HIF-1α-induced expression of m6A reader YTHDF1 drives hypoxia-induced autophagy and malignancy of hepatocellular carcinoma by promoting ATG2A and ATG14 translation

Research progress on the mechanism of tumor cell ferroptosis regulation by epigenetics

Cancer remains a significant barrier to human longevity and a leading cause of mortality worldwide. Despite advancements in cancer therapies, challenges such as cellular toxicity and drug resistance to chemotherapy persist. Regulated cell death (RCD), once regarded as a passive process, is now recognized as a programmed mechanism with distinct biochemical and morphological characteristics, thereby presenting new therapeutic opportunities. Ferroptosis, a novel form of RCD characterized by iron-dependent lipid peroxidation and unique mitochondrial damage, differs from apoptosis, autophagy, and necroptosis. It is driven by reactive oxygen species (ROS)-induced lipid peroxidation and is implicated in tumorigenesis, anti-tumor immunity, and resistance, particularly in tumors undergoing epithelial-mesenchymal transition. Moreover, ferroptosis is associated with ischemic organ damage, degenerative diseases, and aging, regulated by various cellular metabolic processes, including redox balance, iron metabolism, and amino acid, lipid, and glucose metabolism. This review focuses on the role of epigenetic factors in tumor ferroptosis, exploring their mechanisms and potential applications in cancer therapy. It synthesizes current knowledge to provide a comprehensive understanding of epigenetic regulation in tumor cell ferroptosis, offering insights for future research and clinical applications.

Emerging importance of m6A modification in liver cancer and its potential therapeutic role

Liver cancer refers to malignant tumors that form in the liver and is usually divided into several types, the most common of which is hepatocellular carcinoma (HCC), which originates in liver cells. Other rare types of liver cancer include intrahepatic cholangiocarcinoma (iCCA). m6A modification is a chemical modification of RNA that usually manifests as the addition of a methyl group to adenine in the RNA molecule to form N6-methyladenosine. This modification exerts a critical role in various biological processes by regulating the metabolism of RNA, affecting gene expression. Recent studies have shown that m6A modification is closely related to the occurrence and development of liver cancer, and m6A regulators can further participate in the pathogenesis of liver cancer by regulating the expression of key genes and the function of specific cells. In this review, we provided an overview of the latest advances in m6A modification in liver cancer research and explored in detail the specific functions of different m6A regulators. Meanwhile, we deeply analyzed the mechanisms and roles of m6A modification in liver cancer, aiming to provide novel insights and references for the search for potential therapeutic targets. Finally, we discussed the prospects and challenges of targeting m6A regulators in liver cancer therapy.

Biological roles of enhancer RNA m6A modification and its implications in cancer

Enhancers, as distal cis-regulatory elements in the genome, have a pivotal influence on orchestrating precise gene expression. Enhancer RNAs (eRNAs), transcribed from active enhancer regions, are increasingly recognized as key regulators of transcription. N6-methyladenosine (m6A), the most plentiful internal modification in eukaryotic mRNAs, has garnered significant research interest in recent years. With advancements in high-throughput sequencing technologies, it has been established that m6A modifications are also present on eRNAs. An accumulative body of evidence demonstrates that aberrant enhancers, eRNAs, and m6A modifications are intimately connected with carcinoma onset, progression, invasion, metastasis, treatment response, drug resistance, and prognosis. However, the underlying molecular mechanisms governing m6A modification of eRNAs in cancer remain elusive. Here, we review and synthesize current understanding of the regulatory roles of enhancers, eRNAs, and m6A modifications in cancer. Furthermore, we investigate the possible roles of eRNAs m6A modification in tumorigenesis based on existing literature, offering novel perspectives and directions for future research on epigenetic regulatory mechanisms in cancer cells.

Prognostic implication of six m6A-modulated genes signature in the ferroptosis for hepatocellular carcinoma patients

Hepatocellular carcinoma (HCC) remains one of the most prevalent and lethal malignancies worldwide, with survival rates still falling short of expectations. Emerging evidence highlights the pivotal roles of both m6A methylation and ferroptosis-related genes (FRGs) in HCC progression. However, the prognostic significance of m6A-modulated FRGs remains largely unexplored. In this study, we developed a novel prognostic signature based on m6A-regulated FRGs, identifying six key genes (VEGFA, FANCD2, ZFP69B, EIF2S1, SLC7A11, and SRXN1) through multivariate and LASSO Cox regression analyses. A high m6A-FRGs score was strongly associated with poor prognosis, and multivariate analysis confirmed it as an independent prognostic factor. Notably, the high-risk group exhibited increased expression of immune checkpoint genes and a higher frequency of gene mutations. Functional assays further demonstrated that silencing ZFP69B significantly suppressed liver cancer cell proliferation, migration, and invasion. Clinical validation in 144 HCC samples revealed that elevated ZFP69B expression correlated with worse patient outcomes. Moreover, qPCR analysis confirmed CLSPN and HNRNPR as downstream targets of ZFP69B. Collectively, our findings establish the m6A-FRGs signature as a powerful prognostic tool for HCC and identify ZFP69B as a promising therapeutic target, warranting further investigation.

Hypoxia-inducible factor-1 alpha (HIF-1α) inhibitor AMSP-30 m attenuates CCl4-induced liver fibrosis in mice by inhibiting the sonic hedgehog pathway

Liver fibrosis is a passive and irreversible wound healing process caused by chronic liver injury. Research has shown that the upregulation of hypoxia inducible factor-1 alpha (HIF-1α) is closely related to the occurrence and development of liver fibrosis and HIF-1 α may be a promising target for the treatment of liver fibrosis. AMSP-30 m is a newly developed novel HIF-1α inhibitor by our group, which has strong anti-tumor and anti-inflammatory effects. In this study, we described the therapeutic effect and specific mechanism of AMSP-30 m on carbon tetrachloride (CCl4) induced liver fibrosis in mice. Liver fibrosis induced by CCl4 in mice and liver fibrosis induced by cobalt dichloride (CoCl2) in LX-2 cells (human hepatic stellate cell (HSC) line) were studied. Hematoxylin & eosin (H&E)and Masson's trichrome staining were used to observe pathological conditions. Western Blot, immunofluorescence and immunohistochemistry were used to detect protein expression and localization in cells, and quantitative real-time PCR analysis (qRT-PCR) was used to detect mRNA expression. Biochemical detection kits were used to detect alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels. The results demonstrated that AMSP-30 m significantly alleviated pathological symptoms, reduced ALT and AST levels, and inhibited the expression of alpha-smooth muscle actin (α-SMA) and collagen type I (COL1α1) in CCl4-induced liver fibrosis in mice. AMSP-30 m could significantly reduce the expression of HIF-1α and sonic hedgehog (Shh) pathway related proteins (Smoothened (Smo), Shh, and glioma-associated oncogene-1 (Gli-1)) in CCl4 induced liver fibrosis mice. AMSP-30 m also played a similar role in the CoCl2-induced anoxic liver fibrosis model of LX-2 cells. Further experiments showed that Cyclopamine (a Shh inhibitor) could significantly inhibit the increase of α-SMA and COL1α1 resulting from HIF-1α but not significantly inhibit HIF-1α induced by CoCl2 in LX-2 cells. And the combination of Cyclopamine and AMSP-30 m further reduced the expression of α-SMA and COL1α1 induced by HIF-1α. In summary, this study demonstrates that the HIF-1α inhibitor AMSP-30 m exerts a robust anti-fibrotic effect by inhibiting the Shh pathway, which is identified as a critical underlying mechanism. These findings suggest a promising therapeutic strategy for the treatment of liver fibrosis.

New Insights into the Diagnosis and Treatment of Hepatocellular Carcinoma

Hepatocellular carcinoma remains one of the leading contributors to global cancer mortality, frequently stemming from chronic liver conditions, such as viral hepatitis, non-alcoholic fatty liver disease, and alcohol-induced cirrhosis. While antiviral treatments have made significant strides, the rising prevalence of hepatocellular carcinoma linked to non-infectious causes underscores the pressing demand for more effective diagnostic tools and therapeutic interventions. Advances in imaging and liquid biopsy technologies have facilitated early detection and diagnosis, and treatment strategies are diversifying to include immune checkpoint inhibitors, tyrosine kinase inhibitors, and interventional therapies. Translational therapies for advanced hepatocellular carcinoma have improved surgical opportunities and patient survival. Artificial intelligence has played a transformative role in the diagnosis and treatment of hepatocellular carcinoma, in terms of image analysis, histopathologic classification, drug development, and targeted therapy. The future of hepatocellular carcinoma treatment lies in precision oncology and the collaboration of multidisciplinary teams, as well as in early detection. The ultimate goal is to keep patients alive longer and reduce the global burden of this complex malignancy.

