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.

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.

m^(6)A modification of lncRNA in middle ear cholesteatoma

Objective:Middle ear cholesteatoma is a non-tumorous condition that typically leads to hearing loss,bone destruction,and other severe complications.Despite surgery being the primary treatment,the recurrence rate remains high.Therefore,exploring the molecular mechanisms underlying cholesteatoma is crucial for discovering new therapeutic approaches.This study aims to explore the involvement of N6-methyladenosine(m^(6)A)methylation in long non-coding RNAs(lncRNAs)in the biological functions and related pathways of middle ear cholesteatoma.Methods:The m^(6)A modification patterns of lncRNA in middle ear cholesteatoma tissues(n=5)and normal post-auricular skin tissues(n=5)were analyzed using an lncRNA m^(6)A transcriptome microarray.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were conducted to identify potential biological functions and signaling pathways involved in the pathogenesis of middle ear cholesteatoma.Methylated RNA immunoprecipitation(MeRIP)-PCR was used to validate the m^(6)A modifications in cholesteatoma and normal skin tissues.Results:Compared with normal skin tissues,1525 lncRNAs were differentially methylated in middle ear cholesteatoma tissues,with 1048 showing hypermethylation and 477 showing hypomethylation[fold change(FC)≥3 or<1/3,P<0.05].GO enrichment analysis indicated that hypermethylated lncRNAs were involved in protein phosphatase inhibitor activity,neuron-neuron synapse,and regulation ofα-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid(AMPA)receptor activity.Hypomethylated lncRNAs were associated with mRNA methyltransferase activity,secretory granule membrane,and mRNA methylation.KEGG analysis revealed that hypermethylated lncRNAs were mainly associated with 5 pathways:the Hedgehog signaling pathway,viral protein interaction with cytokines and cytokine receptors,mitogen-activated protein kinase(MAPK)signaling pathway,cytokine-cytokine receptor interaction,and adrenergic signaling in cardiomyocytes.Hypomethylated lncRNAs were mainly involved in 4 pathways:Renal cell carcinoma,tumor necrosis factor signaling pathway,transcriptional misregulation in cancer,and cytokine-cytokine receptor interaction.Additionally,MeRIP-PCR confirmed the changes in m^(6)A methylation levels in NR_033339,NR_122111,NR_130744,and NR_026800,consistent with microarray analysis.Real-time PCR also confirmed the significant upregulation of MAPK1 and NF-κB,key genes in the MAPK signaling pathway.Conclusion:This study reveals the m^(6)A modification patterns of lncRNAs in middle ear cholesteatoma,suggests a direction for further research into the role of lncRNA m^(6)A modification in the etiology of cholesteatoma.The findings provide potential therapeutic targets for the treatment of middle ear cholesteatoma.

The landscape of epigenetic regulation and therapeutic application of N^(6)-methyladenosine modifications in non-coding RNAs

RNA N^(6)-methyladenosine(m^(6)A)methylation is the most abundant and conserved RNA modification in eukaryotes.It participates in the regulation of RNA metabolism and various pathophysiological processes.Non-coding RNAs(ncRNAs)are defined as small or long transcripts which do not encode proteins and display numerous biological regulatory functions.Similar to mRNAs,m^(6)A deposition is observed in ncRNAs.Studying RNA m^(6)A modifications on ncRNAs is of great importance specifically to deepen our understanding of their biological roles and clinical implications.In this review,we summarized the recent research findings regarding the mutual regulation between RNA m^(6)A modification and ncRNAs(with a specific focus on microRNAs,long non-coding RNAs,and circular RNAs)and their functions.We also discussed the challenges of m^(6)A-containing ncRNAs and RNA m^(6)A as therapeutic targets in human diseases and their future perspective in translational roles.

