Integrated Transcriptomic, In Silico, and In Vitro Characterization of lncRNA ENST00000615487.1 Reveals Epithelial-Specific Expression, Differential Subcellular Distribution Between Normal and Colorectal Cancer Cells, and Potential Regulatory Functions

Characterization of a novel lncRNA RP3-340N1.2 and its association with a miR-4650-5p/SHC1-related regulatory network in lung adenocarcinoma

Long noncoding RNAs (lncRNAs) are increasingly recognized as regulators of cancer-related biological processes. However, the functional significance of many lncRNAs in lung adenocarcinoma (LUAD) remains incompletely understood. In this study, we identified RP3-340N1.2 as an upregulated lncRNA in LUAD through analyses of public transcriptomic datasets, which was further confirmed by quantitative real-time PCR in LUAD cell lines. Functional assays demonstrated that knockdown of RP3-340N1.2 was associated with reduced proliferation, migration, invasion, and clonogenic growth of LUAD cells in vitro. In addition, suppression of RP3-340N1.2 attenuated tumor growth in a xenograft model. Bioinformatic analysis using the LncBase Experimental v3 database identified hsa-miR-4650-5p as a potential interacting microRNA of RP3-340N1.2. This interaction was further examined by dual-luciferase reporter and RNA immunoprecipitation assays. Functional experiments additionally showed that miR-4650-5p overexpression was associated with reduced proliferative and migratory capacities in LUAD cells. Among the predicted downstream targets of miR-4650-5p, SHC1 was selected for further investigation. Alterations in RP3-340N1.2 or miR-4650-5p expression were accompanied by corresponding changes in SHC1 expression and ERK1/2 phosphorylation. Furthermore, rescue experiments demonstrated that SHC1 knockdown largely reversed RP3-340N1.2-associated cellular phenotypes, supporting the functional involvement of SHC1 within this regulatory framework. Collectively, these findings indicate that RP3-340N1.2 is aberrantly expressed in LUAD and may participate in tumor-associated cellular behaviors through a miR-4650-5p/SHC1-related regulatory mechanism. This study provides preliminary evidence supporting the potential relevance of RP3-340N1.2 in LUAD and offers additional insight into lncRNA-associated regulatory networks in this disease.

Long Noncoding RNAs (lncRNAs) as Biomarkers of Prognosis in TNBC and Non-TNBC Breast Cancer Patients

Functional studies have shown that long noncoding RNAs (lncRNAs) play different roles in gene expression regulation, acting as epigenetic factors. Accumulating evidence indicates that lncRNAs modulate diverse biological processes, and their altered expression is associated with the development and progression of cancer, including BC. Here, aiming to identify lncRNAs associated with breast cancer, we performed a re-analysis of the expression data from 1071 tumors of eligible patients in the LACRN-MPBC Study. Using normalized data, we compared the expression profiles of triple-negative breast cancer (TNBC; 170 cases) and a heterogeneous group of non-TNBC tumors (782 cases). A total of 59 differentially expressed lncRNAs (DELncRNAs) could be identified based on the criteria of |log2FC| ≥ 1 and FDR < 0.05, using the DESeq2 R package. In the Kaplan–Meier survival analysis, we identified DELncRNAs that affect disease-free survival and/or overall survival, with eight of them in TNBC and 27 in non-TNBC patients. Multivariate Cox proportional-hazards models were used to evaluate independent predictors of survival. Two DELncRNAs, VLDLR-AS1 and PART1, were identified as independent prognostic markers for TNBC patients, while seven (LINC00239, FAM30A, LINC00842, LINC01315, EGOT, LY6E-DT, and SLC25A21-AS1) were independent prognostic markers for non-TNBC patients. Our computational study identifies several candidate lncRNAs associated with clinical outcomes in breast cancer. However, the DELncRNAs identified here should be interpreted as preliminary candidates, which require future validation and functional studies to determine their biological roles and evaluate their potential as prognostic biomarkers.

LncRNA ZNF582-AS1 Acts as a Tumor Suppressor in Endometrial Cancer via the miR-21-5p/miR-516a-3p/CREBRF Axis.

