Identification of prognostic biomarkers for hepatocellular carcinoma based on the m6A RNA modification

Skin cutaneous melanoma (SKCM) is a highly aggressive malignancy, and understanding the mechanisms underlying its metastasis is essential for improving patient prognosis. N6-methyladenosine (m6A) RNA modification is involved in tumor progression; however, its specific role in SKCM metastasis remains poorly defined. The present study aimed to identify m6A-related regulatory genes associated with SKCM metastasis and to assess their impact on the tumor immune microenvironment. Expression data from primary and metastatic SKCM samples were obtained from the Gene Expression Omnibus (GSE8401, GSE15605, GSE46517 and GSE65904) and The Cancer Genome Atlas-SKCM databases. A metastasis-risk prediction model was constructed using least absolute shrinkage and selection operator-Cox regression analysis. Differential expression analysis, functional enrichment, Pearson correlation, single-sample gene set enrichment analysis and competing endogenous (ce)RNA network analysis were performed. Key gene expression levels were evaluated using reverse transcription-quantitative PCR and immunohistochemistry. A total of 94 metastasis-related mRNAs were identified as differentially expressed, of which 45 demonstrated significant associations with m6A regulators. Among them, 12 genes were associated with patient prognosis, with cadherin 3 (CDH3), keratin 17 (KRT17), plakophilin 1 (PKP1) and cellular retinoic acid binding protein 2 (CRABP2) identified as key candidates. A ceRNA network comprising these four mRNAs, 13 long noncoding RNAs, and 20 microRNAs was constructed. These core genes demonstrated significantly higher expression levels in tumor tissues compared with in adjacent normal tissues, were associated with a worse overall survival, and revealed strong correlations with immune cell infiltration, particularly mast cells and Th17 cells. In conclusion, m6A RNA modification may contribute to SKCM metastasis by regulating the expression of CDH3, KRT17, PKP1 and CRABP2, as well as modulating the tumor immune microenvironment. These findings offer novel insights into the metastatic mechanisms of SKCM and identify potential biomarkers for its diagnosis, prognosis and targeted immunotherapy.

With the increasing application of nanoparticles (NPs) in medical and consumer applications, it is necessary to ensure their safety. As m6A (N6-methyladenosine) RNA modification is one of the most prevalent RNA modifications involved in many diseases and essential biological processes, the relationship between nanoparticles and m6A RNA modification for the modulation of these events has attracted substantial research interest. However, there is limited knowledge regarding the relationship between nanoparticles and m6A RNA modification, but evidence is beginning to emerge. Therefore, a summary of these aspects from current research on nanoparticle-induced m6A RNA modification is timely and significant. In this review, we highlight the roles of m6A RNA modification in the bioimpacts of nanoparticles and thus elaborate on the mechanisms of nanoparticle-induced m6A RNA modification. We also summarize the dynamic regulation and biofunctions of m6A RNA modification. Moreover, we emphasize recent advances in the application perspective of nanoparticle-induced m6A RNA modification in medication and toxicity of nanoparticles to provide a potential method to facilitate the design of nanoparticles by deliberately tuning m6A RNA modification.

Immunotherapy is a novel clinical approach that has shown clinical efficacy in multiple cancers. However, only a fraction of patients respond well to immunotherapy. Immuno-oncological studies have identified the type of tumors that are sensitive to immunotherapy, the so-called hot tumors, while unresponsive tumors, known as “cold tumors,” have the potential to turn into hot ones. Therefore, the mechanisms underlying cold tumor formation must be elucidated, and efforts should be made to turn cold tumors into hot tumors. N6-methyladenosine (m6A) RNA modification affects the maturation and function of immune cells by controlling mRNA immunogenicity and innate immune components in the tumor microenvironment (TME), suggesting its predominant role in the development of tumors and its potential use as a target to improve cancer immunotherapy. In this review, we first describe the TME, cold and hot tumors, and m6A RNA modification. Then, we focus on the role of m6A RNA modification in cold tumor formation and regulation. Finally, we discuss the potential clinical implications and immunotherapeutic approaches of m6A RNA modification in cancer patients. In conclusion, m6A RNA modification is involved in cold tumor formation by regulating immunity, tumor-cell-intrinsic pathways, soluble inhibitory mediators in the TME, increasing metabolic competition, and affecting the tumor mutational burden. Furthermore, m6A RNA modification regulators may potentially be used as diagnostic and prognostic biomarkers for different types of cancer. In addition, targeting m6A RNA modification may sensitize cancers to immunotherapy, making it a promising immunotherapeutic approach for turning cold tumors into hot ones.

