Characterization of N6-methyladenosine long non-coding RNAs in sporadic congenital cataract and age-related cataract

AIM:To characterize the N6-methyladenosine(m6A)modification patterns in long non-coding RNAs(lncRNAs)in sporadic congenital cataract(CC)and age-related cataract(ARC).METHODS:Anterior capsule of the lens were collected from patients with CC and ARC.Methylated RNA immunoprecipitation with next-generation sequencing and RNA sequencing were performed to identify m6A-tagged lncRNAs and lncRNAs expression.Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and Gene Ontology annotation were used to predict potential functions of the m6A-lncRNAs.RESULTS:Large amount of m6A peaks within lncRNA were identified for both CC and ARC,while the level was much higher in ARC(49870 peaks)than that in CC(18688 peaks),yet those difference between ARC in younger age group(ARC-1)and ARC in elder age group(ARC-2)was quite slight.A total of 1305 hypermethylated and 1178 hypomethylated lncRNAs,as well as 182 differential expressed lncRNAs were exhibited in ARC compared with CC.On the other hand,5893 hypermethylated and 5213 hypomethylated lncRNAs,as well as 155 significantly altered lncRNA were identified in ARC-2 compared with ARC-1.Altered lncRNAs in ARC were mainly associated with the organization and biogenesis of intracellular organelles,as well as nucleotide excision repair.CONCLUSION:Our results for the first time present an overview of the m6A methylomes of lncRNA in CC and ARC,providing a solid basis and uncovering a new insight to reveal the potential pathogenic mechanism of CC and ARC.

Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification

N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.

ALKBH5 suppresses autophagic flux via N6-methyladenosine demethylation of ZKSCAN3 mRNA in acute pancreatitis

BACKGROUND Increasing evidence has demonstrated that N6-methyladenosine(m6A)RNA modification plays an essential role in a wide range of pathological conditions.Impaired autophagy is a critical hallmark of acute pancreatitis(AP).AIM To explore the role of the m6A modification of ZKSCAN3 in the regulation of autophagy in AP.METHODS The AP mouse cell model was established by cerulein-treated mouse pancreatic acinar cells(MPC-83),and the results were confirmed by the levels of amylase and inflammatory factors.Autophagy activity was evaluated by specific identification of the autophagy-related microstructure and the expression of autophagy-related genes.ZKSCAN3 and ALKBH5 were knocked down to study the function in AP.A m6A RNA binding protein immunoprecipitation assay was used to study how the m6A modification of ZKSCAN3 mRNA is regulated by ALKBH.RESULTS The increased expression of amylase and inflammatory factors in the supernatant and the accumulation of autophagic vacuoles verified that the AP mouse cell model was established.The downregulation of LAMP2 and upregulation of LC3-II/I and SQSTM1 demonstrated that autophagy was impaired in AP.The expression of ZKSCAN3 was upregulated in AP.Inhibition of ZKSCAN3 increased the expression of LAMP2 and decreased the expression of the inflammatory factors,LC3-II/I and SQSTM1.Furthermore,ALKBH5 was upregulated in AP.Knockdown of ALKBH5 downregulated ZKSCAN3 expression and restored decreased autophagic flux in AP.Notably,the bioinformatic analysis revealed 23 potential m6A modification sites on ZKSCAN3 mRNA.The m6A modification of ZKSCAN3 mRNA was significantly decreased in AP.Knockdown of ALKBH5 increased the modification of ZKSCAN3 mRNA,which confirmed that ALKBH5 upregulated ZKSCAN3 expression in a m6A-dependent manner.CONCLUSION ALKBH5 inhibits autophagic flux through m6A demethylation of ZKSCAN3 mRNA in AP,thereby aggravating the severity of the disease.

