The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation.Editing the epigenome and epitranscriptome dire...The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation.Editing the epigenome and epitranscriptome directs the fate of the transcript influencing the functional outcome of each mRNA.In this context,non-coding RNAs play a decisive role in addressing the expression regulation at the gene and chromosomal levels.Long-noncoding RNAs,consisting of more than 200 nucleotides,have been shown to act as epigenetic regulators in several key molecular processes involving neurodegenerative disorders,such as Alzheimer’s disease,Parkinson’s disease,amyotrophic lateral sclerosis and Huntington’s disease.Long-noncoding RNAs are abundantly expressed in the central nervous system,suggesting that their deregulation could trigger neuronal degeneration through RNA modifications.The evaluation of their diagnostic significance and therapeutic potential could lead to new treatments for these diseases for which there is no cure.展开更多
Hepatocellular carcinoma(HCC)remains the third leading cause of cancer-related deaths worldwide;however,its therapeutic options are limited.Understanding the molecular mechanisms of HCC could provide insight into new ...Hepatocellular carcinoma(HCC)remains the third leading cause of cancer-related deaths worldwide;however,its therapeutic options are limited.Understanding the molecular mechanisms of HCC could provide insight into new therapies.Emerging studies indicate the important role of long-noncoding RNAs(lncRNAs)in the pathogenesis of HCC.The expression of the well-studied lncRNA taurine upregulated gene 1(TUG1)is upregulated in HCC tissues,but its transcriptomic effects in HCC cells remain unexplored.We established TUG1-knockdown and control HCC cells for RNA-seq experiments.KEGG analysis revealed glycolysis as the top enriched pathway upon TUG1 silencing.Accordingly,TUG1-depleted HCC cells showed impairments in glucose uptake,ATP synthesis,and lactate production.Clinical HCC tissue data revealed positive gene expression correlations between TUG1 and several glycolysis-related genes.To identify a molecular function of TUG1 in glycolysis,we explored the competing endogenous model and used bioinformatic tools to find the five microRNAs(miRNAs)that had the most binding sites for TUG1.Among these miRNAs,miR-122-5p exhibited an inverse correlation in gene expression with most TUG1-regulated glycolysis genes,including PKM,ALDOA,ENO2,and PFKM.Dual-luciferase assays demonstrated the direct interaction between TUG1 and miR-122-5p and between miR-122-5p and the 3ʹuntranslated regions of both PKM and ALDOA.We further showed that inhibition of miR-122-5p alleviated the suppression of glycolysis induced by TUG1 depletion.Together,our RNA-seq analysis of TUG1-depleted HCC cells,combined with clinical data,reveals a critical role of TUG1 in regulating glycolysis and provides new insight into its oncogenic function in HCC.展开更多
Radiation-induced lung fibrosis(RILF) is a common side effect of thoracic irradiation therapy and leads to high mortality rates after cancer treatment. Radiation injury induces inflammatory M1 macrophage polarization ...Radiation-induced lung fibrosis(RILF) is a common side effect of thoracic irradiation therapy and leads to high mortality rates after cancer treatment. Radiation injury induces inflammatory M1 macrophage polarization leading to radiation pneumonitis, the first stage of RILF progression. Fibrosis occurs due to the transition of M1 macrophages to the anti-inflammatory pro-fibrotic M2 phenotype, and the resulting imbalance of macrophage regulated inflammatory signaling. Non-coding RNA signaling has been shown to play a large role in the regulation of the M2 mediated signaling pathways that are associated with the development and progression of fibrosis. While many studies show the link between M2 macrophages and fibrosis, there are only a few that explore their distinct role and the regulation of their signaling by non-coding RNA in RILF. In this review we summarize the current body of knowledge describing the roles of M2 macrophages in RILF, with an emphasis on the expression and functions of non-coding RNAs.展开更多