Long non-coding RNA small nucleolar RNA host gene 6 aggravates pancreatic cancer through upregulation of far upstream element binding protein 1 by sponging microRNA-26a-5p

Background:Pancreatic cancer(PC)is a highly deadly malignancy with few effective therapies.We aimed to unmask the role that long non-coding RNA small nucleolar RNA host gene 6(SNHG6)plays in PC cells by targeting far upstream element binding protein 1(FUBP1)via microRNA-26a-5p(miR-26a-5p).Methods::SNHG6 expression was predicted by bioinformatics,followed by verification via reverse transcription quantitative polymerase chain reaction.Then,the interactions among SNHG6,miR-26a-5p,and FUBP1 were detected through online software analysis,dual luciferase reporter assay and RNA pull-down.After that,cells were treated with different small interfering RNAs and/or mimic to determine the interactions among SNHG6,miR-26a-5p,and FUBP1 and their roles in PC cells.Finally,the role of SNHG6 in tumor growth in vivo was evaluated by measuring the growth and weight of transplanted tumors in nude mice.A t-test,one-way and two-way analysis of variance were used for data analysis.Results::Compared with that in normal tissues,SNHG6 was highly expressed in PC tissues(1.00±0.05 vs.1.56±0.06,t=16.03,P<0.001).Compared with that in human pancreatic duct epithelial cells(HPDE6-C7),SNHG6 showed the highest expression in PANC-1 cells(1.00±0.06 vs.3.87±0.13,t=34.72,P<0.001)and the lowest expression in human pancreatic cancer cells(MIAPaCa-2)(1.00±0.06 vs.1.41±0.07,t=7.70,P=0.0015).Compared with the levels in the si-negative control group,SNHG6(0.97±0.05 vs.0.21±0.06,t=16.85,P<0.001),N-cadherin(0.74±0.05 vs.0.41±0.04,t=8.93,P<0.001),Vimentin(0.55±0.04 vs.0.25±0.03,t=10.39,P<0.001),andβ-catenin(0.62±0.05 vs.0.32±0.03,t=8.91,P<0.001)were decreased,while E-cadherin(0.65±0.06 vs.1.36±0.07,t=13.34,P<0.001)was increased after SNHG6 knockdown or miR-26a-5p overexpression,accompanied by inhibited cell proliferation,migration,and invasion.SNHG6 overexpression exerted the opposite effects.SNHG6 upregulated FUBP1 expression by sponging miR-26a-5p.Silencing SNHG6 blocked the growth of PC in vivo.Conclusion::Silencing SNHG6 might ameliorate PC through inhibition of FUBP1 by sponging miR-26a-5p,thus providing further supporting evidence for its use in PC treatment.

H19 recruited N^(6)-methyladenosine(m^(6)A)reader YTHDF1 to promote SCARB1 translation and facilitate angiogenesis in gastric cancer

Background:Angiogenesis is described as a complex process in which new microvessels sprout from endothelial cells of existing vasculature.This study aimed to determine whether long non-coding RNA(lncRNA)H19 induced the angiogenesis of gastric cancer(GC)and its possible mechanism.Methods:Gene expression level was determined by quantitative real-time polymerase chain reaction and western blotting.Cell counting kit-8,transwell,5-Ethynyl-2′-deoxyuridine(EdU),colony formation assay,and human umbilical vein endothelial cells(HUVECs)angiogenesis assay as well as Matrigel plug assay were conducted to study the proliferation,migration,and angiogenesis of GC in vitro and in vivo.The binding protein of H19 was found by RNA pull-down and RNA Immunoprecipitation(RIP).High-throughput sequencing was performed and next Gene Ontology(GO)as well as Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis was conducted to analyze the genes that are under H19 regulation.Methylated RIP(me-RIP)assay was used to investigate the sites and abundance among target mRNA.The transcription factor acted as upstream of H19 was determined through chromatin immunoprecipitation(ChIP)and luciferase assay.Results:In this study,we found that hypoxia-induced factor(HIF)-1a could bind to the promoter region of H19,leading to H19 overexpression.High expression of H19 was correlated with angiogenesis in GC,and H19 knocking down could inhibit cell proliferation,migration and angiogenesis.Mechanistically,the oncogenic role of H19 was achieved by binding with the N^(6)-methyladenosine(m^(6)A)reader YTH domain-containing family protein 1(YTHDF1),which could recognize the m^(6)A site on the 3′-untransated regions(3′-UTR)of scavenger receptor class B member 1(SCARB1)mRNA,resulting in over-translation of SCARB1 and thus promoting the proliferation,migration,and angiogenesis of GC cells.Conclusion:HIF-1a induced overexpression of H19 via binding with the promoter of H19,and H19 promoted GC cells proliferation,migration and angiogenesis through YTHDF1/SCARB1,which might be a beneficial target for antiangiogenic therapy for GC.