Modulation of host N6-methyladenosine modification by gut microbiota in colorectal cancer

As a research hotspot in the field of molecular biology,N6-methyladenosine(m6A)modification has made progress in the treatment of colorectal cancer(CRC),leukemia and other cancers.Numerous studies have demonstrated that the tumour microenvironment(TME)regulates the level of m6A modification in the host and activates a series of complex epigenetic signalling pathways through interactions with CRC cells,thus affecting the progression and prognosis of CRC.However,with the diversity in the composition of TME factors,this action is reci-procal and complex.Encouragingly,some studies have experimentally revealed that the intestinal flora can alter CRC cell proliferation by directly acting on m6A and thereby altering CRC cell proliferation.This review summarizes the data,supporting the idea that the intestinal flora can influence host m6A levels through pathways such as methyl donor metabolism and thus affect the progression of CRC.We also review the role of m6A modification in the diagnosis,treatment,and prognostic assessment of CRC and discuss the current status,limitations,and potential clinical value of m6A modification in this field.We propose that additional in-depth research on m6A alterations in CRC patients and their TME-related targeted therapeutic issues will lead to better therapeutic outcomes for CRC patients.

N6-methyladenosine methylation regulates the tumor microenvironment of Epstein-Barr virus-associated gastric cancer

BACKGROUND N6-methyladenosine(m6A)methylation modification exists in Epstein-Barr virus(EBV)primary infection,latency,and lytic reactivation.It also modifies EBV latent genes and lytic genes.EBV-associated gastric cancer(EBVaGC)is a distinctive molecular subtype of GC.We hypothesized EBV and m6A methylation regulators interact with each other in EBVaGC to differentiate it from other types of GC.AIM To investigate the mechanisms of m6A methylation regulators in EBVaGC to determine the differentiating factors from other types of GC.METHODS First,The Cancer Gene Atlas and Gene Expression Omnibus databases were used to analyze the expression pattern of m6A methylation regulators between EBVaGC and EBV-negative GC(EBVnGC).Second,we identified Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)functional enrichment of m6A-related differentially expressed genes.We quantified the relative abundance of immune cells and inflammatory factors in the tumor microenvironment(TME).Finally,cell counting kit-8 cell proliferation test,transwell test,and flow cytometry were used to verify the effect of insulin-like growth factor binding protein 1(IGFBP1)in EBVaGC cell lines.RESULTS m6A methylation regulators were involved in the occurrence and development of EBVaGC.Compared with EBVnGC,the expression levels of m6A methylation regulators Wilms tumor 1-associated protein,RNA binding motif protein 15B,CBL proto-oncogene like 1,leucine rich pentatricopeptide repeat containing,heterogeneous nuclear ribonucleoprotein A2B1,IGFBP1,and insulin-like growth factor 2 binding protein 1 were significantly downregulated in EBVaGC(P<0.05).The overall survival rate of EBVaGC patients with a lower expression level of IGFBP1 was significantly higher(P=0.046).GO and KEGG functional enrichment analyses showed that the immunity pathways were significantly activated and rich in immune cell infiltration in EBVaGC.Compared with EBVnGC,the infiltration of activated CD4+T cells,activated CD8+T cells,monocytes,activated dendritic cells,and plasmacytoid dendritic cells were significantly upregulated in EBVaGC(P<0.001).In EBVaGC,the expression level of proinflammatory factors interleukin(IL)-17,IL-21,and interferon-γ and immunosuppressive factor IL-10 were significantly increased(P<0.05).In vitro experiments demonstrated that the expression level of IGFBP1 was significantly lower in an EBVaGC cell line(SNU719)than in an EBVnGC cell line(AGS)(P<0.05).IGFBP1 overexpression significantly attenuated proliferation and migration and promoted the apoptosis levels in SNU719.Interfering IGFBP1 significantly promoted proliferation and migration and attenuated the apoptosis levels in AGS.CONCLUSION m6A regulators could remodel the TME of EBVaGC,which is classified as an immune-inflamed phenotype and referred to as a“hot”tumor.Among these regulators,we demonstrated that IGFBP1 affected proliferation,migration,and apoptosis.