Hepatocellular carcinoma (HCC) is the leading cause of cancer death worldwide;nevertheless, currenttherapeutic options are limited or ineffective for many patients. Therefore, elucidation of molecular mechanisms inHCC...Hepatocellular carcinoma (HCC) is the leading cause of cancer death worldwide;nevertheless, currenttherapeutic options are limited or ineffective for many patients. Therefore, elucidation of molecular mechanisms inHCC biology could yield important insights for the intervention of novel therapies. Recently, various studies havereported dysregulation of long non-coding RNAs (lncRNAs) in the initiation and progression of HCC, including H19;however, the biological function of H19 in HCC remains unclear. Here, we show that knockdown of H19 disruptedHCC cell growth, impaired the G1-to-S phase transition, and promoted apoptosis, while overexpression of H19yielded the opposite results. Screening for expression of cell cycle-related genes revealed a significant downregulationof CDK6 at both RNA and protein levels upon H19 suppression. Bioinformatic analysis of the H19 sequence and the3′ untranslated region (3′ UTR) of CDK6 transcripts showed several binding sites for microRNA-107 (miR-107), andthe dual luciferase reporter assay confirmed their direct interaction with miR-107. Consistently, blockage of miR-107activity alleviated the growth suppression phenotypes induced by H19 downregulation, suggesting that H19 serves asa molecular sponge for miR-107 to promote CDK6 expression and cell cycle progression. Together, this studydemonstrates a mechanistic function of H19 in driving the proliferation of HCC cells and suggests H19 suppressionas a novel approach for HCC treatment.展开更多
Recent advances in deep sequencing technologies have revealed that,while less than 2%of the human genome is transcribed into mRNA for protein synthesis,over 80%of the genome is transcribed,leading to the production of...Recent advances in deep sequencing technologies have revealed that,while less than 2%of the human genome is transcribed into mRNA for protein synthesis,over 80%of the genome is transcribed,leading to the production of large amounts of noncoding RNAs(ncRNAs).It has been shown that ncRNAs,especially long non-coding RNAs(lncRNAs),may play crucial regulatory roles in gene expression.As one of the first isolated and reported lncRNAs,H19 has gained much attention due to its essential roles in regulating many physiological and/or pathological processes including embryogenesis,development,tumorigenesis,osteogen-esis,and metabolism.Mechanistically,H19 mediates diverse regulatory functions by serving as competing endogenous RNAs(CeRNAs),Igf2/H19 imprinted tandem gene,modular scaffold,cooperating with H19 antisense,and acting directly with other mRNAs or lncRNAs.Here,we summarized the current understanding of H19 in embryogenesis and development,cancer development and progression,mesenchymal stem cell lineage-specific differentiation,and metabolic diseases.We discussed the potential regulatory mechanisms underlying H19’s func-tions in those processes although more in-depth studies are warranted to delineate the exact molecular,cellular,epigenetic,and genomic regulatory mechanisms underlying the physiolog-ical and pathological roles of H19.Ultimately,these lines of investigation may lead to the development of novel therapeutics for human diseases by exploiting H19 functions.展开更多
基金funded by a special award to the Department of Pharmacy,Health and Nutritional Sciences of University of Calabria(Italy)(Department of Excellence,Italian Law232/2016)from the Italian Ministry of Research and University(MIUR)to FLC.
文摘The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation.Editing the epigenome and epitranscriptome directs the fate of the transcript influencing the functional outcome of each mRNA.In this context,non-coding RNAs play a decisive role in addressing the expression regulation at the gene and chromosomal levels.Long-noncoding RNAs,consisting of more than 200 nucleotides,have been shown to act as epigenetic regulators in several key molecular processes involving neurodegenerative disorders,such as Alzheimer’s disease,Parkinson’s disease,amyotrophic lateral sclerosis and Huntington’s disease.Long-noncoding RNAs are abundantly expressed in the central nervous system,suggesting that their deregulation could trigger neuronal degeneration through RNA modifications.The evaluation of their diagnostic significance and therapeutic potential could lead to new treatments for these diseases for which there is no cure.
