In China, hepatitis B virus （HBV） infection is the major cause of hepatocellular carcinoma （HCC）, which is called HBV-related HCC （HBV-HCC）, but the pathogenesis has not been clearly elu- cidated. Long non-codin...In China, hepatitis B virus （HBV） infection is the major cause of hepatocellular carcinoma （HCC）, which is called HBV-related HCC （HBV-HCC）, but the pathogenesis has not been clearly elu- cidated. Long non-coding RNAs （lncRNAs） have been paid increasing attention to, as an important regulatory molecule involved in many biological processes, as well as a variety of diseases. This study examined lncRNA that might play an important role in HBV-HCC pathogenesis by conducting lncRNA and mRNA profile comparison between HBV-HCC and normal liver tissues. The differentially ex- pressed lncRNA and mRNA profiles between HBV-HCC and normal liver tissues were analyzed by mi- croarrays. The potential protein-encoding gene regulated by lncRNA, and the biological function （gene ontology, pathway analysis） of the target gene were investigated. The results showed that the expression levels of lncRNA and mRNA in HBV-HCC tissues were different from those in normal liver tissues. As compared with normal liver tissue, 837 （4.30%） lncRNAs exhibited more than two-fold change （P〈0.05）; 325 were up-regulated, and 512 were down-regulated; 991 （5.70%） mRNAs exhibited more than 2-fold change （P〈0.05）; 733 were up-regulated and 258 were down-regulated in HBV-HCC tissue. Besides, there were 7 lncRNAs with above 10-fold elevation, 6 lncRNAs with above 10-fold decrease, 18 mRNAs with above 10-fold elevation and 11 mRNAs with above 10-fold decrease. 444 （53.05%） lncRNAs had their corresponding mRNAs, some of which were adjacent to lncRNAs. The biological analysis showed that the target gene of differentially expressed lncRNAs took part in the important bio- logical regulatory function. Target gene-related pathway analysis revealed the pathways in carcinoma and mitogen-activated protein kinase （MAPK） signaling pathways significantly changed in the HBV-HCC tissues as compared with normal liver tissues （P〈0.05）. It was suggested that as compared with normal liver tissues, the expression of lncRNAs in HBV-HCC tissues changed significantly, and lncRNAs played a key role in the pathogenesis of HBV-HCC probably by mainly regulating the carci- noma-related signaling pathway and MAPK signaling pathways.展开更多
Abstract With the development of genome-wide sequencing technology, 195 types of functional long non-coding RNAs （lncRNAs） have so far been found, and their cellular roles are gradually being revealed. Now lncRNAs h...Abstract With the development of genome-wide sequencing technology, 195 types of functional long non-coding RNAs （lncRNAs） have so far been found, and their cellular roles are gradually being revealed. Now lncRNAs have become a hotspot in the life science. These small molecules exist in almost all higher eukaryotes, and have very important regulatory roles in these organisms. This review briefly summarizes recent progress in researches on antisense non-coding RNA in the INK4 locus.展开更多
The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)e...The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)expression profiles constructed by using bioinformatics methods and tools for biological features of AF-VHD.Fold change and t-test were used to identify differentially expressed(DE)lncRNAs and mRNAs.The enrichment analysis of DE mRNAs was performed.The subgroups formed by lncRNAs and nearby mRNAs were screened,and a transcriptional regulation network among lncRNAs,mRNAs,and transcription factors(TFs)was constructed.The interactions between mRNAs related to lncRNAs and drugs were predicted.The 620 AF-VHDrelated DE lncRNAs and 452 DE mRNAs were identified.The 3 lncRNA subgroups were screened.The 665 regulations mediated by lncRNAs and TFs were identified.The 9 mRNAs related to lncRNAs had 1 or more potential drug interactions,totaling 37 drugs.Of these,9 drugs targeting 3 genes are already known to be able to control or trigger atrial fibrillation(AF)or other cardiac arrhythmias.The found biological features of AF-VHD provide foundations for further biological experiments to better understand the roles of lncRNAs in development from the valvular heart disease(VHD)to AF-VHD.展开更多