Advances of N6-methyladenosine modification on circular RNA in hepatocellular carcinoma

N6-methyladenosine(m6A)is a reversible epigenetic modification, which is one of the most abundant modifiers in eukaryotic cells and has been commonly reported in messenger RNAs and non-coding RNAs. The processing modification of m6A regulates RNA transcription, processing, splicing, degradation, and translation, and plays an important role in the biological process of tumors. Circular RNA, which lacks the 5' cap structure, has been mistakenly regarded as a "junk sequence" generated by accidental shearing during the transcription process. However, it has been found that circRNAs can be involved in tumor invasion and metastasis through microRNAs, binding proteins, translated peptides, and m6A modifications. In this paper, we reviewed the role of m6A modifications in circRNA regulation and their functions in hepatocellular carcinoma and discussed their potential clinical applications and future development in this field.

Long non-coding RNA GATA6-AS1 is mediated by N6-methyladenosine methylation and inhibits the proliferation and metastasis of gastric cancer

BACKGROUND Through experimental research on the biological function of GATA6-AS1,it was confirmed that GATA6-AS1 can inhibit the proliferation,invasion,and migration of gastric cancer cells,suggesting that GATA6-AS1 plays a role as an anti-oncogene in the occurrence and development of gastric cancer.Further experi-ments confirmed that the overexpression of fat mass and obesity-associated protein(FTO)inhibited the expression of GATA6-AS1,thereby promoting the occurrence and development of gastric cancer.AIM To investigate the effects of GATA6-AS1 on the proliferation,invasion and migration of gastric cancer cells and its mechanism of action.METHODS We used bioinformatics methods to analyze the Cancer Genome Atlas(https://portal.gdc.cancer.gov/.The Cancer Genome Atlas)and download expression data for GATA6-AS1 in gastric cancer tissue and normal tissue.We also constructed a GATA6-AS1 lentivirus overexpression vector which was transfected into gastric cancer cells to investigate its effects on proliferation,migration and invasion,and thereby clarify the expression of GATA6-AS1 in gastric cancer and its biological role in the genesis and development of gastric cancer.Next,we used a database(http://starbase.sysu.edu.cn/starbase2/)to analysis GATA6-AS1 whether by m6A methylation modify regulation and predict the methyltransferases that may methylate GATA6-AS1.Furthermore,RNA immunoprecipitation experiments confirmed that GATA6-AS1 was able to bind to the m6A methylation modification enzyme.These data allowed us to clarify the ability of m6A methylase to influence the action of GATA6-AS1 and its role in the occurrence and development of gastric cancer.RESULTS Low expression levels of GATA6-AS1 were detected in gastric cancer.We also determined the effects of GATA6-AS1 overexpression on the biological function of gastric cancer cells.GATA6-AS1 had strong binding ability with the m6A demethylase FTO,which was expressed at high levels in gastric cancer and negatively correlated with the expression of GATA6-AS1.Following transfection with siRNA to knock down the expression of FTO,the expression levels of GATA6-AS1 were up-regulated.Finally,the proliferation,migration and invasion of gastric cancer cells were all inhibited following the knockdown of FTO expression.CONCLUSION During the occurrence and development of gastric cancer,the overexpression of FTO may inhibit the expression of GATA6-AS1,thus promoting the proliferation and metastasis of gastric cancer.