基金supported by the Thailand Science Research and Innovation Fund Chulalongkorn University(Grant No.HEAF67300078)the 90th Anniversary Scholarship,Chulalongkorn University Ratchadapisek Sompoch Fund(Grant No.Batch#55,T.Boonto)the Center of Excellence in Hepatitis and Liver Cancer,Faculty of Medicine,Chulalongkorn University.T.Boonto was supported by the scholarship from the Graduate School,Chulalongkorn University,to commemorate the 72^(nd) anniversary of His Majesty King Bhumibol Adulyadej(Grant No.Batch#22).
文摘Hepatocellular carcinoma(HCC)remains the third leading cause of cancer-related deaths worldwide;however,its therapeutic options are limited.Understanding the molecular mechanisms of HCC could provide insight into new therapies.Emerging studies indicate the important role of long-noncoding RNAs(lncRNAs)in the pathogenesis of HCC.The expression of the well-studied lncRNA taurine upregulated gene 1(TUG1)is upregulated in HCC tissues,but its transcriptomic effects in HCC cells remain unexplored.We established TUG1-knockdown and control HCC cells for RNA-seq experiments.KEGG analysis revealed glycolysis as the top enriched pathway upon TUG1 silencing.Accordingly,TUG1-depleted HCC cells showed impairments in glucose uptake,ATP synthesis,and lactate production.Clinical HCC tissue data revealed positive gene expression correlations between TUG1 and several glycolysis-related genes.To identify a molecular function of TUG1 in glycolysis,we explored the competing endogenous model and used bioinformatic tools to find the five microRNAs(miRNAs)that had the most binding sites for TUG1.Among these miRNAs,miR-122-5p exhibited an inverse correlation in gene expression with most TUG1-regulated glycolysis genes,including PKM,ALDOA,ENO2,and PFKM.Dual-luciferase assays demonstrated the direct interaction between TUG1 and miR-122-5p and between miR-122-5p and the 3ʹuntranslated regions of both PKM and ALDOA.We further showed that inhibition of miR-122-5p alleviated the suppression of glycolysis induced by TUG1 depletion.Together,our RNA-seq analysis of TUG1-depleted HCC cells,combined with clinical data,reveals a critical role of TUG1 in regulating glycolysis and provides new insight into its oncogenic function in HCC.
文摘Radiation-induced lung fibrosis(RILF) is a common side effect of thoracic irradiation therapy and leads to high mortality rates after cancer treatment. Radiation injury induces inflammatory M1 macrophage polarization leading to radiation pneumonitis, the first stage of RILF progression. Fibrosis occurs due to the transition of M1 macrophages to the anti-inflammatory pro-fibrotic M2 phenotype, and the resulting imbalance of macrophage regulated inflammatory signaling. Non-coding RNA signaling has been shown to play a large role in the regulation of the M2 mediated signaling pathways that are associated with the development and progression of fibrosis. While many studies show the link between M2 macrophages and fibrosis, there are only a few that explore their distinct role and the regulation of their signaling by non-coding RNA in RILF. In this review we summarize the current body of knowledge describing the roles of M2 macrophages in RILF, with an emphasis on the expression and functions of non-coding RNAs.
基金financially supported by Thailand Science Research and Innovation Fund Chulalongkorn University(CU_FRB65_hea(46)_053_30_34)Ratchadapiseksompotch Fund,Faculty of Medicine,Chulalongkorn University(Grant No.RA 66/017)+1 种基金Thailand Research Fund(TRF)Senior Research Scholar(Grant No.RTA6280004)the Center of Excellence in Hepatitis and Liver Cancer,Faculty of Medicine,Chulalongkorn University.
