Search Results (404)

The continuous expression of HPV oncogenes E6 and E7 contributes to the maintenance of the cervical cancer (CC) phenotype by altering gene expression programs involved in tumor progression and aggressiveness. MicroRNAs (miRNAs) have emerged as critical regulators of gene expression in CC, including miR-218-5p, which has been described as a tumor suppressor. In this study, we investigated the impact of HPV-16 oncoproteins E6 and E7 on the regulation of miR-218-5p expression and its target gene PIK3C2A, as well as their functional and clinical relevance in CC. We found that miR-218-5p expression is significantly reduced in HPV-16-positive CC cell lines, while PIK3C2A expression is increased. Silencing the expression of the E6/E7 oncogenes in Ca Ski cells restored miR-218-5p levels and reduced PIK3C2A expression. Conversely, overexpression of the E6 and E7 oncogenes in C-33 A cells significantly decreased miR-218-5p expression and increased PIK3C2A expression. Functional assays performed on C-33 A cells expressing E6 and E7 revealed that ectopic expression of miR-218-5p suppresses cell proliferation and migration, effects that are partially mediated by PIK3C2A. Bioinformatics analysis showed that low miR-218-5p expression and high PIK3C2A expression are associated with reduced overall survival in patients with cervical cancer. Our findings identify the miR-218-5p/PIK3C2A axis as a novel regulatory pathway modulated by HPV-16 oncoproteins E6 and E7 that contributes to CC cell proliferation and migration. Furthermore, miR-218-5p and PIK3C2A emerge as potential prognostic biomarkers in CC. Full article

Potyvirus rapae (turnip mosaic virus, TuMV) is widely used as a model system in plant–virus interaction studies. The TuMV RNA genome encodes 11 proteins, some of which remain poorly characterized, while the functions of others are well defined. Studying individual proteins in isolation may not recapitulate native expression levels, subcellular localization, and interaction with host factors during virus replication and movement. An alternative approach is to tag individual viral proteins in the context of an infectious clone. Epitope tags may alter protein functions and affect viral replication, movement, or a combination of essential steps, thus leading to changes in pathogenicity. Because they have central roles in viral infection, here we measured the effect of individually tagging the helper component proteinase (HC-Pro) and nuclear inclusion protein b (NIb) with a 6His-3xFLAG tag. Epitope tags were placed at the N-terminus of HC-Pro and the N- and C-termini of NIb within a TuMV infectious clone carrying coding sequences for the green fluorescent protein (TuMV-GFP). Constructs carrying a tagged HC-Pro displayed pathogenicity similar to that observed for TuMV-GFP in Nicotiana benthamiana and Arabidopsis thaliana plants. In contrast, infectivity of NIb-tagged clones became temperature sensitive and, even at the permissive temperature, showed reduced pathogenicity compared to TuMV-GFP. Providing a silencing suppressor in trans did not restore infection efficiency, suggesting reduced viral fitness due to structural or functional disruption caused by the epitope tags. Structural models generated using AlphaFold2 showed no effect of the tag on HC-Pro. In contrast, structural models illustrated tag interference with the NIb catalytic site. AlphaFold2 was further used to predict the structural impact of several tags on NIb and to predict the effect of a 6HIS-3xFlag tag on all other TuMV proteins. This study provides a broadly applicable framework for selecting suitable epitope tags to mark viral proteins and maintain function in the context of virus infection. Full article

DNA methylation is a key mechanism in epigenetic regulation and plays a pivotal role in tumor initiation, progression, and therapeutic resistance. We begin by elucidating how the dysregulation of key DNA methylation enzymes in tumors drives concurrent global hypomethylation and cytosine-phosphate-guanine (CpG) island hypermethylation. This aberrant epigenetic landscape promotes tumorigenesis through silencing tumor suppressor genes and triggering abnormal activation of oncogenic signaling pathways. Notably, DNA methylation is intimately linked to cellular pyroptosis. In particular, the hypermethylation-mediated silencing of pyroptosis effector genes represents a critical epigenetic mechanism underlying acquired drug resistance. Targeting DNA methylation with epigenetic drugs offers a novel strategy to resensitize tumors to chemotherapy, radiotherapy, and immunotherapy. Moreover, advances in nanomedicine have yielded smart platforms for the precise administration of epigenetic modulators and combination therapies. These platforms enable a coordinated “epigenetic priming-pyroptosis execution” strategy, which holds promises for reversing therapeutic resistance and remodeling the tumor immune microenvironment. By integrating DNA methylation regulation, pyroptosis mechanisms, and nano-targeted strategies, this review aims to provide a theoretical framework and novel perspectives for developing innovative, epigenetically driven anti-tumor therapies. Full article