N6-甲基腺苷甲基化相关基因IGF2BP3在肾透明细胞癌的作用研究

目的筛选肾透明细胞癌(ccRCC)中的关键N6-甲基腺苷(m^(6)A)甲基化相关基因,并研究其与ccRCC预后、ccRCC细胞的迁移和侵袭的关系。方法从癌症基因组图谱(TCGA)和基因型组织表达(GTEx)数据库中下载ccRCC和癌旁组织的RNA测序数据和临床数据,采用R4.1.1分析表达谱和预后,并筛选关键基因。收集10例ccRCC手术临床标本,采用定量PCR(qPCR)和免疫组织化学法分别检测基因mRNA和蛋白表达。在人ccRCC细胞系RCC23中,通过SiRNA敲减关键基因,并用CCK-8检测细胞的存活率,采用划痕试验和Transwell试验分别检测细胞的迁移和侵袭。结果19个m^(6)A甲基化相关基因中仅有胰岛素样生长因子ⅡmRNA结合蛋白3(IGF2BP3)在ccRCC组织中高表达,且IGF2BP3高表达与ccRCC患者预后不良呈正相关。通过qPCR和免疫组织化学法在临床标本中验证了IGF2BP3的高表达。通过小干扰RNA(siRNA)将IGF2BP3敲减后发现,RCC23细胞的存活率明显下降,且细胞的迁移和侵袭能力下降。结论IGF2BP3可能是预测ccRCC患者预后的生物标志物和潜在的药物治疗靶点。

2株H5N6亚型禽流感病毒的遗传进化分析

为了解禽流感病毒(Avian influenza virus,AIV)的遗传进化特点,试验对2022—2023年从我国湖南和福建活禽交易市场分离的2株鸭源H5N6亚型AIV进行全基因组测序、关键氨基酸位点分析和遗传进化树构建,这2株AIV分别为A/duck/Hunan/QG3/2022(H5N6)(简称HN/QG3)和A/duck/Fujian/QG4/2023(H5N6)(简称FJ/QG4)。结果显示:HN/QG3株属于2.3.4.4b分支,其基因组来源于H5N6和H5N8毒株,与鸭、野鸟、环境和人类来源的H5亚型AIV的同源性较高,而FJ/QG4株属于2.3.4.4h分支,HA基因与分离株A/Rattus norvegicus/China/FS21/2021(H5N6)的相似性为97%,而其他基因片段与2021年广东地区分离的人源H5N6亚型AIV的同源性较高;2株H5N6亚型AIV的HA蛋白裂解位点含有多个连续的碱性氨基酸,符合高致病性AIV的分子特征,HA蛋白第226和228位分别为Q和G,说明H5N6亚型AIV具有优先结合禽源α2,3-唾液酸受体的特征,并且NA蛋白第58~68位缺失11个氨基酸,对小鼠的致病性可能增强。研究表明,2株鸭源H5N6亚型AIV分别属于2.3.4.4b分支和2.3.4.4h分支,其对人源α2,6-唾液酸受体的识别能力增强,毒力和传播能力可能增强。

N-6甲基腺苷调节蛋白在胶质瘤中的研究进展

N-6甲基腺苷(m6A)是真核生物中RNA分子上的一种常见化学修饰,这种修饰对RNA的稳定性、翻译和转录等多种生物过程有重要影响。m6A修饰在所有腺苷酸中所占的比例虽然很小(0.1%-0.4%),但它是真核生物mRNA中最丰富的表观遗传修饰之一,在干细胞的更新、分化、转录、翻译、降解等过程中都扮演着重要角色,并可能在特定基因的表达或失活中起决定性作用。m6A修饰是一个动态可逆的过程,由甲基化酶、去甲基化酶及阅读蛋白共同调控,甲基化酶复合物的核心成员包括METTL3、METTL14和WTAP,而FTO和ALKBH5则是已知的去甲基化酶。YTH基因家族中的蛋白,即m6A阅读蛋白,能够识别并结合带有m6A修饰的RNA,从而调节RNA的代谢过程并参与不同的生理活动。研究显示m6A阅读蛋白YTH家族在胶质瘤形成和发展中起关键作用,本文旨在综述m6A及相关蛋白与胶质瘤的关系。

Predicting Standardized Precipitation Evapotranspiration Index for Fada N’Gourma by 2050 Using CMPI-6 Outputs under SSPs Scenarios

