR for DMR identification in the CpG context. Therefore, an epigenetic analysis of colorectal cancer was conducted to identify differentially methylated regions, using the thresholds p < 0.05 and logFC > 1.
RESULTS
DEG analysis reveals that TNIK is significantly upregulated in cancer samples. From DMR analysis, TNIK was observed to be relatively hypomethylated in the murine experimental model, while expression analysis of human CRC microarray data identified TNIK as an upregulated gene, an inverse relationship consistent with established epigenetic regulatory trends.
DISCUSSION
The data analyses and interpretations in this work provide a molecular basis for future pharmacological studies targeting TNIK kinase activity and aberrant DNA methylation in CRC, with potential implications for drug discovery efforts to restore normal Wnt pathway regulation. The study links changes in DNA methylation patterns to gene expression and provides important mechanistic definitions of how epigenetic modifications affect gene regulation.
CONCLUSION
The overall contribution of TNIK overexpression to carcinogenesis and tumor progression through epigenetic modulation in CRC could be applied as a clinical biomarker or candidate for tumor suppressor genes in future studies.
Sherlin Rosita Arokiaraj, R. Prathiviraj, D. A. Gideon et al.· Anti-Cancer Agents in Medici...· 0 citations
A large number of cancer-related single-nucleotide polymorphisms (SNPs) are distributed in the genomic regions of long non-coding RNAs (lncRNAs), yet the mechanisms linking them to cancer risk have not been fully clarified so far. This study explored LINC00578 rs7430456’s association with breast cancer susceptibility and LINC00578’s role/mechanism in triple-negative breast cancer (TNBC). A total of 480 breast cancer patients and 460 controls were enrolled. LINC00578 rs7430456 genotyping and LINC00578 expression detection via RT-qPCR were performed. Functional assays (proliferation, migration, invasion) were conducted in TNBC cell lines, and the LINC00578-miR-143-5p interaction was explored by dual-luciferase reporter assay. LINC00578 rs7430456 G allele and AG/GG genotypes reduced breast cancer risk. LINC00578 was upregulated in breast cancer (especially TNBC) with an AUC of 0.873 for diagnosis. LINC00578 knockdown inhibited TNBC cell proliferation, migration, and invasion. LINC00578 sponged miR-143-5p, and miR-143-5p mediated its oncogenic effects. LINC00578 rs7430456 is associated with breast cancer susceptibility, and LINC00578 promotes TNBC progression via sponging miR-143-5p, being a potential biomarker and therapeutic target for breast cancer, particularly TNBC.
Jing Zhai, Wei Wu, Xiaoyun Mao et al.· Hereditas· 0 citations
This study demonstrates that the long noncoding RNA (lncRNA) LINC00460 is significantly overexpressed in clear cell renal cell carcinoma (ccRCC) and is strongly associated with adverse clinical outcomes. Analysis of data from The Cancer Genome Atlas (TCGA), validated by an independent cohort (GSE53757) and quantitative real-time polymerase chain reaction (qRT-PCR), shows that high LINC00460 expression has robust diagnostic value (area under the curve [AUC] = 0.818) and predicts shorter overall survival, highlighting its potential as a prognostic biomarker. Functional enrichment analyses indicate that LINC00460 is involved in key pathways, including complement and coagulation cascades, cytokine-cytokine receptor interactions, extracellular matrix remodeling, and p53 signaling. In vitro experiments confirm that silencing LINC00460 in ccRCC cell lines (Caki-2 and ACHN) markedly inhibits tumor cell proliferation, migration, and invasion while promoting apoptosis. Mechanistically, LINC00460 knockdown reduces levels of inflammatory factors (interleukin-6 [IL-6], tumor necrosis factor-alpha [TNF-α], and C-X-C motif chemokine ligand 8 [CXCL8]) and coagulation-related proteins (C3, SERPINA1, and PLAU), and activates the p53 pathway by upregulating p21 and BAX while downregulating Bcl-2. Genomic analysis reveals higher mutation rates of BAP1 and LRP2 in LINC00460-high tumors, and drug repurposing screening identifies cinchonine and iproniazid as candidate therapeutic agents. These findings establish LINC00460 as an oncogenic driver in ccRCC and a promising target for both diagnosis and precision therapy.
Bo Dong, Songtao Liu, Wenyu Wang et al.· American journal of translat...· 0 citations
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