The landscape of N 6-methyladenosine RNA methylation in skin diseases

Skin diseases encompass a diverse range of conditions with significant psychological and physiological impacts. N6-methyladenosine (m6A) RNA methylation is a key epitranscriptomic modification that regulates gene expression by influencing RNA stability, splicing, translation, export and degradation. Recent studies have highlighted the crucial role of m6A modification in the pathogenesis and progression of various skin diseases. m6A modification affects critical biologic processes of the skin, such as inflammation, immune response and cellular ageing. This review systematically explores the landscape of m6A modification in nontumour skin diseases, elucidating its regulatory roles and therapeutic implications, including wound healing, scar and keloid, skin ageing, psoriasis, systemic lupus erythematosus, acne vulgaris, rosacea, chronic actinic dermatitis and scleroderma. The intricate mechanisms of m6A modification can lead to the development of novel diagnostic biomarkers and therapeutic strategies, ultimately improving patient outcomes.

Patient-derived xenograft model: Applications and challenges in liver cancer

ABSTRACT

Liver cancer is one of the most common malignant tumors worldwide. Currently, the available treatment methods cannot fully control its recurrence and mortality rate. Establishing appropriate animal models for liver cancer is crucial for developing new treatment technologies and strategies. The patient-derived xenograft (PDX) model preserves the tumor's microenvironment and heterogeneity, which makes it advantageous for biological research, drug evaluation, personalized medicine, and other purposes. This article reviews the development, preparation techniques, application fields, and challenges of PDX models in liver cancer, providing insights for the research and exploration of PDX models in diagnostic and therapeutic strategies of liver cancer.

Identification of autophagy-related biomarker and analysis of immune infiltrates in diabetic nephropathy: PTGER1 protein macromolecular structure and function

Diabetic nephropathy (DKD) is a common complication of diabetic patients, which seriously affects their quality of life and longevity. In recent years, autophagy has been found to play an important role in the pathogenesis of DKD. The aim of this study is to identify markers of autophagy associated with diabetic nephropathy, with special attention to the structural and biological role of PTGER1 protein and its role in immune infiltration. The DKD differential genes were identified by means of various sexually expressed genes (DEGs) analysis, and functional enrichment (GO) and pathway enrichment (KEGG) analysis were performed for the significant differential genes combined with weighted gene co-expression network analysis (WGCNA). Meanwhile, gene collection enrichment analysis (GSEA) was used to further explore the function of autophagy related genes. By constructing protein-protein interaction network (PPI) and GeneMania analysis, PTGER1 was identified as a key hub gene. The diagnostic value of biomarkers was evaluated by ROC curve, and the infiltration of different immune cells was analyzed. The results showed that PTGER1 was significantly up-regulated in the renal tissues of diabetic nephropathy patients. WGCNA and functional enrichment analysis revealed a close correlation between PTGER1-related autophagy pathways and immune responses. The constructed PPI network indicated that PTGER1 had significant interactions with multiple autophagy and inflammation-related proteins, and ROC curve analysis indicated the potential application value of PTGER1 in the early screening of DKD.

Nucleus pulposus cell-mimicking nanoparticles for cell-specific HIF1A editing to modulate SASP-mediated disc inflammation via autophagy activation

Traditional methods of plasmid delivery, including viral vectors, lipofection, and electroporation, are widely used for gene editing but have limitations, such as cellular toxicity, limited transfection efficiency in primary cells, and nonspecific side effects. Here, we report the development of nucleus pulposus cell (NPC)-mimicking nanoparticles (HIF1A@NNP) with an NPC membrane as the shell and pcDNA3.1+-rHIF1A encapsulated in the core via extrusion. HIF1A@NNP exhibited a protein expression pattern similar to that of the NPC membrane and displayed a typical vesicle profile. Compared to liposomes and lentiviruses, HIF1A@NNP overexpressed HIF1A in NPCs while improving cell viability. HIF1A@NNP was more readily internalized by NPCs than by other cell types, with fewer effects on vascularization, nerve growth, and macrophage polarization than HIF1A overexpression using lipo3000. HIF1A@NNP reduced the apoptotic rate and inhibited the senescent phenotype, as evidenced by reduced DNA damage, lower levels of senescence-related proteins, and fewer SA-β-Gal-positive cells. HIF1A@NNP induced a senescence-associated secretory phenotype (SASP), which enhanced macrophage migration and M1 polarization. Additionally, HIF1A@NNP activated autophagy in NPCs. In summary, HIF1A@NNP demonstrated satisfactory biocompatibility, alleviated the SASP, and inhibited SASP-mediated macrophage recruitment and inflammatory polarization, leading to reduced disc degeneration and providing a promising strategy for combating intervertebral disc degeneration. STATEMENT OF SIGNIFICANCE: Conventional plasmid delivery methods like viral vectors, lipofection, and electroporation struggle with cellular toxicity and inefficiency in primary cells. Non-cell-specific HIF1A activation via these methods may exacerbate inflammation and pain, as HIF1A drives angiogenesis and dendritic ingrowth into the disc. Thus, a cell-specific delivery strategy could circumvent such adverse effects. Our study introduces HIF1A@NNP, a nanoparticle mimicking nucleus pulposus cells (NPCs), with an NPC membrane shell encapsulating pcDNA3.1+-rHIF1A. It preferentially targets NPCs, achieving superior HIF1A overexpression and cell viability compared to liposomes and lentiviruses. This represents a highly promising and potentially transformative approach against intervertebral disc degeneration.

An exploration on the involvement of the methyltransferase like 3-m6A‑zinc finger MYM-type containing 1 axis in the progression of liver hepatocellular carcinoma

An existing study has underlined the involvement of Methyltransferase Like 3 (METTL3) and its mediated N6-methyladenosine (m6A) modification on zinc finger MYM-type containing 1 (ZMYM1) in cancers, and we aimed to explore their implication in liver hepatocellular carcinoma (LIHC). The levels of METTL3 and ZMYM1 in LIHC cells were gauged via qPCR. The involvement of METTL3 in LIHC progression was explored via assays in vitro and in vivo, and the mechanisms underlying the effects of METTL3 on LIHC were explored via m6A methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) and confocal immunofluorescence assays. METTL3, the m6A methyltransferase of interest, expressed relatively higher in LIHC. The promoting effects of METTL3 on LIHC progression were confirmed both in vitro and in vivo, and the relevant mechanisms maybe related to ZMYM1, a target of METTL3. Such effects of METTL3-m6A-ZMYM1 axis on the progression of LIHC were confirmed to be related to the inactivation of RAS/ERK/c-FOS pathway and the reduction in E-cadherin expression yet the elevation in N-cadherin and Vimentin expressions, therefore accelerating the metastasis in LIHC. Our study highlighted the possible involvement of METTL3-mediated m6A modification in LIHC and explored METTL3-m6A-ZMYM1 axis as a possible therapeutic target for the anti-metastatic strategy against LIHC.

Placental RTN3L-dependent ER-Phagy Contributes to Fetal Testicular Dysplasia Upon Environmental Stress

Prenatal environmental stress damages fetal testicular development, leading to male infertility. However, the precise mechanisms underlying the impact of gestational environmental stress on fetal testicular development require further investigation. This study demonstrates that gestational environmental stressor cadmium exposure caused placental estradiol synthesis inhibition and fetal testicular dysplasia. Gestational estradiol supplementation restores fetal testicular dysplasia caused by environmental stress-induced placental estradiol synthesis inhibition. Analysis of human placentae and cadmium-stimulated human primary placental trophoblasts confirmed that ER-phagy is associated with the inhibition of estradiol synthesis in placentae. Subsequently, the data reveals that environmental stress significantly activates RTN3L-mediated ER-phagy. RTN3L-deficient cells and placental Rtn3l-specific knockout mice confirm that environmental stress-activated RTN3L-mediated ER-phagy inhibited placental estradiol synthesis. Total N6-methyladenosine level increasing in gestational environmental stress-exposed placentae. METTL3-mediated N6-methyladenosine modification suppression obviously restrains environmental stress-activated RTN3L-dependent ER-phagy. In conclusion, gestational environmental stress activates ER-phagy by increasing placental Rtn3l mRNA N6-methyladenosine modification, inhibiting placental estradiol synthesis, and contributing to fetal testicular dysplasia. The study demonstrates the early prevention and treatment of adult male infertility from the perspective of fetal-derived diseases.

YTHDF1/RNF7/p27 axis promotes prostate cancer progression

Prostate cancer (PCa) is a prevalent malignant tumor of the urinary system and remains the most common cancer among males. In this study, we showed that YTHDF1, one of the reader proteins involved in the N6-methyladenosine (m6A) modification signaling pathway, is highly expressed in PCa cancerous tissues and cells, which correlates with poor clinical outcomes. Our study revealed that YTHDF1 knockdown inhibits tumor cell proliferation, migration, and xenograft tumor formation by decreasing p27 protein stability through proteasome degradation signaling. Consistently, YTHDF1 depletion markedly reduced the clonogenic growth of Pten or/and TP53-deficient organoids. Candidate p27-targeting E3 ubiquitin ligases screening identified RNF7 as the direct downstream target for YTHDF1 in an m6A-dependent manner. The subsequent high translation of RNF7 results in the efficient degradation of the cell cycle inhibitor p27 and malignant tumor cell growth. In addition, we provided evidence showing that YTHDF1 or RNF7 depletion sensitizes tumor cells to chemotherapy drug cisplatin by increasing cellular apoptosis. Our findings revealed that the neddylation inhibitor MLN4924 effectively inhibited prostate cancer progression in vitro and in vivo. Our study highlights the YTHDF1/RNF7/p27 axis as a crucial component in PCa, suggesting its potential as a novel therapeutic target.