Extreme weather events,such as floods and droughts,are expected to rise significantly worldwide as a result of climate change.Investigating future drought patterns is therefore a key approach for elaborating anticipatory water resources management responses to climate change.In this paper,future meteorological drought conditions are investigated based on the SPEI(Standardised Precipitation Evapotranspiration Index).This study makes use of observed and projected data.The simulated data were retrieved from the CMIP6(Coupled Model Intercomparison Project Phase 6)over the period 2025-2050,and the Delta change method was adopted to remove the bias in the dataset.Then SPEI at various scales has been estimated under four future scenarios(SSP1-2.6,SSP2-4.5,SSP3-7.0 and SSP5-8.5).The trend analysis of the projected SPEI was performed at p<0.05 using the MMK(Modified Mann-Kendall)test in order to detect the statistically significant trend of the drought against the null hypothesis of no trend.Results show large variability in the magnitude of drought in the past and future.Based on SPEI at 24 months accumulation,the result shows that under SSP1-2.6,the basin will experience a wet period during the first decade(SPEI=0.60),the second decade will be dry(SPEI24=-0.43).The remaining years will be also dry(SPEI=-0.34).Under SSP2-4.5,SSP3-7.0 and SSP5-8.5 scenarios,the district will experience a wet period during the first two decades with SPEI ranging from 0.38 to 0.59.This wet period will be followed by a dry period under these scenarios ranging from-0.14 to-0.06.Overall,under SSPs scenarios,two main periods characterized by a rainfall recovery spanning from followed by a moderately prolonged drought are identified within the study area.The findings of this study may provide valuable information for developing proactive measures to reduce water insecurity in Fada N’Gourma through effective drought mitigation.

N末端B型脑钠肽前体、白细胞介素-6、血管紧张素Ⅱ与慢性心力衰竭预后及患者心功能的相关性分析

目的探究N末端B型脑钠肽前体(NT-proBNP)、白细胞介素-6(IL-6)、血管紧张素Ⅱ(Ang-Ⅱ)与慢性心力衰竭(CHF)预后及患者心功能的相关性,为临床诊疗提供参考。方法选取2023年1月至12月泰州市第四人民医院收治的132例CHF患者的临床资料,进行回顾性分析。根据CHF患者随访时是否发生不良心血管事件分为预后良好组(81例)和预后不良组(51例)。比较两组患者心功能指标、NT-proBNP、IL-6、Ang-Ⅱ水平,使用Pearson相关性模型分析心功能指标与NT-proBNP、IL-6、Ang-Ⅱ水平的相关性,采用多因素Logistic回归分析影响CHF患者预后的独立危险因素。结果预后不良组患者左心室舒张末期内径(LVEDD)、左心室收缩末期内径(LVESD)均大于预后良好组,左心室射血分数(LVEF)低于预后良好组,左心室后壁收缩末期厚度(LVPWTs)、舒张末期室间隔厚度(IVSTd)均大于预后良好组(均P<0.05)。预后不良组患者NT-proBNP、IL-6、Ang-Ⅱ水平均高于预后良好组(均P<0.05)。Pearson相关性分析结果显示:NT-proBNP、IL-6、Ang-Ⅱ水平与LVEDD、LVESD、LVPWTs、IVSTd均呈正相关(NT-proBNP:r值=0.520、0.662、0.535、0.571,均P<0.05;IL-6:r值=0.575、0.555、0.414、0.463,均P<0.05;Ang-Ⅱ:r值=0.556、0.362、0.581、0.350,均P<0.05),与LVEF均呈负相关(NT-proBNP:r值=-0.540,P<0.05;IL-6:r值=-0.521,P<0.05;Ang-Ⅱ:r值=-0.456,P<0.05)。多因素Logistic回归分析结果显示:NT-proBNP、IL-6、Ang-Ⅱ水平高均为影响CHF患者预后的独立危险因素(均P<0.05)。结论CHF预后不良患者临床均表现出NT-proBNP、IL-6、Ang-Ⅱ水平升高现象,且上述指标均为影响CHF患者预后的独立危险因素,其水平均与患者心功能存在相关性,临床应加强对上述指标的监测和管理,以降低CHF患者不良结局的发生风险。

