Objective Pseudogenes are initially regarded as nonfunctional genomic sequences,but some pseudogenes regulate tumor initiation and progression by interacting with other genes to modulate their transcriptional activiti...Objective Pseudogenes are initially regarded as nonfunctional genomic sequences,but some pseudogenes regulate tumor initiation and progression by interacting with other genes to modulate their transcriptional activities.Olfactory receptor family 7 subfamily E member 47 pseudogene(OR7E47P)is expressed broadly in lung tissues and has been identified as a positive regulator in the tumor microenvironment(TME)of lung adenocarcinoma(LUAD).This study aimed to elucidate the correlation between OR7E47P and tumor immunity in lung squamous cell carcinoma(LUSC).Methods Clinical and molecular information from The Cancer Genome Atlas(TCGA)LUSC cohort was used to identify OR7E47P-related immune genes(ORIGs)by weighted gene correlation network analysis(WGCNA).Based on the ORIGs,2 OR7E47P clusters were identified using non-negative matrix factorization(NMF)clustering,and the stability of the clustering was tested by an extreme gradient boosting classifier(XGBoost).LASSO-Cox and stepwise regressions were applied to further select prognostic ORIGs and to construct a predictive model(ORPScore)for immunotherapy.The Botling cohorts and 8 immunotherapy cohorts(the Samstein,Braun,Jung,Gide,IMvigor210,Lauss,Van Allen,and Cho cohorts)were included as independent validation cohorts.Results OR7E47P expression was positively correlated with immune cell infiltration and enrichment of immune-related pathways in LUSC.A total of 57 ORIGs were identified to classify the patients into 2 OR7E47P clusters(Cluster 1 and Cluster 2)with distinct immune,mutation,and stromal programs.Compared to Cluster 1,Cluster 2 had more infiltration by immune and stromal cells,lower mutation rates of driver genes,and higher expression of immune-related proteins.The clustering performed well in the internal and 5 external validation cohorts.Based on the 7 ORIGs(HOPX,STX2,WFS,DUSP22,SLFN13,GGCT,and CCSER2),the ORPScore was constructed to predict the prognosis and the treatment response.In addition,the ORPScore was a better prognostic factor and correlated positively with the immunotherapeutic response in cancer patients.The area under the curve values ranged from 0.584 to 0.805 in the 6 independent immunotherapy cohorts.Conclusion Our study suggests a significant correlation between OR7E47P and TME modulation in LUSC.ORIGs can be applied to molecularly stratify patients,and the ORPScore may serve as a biomarker for clinical decision-making regarding individualized prognostication and immunotherapy.展开更多
Novel pseudogenes homologous to the mitochondrial(mt) 16S rRNA gene were detected via different approaches. Eight pseudogenes were sequenced. Copynumber polymorphism of the mtDNA pseudogenes wasobserved among randomly...Novel pseudogenes homologous to the mitochondrial(mt) 16S rRNA gene were detected via different approaches. Eight pseudogenes were sequenced. Copynumber polymorphism of the mtDNA pseudogenes wasobserved among randomly chosen individuals, and evenamong siblings. A mtDNA pseudogene in the Ychromosome was observed in a YAC clone carrying onlyrepetitive sequence tag site (STS). PCR screening of human yeast artificial chromosome (YAC) libraries showedthat there were at least 5.7×105 hp of the mtDNA pseudogenes in each haploid nuclear genome. Possible involvement of the mtDNA pseudogenes in the variable part ofthe human nuclear genome is discussed.展开更多
Certain pseudogenes may regulate their protein-coding cousins by competing for miRNAs and play an active biological role in cancer. However, few studies have focused on the association of genetic variations in pseudog...Certain pseudogenes may regulate their protein-coding cousins by competing for miRNAs and play an active biological role in cancer. However, few studies have focused on the association of genetic variations in pseudogenes with cancer prognosis. We selected six potentially functional single nucleotide polymorphisms （SNPs） in cancerrelated pseudogenes, and performed a case-only study to assess the association between those SNPs and the prognosis of hepatocellular carcinoma （HCC） in 331 HBV-positive HCC patients without surgical treatment. Log-rank test and Cox proportional hazard models were used for survival analysis. We found that the A allele of rs9909601 in E2F3P1 was significantly associated with a better prognosis compared with the G allele [adjusted hazard ratio （HR） = 0.69, 95% confidence interval （CI） = 0.56-0.86, P = 0.001]. Additionally, this protective effect was more predominant for patients without chemotherapy and transcatheter hepatic arterial chemoembolization （TACE） treatment. Interestingly, we also detected a statistically significant multiplicative interaction between genotypes of rs9909601 and chemotherapy or TACE status on HCC survival （P for multiplicative interaction 〈 0.001）. These findings indicate that rs9909601 in the pseudogene E2F3P1 may be a genetic marker for HCC prognosis in Chinese.展开更多