Nuclear accumulation of YTHDF1 regulates mRNA splicing in the DNA damage response

YTH domain-containing family protein 1 (YTHDF1), a reader of N6-methyladenosine (m6A), has been implicated in regulating RNA metabolism in the cytosol. Here, we report a role of YTHDF1 within the nucleus in response to genotoxic stress. Upon radiation, YTHDF1 is phosphorylated at serine-182 in an ataxia telangiectasia and Rad3-related-dependent manner. This phosphorylation inhibits exportin 1-mediated nuclear export of YTHDF1, resulting in its accumulation within the nucleus. Nuclear YTHDF1 enhances the binding capacity of serine- and arginine-rich splicing factor 2 to a group of m6A-modified exons, leading to increased exon inclusion. Specifically, YTHDF1 promotes splicing and expression of DNA repair genes, such as BRCA1 and TP53BP1, thereby mitigating excessive DNA damage. Depletion of YTHDF1 sensitizes cancer cells to radiation treatment. Together, our study reveals a crucial role of YTHDF1 in m6A-mediated messenger RNA splicing in the DNA damage response, proposing it as a potential target for radiation therapy.

Estrogen receptor β alleviates colitis in intestinal epithelial cells and activates HIF-1a and ATG-9a-mediated autophagy

Estrogen receptor β (ERβ) plays a pivotal role in regulating intestinal epithelial function and inflammation. Its involvement in inflammatory bowel diseases (IBD), particularly in ulcerative colitis (UC), remains poorly understood, despite emerging evidence pointing to its anti-inflammatory properties. This study investigated ERβ expression in UC patients using quantitative PCR, Western blot, and immunofluorescence. To investigate the functional role of ERβ, a DSS-induced colitis mouse model and LPS-treated HT-29 cells were used. Autophagy activity was evaluated through Western blot, transmission electron microscopy (TEM), and autophagy inhibitors. Co-immunoprecipitation (Co-IP) and dual luciferase reporter assays were employed to explore the interaction between ERβ and hypoxia-inducible factor-1α (HIF-1α), as well as the regulation of ATG-9a expression. The results demonstrated that ERβ expression was significantly downregulated in the inflammatory colons of UC patients. In vivo, ERβ activation by ERB041 alleviated DSS-induced colitis in mice, reducing weight loss, histopathological damage, and inflammatory cytokine levels. In vitro, ERB041 enhanced autophagy in LPS-treated HT-29 cells, accompanied by a reduction in pro-inflammatory cytokines. Furthermore, ERβ activation promoted the expression of tight junction proteins and preserved epithelial barrier integrity. Co-IP and dual luciferase assays revealed that ERβ interacted with HIF-1α and modulated ATG-9a-mediated autophagy. These results indicate that ERβ alleviates intestinal inflammation and activates HIF-1a and ATG-9a-mediated autophagy, providing new insights into the therapeutic potential of targeting ERβ in UC and highlighting its role in maintaining intestinal homeostasis.

The role of hypoxia-senescence co-related molecular subtypes and prognostic characteristics in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is known for its high invasiveness, high fatality rate. Both hypoxia and senescence play crucial roles in the initiation and progression of cancer, yet their prognostic implications in HCC are yet to be fully understood. The hypoxia-senescence co-related genes (HSCRGs) were screened from public databases. Transcriptome data and clinical information were obtained from patients with HCC using the Cancer Genome Atlas, GSE76427, and International Cancer Genome Consortium (ICGC). The random forest tree algorithm was used to identify the characteristic genes of the disease, and the genes were verified by related experiments. SVM algorithm was used to classify HCC patients based on HSCRGs. The prediction model based on HSCRGs was established by LASSO, univariate and multivariate COX regression analysis. We used the ICGC for outside validation. The risk score model was analyzed from subgroup analysis, immune infiltration, and functional strength. The expression patterns of key prognostic genes in tumor microenvironment were decoded by single cell analysis. A total of 184 HSCRGs were identified. The expression pattern and functional characteristics of MLH1 gene in HCC were verified. Two HCC subtypes were identified based on HSCRGs. Then, a prediction model based on HSCRGs was established, and risk score was identified as an independent prognostic indicator of HCC. A new nomogram is constructed and shows good prediction ability. We further determined that the level of infiltration of immune cells and the expression of immune checkpoints are significantly affected by the risk score. The immune microenvironment was different between the two risk groups. The high-risk group was dominated by immunosuppressed cells, and the prognosis was poor. Single-cell analysis revealed the expression of seven key prognostic genes in the tumor microenvironment. Finally, qPCR results further verified the expression levels of seven prognostic genes. HSCRGs are of great significance in the prognosis prediction, risk stratification and targeted therapy of patients with HCC.

METTL3 Plays Regulatory Roles in Acute Pneumonia during Staphylococcus aureus Infection

Pneumonia caused by Staphylococcus aureus infection has consistently been a significant cause of morbidity and mortality worldwide. Extensive research to date indicates that N6-methyladenosine (m6A) modification plays a crucial role in the development and progression of various diseases. However, it remains unknown whether the m6A modification affects the progression of bacterial pneumonia. To explore this question, we assessed the levels of m6A as well as the expression of methyltransferases (METTL3 and METTL14), demethylase fat mass and obesity-related protein (FTO), and methylation reader proteins YTHDF1 and YTHDF2 in mice and MH-S cells during S. aureus infection. The levels of m6A and METTL3 were significantly upregulated in S. aureus-infected mice and MH-S cells. siMETTL3 knockdown resulted in more severe bacterial colonization, lung damage, increased inflammatory cytokines (IL-6, IL-1β, TNF-α), and mortality rates in mice as well as MH-S cells following the bacterial infection. Regulation of lung inflammation levels by METTL3 was associated with the activation of the MAPK/NF-κB/JAK2-STAT3 signaling pathway. Moreover, siMETTL3 mice exhibited an increased release of superoxides and exacerbated oxidative stress in the lungs following S. aureus infection, which was correlated with impaired mitochondrial autophagy mediated by the Pink1/Parkin pathway. Our findings provide previously unrecognized evidence of the protective role of METTL3 in S. aureus-induced acute pneumonia, indicating a potential therapeutic target for S. aureus infections.

METTL3 and HERC4: Elevated Expression and Impact on Hepatocellular Carcinoma Progression

Background: Methyltransferase-like 3 (METTL3) and HECT and RLD domain containing E3 ubiquitin protein ligase 4 (HERC4) have been studied in the field of oncology; however, their roles and interaction in hepatocellular carcinoma (HCC) await elucidation. Methods: Initially, METTL3 and HERC4 expressions in normal and HCC samples were predicted employing the UALCAN database, and the targeting relationship between these two was explored via coimmunoprecipitation assay. Following the quantification on N6-methyladenosine (m6A) enrichment, the localization of METTL3 and HERC4 on HCC cells was visualized via immunofluorescence assay. The effects of METTL3 and HERC4 on HCC cells proliferation and migration were determined in vitro assays. METTL3 and HERC4 expressions were quantified via quantitative polymerase chain reaction, and those of metastasis-related proteins N-cadherin and vimentin were calculated with immunoblotting assay. Furthermore, the levels of angiogenic factors such as vascular endothelial growth factor and basic fibroblast growth factor were measured by enzyme-linked immunosorbent assay. Results: METTL3 and HERC4 expressed highly in HCC and their expressions were positively correlated with tumor grade. METTL3 overexpression enhanced the expression of HERC4 and promoted the proliferation and migration abilities of HCC cells. Specifically, METTL3 overexpression increased vimentin and N-cadherin expressions, while its silencing did conversely. Besides, HERC4 overexpression reversed the effects of METTL3 silencing on the proliferation and migration as well as the levels of angiogenic factors in HCC cells. Conclusion: This study reveals the upregulation of METTL3 and HERC4 expression in HCC and their role in HCC by enhancing the proliferation, migration, and angiogenesis potential of HCC cells.

