Ovarian cancer (OV) has the highest mortality rate among gynecological malignancies, with limited improvement in survival despite emerging treatments, underscoring an urgent need for novel diagnostic and therapeutic targets. Alternative splicing (AS) plays critical roles in OV progression, and long non-coding RNAs (lncRNAs) have recently been implicated as splicing regulators in tumor development. However, the landscape of lncRNA-mediated splicing dysregulation in OV remains unexplored. Here, we performed a genome-wide analysis integrating 207 differentially expressed lncRNAs and 1201 abnormal AS events from OV transcriptomes, identifying 2545 co-expression pairs. By constructing multi-layer regulatory networks incorporating splicing factors, transcription factors, and microRNAs, and applying a restart random walk algorithm seeded with oncogenes, we prioritized 29 hub splicing-regulatory lncRNAs, of which 15 are significantly associated with OV survival. This study provides novel lncRNA biomarkers and mechanistic insights into splicing dysregulation in OV.
Hepatocellular carcinoma (HCC) is a malignant neoplasm characterized by high incidence and mortality rates globally. Its pathogenesis and progression are intricate and multifaceted, necessitating comprehensive analysis and elucidation. Recent studies have demonstrated that non-coding RNAs (such as long non-coding RNAs, circular RNAs, and microRNAs) and alternative splicing, which are central to post-transcriptional regulation, engage in extensive regulatory interactions. These interactions form a complex regulatory network that significantly influences the malignant properties such as stemness, proliferation, invasion, metastasis, metabolic reprogramming, tumor microenvironment, and drug sensitivity in liver cancer cells. This review systematically explores the molecular mechanisms underlying the interactions between non-coding RNAs and alternative splicing events, highlighting the role of this regulatory network in modulating the expression of oncogenes and tumor suppressor genes in HCC. Additionally, this review investigates the prospective application of pivotal molecules within this regulatory network as novel diagnostic biomarkers and therapeutic targets. It also analyzes the challenges and obstacles encountered in the clinical translation process, thereby providing new insights for research on the precision diagnosis and treatment of HCC.
Cystic Fibrosis (CF) is a genetic disease characterized by chronic pulmonary inflammation and infection, principally with Pseudomonas aeruginosa. P. aeruginosa can exhibit resistance to innate immune effectors and antibiotics by expressing virulence factors and forming antibiotic-resistant biofilms, which facilitate chronic infection in immunocompromised hosts. Therefore, new antimicrobials are required. MicroRNAs are mammalian short non-coding RNAs that negatively regulate protein expression. MiR-17-5p, an inhibitor of CXCL8/IL-8, can decrease neutrophil abundance in the CF lung. Here we investigate whether miR-17-5p has anti-P. aeruginosa properties. The sequences of the full-length miRNA and the miR-17-5p isoform miR.17.P4d_5p were tested for their ability to bind to RNA transcripts encoded by P. aeruginosa PAO1 (NC_002516) using the bioinformatics tools RocketmiR and IntaRNA. A miR-17-5p DNA tetrahedron (Td-miR.17.P4d_5p, Size = 118-180 nm) was tested for its delivery into CF bronchial epithelial cells and ability to inhibit IL-8 gene and protein expression, and its effects on P. aeruginosa growth, antimicrobial resistance, and biofilm formation. Successful delivery into CFBE41o- and 16HBE14o- cells inhibited IL-8 expression induced by Pseudomonas-conditioned medium (PAO1, Mucoid strains 1 and 2 p < 0.00001; PA14 p < 0.0001). Delivery into PAO1 and PA14 inhibited growth and biofilm formation while significantly enhancing their sensitivity to the antibiotic cefotaxime. Td-miR.17.P4d_5p also significantly inhibited biofilm formation in two clinical mucoid P. aeruginosa strains. qPCR and EMSA were used to investigate the mechanism of action of miR.17.P4d_5p. The data showed that miR.17.P4d_5p could inhibit expression of kynU (p < 0.00001), a tryptophan metabolism pathway molecule related to PAO1 growth, and the biofilm formation-related molecules pilL, fimX, ppkA and pslA (all p < 0.00001) in P. aeruginosa PAO1. The combined anti-IL-8 and anti-P. aeruginosa properties of miR.17.P4d_5p suggest its potential usefulness as a dual anti-infective and anti-inflammatory therapeutic strategy for CF.
Pulmonary arterial hypertension (PAH) is a progressive vasculopathy characterized by pathological vascular remodeling, in which pulmonary artery smooth muscle cells (PASMCs) undergo phenotypic switching from a contractile to a synthetic state, driving excessive proliferation and migration. Here, we report that miR-199a-3p is significantly downregulated in both hypoxia/SU5416-induced PAH rat models and PDGF-BB-stimulated human PASMCs. Mechanistically, PDGF-BB stimulation induces the phosphorylation of STAT3, which directly binds to the TTCCCGGAA motif within the promoter of miR-199a-3p. This binding transcriptionally represses miR-199a-3p. Functional analyses demonstrated that miR-199a-3p overexpression maintains the PASMC contractile phenotype (upregulating MYH11 and SM22α) and suppresses proliferation and migration. Conversely, miR-199a-3p inhibition promotes synthetic phenotypic switching and activates the ERK/AKT signaling pathway. Furthermore, we identified YAP1 as a novel direct target of miR-199a-3p, linking miRNA downregulation to downstream proliferative signaling. Collectively, these findings establish a PDGF-BB/STAT3/miR-199a-3p/YAP1 regulatory axis that drives pathological PASMC phenotypic switching. This axis represents a promising therapeutic target for mitigating pulmonary vascular remodeling in PAH.
Acute myeloid leukemia (AML) is a malignant hematologic disease with poor prognosis, and improved understanding of its biology is critical for patient outcomes. While protein-coding genes in AML are well characterized, the role of long non-coding RNAs (lncRNAs) remains largely unexplored. Here, we investigated how lncRNAs contribute to AML biology and treatment resistance. Three high-throughput lncRNA-CRISPR-interference (CRISPRi) screens were performed in the AML cell line MOLM-13, targeting 7996 lncRNAs expressed in hematopoietic cells, with knockdowns directed to transcription start sites defined through cap analysis of gene expression (CAGE) sequencing. Effects on proliferation, differentiation, and response to the Bcl-2 inhibitor venetoclax were assessed. In total, 58, 4, and 23 lncRNAs were found to affect proliferation, differentiation, and venetoclax sensitivity, respectively. Three proliferation-associated lncRNAs (MIR17HG, CATG00000106133.1, and CATG00000056792.1) and one venetoclax-associated lncRNA (AC009299.3) were further investigated. CATG00000106133.1 was enriched in de novo and cytogenetically normal AML and correlated with NPM1 and IDH2 mutations. Gene Ontology and Reactome analyses of RNA-seq from CATG00000106133.1 knockout cells revealed roles in cytokine signaling and immune pathways. AC009299.3, linked to venetoclax response, was associated with poor outcome, adverse risk, and increased age in AML patients. Collectively, this study identifies four lncRNAs implicated in key leukemogenic processes, highlighting their potential for understanding AML biology, prognosis, and therapeutic response.