Human pluripotent stem cells (hPSCs) are a promising source for regenerative medicine due to their self-renewal and differentiation capacities. However, genetic instability acquired during reprogramming and in vitro culture presents major safety challenges for clinical translation. Recurrent mutations, especially structural variants (SVs), are of particular concern as they can impair differentiation and increase tumorigenic risk. In this review, we establish and systematically explore a central causal axis: SVs–three dimensional (3D) genome disruption–safety of hPSC-based therapy. We propose that SVs critically compromise therapeutic safety by perturbing the 3D architecture of the genome, leading to pathogenic rewiring of enhancer–promoter interactions. This rewiring, exemplified by “enhancer hijacking” and “enhancer loss,” can aberrantly activate oncogenes or silence tumor suppressors even in the absence of copy number variations. Thus, 3D genome disruption provides a key mechanistic explanation for SV-driven tumorigenic potential and impaired differentiation fidelity in hPSCs. By highlighting this causal axis, our review not only advances the mechanistic understanding of SV-associated risks but also provides actionable insights for the development of more rigorous quality standards for hPSC-based cell therapy products. Full article

The ubiquitously transcribed tetratricopeptide repeat Y-linked gene (UTY/KDM6C), a catalytically impaired histone demethylase encoded on the Y chromosome, has garnered increasing attention for its emerging roles in tumorigenesis and cancer progression. Despite high sequence homology with its X-linked paralog UTX/KDM6A, UTY exhibits markedly reduced or absent H3K27me3 demethylase activity due to critical amino acid substitutions in its Jumonji C domain. Consequently, UTY primarily functions through non-enzymatic mechanisms, acting as a scaffold in chromatin-remodelling complexes like COMPASS and SWI/SNF, or mediating protein–protein interactions that regulate transcriptional programs independent of demethylation. This aligns with epigenetic dysregulation in cancers, where imbalances in repressive H3K27me3 and active H3K4me either drive tumour suppressor silencing or oncogene activation. Unlike frequently mutated UTX in cancers such as breast, renal cell carcinoma, and acute myeloid leukaemia, UTY’s contributions in cancer are less defined, constrained by male-specific expression. Emerging evidence suggests UTY as a context-dependent tumour suppressor in AML and squamous-like pancreatic ductal adenocarcinoma. While direct functional validation remains limited in several cancer types, UTY is increasingly implicated as a potential tumour suppressor in haematological malignancies and prostate cancer. Therapeutically targeting UTY’s scaffold functions shows promise for male-specific cancers and merits future investigation. Full article

Background/Objectives: MicroRNAs (miRNAs) are key regulators of gene expression and have been implicated in multiple aspects of cancer progression. However, the role of miR-214-3p in breast cancer remains controversial. In this study, we investigated the functional role of miR-214-3p and explored its potential regulatory target in breast cancer, particularly in triple-negative breast cancer (TNBC). Methods: miR-214-3p expression was evaluated in breast cancer cell lines. Luciferase reporter assays were performed to assess functional targeting of the FRK 3′-UTR. Functional assays, including proliferation, migration, and invasion assays, were conducted following miR-214-3p overexpression or FRK silencing. Results: miR-214-3p was markedly upregulated in TNBC cells (MDA-MB-231), while Fyn-related kinase (FRK), a potential tumor suppressor, showed an inverse expression trend. Luciferase reporter assays demonstrated that miR-214-3p functionally targets the 3′-UTR of FRK. Functional analyses revealed that overexpression of miR-214-3p significantly increased cell proliferation, migration, and invasion. Notably, silencing of FRK recapitulated these effects, supporting its role as a functional mediator of miR-214-3p. Conclusions: This study identifies a miR-214–FRK regulatory axis in breast cancer and suggests its contribution to aggressive tumor behavior. Targeting miR-214-3p or modulating FRK activity may represent a potential therapeutic strategy. Full article