Epigenetic N6-methyladenosine modification of RNA and DNA regulates cancer

The biological roles of N6 methylation of nucleic acids have been extensively studied.Adenine methylation of RNA is the most prevalent RNA modification and has widespread effects on RNA splicing,translation,localization,and stability.Aberrant dynamic regulation of RNA N6-methyladenosine(m6 A)has been reported in numerous human diseases,including several cancers.In recent years,eukaryotic DNA N6-methyladenosine(6 mA)has also been reported and implicated in cancer progression and tumorigenesis.In this review,we summarize the contributions of N6-methyladenosine modification to cancer biology and pathogenesis in the context of both RNA and DNA.We also highlight the clinical relevance of targeting these modifications as a therapeutic strategy for cancer.

Genome-wide map of N6-methyladenosine circular RNAs identified in mice model of severe acute pancreatitis

BACKGROUND Severe acute pancreatitis(SAP)is a deadly inflammatory disease with complex pathogenesis and lack of effective therapeutic options.N6-methyladenosine(m6A)modification of circRNAs plays important roles in physiological and pathological processes.However,the roles of m6A circRNA in the pathological process of SAP remains unknown.AIM To identify transcriptome-wide map of m6A circRNAs and to determine their biological significance and potential mechanisms in SAP.METHODS The SAP in C57BL/6 mice was induced using 4%sodium taurocholate salt.The transcriptome-wide map of m6A circRNAs was identified by m6A-modified RNA immunoprecipitation sequencing.The biological significance of circRNAs with differentially expressed m6A peaks was evaluated through gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis.The underlying mechanism of m6A circRNAs in SAP was analyzed by constructing of m6A circRNAmicroRNA networks.The expression of demethylases was determined by quantitative polymerase chain reaction and western blot to deduce the possible mechanism of reversible m6A process in SAP.RESULTS Fifty-seven circRNAs with differentially expressed m6A peaks were identified by m6A-modified RNA immunoprecipitation sequencing,of which 32 were upregulated and 25 downregulated.Functional analysis of these m6A circRNAs in SAP found some important pathways involved in the pathogenesis of SAP,such as regulation of autophagy and protein digestion.In m6A circRNA–miRNA networks,several important miRNAs participated in the occurrence and progression of SAP were found to bind to these m6A circRNAs,such as miR-24-3p,miR-26a,miR-92b,miR-216b,miR-324-5p and miR-762.Notably,the total m6A level of circRNAs was reduced,while the demethylase alkylation repair homolog 5 was upregulated in SAP.CONCLUSION m6A modification of circRNAs may be involved in the pathogenesis of SAP.Our findings may provide novel insights to explore the possible pathogenetic mechanism of SAP and seek new potential therapeutic targets for SAP.

Recent progress in N6-methyladenosine modification in ocular surface diseases

N6-methyladenosine(m6A)modification is a reversible process promoted by“writers”,inhibited by“erasers”,and processed by“readers”.During the last decade,increasing emphasis has been placed on the underlying roles of m6A modification owing to their great importance in biological significance.The abnormal regulation of m6A modification will lead to aberrant cellular behavior and various diseases.Recently,studies have demonstrated that m6A modification is closely associated with the genesis and progression of ocular surface diseases(OSDs).This review focus on the role of m6A modification and research progress in OSDs including fungal keratitis,herpes simplex keratitis,immunerelated keratoconjunctival diseases,pterygium,ocular chemical burns,and Graves’ophthalmopathy,which may provide new insights into and prospective applications for OSDs.