INTRODUCTION Endometrial Carcinoma (EC) is a prevalent gynecological malignant tumor with a rising incidence rate. Long non-coding RNAs (lncRNAs) are key regulatory factors in tumorigenesis. Although ZNF582-AS1 is an lncRNA that has been linked to other cancers, its role and mechanism in EC have not yet been explored. METHODS ZNF582-AS1 expression was examined in the GEPIA database and confirmed in 45 pairs of EC/normal tissues and cell lines. Functional assays (including MTT and flow cytometry) were performed after ZNF582-AS1 overexpression. Potential miRNA targets were predicted using bioinformatics and validated using luciferase reporter and RNA Immunoprecipitation (RIP) detection. Downstream targets of miRNA were identified and detected using qPCR and Western blotting. Rescue experiments were conducted to confirm the functional interactions. A xenograft mouse model was used for in vivo validation. RESULTS ZNF582-AS1 exhibits marked downregulation in EC tissues and cell lines. Low ZNF582-AS1 expression is linked to unfavorable prognosis. ZNF582-AS1 overexpression suppresses EC cell proliferation, triggers cell cycle arrest, and decreases miR-21-5p and miR-516a3p mRNA levels. Additionally, miR-21-5p/miR-516a-3p suppresses CREBRF expression by binding directly to the 3'-UTR of CREBRF, and ZNF582-AS1 overexpression attenuates this CREBRF suppression. In the in vivo studies, ZNF582-AS1 overexpression effectively inhibited tumor growth in nude mice. DISCUSSION These findings support a competitive endogenous RNA mechanism, in which ZNF582-AS1 acts as a molecular sponge for miR-21-5p and miR-516a-3p, thereby alleviating their inhibitory effect on CREBRF expression. The recovery of CREBRF subsequently inhibits EC cell proliferation and promotes G0/G1 phase arrest, possibly by downregulating the CDK4/Cyclin D1 signaling pathway. The in vivo anti-tumor effect of ZNF582-AS1 further supports its biological relevance in EC progression. Overall, the ZNF582-AS1/miR-21-5p/miR516a-3p/CREBRF regulatory axis provides mechanistic insights into EC tumorigenesis and emphasizes the tumor suppressive effect of ZNF582-AS1. CONCLUSION LncRNA ZNF582-AS1 inhibits cell proliferation in EC by regulating the miR-21- 5p/miR-516a-3p/CREBRF axis. ZNF582-AS1 represents a potential treatment target and prognostic marker for EC.

Elevated Expression of LINC02257 and LINC00659 in Breast Cancer is Associated with Poor Survival and Immune Cell Infiltration

LncRNA SLC12A9-AS1 Drives Malignant Progression in Colorectal Cancer by Regulating miR-139-3p.

This study investigated the function of long noncoding RNA SLC12A9-AS1 in colorectal cancer (CRC) cells and its potential regulatory mechanism. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to measure SLC12A9-AS1 and miR-139-3p expression in CRC cell lines. Cell viability was assessed using the Cell Counting Kit-8 (CCK-8) assay, whereas migration and invasion were evaluated using permeable cell culture insert assays. The interaction between SLC12A9-AS1 and miR-139-3p was examined using dual-luciferase reporter (DLR) and RNA immunoprecipitation (RIP) assays. SLC12A9-AS1 was significantly upregulated, whereas miR-139-3p was downregulated, in CRC cells. Silencing SLC12A9-AS1 markedly reduced cell viability, migration, invasion, and epithelial-mesenchymal transition (EMT). The DLR and RIP assays supported an interaction between SLC12A9-AS1 and miR-139-3p. In addition, inhibition of miR-139-3p reversed the suppressive effects of SLC12A9-AS1 knockdown on malignant cellular phenotypes. Collectively, these findings indicate that SLC12A9-AS1 is abnormally overexpressed in CRC cells and that its knockdown attenuates malignant phenotypes, at least in part through regulation of miR-139-3p. These results provide new in vitro experimental evidence for understanding the molecular mechanisms involved in CRC pathogenesis.

LINC00673-V4 Promotes Colorectal Cancer Cell Proliferation by Interacting With FUS and Restoring the Expression of Hippo-YAP Target Genes.

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.