The crosstalk between cellular survival pressures and N6-methyladenosine modification in hepatocellular carcinoma.

Within the tumor microenvironment, survival pressures are prevalent with potent drivers of tumor progression, angiogenesis, and therapeutic resistance. N6-methyladenosine (m6A) methylation has been recognized as a critical post-transcriptional mechanism regulating various aspects of mRNA metabolism. Understanding the intricate interplay between survival pressures and m6A modification provides new insights into the molecular mechanisms underlying hepatocellular carcinoma (HCC) progression and highlights the potential for targeting the survival pressures-m6A axis in HCC diagnosis and treatment. A literature search was conducted in PubMed, MEDLINE, and Web of Science for relevant articles published up to April 2024. The keywords used for the search included hepatocellular carcinoma, cellular survival, survival pressure, N6-methyladenosine, tumor microenvironment, stress response, and hypoxia. This review delves into the multifaceted roles of survival pressures and m6A RNA methylation in HCC, highlighting how survival pressures modulate the m6A landscape, the impact of m6A modification on survival pressure-responsive gene expression, and the consequent effects on HCC cell survival, proliferation, metastasis, and resistance to treatment. Furthermore, we explored the therapeutic potential of targeting this crosstalk, proposing strategies that leverage the understanding of survival pressures and m6A RNA methylation mechanisms to develop novel, and more effective treatments for HCC. The interplay between survival pressures and m6A RNA methylation emerges as a complex regulatory network that influences HCC pathogenesis and progression.

Fu CL ，Zhao ZW ，Zhang QN 《Hepatobiliary & Pancreatic Diseases International》

PIWIL genes in hepatocellular carcinoma: a multi-omics approach uncovering dysregulated expression and ceRNA networks in mice.

This multi-omics study delves into the expression patterns of PIWIL genes and their correlation with hepatocellular carcinoma (HCC) progression, utilizing whole transcriptome sequencing, bioinformatics, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) in mice. We identified differential expression levels of PIWIL genes between HCC and control tissues and analyzed their roles within the competing endogenous RNA (ceRNA) network related to regulatory non-coding RNA-mediated gene silencing (RNGS). Our findings showed that Piwil1 and Piwil4 were overexpressed while Piwil2 is underexpressed. As ceRNAs, specific lncRNAs, including Pvt1, Gas5, and BGIGI10090_38749, might sponge up miR-351-5p and miR-31-5p, promoting Piwil1 and Piwil4 expression, while miR-133b-3p, lacking ceRNA sponge absorption, continues to inhibit Piwil2. Through their interactions with PPI proteins encoded by RNGS genes, especially Dhx9, Drosha, Mov10, and Tdrd1, PIWI family members might play a multifaceted role in regulating gene expression and metabolic processes, thereby involving the development and progression of HCC. These interactions within the PPI network could influence the stability and activity of PIWIL proteins and contribute to the overall regulation of gene expression and HCC progression. In the RNGS, a diverse array of miRNAs, genes, lncRNAs, circRNAs, and pseudogenes have been observed, which are suggested to intricately interplay, potentially weaving a complex ceRNA regulatory network. Abnormally expressed miRNA-targeted genes in RNGS are associated with key biological processes, such as lipid metabolism and immune responses, crucial for tumor cell survival, and processes supporting tumor growth and invasion, like translation and cytoskeleton organization. This regulation is reflected in distinct KEGG pathways for downregulated and upregulated targets, highlighting the dualistic role of PIWIL genes in modulating HCC progression. The study concludes that PIWI family members have a correlation with HCC progression and play divergent roles in the pathogenesis, with overexpression of the Piwil1 and Piwil4 potentially promoting HCC progression and underexpression of Piwil2 likely suppressing tumor development. The ceRNA mechanism and PPI network are crucial in regulating the expression and function of PIWIL genes, respectively. The intricate ceRNA network potentially regulates the expression of miRNA-targeted genes in RNGS, which might be crucial for tumor survival and promotion, with impacts on immune responses and cell growth based on enriching results of dysregulated miRNA-targeted genes in HCC. By shedding light on the molecular intricacies of HCC, this multi-omics study underscores the pivotal roles of epigenetic regulations, especially the influence of PIWI family genes with other genes and ncRNAs in the RNGS process in HCC pathology. The findings offer valuable insights into the molecular mechanisms underpinning HCC, which may inform future research into potential targets for therapeutic intervention. The future research could benefit from integrating a diverse range of methodologies to further elucidate the roles of PIWIL genes in HCC progression, building upon the findings presented here.