Long noncoding RNA (lncRNA) is a leader of the degree of more than 200 nucleotides, almost do not have the function of protein coding endogenous RNA molecules. Recent studies show that, lncRNA is not encoded protein, ...Long noncoding RNA (lncRNA) is a leader of the degree of more than 200 nucleotides, almost do not have the function of protein coding endogenous RNA molecules. Recent studies show that, lncRNA is not encoded protein, but it has a wide range of biological functions, and lncRNA in human diseases, especially in oncology, more and more attention has been paid to its role. Nasopharyngeal carcinoma (NPC) is a common malignant tumor of the head and neck in South China, which poses a serious threat to people’s health and life. Studies found that lncRNA is widely involved in the invasion, metastasis and prognosis of nasopharyngeal carcinoma (NPC). In this article, we will review the research progress of lncRNA in nasopharyngeal carcinoma.展开更多
Long non-coding RNAs(lncRNAs)play a significant role in maintaining tissue morphology and functions,and their precise regulatory effectiveness is closely related to expression patterns.However,the spatial expression p...Long non-coding RNAs(lncRNAs)play a significant role in maintaining tissue morphology and functions,and their precise regulatory effectiveness is closely related to expression patterns.However,the spatial expression patterns of lncRNAs in humans are poorly characterized.Here,we constructed five comprehensive transcriptomic atlases of human lncRNAs covering thousands of major tissue samples in normal and disease states.The lncRNA transcriptomes exhibited high consistency within the same tissues across resources,and even higher complexity in specialized tissues.Tissue-elevated(TE)lncRNAs were identified in each resource and robust TE lncRNAs were refined by integrative analysis.We detected 1 to 4684 robust TE lncRNAs across tissues;the highest number was in testis tissue,followed by brain tissue.Functional analyses of TE lncRNAs indicated important roles in corresponding tissue-related pathways.Moreover,we found that the expression features of robust TE lncRNAs made them be effective biomarkers to distinguish tissues;TE lncRNAs also tended to be associated with cancer,and exhibited differential expression or were correlated with patient survival.In summary,spatial classification of lncRNAs is the starting point for elucidating the function of lncRNAs in both maintenance of tissue morphology and progress of tissue-constricted diseases.展开更多
Objective To explore the expression characteristics of long non-coding RNA-Co7Rik and to discuss its potential impacts on hepatic gluconeogenesis.Methods Building fasting-feeding model and high fat diet(HFD)feeding mo...Objective To explore the expression characteristics of long non-coding RNA-Co7Rik and to discuss its potential impacts on hepatic gluconeogenesis.Methods Building fasting-feeding model and high fat diet(HFD)feeding model to detect the expression level of LncRNACo7Rik.Separating different parts of C57BL/6J mice展开更多
As a leading cause of cancer deaths worldwide, lung cancer is a collection of diseases with diverse etiologies which can be broadly classified into small-cell lung cancer （SCLC） and non-small-cell lung cancer （NSCL...As a leading cause of cancer deaths worldwide, lung cancer is a collection of diseases with diverse etiologies which can be broadly classified into small-cell lung cancer （SCLC） and non-small-cell lung cancer （NSCLC）. Lung cancer is characterized by genomic and epigenomic alterations; however, mechanisms underlying lung tumorigenesis remain to be elucidated. Long noncoding RNAs （lncRNAs） are a group of non-coding RNAs that consist of ≥ 200 nucleotides but possess low or no protein-coding potential. Accumulating evidence indicates that abnormal expression of lncRNAs is associated with tumorigenesis of various cancers, including lung cancer, through multiple biological mechanisms involving epigenetic, transcriptional, and post-transcriptional alterations. In this review, we highlight the expression and roles of lncRNAs in NSCLC and discuss their potential clinical applications as diagnostic or prognostic biomarkers, as well as therapeutic targets.展开更多