Objective: To clone cytochrome P450 from Aedes aegypti(Ae. aegypti) and determine the characteristics using bioinformatics tools. Methods: Cytochrome P450 of Ae. aegypti was amplified using polymerase chain reaction, ...Objective: To clone cytochrome P450 from Aedes aegypti(Ae. aegypti) and determine the characteristics using bioinformatics tools. Methods: Cytochrome P450 of Ae. aegypti was amplified using polymerase chain reaction, cloned and sequenced. Evolutionary relationship of the sequence was inferred and bioinformatics tools were used to predict subcellular localisation, signal peptide, transmembrane helix, phosphorylation, O-glycosylation, secondary and tertiary structures of the deduced protein. Results: Polymerase chain reaction rather amplified a cytochrome P450 pseudogene which was named CYP4H44P(Gen Bank accession number KF779932). The pseudogene has 1537 nucleotides and an open reading frame of 335 amino acids containing cytochrome P450 motifs except the Wxxx R motif. It is highly homologous to CYP4H28 and CYP4H28v2. Phylogenetic analysis and evolutionary divergence showed strong clustering with CYP4H28 alleles and least divergence from the alleles respectively. The deduced protein was predicted to be found in the cytoplasm and likely to be phosphorylated but devoid of signal peptide, transmembrane helix and O-glycosylated sites. The secondary and tertiary structures were also generated. Conclusions: A cytochrome P450 pseudogene, CYP4H44 P was cloned from Ae. aegypti. The pseudogene is homologous with CYP4H28 alleles and seems to have recently diverged from this group. Isolating this pseudogene is an important step for evaluating its biological role in the mosquito and for the evolutionary analysis of Ae. aegypti CYPs.展开更多
Olfactory receptors（ORs）,the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation,constitute the largest gene family in vertebrates.Dogs and wolves,like many other mamma...Olfactory receptors（ORs）,the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation,constitute the largest gene family in vertebrates.Dogs and wolves,like many other mammals,have a highly developed capability to detect and identify odorant molecules,even at minimum concentrations.In this study,the olfactory receptor repertoire from domestic dog and its closest relative,the wolf,were sequenced to estimate the fraction of pseudogenes in each subspecies.The fraction of disrupted olfactory receptor genes in dog was 17.78%,whereas,that in wolf was 12.08%.As expected the dog was less dependent on olfaction than the wolf,and the dog had more olfactory receptor pseudogenes.However,the observed difference between the two subspecies was not at the significant level（χ2 = 1.388,p = 0.239 0.05）.The values indicated that although domestication might play a role in the reduction of OR genes,it could not be concluded that the living environment provided by domestication lead to a significant reduction of the functional olfactory receptor repertoire.Furthermore,the purpose of domestication may also have influence on the ratio of functional olfactory receptor genes reduction.展开更多
The outcomes of ovarian cancer are complicated and usually unfavorable due to their diagnoses at a late stage.Identifying the efficient prognostic biomarkers to improve the survival of ovarian cancer is urgently warra...The outcomes of ovarian cancer are complicated and usually unfavorable due to their diagnoses at a late stage.Identifying the efficient prognostic biomarkers to improve the survival of ovarian cancer is urgently warranted.The survival-related pseudogenes retrieved from the Cancer Genome Atlas database were screened by univariate Cox regression analysis and further assessed by least absolute shrinkage and selection operator(LASSO)method.A risk score model based on the prognostic pseudogenes was also constructed.The pseudogene-mRNA regulatory networks were established using correlation analysis,and their potent roles in the ovarian cancer progression were uncovered by functional enrichment analysis.Lastly,ssGSEA and ESTIMATE algorithms was used to evaluate the levels of immune cell infiltrations in cancer tissues and explore their relationship with risk signature.A prediction model of 10-pseudogenes including RPL10P6,AC026688.1,FAR2P4,AL391840.2,AC068647.2,FAM35BP,GBP1P1,ARL4AP5,RPS3AP2,and