Mechanosensitive ion channel-related genes in hepatocellular carcinoma: Unraveling prognostic genes and their roles in drug resistance and immune modulation.

Hepatocellular carcinoma (HCC) is a life-threatening cancer with rising incidence and mortality rates. Identifying new prognostic biomarkers is crucial for improving HCC management. This study investigates the role of Double PHD Fingers 1 (DPF1) in hepatocellular carcinoma (HCC), exploring its potential as a prognostic indicator and therapeutic target. We analyzed DPF1 expression in 374 hepatocellular carcinoma (HCC) tissues and 50 normal tissues from the TCGA-HCC database, as well as in 240 HCC tissues and 202 normal tissues from the ICGC-HCC repository. We examined the correlation between DPF1 expression and clinical parameters, immune cell infiltration, drug response profiles, cancer stem cell (CSC) characteristics, and its diagnostic/prognostic potential using various bioinformatics tools and statistical analyses. Validation was performed using the ICGC and HPA databases, and qRT-PCR was used to confirm DPF1 expression in HCC cell lines. DPF1 exhibited abnormal expression in HCC and several other malignancies. Elevated DPF1 levels were significantly associated with higher Alpha-fetoprotein (AFP) levels (p = 0.043) and poorer clinical outcomes, including diminished overall survival (OS) (p = 0.002), progression-free survival (PFS) (p = 0.018), and disease-specific survival (DSS) (p = 0.001). DPF1 expression was also linked to immune cell infiltration, immune checkpoint gene expression, drug sensitivity, and CSC characteristics. Notably, DPF1 was significantly overexpressed in HCC tissues and cell lines at both transcriptional and translational levels. Our study reveals that DPF1 is a novel prognostic biomarker in HCC, with potential implications for immunotherapy and drug resistance. Elevated DPF1 expression is associated with adverse clinical outcomes and may serve as a target for future therapeutic interventions in HCC.

Regulatory role and mechanism of m6A RNA modification in human metabolic diseases

The epitranscriptomics field has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here, we show that using direct RNA sequencing, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Specifically, we find that our algorithm, trained with m6A-modified and unmodified synthetic sequences, can predict m6A RNA modifications with ~90% accuracy. We then extend our findings to yeast data sets, finding that our method can identify m6A RNA modifications in vivo with an accuracy of 87%. Moreover, we further validate our method by showing that these ‘errors’ are typically not observed in yeast ime4-knockout strains, which lack m6A modifications. Our results open avenues to investigate the biological roles of RNA modifications in their native RNA context.

Parkinson's disease (PD) is a neurodegenerative disease with a high prevalence among the middle-aged and elderly population. The pathogenesis of PD is closely linked to the misfolding and aggregation of α-synuclein, which contributes to the formation of Lewy bodies. These processes are associated with the degeneration of dopaminergic neurons, a key neuropathological change that underlies the motor symptoms of PD. In addition, genetic susceptibility, mitochondrial dysfunction, oxidative stress and neuroinflammation are involved in the progress of the disease. Previous studies indicated that the dysregulation of epigenetic modifications, including DNA methylation and histone acetylation, may be the key pathophysiological factors in PD. N6-methyladenosine (m6A) is a dynamically reversible modification in eukaryotes RNA, and could regulate mRNA degradation, stability, maturation, and translation. Recently, clinical research has shown that the global m6A level is significantly reduced in PD patients as well as the expression changes in m6A-associated proteins. Moreover, the dysregulation of m6A modification was shown to impact dopamine metabolism and damage dopaminergic neurons, indicating that m6A RNA modification may play a critical role in the pathogenesis of PD. In this review, we summarize recent clinical studies on m6A RNA modification in PD patients and discuss the regulatory role of m6A modification in dopamine metabolism and dopaminergic neurons death. Furthermore, based on the different m6A modification databases and prediction websites, we analyzed the potential m6A modification sites on the mRNA of key PD pathogenic genes (SNCA, PRKN, PINK1, and LRRK2) for the first time, aiming to offer new gene targets and perspectives understanding the pathogenesis of PD.