Analysis of N6-methyladenosine-modified mRNAs in diabetic cataract

BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic complication,usually occurs at an earlier age and progresses faster than age-related cataracts.Evidence has linked N6-methyladenosine(m6A)to DC progression.However,there exists a lack of understanding regarding RNA m6A modifications and the role of m6A in DC pathogenesis.AIM To elucidate the role played by altered m6A and differentially expressed mRNAs(DEmRNAs)in DC.METHODS Anterior lens capsules were collected from the control subjects and patients with DC.M6A epitranscriptomic microarray was performed to investigate the altered m6A modifications and determine the DEmRNAs.Through Gene Ontology and pathway enrichment(Kyoto Encyclopedia of Genes and Genomes)analyses,the potential role played by dysregulated m6A modification was predicted.Real-time polymerase chain reaction was further carried out to identify the dysregulated expression of RNA methyltransferases,demethylases,and readers.RESULTS Increased m6A abundance levels were found in the total mRNA of DC samples.Bioinformatics analysis predicted that ferroptosis pathways could be associated with m6A-modified mRNAs.The levels of five methylation-related genes-RBM15,WTAP,ALKBH5,FTO,and YTHDF1-were upregulated in DC samples.Upregulation of RBM15 expression was verified in SRA01/04 cells with high-glucose medium and in samples from DC patients.CONCLUSION M6a mRNA modifications may be involved in DC progression via the ferroptosis pathway,rendering novel insights into therapeutic strategies for DC.

N^(6)-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance

Background:Stemness and chemoresistance contribute to cervical cancer recurrence and metastasis.In the current study,we determined the relevant players and role of N^(6)-methyladenine(m^(6)A)RNA methylation in cervical cancer progression.Methods:The roles of m^(6)A RNA methylation and centromere protein K(CENPK)in cervical cancer were analyzed using bioinformatics analysis.Methylated RNA immunoprecipitation was adopted to detect m^(6)A modification of CENPK mRNA.Human cervical cancer clinical samples,cell lines,and xenografts were used for analyzing gene expression and function.Immunofluorescence staining and the tumorsphere formation,clonogenic,MTT,and EdU assays were performed to determine cell stemness,chemoresistance,migration,invasion,and proliferation in HeLa and SiHa cells,respectively.Western blot analysis,co-immunoprecipitation,chromatin immunoprecipitation,and luciferase reporter,cycloheximide chase,and cell fractionation assays were performed to elucidate the underlying mechanism.Results:Bioinformatics analysis of public cancer datasets revealed firm links between m^(6)A modification patterns and cervical cancer prognosis,especially through ZC3H13-mediated m^(6)A modification of CENPK mRNA.CENPK expression was elevated in cervical cancer,associated with cancer recurrence,and independently predicts poor patient prognosis[hazard ratio=1.413,95%confidence interval=1.078−1.853,P=0.012].Silencing of CENPK prolonged the overall survival time of cervical cancer-bearing mice and improved the response of cervical cancer tumors to chemotherapy in vivo(P<0.001).We also showed that CENPK was directly bound to SOX6 and disrupted the interactions of CENPK withβ-catenin,which promotedβ-catenin expression and nuclear translocation,facilitated p53 ubiquitination,and led to activation of Wnt/β-catenin signaling,but suppression of the p53 pathway.This dysregulation ultimately enhanced the tumorigenic pathways required for cell stemness,DNA damage repair pathways necessary for cisplatin/carboplatin resistance,epithelial-mesenchymal transition involved in metastasis,and DNA replication that drove tumor cell proliferation.Conclusions:CENPK was shown to have an oncogenic role in cervical cancer and can thus serve as a prognostic indicator and novel target for cervical cancer treatment.