Colorectal cancer (CRC) is the third most commonly diagnosed malignancy worldwide, with molecular heterogeneity complicating early detection and treatment stratification. The insulin-like growth factor (IGF) axis interacts bidirectionally with immune regulatory mechanisms in ways that shape tumor phenotype and therapeutic vulnerability. This review synthesizes evidence on how IGF signaling orchestrates immunosuppression through effects on tumor-associated macrophages, regulatory T cells, and myeloid-derived suppressor cells, while inflammatory cytokines reciprocally modulate IGF bioavailability. Three mechanistic principles emerge: IGF binding protein 2 (IGFBP-2) functions as a central coordinator linking growth factor signaling to immune evasion through STAT3-dependent pathways driving M2 macrophage polarization and regulatory T cell differentiation; IGF–immune crosstalk varies considerably across molecular subtypes, with microsatellite-stable tumors exhibiting high reliance on IGF-I receptor-mediated immune silencing; and local paracrine IGF production increasingly dominates over systemic regulation as disease progresses. These bidirectional connections establish self-reinforcing circuits that determine whether tumors remain immunologically responsive or develop immune exclusion. Multi-marker panels incorporating IGFBP-2 alongside complementary biomarkers have shown improved diagnostic performances for early CRC detection, underscoring the need for the large-scale prospective clinical evaluation of IGF network components as biomarkers for CRC in diverse populations. The convergence of IGF signaling with checkpoint regulation suggests that combined targeting warrants investigation for resistance in tumors lacking effective immunotherapy options. Full article

Background: Breast cancer susceptibility gene 1 (BRCA1) is a pivotal regulator of DNA repair, and its loss through germline mutations is strongly linked to the development of aggressive breast cancers with characteristic clinical and pathological features. Beyond genetic disruption, epigenetic silencing via promoter hypermethylation has emerged as a non-mutational mechanism of tumour suppressor inactivation and a potential biomarker for guiding therapeutic decisions. Here, we investigate BRCA1 promoter methylation, its impact on gene expression, and its association with clinicopathological features in a cohort of African women with breast cancer. Methods: Matched tumour and adjacent normal tissues from 27 Black African women with breast cancer were analysed for BRCA1 promoter methylation and gene expression using bisulfite pyrosequencing and quantitative real-time PCR. Associations with clinicopathological variables were assessed using Spearman’s correlation analyses. Results: Five CpG sites within the BRCA1 promoter were significantly hypermethylated in breast tumours compared with matched adjacent normal tissues and showed an inverse association with BRCA1 mRNA expression. Elevated promoter methylation was enriched in hormone receptor-negative and triple-negative breast cancer subtypes and was not influenced by neoadjuvant chemotherapy. BRCA1 promoter methylation occurred independently of BRCA1 mutational status. No significant associations were observed between BRCA1 methylation and age, body mass index, smoking status, or alcohol consumption. Conclusions: Our findings provide evidence of BRCA1 epigenetic silencing in breast tumours from African women, particularly within aggressive hormone receptor-negative subtypes. These results suggest that BRCA1 promoter methylation may represent a clinically informative biomarker for patient stratification and highlight the importance of validation in larger, population-representative cohorts before clinical translation. Full article

Studying epigenetic changes in cancer development can reveal the role of tumor suppressor genes and their regulation by DNA methylation. CpG islands, found in promoter regions, are of particular interest, as their hypermethylation can silence tumor suppressor gene expression. Here, we present a practical analysis pipeline for wet-lab biologists with the aim of identify novel epigenetically regulated tumor suppressors using freely available online tools. Bioinformatic platforms such as the R2 Genomics Analysis and Visualization Platform enable analysis of genomic organization, CpG islands, and regulatory elements. Differential methylation and gene expression analyses are based on datasets including TCGA, using tools such as MethSurv, TCGA Wanderer, and GEPIA2 to correlate DNA methylation with gene expression. This bioinformatic step is the basis for the tumor suppressor verification in the wet-lab. Using this pipeline, we identified CLDN10 and GJB2 as potential tumor suppressors in melanoma. Experimentally, our approach includes DNA methylation analysis based on DNA bisulfite conversion, combined bisulfite restriction analysis (CoBRA), pyrosequencing for specific CpG methylation quantification, and RT-PCR for RNA expression quantification. We verify these results in primary tumors, metastases, and cell line models. This approach supports efficient identification of novel epigenetically regulated tumor suppressors, providing practical research guidelines. Full article