Abnormal changes in metabolites caused by m6A methylation modification: The leading factors that induce the formation of immunosuppressive tumor microenvironment and their promising potential for clinical application

BACKGROUND

N6-methyladenosine (m6A) RNA methylation modifications have been widely implicated in the metabolic reprogramming of various cell types within the tumor microenvironment (TME) and are essential for meeting the demands of cellular growth and maintaining tissue homeostasis, enabling cells to adapt to the specific conditions of the TME. An increasing number of research studies have focused on the role of m6A modifications in glucose, amino acid and lipid metabolism, revealing their capacity to induce aberrant changes in metabolite levels. These changes may in turn trigger oncogenic signaling pathways, leading to substantial alterations within the TME. Notably, certain metabolites, including lactate, succinate, fumarate, 2-hydroxyglutarate (2-HG), glutamate, glutamine, methionine, S-adenosylmethionine, fatty acids and cholesterol, exhibit pronounced deviations from normal levels. These deviations not only foster tumorigenesis, proliferation and angiogenesis but also give rise to an immunosuppressive TME, thereby facilitating immune evasion by the tumor.

AIM OF REVIEW

The primary objective of this review is to comprehensively discuss the regulatory role of m6A modifications in the aforementioned metabolites and their potential impact on the development of an immunosuppressive TME through metabolic alterations.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review aims to elaborate on the intricate networks governed by the m6A-metabolite-TME axis and underscores its pivotal role in tumor progression. Furthermore, we delve into the potential implications of the m6A-metabolite-TME axis for the development of novel and targeted therapeutic strategies in cancer research.

Distinct 5-methylcytosine profiles of LncRNA in breast cancer brain metastasis

BACKGROUND

Recent studies have identified a complex relationship between methylation patterns and the development of various cancers. Breast cancer (BC) is the second leading cause of cancer mortality among women. Approximately 5-20% of BC patients are at risk of BC brain metastases (BCBM). Although 5-methylcytosine (m5C) has been identified as an important regulatory modifier, its distribution in BCBM is not well understood. This study aimed to investigate the distribution of m5C in BCBM.

MATERIALS AND METHODS

Samples from BCBM (231-BR cells) and BC (MDA-MB-231 cells) groups were subjected to a comprehensive analysis of the m5C methylation in long non-coding RNA (lncRNA) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq). The expression levels of methylated genes in BC and adjacent tissues were verified through quantitative real-time polymerase chain reaction (RT-qPCR). Enrichment pathway analyses were through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to predict the potential functions of m5C in BCBM.

RESULTS

The MeRIP-seq analysis identified 23,934 m5C peaks in BCBM and 21,236 m5C in BC. A total of 9,480 annotated genes (BCBM) and 8,481 annotated genes (BC) were mapped. Notably, 1,819 methylation sites in lncRNA were upregulated in BCBM, whereas 2,415 methylation sites were upregulated in BC. Significant m5C hypermethylated lncRNAs included ENST00000477316, ENST00000478098 and uc002gtt.1, whereas hypomethylated lncRNAs included ENST00000600912, ENST00000493668, ENST00000544651 and ENST00000464989. These results were verified by qPCR and MeRIP-qPCR in BC and BCBM. Considering the strong association between m5C RNA methylation regulators and lncRNA, we examined the expression levels of 13 m5C RNA methylation regulators and observed significant differences between BC tissues and adjacent normal tissues. In addition, the interaction between regulators of altered expression and the differentially expressed genes in vitro was analyzed. The GO and KEGG pathways analyses revealed that genes significantly associated with m5C sites in lncRNA were linked to the BCBM signaling pathways.

CONCLUSION

This uncovered significant variations in the levels and distribution of m5C in BCBM compared to BC. The findings provide a new theoretical understanding of the mechanisms of BCBM.

Epitranscriptomic regulation of HIF-1: bidirectional regulatory pathways

BACKGROUND

Epitranscriptomics, the study of RNA modifications such as N6-methyladenosine (m6A), provides a novel layer of gene expression regulation with implications for numerous biological processes, including cellular adaptation to hypoxia. Hypoxia-inducible factor-1 (HIF-1), a master regulator of the cellular response to low oxygen, plays a critical role in adaptive and pathological processes, including cancer, ischemic heart disease, and metabolic disorders. Recent discoveries accent the dynamic interplay between m6A modifications and HIF-1 signaling, revealing a complex bidirectional regulatory network. While the roles of other RNA modifications in HIF-1 regulation remain largely unexplored, emerging evidence suggests their potential significance.

MAIN BODY

This review examines the reciprocal regulation between HIF-1 and epitranscriptomic machinery, including m6A writers, readers, and erasers. HIF-1 modulates the expression of key m6A components, while its own mRNA is regulated by m6A modifications, positioning HIF-1 as both a regulator and a target in this system. This interaction enhances our understanding of cellular hypoxic responses and opens avenues for clinical applications in treating conditions like cancer and ischemic heart disease. Promising progress has been made in developing selective inhibitors targeting the m6A-HIF-1 regulatory axis. However, challenges such as off-target effects and the complexity of RNA modification dynamics remain significant barriers to clinical translation.

CONCLUSION

The intricate interplay between m6A and HIF-1 highlights the critical role of epitranscriptomics in hypoxia-driven processes. Further research into these regulatory networks could drive therapeutic innovation in cancer, ischemic heart disease, and other hypoxia-related conditions. Overcoming challenges in specificity and off-target effects will be essential for realizing the potential of these emerging therapies.

Unraveling the triad of hypoxia, cancer cell stemness, and drug resistance

In the domain of addressing cancer resistance, challenges such as limited effectiveness and treatment resistance remain persistent. Hypoxia is a key feature of solid tumors and is strongly associated with poor prognosis in cancer patients. Another significant portion of the development of acquired drug resistance is attributed to tumor stemness. Cancer stem cells (CSCs), a small tumor cell subset with self-renewal and proliferative abilities, are crucial for tumor initiation, metastasis, and intra-tumoral heterogeneity. Studies have shown a significant association between hypoxia and CSCs in the context of tumor resistance. Recent studies reveal a strong link between hypoxia and tumor stemness, which together promote tumor survival and progression during treatment. This review elucidates the interplay between hypoxia and CSCs, as well as their correlation with resistance to therapeutic drugs. Targeting pivotal genes associated with hypoxia and stemness holds promise for the development of novel therapeutics to combat tumor resistance.

Targeting m6A RNA Modification in Tumor Therapeutics

The prevalent eukaryotic RNA modification N6-methyladenosine (m6A), which is distributed in more than 50% of cases, has demonstrated significant implications in both normal development and disease progression, particularly in the context of cancer. This review aims to discuss the potential efficacy of targeting tumor cells through modulation of m6A RNA levels. Specifically, we discuss how the upregulation or downregulation of integral or specific targets is effective in treating different tumor types and patients. Additionally, we will cover the factors influencing the efficacy of m6A RNA targeting in tumor treatment. Our review will focus on the impact of targeting m6A mRNA on genes and cells and assess its potential as a therapeutic strategy for tumors. Despite the challenges involved, further research on m6A RNA in tumors and its integration with existing tumor therapy approaches is warranted.

The m6A reader IGF2BP3 promotes HCC progression by enhancing MCM10 stability

Abnormal N6-methyladenosine (m6A) modifications were associated with the occurrence, development, and metastasis of cancer. However, the functions and mechanisms of m6A regulators in cancer remained largely elusive and should be explored. Here, we identified that insulin like growth Factor 2 mRNA binding protein 3 (IGF2BP3) was specifically overexpressed and associated with poor prognosis in liver hepatocellular carcinoma (HCC). Importantly, IGF2BP3 promoted HCC cells progression in an m6A-dependent manner, IGF2BP3 silencing significantly inhibited proliferation and migratory ability of tumor cells in vitro and in in vivo. Mechanistically, IGF2BP3 interacted with minichromosomal maintenance complex component (MCM10) mRNAs to prolong stability of m6A-modified RNA. Therefore, our findings indicated that m6A reader IGF2BP3 contributed to tumorigenesis and poor prognosis, providing a potential prognostic biomarker and therapeutic target for HCC.

Parvimonas micra promotes oral squamous cell carcinoma metastasis through TmpC-CKAP4 axis

Parvimonas micra (P. micra), an opportunistic oral pathogen associated with multiple cancers, has limited research on its role in oral squamous cell carcinoma (OSCC). This study shows that P. micra is enriched in OSCC tissues and positively correlated with tumor metastasis and stages. P. micra infection promotes OSCC metastasis by inducing hypoxia/HIF-1α, glycolysis, and autophagy. Mechanistically, P. micra surface protein TmpC binds to CKAP4, a receptor overexpressed in OSCC, facilitating bacterial attachment and invasion. This interaction activates HIF-1α and autophagy via CKAP4-RanBP2 and CKAP4-NBR1 pathways, driving metastasis. Targeting CKAP4 with masitinib or antibodies impairs P. micra attachment and abolishes P. micra-promoted OSCC metastasis in vitro and in vivo. Together, our findings identify P. micra as a pathogen that promotes OSCC metastasis and highlight that TmpC-CKAP4 interaction could be a potential therapeutic target for OSCC.

m6A modified ATG9A is required in regulating autophagy to promote HSCs activation and liver fibrosis

Hepatic stellate cells (HSCs) are the central link of the occurrence and development of hepatic fibrosis, and autophagy promotes HSCs activation. N6-methyladenosine (m6A) RNA modification can also control autophagy by targeting selected autophagy-associated genes. but up to now, little research has been done on the m6A modification autophagy-related genes (ATGs) in hepatic fibrosis. Here, we identify ATG9A as a previously unrecognized m6A modified ATG using m6A-sequencing (m6A-seq). Importantly, ATG9A is upregulated in liver fibrosis mice and primary biliary cirrhosis (PBC) patient liver tissue. Mechanistically, based on the presence of m6A binding sites on ATG9A, ATG9A promotes HSCs autophagy in an m6A dependent manner, thereby enhancing HSCs activation. Noteworthy, FTO is identified as the upstream of ATG9A, and knockdown of ATG9A can prevent FTO-induced HSCs autophagy and activation. In bile duct ligation (BDL) or CCL4-induced liver fibrosis mouse models, lowering ATG9A alleviated liver fibrosis through PI3K/AKT/mTOR pathway and TGFβ1/smad3 pathway. Taken together, our results provided that ATG9A is a potential prognostic biomarker and therapeutic target for patients with liver fibrosis.