Multilevel regulation of N6-methyladenosine RNA modifications: Implications in tumorigenesis and therapeutic opportunities

Liquid–liquid phase separation (LLPS) has been linked to the initiation and progression of cancers. This study aimed to investigate the LLPS-related molecular features and develop a prognostic signature for hepatocellular carcinoma (HCC). Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data were obtained from open-source repositories. The Seurat package was used for processing and analyzing scRNA-seq data. LLPS-related genes (LLPSRGs) were identified by integrating scRNA-seq and bulk RNA-seq data. Univariate Cox and LASSO regression analyses were employed to construct an LLPS-related prognostic risk model. A predictive nomogram was also developed based on the risk score and clinicopathologic features. Additionally, correlations between clinicopathological features, biological functions, and tumor mutations with prognostic risk were explored. Experimental validation included cell transfection, wound healing, and transwell assays. Fourteen distinct cell clusters were identified, with malignant hepatocytes exhibiting the highest LLPS score. High-LLPS hepatocytes strongly interacted with other cells, showing elevated expression of EGFR-ERGF, EGFR-AREG, MIF-CD44, and MIF-CXCR4 interactions. The LLPS score was associated with malignant differentiation of hepatocytes. Ten LLPSRGs were identified as part of the LLPS-related risk signature, and potential agents were predicted: Olitigaltin and Lactose for LGALS3, and Sitamaquine, Phenazopyridine, Sulfanilamide, Pamaquine, Sodium ascorbate, and Co-trimoxazole for G6PD. Knockdown of LGALS3 inhibited HCC cell migration and invasion. LLPS-related molecular characteristics were identified, and an LLPS-related prognostic model was developed, offering novel insights into HCC research and providing potential therapeutic targets.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-20691-6.

BackgroundHepatocellular carcinoma (HCC) is a prevalent malignant tumor. Long non-coding RNAs (lncRNAs) have been demonstrated to be abnormally expressed in many tumors and act as crucial regulators in various biological processes. However, the expression and function of the recently identified macrophage-associated lncRNA ELMO1 antisense RNA 1 (ELMO1-AS1) in HCC are unclear.MethodsThe expression of ELMO1-AS1 was determined in HCC tissues and adjacent nontumorous tissues by quantitative real-time polymerase chain reaction (qRT-PCR). The Kaplan-Meier survival analysis and Cox regression analysis were performed to establish the correlation between the expression level and survival of HCC patients in a training set and a validation set, respectively. The overexpression experiments were also conducted to investigate the biological role of ELMO1-AS1 in HCC cells.ResultsWe uncovered that ELMO1-AS1 was significantly downregulated in HCC tissues, and high expression of ELMO1-AS1 is correlated with optimistic treatment outcome suggesting its potential as an independent prognostic biomarker for HCC. It was also found that overexpression of ELMO1-AS1 in HCC cells suppressed cell proliferation, migration and invasion and engulfment and cell motility 1 (ELMO1) may be a target of ELMO1-AS1.ConclusionOur results suggested that macrophage-associated lncRNA ELMO1-AS1 could be a crucial regulator involved in HCC progression and considered as a potential prognostic biomarker and therapeutic target for HCC.

Despite advances in hepatocellular carcinoma (HCC) management, prognosis remains poor. Advanced-stage diagnosis often excludes curative treatments, and current biomarkers (e.g., alpha-fetoprotein [AFP]) have limited utility in early detection. Liquid biopsy has emerged as a promising cancer detection tool, with circulating cell-free DNA (ccfDNA) showing significant diagnostic potential. This proof-of-concept study aimed to investigate the potential role of tumor fraction (TF) within ccfDNA as a biomarker in HCC patients. A total of sixty patients were recruited, including thirteen with chronic liver disease (CLD), twenty-four with cirrhosis, and twenty-three with HCC. Plasma samples were collected, and ccfDNA was extracted for shallow whole genome sequencing (sWGS) analysis. The TF was calculated by focusing on somatic copy number alterations (SCNAs) within the ccfDNA. Among patients with CLD and cirrhosis (n = 37), ctDNA was undetectable in all but one cirrhotic patient who exhibited a significant tumor fraction (TF) of 17% and subsequently developed HCC. Conversely, five out of twenty-three HCC patients (21.7%) displayed detectable ctDNA with TF levels ranging from 3.0% to 32.6%. Patients with detectable ctDNA were characterized by more aggressive oncological features, including a higher number of nodules (p = 0.005), advanced-stage disease (60% BCLC C, p = 0.010), and poorer response to therapy (80% PD, p = 0.001). Moreover, the overall survival (OS) was significantly reduced in patients with detectable ctDNA (median OS: 17 months; CI 95% 4.5-26.5) compared to those without (median OS: 24.0 months; CI 95% 7.0-66.0; log-rank p = 0.002). Our results suggest that the analysis of TF by sWGS is a promising non-invasive tool for the identification of HCC with aggressive clinical behavior, whereas it is not sensitive enough for early HCC detection. This molecular assay can improve prognostic stratification in HCC patients.