文摘Hepatocellular carcinoma (HCC) is the leading cause of cancer death worldwide;nevertheless, currenttherapeutic options are limited or ineffective for many patients. Therefore, elucidation of molecular mechanisms inHCC biology could yield important insights for the intervention of novel therapies. Recently, various studies havereported dysregulation of long non-coding RNAs (lncRNAs) in the initiation and progression of HCC, including H19;however, the biological function of H19 in HCC remains unclear. Here, we show that knockdown of H19 disruptedHCC cell growth, impaired the G1-to-S phase transition, and promoted apoptosis, while overexpression of H19yielded the opposite results. Screening for expression of cell cycle-related genes revealed a significant downregulationof CDK6 at both RNA and protein levels upon H19 suppression. Bioinformatic analysis of the H19 sequence and the3′ untranslated region (3′ UTR) of CDK6 transcripts showed several binding sites for microRNA-107 (miR-107), andthe dual luciferase reporter assay confirmed their direct interaction with miR-107. Consistently, blockage of miR-107activity alleviated the growth suppression phenotypes induced by H19 downregulation, suggesting that H19 serves asa molecular sponge for miR-107 to promote CDK6 expression and cell cycle progression. Together, this studydemonstrates a mechanistic function of H19 in driving the proliferation of HCC cells and suggests H19 suppressionas a novel approach for HCC treatment.
基金supported by the National Natural Science Foundation of China(NSFC)(No.82002312,81972069)supported in part by research grants from the National Institutes of Health,USA(No.CA226303 to TCH,No.DE030480 to RRR)+10 种基金supported by the Science and Technology Research Program of Chongqing Education Commission,China(No.KJQN202100431,KJZD-M202100401)the Top Talent Award from The First Affiliated Hospital of Chongqing Medical University,China(No.BJRC2021-04)Cultivation Program of Postdoctoral Research of The First Affiliated Hospital of Chongqing Medical University,China(No.CYYY-BSHPYXM-202202)supported by a post-doctoral fellowship from Chongqing Medical University and rewarded by China Postdoctoral Science Foundation(No.2022M720605)supported in part by research grants from the 2019 Science and Technology Project of Chongqing Education Commission,China(No.KJQN201900410)the 2019 Funding for Postdoctoral Research(Chongqing Human Resources and Social Security Bureau No.298)the Natural Science Foundation of China(No.82102696)supported by the Medical Scientist Training Program of the National Institutes of Health,USA(No.T32 GM007281)supported in part by The University of Chicago Cancer Center Support Grant,USA(No.P30CA014599)the National Center for Advancing Translational Sciences(NCATS)of the National Institutes of Health,USA(No.5UL1TR002389)supported by the Mabel Green Myers Research Endowment Fund and The University of Chicago Orthopedics Alumni Fund.
文摘Recent advances in deep sequencing technologies have revealed that,while less than 2%of the human genome is transcribed into mRNA for protein synthesis,over 80%of the genome is transcribed,leading to the production of large amounts of noncoding RNAs(ncRNAs).It has been shown that ncRNAs,especially long non-coding RNAs(lncRNAs),may play crucial regulatory roles in gene expression.As one of the first isolated and reported lncRNAs,H19 has gained much attention due to its essential roles in regulating many physiological and/or pathological processes including embryogenesis,development,tumorigenesis,osteogen-esis,and metabolism.Mechanistically,H19 mediates diverse regulatory functions by serving as competing endogenous RNAs(CeRNAs),Igf2/H19 imprinted tandem gene,modular scaffold,cooperating with H19 antisense,and acting directly with other mRNAs or lncRNAs.Here,we summarized the current understanding of H19 in embryogenesis and development,cancer development and progression,mesenchymal stem cell lineage-specific differentiation,and metabolic diseases.We discussed the potential regulatory mechanisms underlying H19’s func-tions in those processes although more in-depth studies are warranted to delineate the exact molecular,cellular,epigenetic,and genomic regulatory mechanisms underlying the physiolog-ical and pathological roles of H19.Ultimately,these lines of investigation may lead to the development of novel therapeutics for human diseases by exploiting H19 functions.