RNA methylation homeostasis in ocular diseases: All eyes on Me

RNA methylation is a pivotal epigenetic modification that adjusts various aspects of RNA biology, including nuclear transport, stability, and the efficiency of translation for specific RNA candidates. The methylation of RNA involves the addition of methyl groups to specific bases and can occur at different sites, resulting in distinct forms, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G). Maintaining an optimal equilibrium of RNA methylation is crucial for fundamental cellular activities such as cell survival, proliferation, and migration. The balance of RNA methylation is linked to various pathophysiological conditions, including senescence, cancer development, stress responses, and blood vessel formation, all of which are pivotal for comprehending a spectrum of eye diseases. Recent findings have highlighted the significant role of diverse RNA methylation patterns in ophthalmological conditions such as age-related macular degeneration, diabetic retinopathy, cataracts, glaucoma, uveitis, retinoblastoma, uveal melanoma, thyroid eye disease, and myopia, which are critical for vision health. This thorough review endeavors to dissect the influence of RNA methylation on common and vision-impairing ocular disorders. It explores the nuanced roles that RNA methylation plays in key pathophysiological mechanisms, such as oxidative stress and angiogenesis, which are integral to the onset and progression of these diseases. By synthesizing the latest research, this review offers valuable insights into how RNA methylation could be harnessed for therapeutic interventions in the field of ophthalmology.

Acetoacetate Ameliorates Hepatic Fibrosis by Targeting Peroxisome Proliferator-Activated Receptor Gamma to Restore Lipid Droplets in Activated Hepatic Stellate Cells

Background: Hepatic fibrosis (HF) is a progressive liver disease characterized by the activation of hepatic stellate cells (HSCs) and changes in lipid metabolism. Abnormal ketone body (KD) levels, including acetoacetate (AcAc) and beta-hydroxybutyrate (BHB), have been observed in patients with HF, but the mechanisms linking ketone metabolism to fibrosis progression remain unclear. Objectives: This study aimed to investigate the role of AcAc in modulating HSCs activation and its potential mechanisms in HF. Methods: We examined the effects of AcAc on HSCs activation by Western blot analysis and RT-PCR both in vivo and in vitro. The impact of AcAc on lipid droplet accumulation in HSCs was assessed using total cholesterol (TC), triglyceride (TG), and Retinol (RET) kits, along with Nile Red and Oil Red O staining. RT-PCR screening was performed to analyze the expression of genes involved in lipid droplet formation and lipid metabolism. Results: Our findings show that AcAc inhibited HSCs activation by restoring LD levels. Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) was identified as a key regulator through gene screening. AcAc primarily regulated PPARγ expression, and knocking down PPARγ significantly aggravated HF progression. Conclusions: The ability of AcAc to restore LD levels and regulate PPARγ suggests that it may represent a promising therapeutic strategy for HF by inhibiting HSCs activation.

Oncometabolite D-2HG drives tumor metastasis and protumoral macrophage polarization by targeting FTO/m6A/ANGPTL4/integrin axis in triple-negative breast cancer

BACKGROUND

D-2-hydroxyglutarate (D-2HG), an oncometabolite derived from the tricarboxylic acid cycle. Previous studies have reported the diverse effects of D-2HG in pathophysiological processes, yet its role in breast cancer remains largely unexplored.

METHODS

We applied an advanced biosensor approach to detect the D-2HG levels in breast cancer samples. We then investigated the biological functions of D-2HG through multiple in vitro and in vivo assays. A joint MeRIP-seq and RNA-seq strategy was used to identify the target genes regulated by D-2HG-mediated N6-methyladenosine (m6A) modification. RNA pull-down assays were further applied to identify the reader that could specifically recognize the m6A modification on angiopoietin like 4 (ANGPTL4) mRNA and RNA immunoprecipitation was used to confirm the findings.

RESULTS

We found that D-2HG accumulated in triple-negative breast cancer (TNBC), exerting oncogenic effects both in vitro and in vivo by promoting TNBC cell growth and metastasis. Mechanistically, D-2HG enhanced global m6A RNA modifications in TNBC cells, notably upregulating m6A modification on ANGPTL4 mRNA, which was mediated by the inhibition of Fat-mass and obesity-associated protein (FTO), resulting in increased recognition of m6A-modified ANGPTL4 by YTH N6-methyladenosine RNA binding protein F1 (YTHDF1), thereby promoting the enhanced translation of ANGPTL4. As a secretory protein, ANGPTL4 subsequently activated the integrin-mediated JAK2/STAT3 signaling cascade in TNBC cells through autocrine signaling. Notably, the knockdown of ANGPTL4 or treatment with GLPG1087 (an integrin antagonist) significantly reduced D-2HG-induced proliferation and metastasis in TNBC cells. Additionally, ANGPTL4 was found to promote macrophage M2 polarization within the tumor microenvironment via paracrine signaling, further driving TNBC progression. The association of ANGPTL4 with poor prognosis in TNBC patients underscores its clinical relevance.

CONCLUSIONS

Our study unveils a previously unrecognized role for D-2HG-mediated RNA modification in TNBC progression and targeting the D-2HG/FTO/m6A/ANGPTL4/integrin axis can serve as a promising therapeutic target for TNBC patients.

USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation

The N6-methyladenosine binding protein YTHDF1, often upregulated in cancer, promotes tumor growth and hinders immune checkpoint blockade treatment. A comprehensive understanding of the molecular mechanisms governing YTHDF1 protein stability is pivotal for enhancing clinical response rates and the effectiveness of immune checkpoint blockade in cancer patients. Here, we report that USP5 interacts with YTHDF1, stabilizing it by removing K11-linked polyubiquitination. Insulin activates mTORC1, phosphorylating USP5 and promoting its dimerization, which binds to and protects YTHDF1 from degradation. Conversely, the CUL7-FBXW8 E3 ligase promotes YTHDF1 degradation. Deficiency in YTHDF1 or USP5 increases PD-L1 expression and suppresses immune-related gene expression, facilitating immune evasion. Combining USP5 inhibition with anti-PD-L1 therapy enhances anti-tumor immunity, suggesting USP5 as a potential biomarker for patient stratification. This study reveals a ubiquitination-dependent regulation of YTHDF1, proposing USP5 inhibition alongside PD-(L)1 blockade as a promising cancer treatment strategy.

WTAP Regulates SOX1 Expression to Affect the Tumorigenicity of Colorectal Cancer via an m6A-YTHDF2-Dependent Manner

BACKGROUND

Wilms tumor 1-associated protein (WTAP) plays a critical role in various cancers, including colorectal cancer (CRC). However, the biological function and molecular mechanisms of WTAP in CRC remain to be elucidated.

METHODS

We determined the expression of WTAP and its correlation with unfavorable prognosis of CRC using RNA-seq and the UALCAN dataset. And we investigated the effects of WTAP on CRC cells using cell proliferation assay, colony formation, cell migration and invasion, and subcutaneous xenograft experiments. We then knockdown of WTAP to identify candidate targets of WTAP. Moreover, the mRNA stability of SRY-box transcription factor 1 (SOX1) was assessed by overexpressing YTHDF2. Finally, we investigated the regulatory mechanism of WTAP in CRC by MeRIP assay, RNA pulldown, dual-luciferase reporter assay, and RIP assay.

RESULTS

We demonstrated that CRC patients with a high expression of WTAP have a risk prognosis. Additionally, WTAP expression can serve as a predictor of survival in CRC. WTAP promoted the proliferation and tumor growth of CRC cells. Moreover, WTAP has been recognized as the upstream regulator of SOX1. WTAP regulated the m6A modification, resulting in the post-transcriptional inhibition of SOX1. YTHDF2 plays a role in promoting mRNA degradation. Then, SOX1 can hinder the progression of CRC. Furthermore, WTAP can regulate the proliferation, migration, and invasion of CRC cells by SOX1 via an m6A-YTHDF2-dependent manner.