With the development of genome-wide sequencing technology, 195 types of functional, long non-coding RNAs(lnc RNAs) have been identified so far, and their cellular roles are gradually being revealed. Lnc RNAs have now ...With the development of genome-wide sequencing technology, 195 types of functional, long non-coding RNAs(lnc RNAs) have been identified so far, and their cellular roles are gradually being revealed. Lnc RNAs have now become a hotspot in the field of life sciences. These small molecules exist in almost all higher eukaryotes and play very important regulatory roles in these organisms. This review briefly summarizes the recent progress in research on plasmacytoma variant translocation 1 gene(PVT1), an lnc RNA.展开更多
Objective: To explore the action mechanisms of Huangqi Decoction Granules(黄芪汤颗粒剂, HQDG) on hepatitis B cirrhosis. Methods: A total of 85 patients with hepatitis B cirrhosis were randomly divided into HQDG group(...Objective: To explore the action mechanisms of Huangqi Decoction Granules(黄芪汤颗粒剂, HQDG) on hepatitis B cirrhosis. Methods: A total of 85 patients with hepatitis B cirrhosis were randomly divided into HQDG group(42 cases) and control group(43 cases) by a random number table and were treated with HQDG or placebo for 48 weeks(6 g per times and orally for 3 times a day), respectively. After RNA-sequencing of serum samples extracted from the patients, the differentially expressed genes(DEGs) in HQDG and control groups before and after treatment were separately screened. The DEGs were then performed pathway enrichment analysis and proteinprotein interaction(PPI) network analysis. The expression levels of key genes were detected by quantitative realtime polymerase chain reaction(qRT-PCR). Results: After the investigation, 4 and 3 cases were respectively excluded from HQD and control groups because of the incomplete data. Additionally, 3 and 5 cases were lost to follow up in HQD and control groups, respectively. Finally, a total of 70 cases with good compliance were included for further DEGs analysis. A total of 1,070 DEGs(including 455 up-regulated genes and 615 down-regulated genes) in HQDG group and 227 DEGs(including 164 up-regulated genes and 63 down-regulated genes) in the control group were identified after treatment. Compared with the control group, 1,043 DEGs were specific in HQDG group. Besides, 1 up-regulated transcription factor(TF, such as GLI family zinc finger 1, GLI1) and 25 down-regulated TFs(such as drosophila mothers against decapentaplegic proteinfamily member 2, SMAD2) were identified. Pathway enrichment analysis showed that down-regulated Ras homolog gene family member A(RHOA) was enriched in pathogenic Escherichia coli infection. In the PPI network, up-regulated epidermal growth factor receptor(EGFR), and down-regulated cell division cycle 42(CDC42) as well as v-akt murine thymoma viral oncogene homolog 1(AKT1) had higher degrees. Moreover, long non-coding RNAs(lncR NA) growth arrest-specific 5(GAS5) was involved in the lncR NA-target regulatory network. Furthermore, qR T-PCR revealed that expression levels of CDC42 and GLI1 had significant differences in HQDG group before and after treatment(P<0.05). Conclusions: CDC42 and GLI1 may be the targets of HQDG in patients with hepatitis B cirrhosis. Additionally, SMAD2, EGFR, AKT1, RHOA and GAS5 might be associated with the curative effect of HQDG on hepatitis B cirrhosis patients.展开更多
Aim: Plasmacytoma variant translocation 1 (PVT1), a long intergenic non-coding RNA, was overexpressed in liver cancer. A single nucleotide polymorphism (SNP) rs4733586 was identified as an expression quantitative trai...Aim: Plasmacytoma variant translocation 1 (PVT1), a long intergenic non-coding RNA, was overexpressed in liver cancer. A single nucleotide polymorphism (SNP) rs4733586 was identified as an expression quantitative trait loci (eQTL) for PVT1 using bioinformatics analysis. This study was to assess the association of PVT1 eQTL with hepatocellular carcinoma (HCC) prognosis. Methods: A case-only study was performed to assess the association between SNP and HCC overall survival in 331 HCC patients with hepatitis B virus. Cox proportional hazard regression models were conducted for survival analysis with adjustment for age, gender, smoking status, drinking status, Barcelona-Clinic Liver Cancer stages, and chemotherapy or transcatheter hepatic arterial chemoembolization (TACE) status. Results: The variant genotype C allele of rs4733586 was significantly associated with a higher death risk compared with T allele (adjusted hazard ratio = 1.26, 95% confidence intervals = 1.05-1.51,P = 0.012 in the additive model). By stepwise Cox proportional hazard analysis, four variables (age, drinking status, chemotherapy or TACE status, PVT1 eQTL) were remained in the final regression model. In the stratified analysis, no heterogeneity was observed among different subgroups. Conclusion: These findings suggest that eQTL SNP for PVT1 may be susceptibility marker for the HCC overall survival.展开更多