Hepatocellular carcinoma (HCC) remains the main type of liver cancer. Understanding the molecular and immune mechanisms of HCC tumorigenesis are required to develop effective biomarkers. This study is designed to measure the circulating MMP9 and CEBPα to provide a diagnostic and prognostic biomarker for HCV-genotype (4) induced liver cirrhosis and carcinogenesis. This study included one hundred Egyptian patients, divided into two groups 50 patients each. The first group: classified into Chronic Liver Disease (CLD) without cirrhosis (n=25) and CLD with cirrhosis (n=25). The second group: classified into CLD patients with HCC, (n=25), and healthy control (25 volunteers). The expression of MMP9 and CEBPα genes were analysed using Real-Time PCR. Our results showed significant downregulation in MMP9 and CEBPα genes in cirrhotic and HCC patients (p< 0.001 and p<0.001) respectively. There was a significant (p< 0.001) diagnostic capacity between HCC patients against CLD with or without cirrhosis patients. Bioinformatics analysis revealed a relationship between MMP9 and CEBPα genes. In conclusion, the gradual decrease in the expression of MMP9 and CEBPα gene during the progression of the disease recommended use of MMP9 and CEBPα genes as a diagnostic and prognostic biomarker for both cirrhosis and HCC in HCV-genotype (4) patients.

Recently, increasing data have suggested that the lncRNA small nucleolar RNA host genes (SNHGs) were aberrantly expressed in hepatocellular carcinoma (HCC), but the association between the prognosis of HCC and their expression remained unclear. The purpose of this meta-analysis was to determine the prognostic significance of lncRNA SNHGs in HCC. We systematically searched Embase, Web of Science, PubMed, and Cochrane Library for eligible articles published up to February 2024. The prognostic significance of SNHGs in HCC was evaluated by hazard ratios (HRs) and 95% confidence intervals (CIs). Odds ratios (ORs) were used to assess the clinicopathological features of SNHGs. This analysis comprised a total of 25 studies covering 2314 patients with HCC. The findings demonstrated that over-expressed SNHGs were associated with larger tumor size, multiple tumor numbers, poor histologic grade, earlier lymphatic metastasis, vein invasion, advanced tumor stage, portal vein tumor thrombosis (PVTT), and higher alpha-fetoprotein (AFP) level, but not with hepatitis B virus (HBV) infection, and cirrhosis. In terms of prognosis, patients with higher SNHG expression were more likely to have shorter overall survival (OS), relapse-free survival (RFS), and disease-free survival (DFS). In conclusion, upregulation of SNHGs expression correlates with shorter OS, RFS, DFS, tumor size and numbers, histologic grade, lymphatic metastasis, vein invasion, tumor stage, PVTT, and AFP level, suggesting that SNHGs may serve as prognostic biomarkers in HCC.

Cell division cycle associated 5 (CDCA5) has been associated with the progression of several types of cancers. However, its possible role and mechanism in hepatocellular carcinoma (HCC) remain unknown. In the present study, immunohistochemical staining and real-time PCR were used to assess CDCA5 protein and mRNA levels in clinical samples. Statistical analysis was performed to explore the clinical correlation between CDCA5 protein expression and clinicopathological features and overall survival in HCC patients. Cell counting and colony formation assays were employed to analyse the effect of CDCA5 on cell proliferation, and flow cytometry was used to study the role of CDCA5 in cell cycle progression and apoptosis. Moreover, subcutaneous xenograft tumour models were implemented to predict the efficacy of targeting CDCA5 in HCC in vivo. We found that CDCA5 expression was significantly higher in HCC tumour tissues, was associated with clinicopathological characteristics, and predicted poor overall survival in HCC patients. Silencing of CDCA5 with small interfering RNA (siRNA) inhibited cell proliferation and induced G2/M cell cycle arrest in vitro. The xenograft growth assay revealed that CDCA5 downregulation impeded HCC growth in vivo. Further study indicated that CDCA5 depletion decreased the levels of ERK1/2 and AKT phosphorylation in vitro and in vivo. Taken together, these results indicate that CDCA5 may act as a novel prognostic biomarker and therapeutic target for HCC.