Jun 2026· Omics· Vol 30, pp. 493 - 504· 0 citations· 40 references
Medicine
TL;DR
Experimental analyses demonstrated that miR-708-5p directly targets the ENTPD2 3′UTR in HCT116 cells and suppresses ENTPD2 expression in both HCT116 and HT-29 cells, supporting a potential contribution of miR-708-5p to ENTPD2 regulation in CRC.
Abstract
Ectonucleoside triphosphate diphosphohydrolase 2 (ENTPD2), an enzyme involved in extracellular nucleotide metabolism and purinergic signaling, has been linked to tumor–immune interactions, although its role in colorectal cancer (CRC) remains unclear. This study examined the expression pattern and regulatory context of ENTPD2 through integrative analysis of transcriptomic, proteomic, microRNA (miRNA), and single-cell transcriptomic datasets. Transcriptomic analyses showed that ENTPD2 mRNA levels are elevated in colorectal tumors compared with normal tissues and that higher expression is associated with shorter relapse-free survival. In contrast, proteomic analyses indicated reduced ENTPD2 protein abundance in tumor samples, suggesting a divergence between transcript and protein expression. Analysis of candidate miRNAs identified miR-708-5p as a potential post-transcriptional regulator, supported by its increased expression in CRC and a predicted binding site within the ENTPD2 3′-untranslated region (UTR). Single-cell transcriptomic datasets further indicated that ENTPD2 transcripts are mainly detected in malignant epithelial cells. We performed a functional validation using dual-luciferase reporter assays, qRT-PCR, and Western blot analysis in CRC cell lines. Experimental analyses demonstrated that miR-708-5p directly targets the ENTPD2 3′UTR in HCT116 cells and suppresses ENTPD2 expression in both HCT116 and HT-29 cells. These findings support a potential contribution of miR-708-5p to ENTPD2 regulation in CRC.
ENST00000615487.1 is a structurally stable lncRNA exhibiting context-dependent expression and localization patterns in CRC, suggesting a potential shift from nuclear transcriptional regulation toward cytoplasmic post-transcriptional functions during colorectal carcinogenesis.
Nataša Đokić, Anastasija Bubanja, Jelena Karanović et al.· Non-Coding RNA· 0 citations
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.
Fang Chen, Yan Yan, Wenting Yang et al.· PLoS ONE· 0 citations
OBJECTIVES
To investigate the functional role of OTU deubiquitinase 6B-antisense transcript 1 (OTUD6B-AS1) and its potential association with parthanatos - a poly (ADP-ribose) polymerase 1 (PARP-1)/apoptosis-inducing factor (AIF)-mediated regulated cell death pathway - in esophageal adenocarcinoma (EAC), which remains poorly understood.
METHODS
The expression patterns of OTUD6B-AS1, miR-145-5p, and its downstream target AIF protein were investigated in EAC cell lines. Gain- and loss-of-function assays were performed in vitro and in vivo to evaluate biological effects. The competing endogenous RNA (ceRNA) regulatory mechanism was verified using dual-luciferase reporter assays and RNA immunoprecipitation (RIP) assays. Activation of parthanatos was assessed by detecting AIF nuclear translocation and DNA damage levels.
RESULT
OTUD6B-AS1 was reduced significantly, and predominantly localized in the cytoplasm of EAC cells. OTUD6B-AS1 overexpression significantly inhibited EAC cell proliferation, migration, and invasion, and induced cellular apoptosis. Mechanistically, OTUD6B-AS1 functioned as a ceRNA, competitively binging to miR-145-5p and thereby relieving its translational suppression of AIF. This biological pathway promoted parthanatos activation, as evidenced by PARP-1 upregulation, extensive DNA damage (with γ-H2AX deposition), and nuclear translocation of AIF. OTUD6B-AS1-induced antitumor activities were abolished by miR-145-5p overexpression or AIF knockdown. Consistently, OTUD6B-AS1 overexpression substantially suppressed xenograft tumor growth in vivo.
CONCLUSION
OTUD6B-AS1 suppresses EAC progression by sponging miR-145-5p and upregulating AIF to induce parthanatos activation. Targeting this ceRNA regulatory axis may be a therapeutic strategy for EAC.