文摘In China, hepatitis B virus （HBV） infection is the major cause of hepatocellular carcinoma （HCC）, which is called HBV-related HCC （HBV-HCC）, but the pathogenesis has not been clearly elu- cidated. Long non-coding RNAs （lncRNAs） have been paid increasing attention to, as an important regulatory molecule involved in many biological processes, as well as a variety of diseases. This study examined lncRNA that might play an important role in HBV-HCC pathogenesis by conducting lncRNA and mRNA profile comparison between HBV-HCC and normal liver tissues. The differentially ex- pressed lncRNA and mRNA profiles between HBV-HCC and normal liver tissues were analyzed by mi- croarrays. The potential protein-encoding gene regulated by lncRNA, and the biological function （gene ontology, pathway analysis） of the target gene were investigated. The results showed that the expression levels of lncRNA and mRNA in HBV-HCC tissues were different from those in normal liver tissues. As compared with normal liver tissue, 837 （4.30%） lncRNAs exhibited more than two-fold change （P〈0.05）; 325 were up-regulated, and 512 were down-regulated; 991 （5.70%） mRNAs exhibited more than 2-fold change （P〈0.05）; 733 were up-regulated and 258 were down-regulated in HBV-HCC tissue. Besides, there were 7 lncRNAs with above 10-fold elevation, 6 lncRNAs with above 10-fold decrease, 18 mRNAs with above 10-fold elevation and 11 mRNAs with above 10-fold decrease. 444 （53.05%） lncRNAs had their corresponding mRNAs, some of which were adjacent to lncRNAs. The biological analysis showed that the target gene of differentially expressed lncRNAs took part in the important bio- logical regulatory function. Target gene-related pathway analysis revealed the pathways in carcinoma and mitogen-activated protein kinase （MAPK） signaling pathways significantly changed in the HBV-HCC tissues as compared with normal liver tissues （P〈0.05）. It was suggested that as compared with normal liver tissues, the expression of lncRNAs in HBV-HCC tissues changed significantly, and lncRNAs played a key role in the pathogenesis of HBV-HCC probably by mainly regulating the carci- noma-related signaling pathway and MAPK signaling pathways.
文摘Abstract With the development of genome-wide sequencing technology, 195 types of functional long non-coding RNAs （lncRNAs） have so far been found, and their cellular roles are gradually being revealed. Now lncRNAs have become a hotspot in the life science. These small molecules exist in almost all higher eukaryotes, and have very important regulatory roles in these organisms. This review briefly summarizes recent progress in researches on antisense non-coding RNA in the INK4 locus.
基金the National Natural Science Foundation of China under Grants No.61872405 and No.61720106004the Key Project of Natural Science Foundation of Guangdong Province under Grant No.2016A030311040.
文摘The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)expression profiles constructed by using bioinformatics methods and tools for biological features of AF-VHD.Fold change and t-test were used to identify differentially expressed(DE)lncRNAs and mRNAs.The enrichment analysis of DE mRNAs was performed.The subgroups formed by lncRNAs and nearby mRNAs were screened,and a transcriptional regulation network among lncRNAs,mRNAs,and transcription factors(TFs)was constructed.The interactions between mRNAs related to lncRNAs and drugs were predicted.The 620 AF-VHDrelated DE lncRNAs and 452 DE mRNAs were identified.The 3 lncRNA subgroups were screened.The 665 regulations mediated by lncRNAs and TFs were identified.The 9 mRNAs related to lncRNAs had 1 or more potential drug interactions,totaling 37 drugs.Of these,9 drugs targeting 3 genes are already known to be able to control or trigger atrial fibrillation(AF)or other cardiac arrhythmias.The found biological features of AF-VHD provide foundations for further biological experiments to better understand the roles of lncRNAs in development from the valvular heart disease(VHD)to AF-VHD.