Profiling of N6-methyladenosine methylation in porcine longissimus dorsi muscle and unravelling the hub gene ADIPOQ promotes adipogenesis in an m^(6)A-YTHDF1–dependent manner

Background Intramuscular fat(IMF)content is a critical indicator of pork quality,and abnormal IMF is also relevant to human disease as well as aging.Although N6-methyladenosine(m^(6)A)RNA modification was recently found to regulate adipogenesis in porcine intramuscular fat,however,the underlying molecular mechanisms was still unclear.Results In this work,we collected 20 longissimus dorsi muscle samples with high(average 3.95%)or low IMF content(average 1.22%)from a unique heterogenous swine population for m^(6)A sequencing(m^(6)A-seq).We discovered 70genes show both differential RNA expression and m^(6)A modification from high and low IMF group,including ADIPOQ and SFRP1,two hub genes inferred through gene co-expression analysis.Particularly,we observed ADIPOQ,which contains three m^(6)A modification sites within 3’untranslated and protein coding region,could promote porcine intramuscular preadipocyte differentiation in an m^(6)A-dependent manner.Furthermore,we found the YT521-B homology domain family protein 1(YTHDF1)could target and promote ADIPOQ mRNA translation.Conclusions Our study provided a comprehensive profiling of m^(6)A methylation in porcine longissimus dorsi muscle and characterized the involvement of m^(6)A epigenetic modification in the regulation of ADIPOQ mRNA on IMF deposition through an m^(6)A-YTHDF1-dependent manner.

N^(6)-methyladenosine(m^(6)A)RNA modification in tumor immunity

Growing evidence supports that cancer progression is closely associated with the tumor microenvironment and immune evasion.Importantly,recent studies have revealed the crucial roles of epigenetic regulators in shaping the tumor microenvironment and restoring immune recognition.N^(6)-methyladenosine(m^(6)A)modification,the most prevalent epigenetic modification of mammalian mRNAs,has essential functions in regulating the processing and metabolism of its targeted RNAs,and therefore affects various biological processes including tumorigenesis and progression.Recent studies have demonstrated the critical functions and molecular mechanisms underlying abnormal m^(6)A modification in the regulation of tumor immunity.In this review,we summarize recent research progress in the potential roles of m^(6)A modification in tumor immunoregulation,with a special focus on the anti-tumor processes of immune cells and involvement in immune-associated molecules and pathways.Furthermore,we review current knowledge regarding the close correlation between m6A-related risk signatures and the tumor immune microenvironment landscape,and we discuss the prognostic value and therapeutic efficacy of m^(6)A regulators in a variety of cancer types.

N6-甲基腺苷相关调节因子与骨关节炎:生物信息学和实验验证分析

背景:越来越多证据表明N6-甲基腺苷(N6-methyladenosine,m6A)调节因子与骨关节炎密切相关,被认为是防治骨关节炎新方向,但具体作用机制不明。目的:通过对骨关节炎基因芯片数据集进行生物信息学分析,探讨m6A对骨关节炎的作用,解析骨关节炎发病机制。方法:首先利用R软件提取GEO数据库中GSE1919数据集中骨关节炎相关m6A调节因子及其表达量,进而对提取结果行基因差异分析及GO、KEGG富集分析;接着对PPI网络拓扑学分析结果和机器学习结果取交集得到m6A关键调节因子,并通过体外细胞实验验证。结果与结论:①提取得到16个骨关节炎相关m6A调节因子表达量,通过差异分析获得ZC3H13、YTHDC1、YTHDF3、HNRNPC等11个m6A差异调节因子;②GO富集分析显示,骨关节炎相关m6A差异调节因子在生物过程中主要于mRNA转运、RNA分解代谢、胰岛素样生长因子受体信号通路调控等发挥作用;③KEGG富集分析显示,差异调节因子主要参与p53、白细胞介素17和AMPK信号通路;④综合PPI网络拓扑学分析和机器学习结果获得m6A关键调节因子——YTHDC1;⑤体外细胞实验结果表明,m6A关键调节因子——YTHDC1在对照组与骨关节炎组中表达存在显著差异(P<0.05);⑥结果显示,YTHDC1与骨关节炎发生发展密切相关,有望成为m6A治疗骨关节炎的分子靶点。