CONCLUSION

Our findings demonstrate that WTAP-mediated m6A modification facilitated the progression of CRC through the YTHDF2-SOX1 axis and could serve as a potential therapeutic targeting for CRC.

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

BACKGROUND

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.

DATA SOURCES

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.

RESULTS

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.

CONCLUSIONS

The interplay between survival pressures and m6A RNA methylation emerges as a complex regulatory network that influences HCC pathogenesis and progression.

Hypoxia-induced autophagy in pancreatic cancer counteracts the cytotoxicity of CD8+ T cells by inhibiting the expression of MHC-I

The hypoxic microenvironment is an essential feature of solid tumors. Autophagy has been controversial in its role in immune regulation. This project aims to elucidate the impact of autophagy in pancreatic cancer (PC) under specific conditions (hypoxia) on CD8+ T cells and the regulatory mechanisms behind it.The levels of HIF1α and autophagy were analyzed by western blot (WB) and immunofluorescence (IF). The effects of HIF1α on cell autophagy were assessed in normoxic or hypoxic treatments using KC7F2 (HIF-1 channel inhibitor) or chloroquine (autophagy inhibitor). CD8+ T cells were co-cultured with PC cells to assess the cytotoxicity using lactate dehydrogenase (LDH) and Hoechst/PI staining. The content of cytokines and the activation level of CD8+ T cells were measured by enzyme-linked immunosorbent assay (ELISA) and flow cytometry. MHC-I expression in PC cells (membranes) was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR), WB, IF, and flow cytometry. Humanized immune-reconstituted mice were applied to investigate the impact of HIF1α-induced autophagy on in vivo immunity.When cells were in hypoxia, the levels of HIF1α and autophagy were higher compared to normoxic conditions. Treatment with KC7F2 resulted in similar levels of HIF1α and autophagy as those in normoxic state. Chloroquine treatment reversed the autophagy level to the normoxic state. The autophagy level of PC cells transfected with oe-HIF1α was increased, with reduced MHC-I expression on cells (membranes), which impaired the cytotoxicity of CD8+ T cells, and thus decreasing the probability of recognition and attack by CD8+ T cells when co-cultured with them. In mice, overexpression of HIF1α hindered the immune suppressive function of CD8+ T cells and facilitated the immune escape of PC by reducing antigen presentation of MHC-I.Under hypoxia, HIF1α-induced autophagy reduces the cytotoxicity of CD8+ T cells by repressing MHC-I expression.

The diverse landscape of RNA modifications in cancer development and progression

BACKGROUND

RNA modifications, a central aspect of epitranscriptomics, add a regulatory layer to gene expression by modifying RNA function without altering nucleotide sequences. These modifications play vital roles across RNA species, influencing RNA stability, translation, and interaction dynamics, and are regulated by specific enzymes that add, remove, and interpret these chemical marks.

OBJECTIVE

This review examines the role of aberrant RNA modifications in cancer progression, exploring their potential as diagnostic and prognostic biomarkers and as therapeutic targets. We focus on how altered RNA modification patterns impact oncogenes, tumor suppressor genes, and overall tumor behavior.

METHODS

We performed an in-depth analysis of recent studies and advances in RNA modification research, highlighting key types and functions of RNA modifications and their roles in cancer biology. Studies involving preclinical models targeting RNA-modifying enzymes were reviewed to assess therapeutic efficacy and potential clinical applications.

RESULTS

Aberrant RNA modifications were found to significantly influence cancer initiation, growth, and metastasis. Dysregulation of RNA-modifying enzymes led to altered gene expression profiles in oncogenes and tumor suppressors, correlating with tumor aggressiveness, patient outcomes, and response to immunotherapy. Notably, inhibitors of these enzymes demonstrated potential in preclinical models by reducing tumor growth and enhancing the efficacy of existing cancer treatments.

CONCLUSIONS

RNA modifications present promising avenues for cancer diagnosis, prognosis, and therapy. Understanding the mechanisms of RNA modification dysregulation is essential for developing targeted treatments that improve patient outcomes. Further research will deepen insights into these pathways and support the clinical translation of RNA modification-targeted therapies.

Exploration of the mechanism of 5-Methylcytosine promoting the progression of hepatocellular carcinoma

5-Methylcytosine (m5C) is a ubiquitous RNA modification that is closely related to various cellular functions. However, no studies have comprehensively demonstrated the role of m5C in hepatocellular carcinoma (HCC) progression. In this study, six pairs of HCC and adjacent tissue samples were subjected to methylated RNA immunoprecipitation sequencing to identify precise m5C loci. Non-negative matrix factorization (NMF) was used to identify HCC subtypes in TCGA-LIHC cohort. Immune, metabolic, and tumor-related pathways in HCC subtypes with differences in methylation status were analyzed and a prognostic model based on m5C-related genes was constructed. Finally, using RIP and molecular interaction analysis, we demonstrated that YBX1 binds to TPM3 in an m5C dependent manner and regulates HCC progression. Widespread m5C sites were identified and found to be differentially distributed in HCC compared with adjacent tissues. Metabolic processes were inhibited in hypermethylated HCC, whereas immune checkpoint and multiple classical tumor pathways were significantly upregulated. More importantly, we have identified an m5C dependent regulatory axis. The m5C reader YBX1 binds to TPM3 in an M5C dependent manner and promotes the progression of hepatocellular carcinoma. These results provide new evidence for further understanding the comprehensive role of m5C in HCC and the regulatory mechanism of m5C.

Rapamycin Increases the Development Competence of Yak (Bos grunniens) Oocytes by Promoting Autophagy via Upregulating 17β-Estradiol and HIF-1α During In Vitro Maturation

High-quality oocyte production strategies play an important role in animal-assisted reproductive biotechnologies, and rapamycin (Rap) has been commonly used to increase the development potential of mammalian oocytes. The purpose of this study is to evaluate the effects and possible molecular mechanisms of rap on the maturation of yak oocytes. Different concentrations of Rap were supplemented during in vitro maturation (IVM) of yak oocytes. The maturation rates of oocytes and development rates of parthenogenetically activated embryos were assessed. The levels of 17β-estradiol (E2) were detected via ELISA, and the expression of autophagy-related factors, steroidogenic enzymes, and HIF-1α was detected via qRT-PCR, western blotting, and fluorescence microscopy, respectively. In addition, the impacts of E2 and HIF-1α on Rap-mediated oocyte autophagy were investigated by investigating the activities of E2 and HIF-1α. Our results showed that 0.1 nM Rap substantially enhanced the developmental ability of yak oocytes. In this group, the levels of E2, CYP19A1, CYP17A1, and autophagy-related factors were also significantly increased, and the expression of ATG5 and BECN1 in subsequent embryos was also increased. Further analysis revealed that Rap tends to enhance the development competence of yak oocytes and that the levels of autophagy-related factors are reduced when the activity of E2 or HIF-1α is inhibited. Furthermore, the levels of E2, CYP19A1, and CYP17A1 were downregulated when the activity of HIF-1α was inhibited, and the levels of HIF-1α were also significantly reduced by the estrogen receptor antagonist G15. Nevertheless, the levels of CYP11A1 mRNA in mature yak COCs were not significantly different among these groups, a phenomenon which implies that the levels of E2 were not correlated with the CYP11A1 content in yak COCs. There was an increasing tendency for the development competence of yak oocytes at the optimum concentration of Rap during IVM. The potential underlying mechanism is that Rap can activate autophagy and upregulate the levels of E2 and HIF-1α in mature oocytes. Additionally, the levels of both E2 and HIF-1α are regulated by each other and involve Rap-regulated autophagy in oocytes.

Melatonin antagonizes bone loss induced by mechanical unloading via IGF2BP1-dependent m6A regulation

Disuse bone loss is prone to occur in individuals who lack mechanical stimulation due to prolonged spaceflight or extended bed rest, rendering them susceptible to fractures and placing an enormous burden on social care; nevertheless, the underlying molecular mechanisms of bone loss caused by mechanical unloading have not been fully elucidated. Numerous studies have focused on the epigenetic regulation of disuse bone loss; yet limited research has been conducted on the impact of RNA modification bone formation in response to mechanical unloading conditions. In this study, we discovered that m6A reader IGF2BP1 was downregulated in both osteoblasts treated with 2D clinostat and bone tissue in HLU mice. Supplementing IGF2BP1 could promote osteoblast proliferation and partially alleviate the adverse effects of mechanical unloading on bone formation. Mechanistically, IGF2BP1 inhibited the degradation of Lef1 mRNA by directly binding to its mRNA and recognizing the m6A modification. Furthermore, LEF1 promoted osteoblast proliferation by upregulating c-Myc and Cyclin D1 expression, as well as participated in mediating IGF2BP1-induced osteoblast activity under mechanical unloading. Notably, Melatonin (MT) might participate in the regulation of the IGF2BP1/LEF1 axis, thereby regulating the proliferation of osteoblasts and bone formation. Collectively, this study revealed a new insight into the regulation of the MT/IGF2BP1/LEF1 pathway in the process of unloading-induced bone loss, which could potentially contribute to establishing therapeutic strategies for disuse osteoporosis.

Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications heterogeneity

Understanding the heterogeneity of epigenetic modifications within single cells is pivotal for unraveling the nature of the complexity of gene expression and cellular function. In this study, we have developed a strategy based on multichrome encoding and "AND" Boolean logic recognition for multiplexed, spatially resolved imaging of single-cell RNA epigenetic modifications, termed as PRoximity Exchange-assisted Encoding of Multichrome (PREEM). Through the implementation of this strategy, we can now map the expression and nuclear distribution of multiple site-specific RNA N6-methyladenosine (m6A) modifications at the single-molecule resolution level in single-cells, and reveal the previously unknown heterogeneity. Notably, we demonstrate how these patterns change after treatment with various drugs. Moreover, cyclic imaging with tailed DNA self-assembly further suggest the scalability and adaptability of PREEM's design. As an innovative epigenetic modification imaging tool, PREEM not only broadens the horizons of single-cell epigenetics research, enabling joint analysis of multiple targets beyond the limitations of imaging channels, but also reveals cell-to-cell variability, thereby enhancing our capacity to explore cellular functions.

New insights into N6-methyladenosine in hepatocellular carcinoma immunotherapy

N6-methylation is a modification in which a methyl group is added to the adenine base of a nucleotide. This modification is crucial for controlling important functions that are vital for gene expression, including mRNA splicing, stability, and translation. Due to its intricate participation in both normal cellular processes and the course of disease, as well as its critical role in determining cell fate, N6-methyladenosine (m6A) alteration has recently attracted a lot of interest. The formation and progression of many diseases, especially cancer, can be attributed to dysregulated m6A alteration, which can cause disturbances in a variety of cellular functions, such as immunological responses, cell proliferation, and differentiation. In this study, we examine how m6A dysregulation affects hepatocellular carcinoma (HCC), with a particular emphasis on how it contributes to immunological evasion and carcinogenesis. We also investigate its potential as a novel therapeutic target, providing new perspectives on potential therapeutic approaches meant to enhance clinical results for patients with HCC.

Arsenic trioxide preconditioning attenuates hepatic ischemia- reperfusion injury in mice: Role of ERK/AKT and autophagy

BACKGROUND

Arsenic trioxide (ATO) is indicated as a broad-spectrum medicine for a variety of diseases, including cancer and cardiac disease. While the role of ATO in hepatic ischemia/reperfusion injury (HIRI) has not been reported. Thus, the purpose of this study was to identify the effects of ATO on HIRI.

METHODS

In the present study, we established a 70% hepatic warm I/R injury and partial hepatectomy (30% resection) animal models in vivo and hepatocytes anoxia/reoxygenation (A/R) models in vitro with ATO pretreatment and further assessed liver function by histopathologic changes, enzyme-linked immunosorbent assay, cell counting kit-8, and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay. Small interfering RNA (siRNA) for extracellular signal-regulated kinase (ERK) 1/2 was transfected to evaluate the role of ERK1/2 pathway during HIRI, followed by ATO pretreatment. The dynamic process of autophagic flux and numbers of autophagosomes were detected by Green fluorescent protein-monomeric Red fluorescent protein-LC3 (GFP-mRFP-LC3) staining and transmission electron microscope.

RESULTS

A low dose of ATO (0.75 μmol/L in vitro and 1 mg/kg in vivo) significantly reduced tissue necrosis, inflammatory infiltration, and hepatocyte apoptosis during the process of hepatic I/R. Meanwhile, ATO obviously promoted the ability of cell proliferation and liver regeneration. Mechanistically, in vitro studies have shown that nontoxic concentrations of ATO can activate both ERK and phosphoinositide 3-kinase-serine/threonine kinase (PI3K-AKT) pathways and further induce autophagy. The hepatoprotective mechanism of ATO, at least in part, relies on the effects of ATO on the activation of autophagy, which is ERK-dependent.

CONCLUSION

Low, non-toxic doses of ATO can activate ERK/PI3K-AKT pathways and induce ERK-dependent autophagy in hepatocytes, protecting liver against I/R injury and accelerating hepatocyte regeneration after partial hepatectomy.

LINC02987 suppression hepatocellular carcinoma progression by modulating autophagy via the miR-338-3p/ATG12 axis

Hepatocellular carcinoma (HCC), the most common primary liver cancer, is marked by a high mortality rate, with the misregulation of long non-coding RNAs (LncRNAs) playing a key role in its development. Here, we studied the role of LINC02987 in HCC. We employed bioinformatics tools to identify LncRNAs and miRNAs that exhibit differential expression in HCC. Quantitative real-time reverse transcription PCR (RT-qPCR) and Western blot analysis were utilized to quantify gene and protein expression levels. The interaction between miR-338-3p and LINC02987 or ATG12 was confirmed through dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. We observed that LINC02987 was overexpressed in HCC tumor tissues and cell lines. Silencing of LINC02987 led to a reduction in cell viability, diminished clonogenic potential, and attenuated invasive and migratory capabilities. Also, decreasing protein level and fluorescence intensity of the autophagy-associated LC3 I/II. In HCC, miR-338-3p expression was downregulated, while inversely correlates with the overexpression of the autophagy protein ATG12. Mimicking miR-338-3p suppresses the activity of both LINC02987 and ATG12, as evidenced by reduced luciferase signals in corresponding reporter assays. Mimicking miR-338-3p suppresses the activity of both LINC02987 and ATG12, as evidenced by reduced luciferase signals in reporter assays. Transfection with si-LINC02987 decreased ATG12 expression, an effect that was partially reversed by miR-338-3p knockdown. Inhibition of miR-338-3p or overexpression of ATG12 increased LC3 I/II protein levels. Our results indicate that LINC02987 sequesters miR-338-3p, leading to increased ATG12 and promoting autophagy in HCC cells. These results highlight the potential of LINC02987 as a therapeutic target for the treatment of HCC.

The Mechanism and Latest Progress of m6A Methylation in the Progression of Pancreatic Cancer

Pancreatic cancer (PC), known as the "king of cancers," is characterized by an exceptionally low five-year survival rate, posing a formidable challenge to global public health. N6-methyladenosine (m6A) methylation is prevalent across various stages of eukaryotic RNA expression, including splicing, maturation, stability, translation, and localization, and represents a pivotal mechanism of epigenetic regulation. m6A methylation influences tumor initiation and progression by modulating post-transcriptional processes, playing a critical role in sustaining cancer cell stemness, promoting cell proliferation, and mediating drug resistance. Extensive research underscores the substantial contribution of m6A modifications to PC development. However, the multiplicity of m6A regulators and their intricate mechanisms of action complicate the landscape. This review aims to deepen the understanding of m6A's role in PC by delineating its involvement in four key areas of tumorigenesis: the hypoxic tumor microenvironment, metabolic reprogramming, immune microenvironment, and resistance mechanisms. Additionally, the review addresses the emerging frontier of m6A interactions with non-coding RNAs (ncRNAs), offering insights into the potential therapeutic and prognostic applications of m6A in the treatment and prognosis prediction of PC.

ALKBH5 controlled autophagy of peripheral blood mononuclear cells by regulating NRG1 mRNA stability in ankylosing spondylitis

Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease which is characterized by pathological osteogenesis. N6-methyladenosine (m6A) RNA modification is pivotal in immunity and inflammation. In this study, the peripheral blood mononuclear cells (PBMCs) were isolated from healthy or AS patients blood samples in Fuyang People's Hospital, which was utilized to clarify the role of m6A modification in AS pathogenesis. The results showed that the autophagy levels showed a decreasing trend; meanwhile, the m6A demethylase ALKBH5 expression was downregulation in AS-PBMCs. The RNA-seq analysis identified 201 significantly altered genes including NRG1, FOS, CAMKK2, NLRC4, and DAPK1; and NRG1 mRNA expression levels showed significant improvement in AS. After ALKBH5 knockdown, the autophagy levels significantly decreased through increasing NRG1 m6A modification and enhancing its mRNA stability, while ALKBH5 overexpression promoted autophagy by reduceing NRG1 mRNA stability. Additionally, the results found that the "reader" IGF2BP3 substantially enhanced NRG1 expression and mRNA stability in AS patients PBMCs. Silencing ALKBH5 increased IGF2BP3 binding to the m6A-enriched NRG1 transcript, and enhancing NRG1 mRNA stability and protein expression. However, ALKBH5 modification site mutation may increase IGF2BP3 binding to NRG1 mRNA. These finding suggested that ALKBH5 downregulation inhibited AS-PBMCs autophagy leves through regulating post-transcriptional m6A modification to upregulate NRG1 protein expression, which provided novel and effective approaches for AS clinical therapy.