文摘Long noncoding RNA (lncRNA) is a leader of the degree of more than 200 nucleotides, almost do not have the function of protein coding endogenous RNA molecules. Recent studies show that, lncRNA is not encoded protein, but it has a wide range of biological functions, and lncRNA in human diseases, especially in oncology, more and more attention has been paid to its role. Nasopharyngeal carcinoma (NPC) is a common malignant tumor of the head and neck in South China, which poses a serious threat to people’s health and life. Studies found that lncRNA is widely involved in the invasion, metastasis and prognosis of nasopharyngeal carcinoma (NPC). In this article, we will review the research progress of lncRNA in nasopharyngeal carcinoma.
基金This work was supported by the National Natural Science Foundation of China(Nos.31970646,32060152,32070673,and 32170676)the Hainan Province Science and Technology Special Fund(No.ZDYF2021SHFZ051)+2 种基金the Harbin Medical University Marshal Initiative Funding(No.HMUMIF-21024)the Marshal Initiative Funding of Hainan Medical University(No.JBGS202103)the Heilongjiang Touyan Innovation Team Program.
文摘Long non-coding RNAs(lncRNAs)play a significant role in maintaining tissue morphology and functions,and their precise regulatory effectiveness is closely related to expression patterns.However,the spatial expression patterns of lncRNAs in humans are poorly characterized.Here,we constructed five comprehensive transcriptomic atlases of human lncRNAs covering thousands of major tissue samples in normal and disease states.The lncRNA transcriptomes exhibited high consistency within the same tissues across resources,and even higher complexity in specialized tissues.Tissue-elevated(TE)lncRNAs were identified in each resource and robust TE lncRNAs were refined by integrative analysis.We detected 1 to 4684 robust TE lncRNAs across tissues;the highest number was in testis tissue,followed by brain tissue.Functional analyses of TE lncRNAs indicated important roles in corresponding tissue-related pathways.Moreover,we found that the expression features of robust TE lncRNAs made them be effective biomarkers to distinguish tissues;TE lncRNAs also tended to be associated with cancer,and exhibited differential expression or were correlated with patient survival.In summary,spatial classification of lncRNAs is the starting point for elucidating the function of lncRNAs in both maintenance of tissue morphology and progress of tissue-constricted diseases.
文摘Objective To explore the expression characteristics of long non-coding RNA-Co7Rik and to discuss its potential impacts on hepatic gluconeogenesis.Methods Building fasting-feeding model and high fat diet(HFD)feeding model to detect the expression level of LncRNACo7Rik.Separating different parts of C57BL/6J mice
基金supported by the National Natural Science Funds for Distinguished Young Scholar(Grant No.81425025)the National Basic Research Program of China(Grant No.2012CB910800)
文摘As a leading cause of cancer deaths worldwide, lung cancer is a collection of diseases with diverse etiologies which can be broadly classified into small-cell lung cancer （SCLC） and non-small-cell lung cancer （NSCLC）. Lung cancer is characterized by genomic and epigenomic alterations; however, mechanisms underlying lung tumorigenesis remain to be elucidated. Long noncoding RNAs （lncRNAs） are a group of non-coding RNAs that consist of ≥ 200 nucleotides but possess low or no protein-coding potential. Accumulating evidence indicates that abnormal expression of lncRNAs is associated with tumorigenesis of various cancers, including lung cancer, through multiple biological mechanisms involving epigenetic, transcriptional, and post-transcriptional alterations. In this review, we highlight the expression and roles of lncRNAs in NSCLC and discuss their potential clinical applications as diagnostic or prognostic biomarkers, as well as therapeutic targets.
基金Supported by Science and Technology Plan of Guangdong Provincial Department of Science and Technology(2011B031800012)
文摘With the development of genome-wide sequencing technology, 195 types of functional, long non-coding RNAs(lnc RNAs) have been identified so far, and their cellular roles are gradually being revealed. Lnc RNAs have now become a hotspot in the field of life sciences. These small molecules exist in almost all higher eukaryotes and play very important regulatory roles in these organisms. This review briefly summarizes the recent progress in research on plasmacytoma variant translocation 1 gene(PVT1), an lnc RNA.