Qingfeng Zheng, Qiu-ping Wu, Yuling Lin et al.· American journal of translat...· 0 citations
Background Identifying upstream molecular regulators linking tumor proliferation with immune-related alterations remains an important challenge in cancer therapy. NTMT1 (METTL11A), a protein N-terminal methyltransferase, has been implicated in tumorigenesis; however, its role in coordinating tumor–immune interaction is poorly understood. Methods We performed integrative single-cell RNA sequencing (GSE208653) and spatial transcriptomics (GSE208654) analyses to characterize NTMT1 expression and function in cervical cancer. Spatial deconvolution and microenvironmental co-localization analyses were used to define context-specific effects. Functional validation was conducted using RT–qPCR, Western blotting, multiplex immunofluorescence, and flow cytometry-based assays. Results NTMT1 exhibited heterogeneous expression across epithelial and immune cell populations, with enrichment in squamous cell carcinoma. Spatial transcriptomics revealed that NTMT1-positive regions were associated with altered immune composition, including reduced macrophage and increased NK/T cell infiltration. In epithelial-enriched regions, NTMT1 expression correlated with activation of cell cycle pathways, including MYC, E2F1, CDK1, and CCNB1. Functional experiments demonstrated that NTMT1 promotes cell cycle progression via MYC upregulation. In epithelial–NK/T co-localization niches, NTMT1 was associated with modulation of antigen presentation pathways and suppression of HLA-A expression. Functionally, NTMT1 overexpression reduced IFN-γ production by CD8+ T cells under the co-culture conditions used in this study, which was partially restored by HLA-A re-expression. Conclusion NTMT1 was identified as a candidate regulator associated with MYC activation and HLA-A suppression. Although the precise molecular mechanism remains to be elucidated, functional experiments demonstrated that NTMT1 overexpression was accompanied by increased MYC expression, reduced HLA-A expression, enhanced cell-cycle progression, and impaired CD8+ T-cell function. These findings identify NTMT1 as a candidate regulatory node associated with MYC activation and downstream HLA-A suppression, warranting further mechanistic and in-vivo investigation, highlighting NTMT1 as a promising candidate for future therapeutic investigation. Further in vivo studies will be required to determine its suitability as a target for combination immunotherapy.
Jinling Zhang, Chen Chen, Huibin Song et al.· Frontiers in Immunology· 0 citations
The role of T-box transcription factor 6 (TBX6), a developmental transcription factor, in tumor initiation and progression in colorectal cancer (CRC) remains unclear. The present study investigated the expression pattern, biological functions, and downstream transcriptional regulatory networks of TBX6 in CRC. Public databases, clinical cohorts, functional assays, xenograft models, and RNA sequencing coupled with Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction analyses were used to define TBX6-associated molecular alterations. TBX6 was markedly upregulated in CRC tissues and cell lines, and its high expression was associated with advanced stage, lymph node metastasis, and poor survival. Functionally, TBX6 promoted proliferation, migration, invasion, and epithelial-mesenchymal transition in CRC cells in vitro, whereas TBX6 knockdown suppressed these malignant phenotypes and inhibited tumor growth with reduced proliferation and increased apoptosis in vivo. Transcriptomic analyses showed that TBX6 knockdown induced coordinated gene expression reprogramming and altered multiple tumor-related pathways. Protein-protein interaction analysis identified C-X-C motif chemokine ligand 14 (CXCL14), NOTUM, adrenoceptor α2A (ADRA2A), and melanin-concentrating hormone receptor 1 (MCHR1) as hub nodes within the TBX6-regulated network. Mechanistically, TBX6 knockdown regulated CXCL14 expression and attenuated Wnt/β-catenin signaling, findings that were further validated in xenograft tissues. These results indicate that TBX6 is aberrantly reactivated in CRC and promotes tumor progression through transcriptional network remodeling, suggesting that TBX6 may represent a potential prognostic biomarker and therapeutic target.
Nianjie Zhang, Leiting Wan, N. He et al.· Gene· 0 citations
Long non-coding RNAs (lncRNAs) have emerged as a class of molecules that play key roles in a number of biological processes and diseases, yet their mechanisms remain largely understudied. Second Chromosome Locus Associated with Prostate-1 (SChLAP1) is one such lncRNA that is overexpressed in prostate cancer (PCa) and is associated with worse patient outcomes. Previously published work in our lab defined the secondary structure of SChLAP1 and identified conserved functional regions including potential protein binding hotspots and locations that may undergo dynamic rearrangements in a cellular context. In PCa cell culture, overexpression of SChLAP1 has been shown to increase proliferation and invasion. In this study, we confirm the oncogenicity of SChLAP1 in the AR dependent LNCaP and 22Rv1 cell lines but demonstrate that the same effect is not seen in AR independent PC3 and Du145 cell lines. Similarly in the AR dependent cell lines, RNA-seq was used to identify differentially expressed genes associated with SChLAP1 overexpression, including upregulation of ribosomal biogenesis and protein synthesis pathways, and downregulation of olfactory transduction, interferon-gamma (IFN-[gamma]) response, and G-protein-coupled receptor (GPCR) signaling. RNA-seq in AR independent cell lines, however, did not have any differentially expressed genes upon SChLAP1 overexpression. Additionally, previous work in our lab [data not shown] identifies the histone H2A deubiquitinase and AR coregulator, MYSM1, as a novel protein binding partner of SChLAP1. Taken together, these results suggest a mechanism wherein SChLAP1 modulates AR signaling to promote PCa growth and progression. Our work on the structure and function of SChLAP1 lays out the groundwork for further investigation of its molecular mechanism and potential to be used as a therapeutic target or biomarker.