Defining epitranscriptomic hallmarks at the host-parasite interface and their roles in virulence and disease progression in Theileria annulata-infected leukocytes

Theileria parasites are known to induce the transformation of host bovine leukocytes, involved in rapid proliferation, evasion from apoptotic mechanisms, and increased dissemination. In this study, we reveal the involvement of m6A RNA modification in T. annulata infection-induced transformation of bovine leukocytes. We conducted m6A sequencing and bioinformatics analysis to map the mRNA methylation patterns of T. annulata-infected host leukocytes. We observe specific mRNA modifications for T. annulata-infected leukocytes and a strong correlation between the proliferation rate of the infected Leukocytes with m6A modifications We observe that the increased amounts of m6A seem to impact some cell cycle dynamics, potentially via modifications of E2F4 mRNA. Moreover, we further identify HIF-1α as a possible driver of these m6A RNA modifications that have clear relevance to cellular proliferation dynamics. Overall, our results provide insights into the role of m6A mRNA methylation in the molecular crosstalk between Theileria and their host leukocytes, emphasizing the critical role of mRNA methylation in host-parasite interaction.

Betaine inhibits the stem cell-like properties of hepatocellular carcinoma by activating autophagy via SAM/m6A/YTHDF1-mediated enhancement on ATG3 stability

Background: Stem cell-like properties are known to promote the recurrence and metastasis of hepatocellular carcinoma (HCC), contributing to a poor prognosis for HCC patients. Betaine, an important phytochemical and a methyl-donor related substance, has shown protective effects against liver diseases. However, its effect on HCC stem cell-like properties and the underlying mechanisms remains uninvestigated. Methods: We measured the effects of betaine on the stem cell-like properties and malignant progression of HCC using patient-derived xenografts, cell-derived xenografts, tail vein-lung metastasis models, in vitro limiting dilution, tumor sphere formation, colony formation, and transwell assays. Mechanistic exploration was conducted using western blots, dot blots, methylated RNA immunoprecipitation-qPCR, RNA stability assays, RNA immunoprecipitation-qPCR, RNA pull-down, and gene mutation assays. Results: A cohort study of HCC found that a higher serum concentration of betaine was associated with decreased levels of stemness-related markers. Furthermore, in HCC cells and xenograft mice, betaine suppressed the stem cell-like properties of HCC by activating autophagy. Mechanistically, betaine increased the m6A modification in HCC by producing S-adenosylmethionine (SAM) via betaine-homocysteine S-methyltransferase (BHMT). This increase in SAM subsequently triggered autophagy by enhancing the stability of autophagy-related protein 3 (ATG3) via YTHDF1 in an m6A-dependent manner, thereby inhibiting the stem cell-like properties of HCC cells. Conclusions: These findings indicate that betaine inhibits the stem cell-like properties of HCC via the SAM/m6A/YTHDF1/ATG3 pathway. This study underscores the potential anti-tumor effects of betaine on HCC and offers novel therapeutic prospects for HCC patients.

The ubiquitin ligase STUB1 suppresses tumorigenesis of renal cell carcinomas through regulating YTHDF1 stability

STIP1 homology and U-box protein 1 (STUB1), a crucial member of the RING family E3 ubiquitin ligase, serve dual roles as an oncogene and a tumor suppressor in various human cancers. However, the role and mechanism of STUB1 in clear cell renal cell carcinoma (ccRCC) remain poorly defined. Here, we identified YTHDF1 as a novel STUB1 interaction partner using affinity purification mass spectrometry. Furthermore, we revealed that STUB1 promotes the ubiquitination and degradation of YTHDF1. Consequently, STUB1 depletion leads to YTHDF1 upregulation in renal cancer cells. Functionally, STUB1 depletion promoted migration and invasion of ccRCC cells in a YTHDF1-dependent manner. Additionally, the depletion of STUB1 also increased the tumorigenic potential of ccRCC in a xenograft model. Importantly, STUB1 expression is downregulated in ccRCC tissues, and its low expression level correlates with advanced tumor stage and poor overall survival in ccRCC patients. Taken together, these findings reveal that STUB1 inhibits the tumorigenicity of ccRCC by regulating YTHDF1 stability.

Programmed cell death pathways in lung adenocarcinoma: illuminating tumor drug resistance and therapeutic opportunities through single-cell analysis

Lung adenocarcinoma (LUAD) is a major contributor to cancer-related deaths, distinguished by its pronounced tumor heterogeneity and persistent challenges in overcoming drug resistance. In this study, we utilized single-cell RNA sequencing (scRNA-seq) to dissect the roles of programmed cell death (PCD) pathways, including apoptosis, necroptosis, pyroptosis, and ferroptosis, in shaping LUAD heterogeneity, immune infiltration, and prognosis. Among these, ferroptosis and pyroptosis were most significantly associated with favorable survival outcomes, highlighting their potential roles in enhancing anti-tumor immunity. Distinct PCD-related LUAD subtypes were identified, characterized by differential pathway activation and immune cell composition. Subtypes enriched with cytotoxic lymphocytes and dendritic cells demonstrated improved survival outcomes and increased potential responsiveness to immunotherapy. Drug sensitivity analysis revealed that these subtypes exhibited heightened sensitivity to targeted therapies and immune checkpoint inhibitors, suggesting opportunities for personalized treatment strategies. Our findings emphasize the interplay between PCD pathways and the tumor microenvironment, providing insights into the mechanisms underlying tumor drug resistance and immune evasion. By linking molecular and immune features to clinical outcomes, this study highlights the potential of targeting PCD pathways to enhance therapeutic efficacy and overcome resistance in LUAD. These results contribute to a growing framework for developing precise and adaptable cancer therapies tailored to specific tumor characteristics.

Role of N6-methyladenosine methylation in nasopharyngeal carcinoma: current insights and future prospective

Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck squamous cell carcinoma prevalent in Southern China, Southeast Asia, and North Africa. Despite advances in treatment options, the prognosis for advanced NPC remains poor, underscoring the urgent need to explore its underlying mechanisms and develop novel therapeutic strategies. Epigenetic alterations have been shown to play a key role in NPC progression. Recent studies indicate that dysregulation of RNA modifications in NPC specifically affects tumor-related transcripts, influencing various oncogenic processes. This review provides a comprehensive overview of altered RNA modifications and their regulators in NPC, with a focus on m6A and its regulatory mechanisms. We discuss how m6A RNA modification influences gene expression and affects NPC initiation and progression at the molecular level, analyzing its impact on cancer-related biological functions. Understanding these modifications could reveal new biomarkers and therapeutic targets for NPC, offering promising directions for future research and precision medicine.

Highly Efficient Delivery of Novel MiR-13896 by Human Umbilical Cord Mesenchymal Stem Cell-Derived Small Extracellular Vesicles Inhibits Gastric Cancer Progression by Targeting ATG2A-Mediated Autophagy

Gastric cancer (GC) is the fourth most common cancer and the second leading cause of cancer-related deaths worldwide. Despite recent advancements, clinical outcomes for GC remain unsatisfactory. Mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) have shown promise in inhibiting tumor progression, but their role in GC, specifically human umbilical cord MSC-derived small EVs (hucMSC-sEVs), is not well understood. This study investigates the therapeutic potential of hucMSC-sEVs in GC treatment. We found that hucMSC-sEVs are captured by GC cells, substantially inhibiting their proliferation and inducing apoptosis. MiRNA sequencing revealed that hucMSC-sEVs were enriched with miRNAs having anticancer properties. Among these, miR-13896, a new miRNA, was identified as a potent inhibitor of GC cell proliferation and a promoter of apoptosis. Mechanistic studies revealed that miR-13896 targets and down-regulates the ATG2A-mediated autophagy pathway, suppressing GC cell growth and metastasis. Furthermore, we enriched hucMSC-sEVs with miR-13896 through electroporation. These engineered EVs specifically targeted tumor sites and significantly reduced GC cell growth and migration in vitro and in vivo. MiR-13896 emerged as a promising therapeutic target for GC. The delivery of miR-13896 via hucMSC-sEVs represents a novel and effective strategy for GC treatment, highlighting the potential of EV-based therapies to combat this malignancy.

N6-methyladenosine (m6A) modification in inflammation: a bibliometric analysis and literature review

N6-methyladenosine (m6A) is the most abundant internal messenger RNA modification in eukaryotes, influencing various physiological and pathological processes by regulating RNA metabolism. Numerous studies have investigated the role of m6A in inflammatory responses and inflammatory diseases. In this study, VOSviewer and Citespace were used to perform bibliometric analysis to systematically evaluating the current landscape of research on the association between m6A and inflammation. The literature was sourced from the Web of Science Core Collection, with characteristics including year, country/region, institution, author, journal, citation, and keywords. According to the bibliometric analysis results of keywords, we present a narrative summary of the potential mechanisms by which m6A regulates inflammation. The results showed that the key mechanisms by which m6A modulates inflammation include apoptosis, autophagy, oxidative stress, immune cell dysfunction, and dysregulation of signaling pathways.