Lnc-TCL6 is a potential biomarker for early diagnosis and grade in liver-cirrhosis patients

Background:Long non-coding RNAs(lncRNAs)have been applied as biomarkers in many diseases.However,scarce biomarkers are available in single lncRNA differential expression associated with different clinical stages of liver cirrhosis(LC).The aim of the study is to identify some lncRNAs that can serve as non-invasive sensitive biomarkers for early diagnosis and grade of LC.Methods:Blood lncRNA expression was evaluated in three independent cohorts with 305 participants including healthy controls,hepatitis B virus(HBV)carriers,and patients with chronic hepatitis B(CHB)or LC.First,candidate lncRNAs were screened by CapitalBiotech microarray to diagnose cirrhosis.Quantitative reverse-transcriptase polymerase chain reaction was then used to investigate the expression of selected lncRNAs in the whole group of cirrhosis and different Child–Pugh classes.Ultimately,the diagnostic accuracy of the promising biomarker was examined and validated via Mann–Whitney test and receiver-operating characteristics analysis.Results:Lnc-TCL6 was identified as a sensitive biomarker for early diagnosis of LC(Child–Pugh A)compared with healthy controls(area under the ROC curve[AUC]=0.636),HBV carriers(AUC=0.671),and CHB patients(AUC=0.672).Furthermore,lnc-TCL6 showed a favourable capacity in discriminating among different Child–Pugh classes(AUC:0.711–0.837).Compared with healthy controls,HBV carriers,and CHB patients,the expression of lnc-TCL6 was obviously up-regulated in Child–Pugh A patients and,conversely,significantly down-regulated in Child–Pugh C patients.Conclusions:Lnc-TCL6 is a novel potential biomarker for early diagnosis of LC and is a possible predictor of disease progression.

LncRNA AFAP1-AS1/miR-27b-3p/VEGF-C axis modulates stemness characteristics in cervical cancer cells

Background:Long non-coding RNA(lncRNA)actin filament-associated protein 1 antisense RNA 1(AFAP1-AS1)functions as a competing endogenous RNA to regulate target genes expression by sponging microRNAs(miRs)to play cancer-promoting roles in cancer stem cells.However,the regulatory mechanism of AFAP1-AS1 in cervical cancer(CC)stem cells is unknown.The present study aimed to provide a new therapeutic target for the clinical treatment of CC.Methods:Hyaluronic acid receptor cluster of differentiation 44 variant exon 6(CD44v6)(+)CC cells were isolated by flow cytometry(FCM).Small interfering RNAs of AFAP1-AS1(siAFAP1-AS1)were transfected into the(CD44v6)(+)cells.The levels of AFAP1-AS1 were measured by quantitative real-time PCR(qRT-PCR).Sphere formation assay,cell cycle analysis,and Western blotting were used to detect the effect of siAFAP1-AS1.RNA pull-down and luciferase reporter assay were used to verify the relationship between miR-27b-3p and AFAP1-AS1 or vascular endothelial growth factor(VEGF)-C.Results:CD44v6(+)CCcells had remarkable stemness and a high level ofAFAP1-AS1.However,AFAP1-AS1knockdownwithsiAFAP1-AS1suppressed the cell cycle transitionofG(1)/S phase and inhibited self-renewal ofCD44v6(+)CCcells,the levels of the stemnessmarkers octamer-binding transcription factor 4(OCT4),osteopontin(OPN),and cluster of differentiation 133(CD133),and the epithelialmesenchymal transition(EMT)-related proteins Twist1,matrix metalloprotease(MMP)-9,and VEGF-C.In the mechanism study,miR-27b-3p/VEGF-C signaling was demonstrated to be a key downstream of AFAP1-AS1 in the CD44v6(+)CC cells.Conclusions:LncRNA AFAP1-AS1 knockdown inhibits the CC cell stemness by upregulating miR-27b-3p to suppress VEGF-C.