基金Supported by National Natural Science Foundation of China(No.81774098)Outstanding Leaders Training Program of Pudong Health Bureau of Shanghai(No.PWRL2016-01)
文摘Objective: To explore the action mechanisms of Huangqi Decoction Granules(黄芪汤颗粒剂, HQDG) on hepatitis B cirrhosis. Methods: A total of 85 patients with hepatitis B cirrhosis were randomly divided into HQDG group(42 cases) and control group(43 cases) by a random number table and were treated with HQDG or placebo for 48 weeks(6 g per times and orally for 3 times a day), respectively. After RNA-sequencing of serum samples extracted from the patients, the differentially expressed genes(DEGs) in HQDG and control groups before and after treatment were separately screened. The DEGs were then performed pathway enrichment analysis and proteinprotein interaction(PPI) network analysis. The expression levels of key genes were detected by quantitative realtime polymerase chain reaction(qRT-PCR). Results: After the investigation, 4 and 3 cases were respectively excluded from HQD and control groups because of the incomplete data. Additionally, 3 and 5 cases were lost to follow up in HQD and control groups, respectively. Finally, a total of 70 cases with good compliance were included for further DEGs analysis. A total of 1,070 DEGs(including 455 up-regulated genes and 615 down-regulated genes) in HQDG group and 227 DEGs(including 164 up-regulated genes and 63 down-regulated genes) in the control group were identified after treatment. Compared with the control group, 1,043 DEGs were specific in HQDG group. Besides, 1 up-regulated transcription factor(TF, such as GLI family zinc finger 1, GLI1) and 25 down-regulated TFs(such as drosophila mothers against decapentaplegic proteinfamily member 2, SMAD2) were identified. Pathway enrichment analysis showed that down-regulated Ras homolog gene family member A(RHOA) was enriched in pathogenic Escherichia coli infection. In the PPI network, up-regulated epidermal growth factor receptor(EGFR), and down-regulated cell division cycle 42(CDC42) as well as v-akt murine thymoma viral oncogene homolog 1(AKT1) had higher degrees. Moreover, long non-coding RNAs(lncR NA) growth arrest-specific 5(GAS5) was involved in the lncR NA-target regulatory network. Furthermore, qR T-PCR revealed that expression levels of CDC42 and GLI1 had significant differences in HQDG group before and after treatment(P<0.05). Conclusions: CDC42 and GLI1 may be the targets of HQDG in patients with hepatitis B cirrhosis. Additionally, SMAD2, EGFR, AKT1, RHOA and GAS5 might be associated with the curative effect of HQDG on hepatitis B cirrhosis patients.
文摘Aim: Plasmacytoma variant translocation 1 (PVT1), a long intergenic non-coding RNA, was overexpressed in liver cancer. A single nucleotide polymorphism (SNP) rs4733586 was identified as an expression quantitative trait loci (eQTL) for PVT1 using bioinformatics analysis. This study was to assess the association of PVT1 eQTL with hepatocellular carcinoma (HCC) prognosis. Methods: A case-only study was performed to assess the association between SNP and HCC overall survival in 331 HCC patients with hepatitis B virus. Cox proportional hazard regression models were conducted for survival analysis with adjustment for age, gender, smoking status, drinking status, Barcelona-Clinic Liver Cancer stages, and chemotherapy or transcatheter hepatic arterial chemoembolization (TACE) status. Results: The variant genotype C allele of rs4733586 was significantly associated with a higher death risk compared with T allele (adjusted hazard ratio = 1.26, 95% confidence intervals = 1.05-1.51,P = 0.012 in the additive model). By stepwise Cox proportional hazard analysis, four variables (age, drinking status, chemotherapy or TACE status, PVT1 eQTL) were remained in the final regression model. In the stratified analysis, no heterogeneity was observed among different subgroups. Conclusion: These findings suggest that eQTL SNP for PVT1 may be susceptibility marker for the HCC overall survival.
