Jul 2026· Journal of Advanced Research· 0 citations· 64 references
Medicine
TL;DR
TPL1 is identified as a functionally relevant lncRNA associated with TNBC growth, invasion, and molecular regulatory programs and provides a framework for further mechanistic and translational investigation.
Abstract
INTRODUCTION
Despite the rapidly expanding catalog of long noncoding RNAs (lncRNAs), the functional roles of most remain poorly characterized in cancer. In triple-negative breast cancer (TNBC), an aggressive subtype with limited targeted treatment options, defining lncRNA-associated molecular mechanisms could uncover novel therapeutic vulnerabilities.
Objectives
This study aimed to systematically identify TNBC-enriched lncRNAs associated with cellular fitness, and drug response, and to functionally characterize prioritized lncRNA candidates with potential therapeutic relevance.
Methods
We generated comprehensive lncRNA annotation by integrating GENCODE, BIGTranscriptome, and MiTranscriptome databases. CRISPR-Cas9 deletion screen targeting 1,029 TNBC-enriched lncRNAs was conducted. Functional validation included proliferation assays in 2D and 3D cultures, invasion assays using an organ-on-chip model, and transcriptomic and proteomic profiling following lncRNA knockdown. Candidate lncRNA-protein associations were assessed using proteomic array analysis. miRNA expression profiling, miRanda-based interaction prediction, and Ingenuity Pathway Analysis (IPA) were used to construct candidate competing endogenous RNA (ceRNA)-like regulatory networks and downstream signaling pathways.
Results
Our CRISPR screen identified fourteen recurrent candidate lncRNA dependencies across both TNBC models, with TNBC Promoting LncRNA 1 (TPL1) emerging among the top candidates. ASO-mediated TPL1 suppression significantly reduced TNBC cell proliferation, clonogenic growth, three-dimensional growth, and invasive capacity. TPL1 was significantly overexpressed in TNBC tissues, particularly within the basal-like immune-suppressed (BLIS) subtype. RNA-FISH analysis showed nuclear/perinuclear and cytoplasmic TPL1 localization. Transcriptomic and proteomic analyses revealed suppression of pathways related to extracellular matrix-receptor interaction, focal adhesion, cell migration, and PI3K-Akt signaling following TPL1 knockdown. Proteomic array, RBPsuite, TLC-CLIP, miRNA profiling, and transcriptomic integration supported candidate protein-associated and ceRNA-like regulatory mechanisms involving TPL1.
Conclusion
This study identifies TPL1 as a functionally relevant lncRNA associated with TNBC growth, invasion, and molecular regulatory programs. These findings support TPL1 as a candidate RNA-targetable vulnerability in TNBC and provide a framework for further mechanistic and translational investigation.
Triple-negative breast cancer (TNBC) remains a major therapeutic challenge due to pronounced molecular heterogeneity, transcriptional plasticity, and frequent treatment resistance. MicroRNA (miRNA)-based strategies have emerged as potential approaches for modulating dysregulated gene expression networks in TNBC; however, the contribution of understudied miRNA families to TNBC-associated regulatory programs remains incompletely understood. This study aimed to investigate the tumor-suppressive role of miR-548f-3p in TNBC and to identify candidate downstream effectors, with particular focus on ANP32E. An integrative analysis combining public transcriptomic datasets, clinical expression profiling, computational target prediction, network-based prioritization, pathway analysis, and single-cell transcriptomic assessment identified miR-548f-3p as consistently downregulated in TNBC. Among candidate downstream targets, ANP32E, a chromatin-associated regulator involved in H2A.Z histone variant dynamics, was identified as a potential effector exhibiting increased expression in TNBC and enrichment within malignant epithelial cell populations. An inverse association between miR-548f-3p and ANP32E expression was observed in patient-derived samples. In breast cancer cell models, miR-548f-3p mimic restoration increased apoptosis, promoted G0/G1 accumulation, and reduced migration- and invasion-associated readouts, although measurable effects were also observed in non-tumorigenic MCF-10A cells. These phenotypic changes were accompanied by reduced ANP32E expression at the protein level, indicating that ANP32E expression is responsive to miR-548f-3p restoration. This study supports miR-548f-3p as a candidate tumor-suppressive miRNA in TNBC. The reduction in ANP32E protein expression following miR-548f-3p restoration, together with computational, single-cell, and clinical expression evidence, supports ANP32E as an expression-responsive candidate downstream effector of miR-548f-3p. Further reporter-based and rescue experiments are required to confirm direct 3′UTR-mediated targeting and to define the mechanistic contribution of ANP32E within the broader miR-548f-3p regulatory network.
Samira Behroozi, Mahdieh Salimi, H. Lanjanian et al.· International Journal of Mol...· 0 citations
This computational study identifies several candidate lncRNAs associated with clinical outcomes in breast cancer, which 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.
M. Acencio, Xin-Hui Wang, Flavia R. Rotea Mangone et al.· International Journal of Mol...· 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
This study integrates multi-omics datasets to identify candidate biomarkers that may influence TNBC progression and modulate therapeutic response and nominate CCND2 and KIF1A as candidate biomarkers and potential therapeutic targets in TNBC.
Roberto Aguilar, Victor Wang, Shane Deng· Journal of Immunology· 0 citations