Huang H ，Lu R ，Peng S ，Huang S ，Mo Y ，Li G ... -  《-》

Integrating single-cell RNA-Seq and bulk RNA-Seq data to explore the key role of fatty acid metabolism in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a predominant cause of cancer-related mortality globally, noted for its propensity towards late-stage diagnosis and scarcity of effective treatment modalities. The process of metabolic reprogramming, with a specific emphasis on lipid metabolism, is instrumental in the progression of HCC. Nevertheless, the precise mechanisms through which lipid metabolism impacts HCC and its viability as a therapeutic target have yet to be fully elucidated. In the current investigation, single-cell RNA sequencing in conjunction with weighted gene co-expression network analysis (WGCNA) was utilized to delineate lipid metabolism-related genes correlated with the prognostic outcomes of hepatocellular carcinoma (HCC). Data procurement encompassed transcriptomic and clinical datasets from HCC patients, sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) repositories. Subsequent to this, consensus clustering analysis was implemented to stratify patients into distinct subgroups, contingent upon the expression patterns of lipid metabolism genes. Further analytical procedures involved functional enrichment analysis, evaluation of immune infiltration, and examination of the mutation landscape.PTGES3 was identified as a pivotal gene associated with lipid metabolism. Subsequent to its identification, cellular communication analysis was employed to assess the immunological attributes of PTGES3 within the tumor microenvironment. The functional role of PTGES3 was further corroborated through molecular docking simulations and in vitro experimental assays. We identified 27 genes associated with lipid metabolism, 18 of which exhibited significant correlation with overall survival in HCC patients. PTGES3 emerged as a central gene, demonstrating a robust association with immune cell infiltration and unfavorable prognosis. Cellular communication analysis revealed that PTGES3 exhibits the highest communication intensity with T cells, modulating the tumor microenvironment by potentiating the FN1/CD44 + MDK/NCL signaling pathway. Elevated expression of PTGES3 was linked to immunosuppressive cascades, diminished responsiveness to immunotherapy, and inferior overall survival outcomes. Molecular docking analysis indicated that etoposide, methotrexate, and doxorubicin could effectively bind to PTGES3. In vitro experiments confirmed that PTGES3 knockdown significantly impaired the proliferation, invasion, and migration of HCC cells. This study highlights the pivotal role of lipid metabolism in HCC progression and identifies PTGES3 as a potential prognostic biomarker and therapeutic target. These findings offer new insights into the development of targeted therapies for HCC, particularly in patients with high PTGES3 expression.

Dai H ，Tao X ，Shu Y ，Liu F ，Cheng X ，Li X ，Shu B ，Luo H ，Chen X ，Cheng Z ... -  《Scientific Reports》

N6-methyladenosine-modified long non-coding RNA KIF9-AS1 promotes stemness and sorafenib resistance in hepatocellular carcinoma by upregulating SHOX2 expression.

Hepatocellular carcinoma (HCC) is a prevalent and aggressive tumor. Sorafenib is the first-line treatment for patients with advanced HCC, but resistance to sorafenib has become a significant challenge in this therapy. Cancer stem cells play a crucial role in sorafenib resistance in HCC. Our previous study revealed that the long non-coding RNA (lncRNA) KIF9-AS1 is an oncogenic gene in HCC. However, the role of KIF9-AS1 in drug resistance and cancer stemness in HCC remains unclear. Herein, we aimed to investigate the function and mechanism of the lncRNA KIF9-AS1 in cancer stemness and drug resistance in HCC. To describe the role of the lncRNA KIF9-AS1 in cancer stemness and drug resistance in HCC and elucidate the underlying mechanism. Tumor tissue and adjacent non-cancerous tissue samples were collected from HCC patients. Sphere formation was quantified via a tumor sphere assay. Cell viability, proliferation, and apoptosis were evaluated via Cell Counting Kit-8, flow cytometry, and colony formation assays, respectively. The interactions between the lncRNA KIF9-AS1 and its downstream targets were confirmed via RNA immunoprecipitation and coimmunoprecipitation. The tumorigenic role of KIF9-AS1 was validated in a mouse model. Compared with that in normal controls, the expression of the lncRNA KIF9-AS1 was upregulated in HCC tissues. Knockdown of KIF9-AS1 inhibited stemness and attenuated sorafenib resistance in HCC cells. Mechanistically, N6-methyladenosine modification mediated by methyltransferase-like 3/insulin-like growth factor 2 mRNA-binding protein 1 stabilized and increased the expression of KIF9-AS1. Additionally, KIF9-AS1 increased the stability and expression of short stature homeobox 2 by promoting ubiquitin-specific peptidase 1-induced deubiquitination. Furthermore, depletion of KIF9-AS1 alleviated sorafenib resistance in a xenograft mouse model of HCC. The N6-methyladenosine-modified lncRNA KIF9-AS1 promoted stemness and sorafenib resistance in HCC by upregulating short stature homeobox 2 expression.

Yu Y ，Lu XH ，Mu JS ，Meng JY ，Sun JS ，Chen HX ，Yan Y ，Meng K ... -  《-》

ALKBH5 acts a tumor-suppressive biomarker and is associated with immunotherapy response in hepatocellular carcinoma.

As immune-checkpoint inhibitors (ICIs) therapy has made great strides in hepatocellular carcinoma (HCC) treatment, improving patient response to this strategy has become the main focus of research. Accumulating evidence has shown that m6A methylation plays a crucial role in the tumorigenesis and progression of HCC, while the precise impact of the m6A demethylase ALKBH5 on the tumor immune microenvironment (TIME) of HCC remains poorly defined. The clinical significance of ALKBH5 and TIM3 were evaluated in human HCC tissues. The biological function of ALKBH5 was analyzed in vitro and in vivo. The HCC molecular subtypes were identified based on key ALKBH5-regulated methylation-related genes (MRGs). The differences in survival, clinical features, TIME and immunotherapy response between these two subtypes were then evaluated. The regulation of ALKBH5 on TIM3 was detected by qPCR, western blotting and MeRIP. ALKBH5 was downregulated in HCC and associated with worse prognosis. ALKBH5 inhibited the proliferation and migration activities of HCC cells in vitro and in vivo. The HCC subtype with high expression of key MRGs was characterized by immunosuppression phenotypes and a worse response to ICIs. Moreover, TIM3 was identified as a target of ALKBH5. Upregulated TIM3 level was negatively correlated with survival in HCC. The results of this study suggest that ALKBH5 is an important regulator in HCC progression. ALKBH5 exerts its influence on the TIME and immunotherapy response by targeting TIM3 in HCC. This work provides new insight into the correlation between m6A modification and ICI response, which may help provide therapeutic benefits to HCC patients.

Ma H ，Hong Y ，Xu Z ，Weng Z ，Yang Y ，Jin D ，Chen Z ，Zhou X ，Xu Z ，Fei F ，Song W ，Li J ... -  《Scientific Reports》