Colorectal cancer (CRC) is a significant cause of cancer mortality in the world, and its etiology is complicated by genetic and epigenetic changes. As one of the most important tumor progression regulators, Zinc Finger E-box Binding Homeobox 1 (ZEB1) is a transcription factor that has a key role in epithelial–mesenchymal transition (EMT), which is essential in the metastasis, drug resistance, and plasticity of cancer cells in CRC. ZEB1 silences the expression of epithelial markers, including E-cadherin, and it induces the development of mesenchymal properties, such as invasion and metastasis, i.e., tumor aggressiveness. ZEB1 drives epigenetic reprogramming in CRC by coordinating histone deacetylation, histone methylation, and DNA methylation of epithelial tumor suppressor gene promoters and by engaging in reciprocal regulatory interactions with non-coding RNAs, including the miR-200 family. Furthermore, multiple oncogenic signaling cascades, including Wnt/β-catenin, TGF-β, NF-κB, MEK-ERK, JAK/STAT3, and HIF-1α, converge on ZEB1 to amplify its transcriptional and epigenetic activity, positioning ZEB1 as a nodal integrator of extracellular cues and epigenetic reprogramming in CRC metastasis. This review integrates three interconnected regulatory layers, i.e., (1) ZEB1’s direct epigenetic control of target gene expression via histone modification and DNA methylation, (2) post-transcriptional regulation of ZEB1 itself by ncRNAs (miRNAs, circRNAs, and lncRNAs) that create feedback circuits modulating layer 1, and (3) upstream modulation of ZEB1 transcriptional activity by oncogenic signaling pathways (Wnt/β-catenin, TGF-β, NF-κB, MEK-ERK, JAK/STAT3, and HIF-1α) to provide a comprehensive picture of ZEB1 in CRC metastasis and its therapeutic implications. Full article

Tubule-derived pro-fibrotic mediators are central for the development of kidney fibrosis. We previously showed that fibrotic stimuli activate and elevate GEF-H1 (ARHGEF2) in tubular cells, leading to RhoA-dependent fibrotic reprogramming. In search of new mechanisms of GEF-H1 regulation, here we used immunoprecipitation and proximity ligation assay to show interaction between GEF-H1 and Myotonic Dystrophy Kinase-related Cdc42-binding kinase (MRCK)α in tubular cells. MRCKα silencing elevated GEF-H1 activity, and induced GEF-H1-dependent RhoA activation, stress fibre formation and myosin light chain phosphorylation. MRCKα depletion also elevated phospho-cofilin levels in a RhoA-dependent manner. The fibrogenic cytokine TGFβ1 rapidly increased binding between GEF-H1 and MRCKα, while MRCKα silencing augmented TGFβ1-induced GEF-H1 activation, suggesting a negative feedback loop. An mRNA array detecting fibrogenic genes revealed increase in a subset of basal and TGFβ1-induced genes following MRCKα depletion. MRCKα silencing promoted nuclear translocation of the profibrotic transcriptional co-activator Myocardin-Related Transcription Factor (MRTF), and MRTF-A+B depletion prevented increase in ACTA2 (α-smooth muscle actin), a key marker of fibrotic reprogramming. Finally, total MRCKα mRNA was reduced in a murine kidney fibrosis model, and immunohistochemistry revealed a decrease in tubular MRCKα. Taken together, we identified MRCKα as a new suppressor of GEF-H1/RhoA/MRTF signaling. Reduced MRCKα expression in kidney fibrosis may promote tubular fibrotic gene expression. Full article

Background: Extracellular vesicles (EVs) play an important role in tumor progression and intercellular communication, yet the contribution of specific cancer-related genes to EV secretion remains incompletely defined. Methods: To address this, we performed an siRNA-based loss-of-function screen targeting 30 frequently altered (proto-)oncogenes and tumor suppressor genes in the colorectal carcinoma cell line HCT-116 to assess their impact on EV release. EVs were isolated by sequential ultracentrifugation to obtain P14 and P100 fractions pelleting at 14,000× g or 100,000× g, respectively, and were characterized by nanoparticle tracking analysis, EV marker expression, and total protein quantification. Cell viability was assessed to control for potential apoptosis-related effects. Results: With few exceptions, knockdown of the investigated genes led to an increase in EV secretion. Silencing of KRAS and BRAF resulted in significantly elevated P14 EV levels, increased EV marker expression, and higher total protein content, while KRAS knockdown was additionally associated with a shift toward larger particle sizes. Downregulation of CTNNB1 increased P14 and decreased P100 EV secretion, whereas CDH1 knockdown reduced P14 EV levels and slightly increased P100 EVs. No general distinction between tumor suppressor genes and (proto-)oncogenes regarding their effects on EV secretion was observed, and cell viability was not significantly altered under the experimental conditions. Conclusions: These findings suggest that components of the Ras/Raf/MAPK and Wnt signaling pathways may contribute to the regulation of EV secretion in colorectal cancer cells. Full article

Coding transcripts-derived small interfering RNAs (ct-siRNAs) have emerged as a special class of endogenous siRNAs and have been implicated in the regulation of gene expression in plants, particularly under conditions where RNA metabolic pathways are perturbed. When the RNA quality control (RQC) system is impaired, the aberrant mRNA fragments were converted to double stranded forms by RNA-directed RNA polymerase 6 (RDR6) with the assistance of Suppressor of Gene Silencing 3 (SGS3) and subsequently processed by DICER-LIKE proteins into 21-nt and 22-nt ct-siRNAs. The accumulation of ct-siRNAs and the resulting suppression of their cognate genes are usually associated with altered plant growth and stress response. In this review, we summarize our current understanding of the ct-siRNAs, particularly their biogenesis under different RNA metabolic defective conditions. Comparative analysis of these genetic contexts indicates that ct-siRNAs act through translation inhibition and/or mRNA cleavage, with regulatory outcomes influenced by siRNA length and genetic background. We further summarize the biological consequence of ct-siRNA accumulation, which are frequently associated with impaired plant growth and stress adaptation. Finally, we discuss current controversies on ct-siRNAs research and highlight key unsolved questions for future investigation. Collectively, this review highlights ct-siRNAs as a link between impaired RNA metabolisms and post-transcriptional gene silencing, with context-dependent effects on plant growth and stress responses. Full article

Insect infestation poses a significant threat to global agriculture by impairing plant growth and reducing crop yields. The western flower thrip (WFT) causes substantial damage through both direct feeding and transmission of plant viruses. Although the jasmonic acid (JA) signaling pathway is known to participate in plant defense against WFTs, the underlying molecular mechanisms in non-model crops such as peppers, remain largely elusive. This study investigates the role of suppressor of prosystemin-mediated responses2 (Spr2) within JA-mediated defense against WFTs in pepper. Through an integrated approach employing virus-induced gene silencing (VIGS), transcription analysis, phytohormone quantification, insect behavior assays and life history investigations, we demonstrated that silencing CaSpr2 significantly reduced JA and JA-Ile accumulation, and led to a strong feeding preference of WFTs for CaSpr2-silenced plants. Furthermore, the adult lifespan, survival rate, female fecundity, oviposition rate, and population parameters of WFTs were significantly improved on CaSpr2-silenced plants. Spr2 functions as an essential component within the JA signaling pathway, thereby playing a critical role in conferring resistance to WFTs in cultivated pepper. These findings provide profound insights and practical implications for breeding thrips-resistant cultivars in non-model plants, through genetic manipulation of JA signaling, offering a promising avenue for sustainable agricultural pest management. Full article

Plant RNA interference (RNAi) is a fundamental antiviral defense that relies on coordinated activities of DICER-like endonucleases (DCLs), Argonaute proteins (AGOs) and RNA-dependent RNA polymerases (RDRs). Over the past decades, studies using model and crop species have uncovered complex and often redundant roles for DCLs and RDRs in generating and amplifying virus-derived small interfering RNAs (vsiRNAs), in addition to connections with transcriptional gene silencing (TGS) and epigenetic defenses against DNA viruses. Concurrently, plant viruses have evolved diverse counterstrategies—proteinaceous RNA silencing suppressors (RSSs), exoribonuclease (XRN)-resistant noncoding RNAs, and indirect manipulation of host pathways—to evade RNAi. Driven by the co-evolutionary arms race, plants have developed sophisticated counter-countermeasures that modulate or overcome viral anti-RNAi activity. Accumulated evidence suggests that plants encode host factor genes that are activated to degrade or sequester viral components such as RSSs against viral infection. On the other hand, plants have also evolved endogenous host modulators of antiviral RNAi that can either reinforce the antiviral response or be co-opted by viruses to antagonize it, representing a furious dynamic molecular battling mechanism. Here, we review recent advances in the molecular functions of DCLs and RDRs across species, summarize newly discovered viral counter-defenses (including RNA-based suppressors), and discuss host counter-countermeasures. We research key areas—such as the roles of RDRγ-class proteins, RTL1 (RNase three-like 1)-mediated competition with DCLs, and the mechanistic impact of viral noncoding RNAs—and outline translational opportunities for improving virus resistance in crops through breeding, biotechnological approaches, and RNA-based applications. Full article