AMD1P1 was established.The 10-pseudogenes signature was demonstrated to be an independent prognostic factor in patient with ovarian cancer in the random set(hazard ratio[HR]=2.512,95%confidence interval[CI]=2.03–3.11,P<0.001)and total set(HR=1.71,95%CI=1.472–1.988,P<0.001).When models integrating with age,grade,stage,and risk signature,the Area Under Curve(AUC)of the 1-year,3-year,5-year and 10-year Receiver Operating Characteristic curve in the random set and total set were 0.854,0.824,0.855,0.805 and 0.679,0.697,0.739,0.790,respectively.The results of functional enrichment analysis indicated that the underlying mechanisms by which these pseudogenes influence cancer prognosis may involve the immune-related biological processes and signaling pathways.Correlation analysis showed that risk signature was significantly correlated with immune cell infiltration and immune score.We identified a novel 10-pseudogenes signature to predict the survival of patients with ovarian cancer,and that may serve as novel possible prognostic biomarkers and therapeutic targets for ovarian cancer.展开更多
HMGN2 have functions in inflammatory response.However,the role of HMGN2 in severe acute pancreatitis(SAP)remains unclear.Here,our study was to discuss the role and regulatory mechanism ofHMGN2 in SAP.In this study,the...HMGN2 have functions in inflammatory response.However,the role of HMGN2 in severe acute pancreatitis(SAP)remains unclear.Here,our study was to discuss the role and regulatory mechanism ofHMGN2 in SAP.In this study,the SAP cell model of AR42J was used to study the function and mechanism of HMGN2 in SAP.The protein expression in cells and serums were examined by western blot and ELISA assay.qPCR was used to test the transcriptional RNA level.Cell viability were examined by MTT assay.Luciferase assay was used to evaluate the interaction between gene and gene.Our results showed that HMGN2 was significantly upregulated in SAP patients.The database predicted and luciferase assay data indicated the HMGN2 was directly binding with miR-590-3p.ELISA,MTT and western blot experiments showed that the HMGN2 were promoted the cell proliferation,reduced the inflammation,and repressed the cell autophagy.Mechanism studies showed that the pseudogene HMGN2P46 level was positively correlated with HMGN2 and upregulated HMGN2 expression by competing for miR-590-3p in SAP.Taken together,all over these results showed upregulation of HMGN2 alleviates SAP,this process was regulated by HMGN2P46 competitively binding with miR-590-3p,which may provide a new insight for the treatment and intervention in SAP.Pseudogene HMGN2P46 was a miRNA sponge to regulate HMGN2 level by competing for miR-590-3p to alleviate the process of SAP.It provided a novel strategy for the diagnosis and treatment of severe acute pancreatitis.展开更多
GAPDH is a conserved enzyme that binds diverse proteins, such as Siah during apoptotic nuclear translocation. There is one somatic GAPDH gene, but over 60 pseudogenes, the expression of which is nebulous. A single nuc...GAPDH is a conserved enzyme that binds diverse proteins, such as Siah during apoptotic nuclear translocation. There is one somatic GAPDH gene, but over 60 pseudogenes, the expression of which is nebulous. A single nucleotide polymorphism (SNP) in the GAPDHP44 pseudogene exhibits a beneficial allele in AD. The objective of this study was to examine the P44 gene and to propose a mechanism for the putative protein and its impact on AD. We examined the sequences in the putative coding region of the human GAPDHP44 gene and the upstream genetic elements usinga bioinformatics approach. We compared the amino acid sequences of the putative gene product with that of the parent GAPDH protein. There is a TATA box 24 nt upstream from, and a Kozak sequence at, putative transcription and translation start sites, respecttively. The upstream region also has sequences (7 - 16 nt) paralogous to those in parent gene introns;one shows homology to a known enhancer element. The resulting protein would contain 139 aa due to a stop codon, roughly the same size as the dinucleotide domain (151 aa) of the parent protein. The SNP is in a region (residues 80 - 120) that binds to the protein GOSPEL. We propose that the beneficial SNP may cause a glutamine to glutamate substitution. NMDA-stmulated neurons undergo GAPDH nitrosylation, Siah translocation, but can be rescued by GOSPEL binding to GAPDH. Our model suggests that the putative P44 protein may regulate GAPDH-GO-SPEL interaction and the beneficial SNPmay ameliorate AD.展开更多
The p53 tumor suppressor gene is either non- functional or highly and frequently mutated in majority of cancers. In our study towards understanding cellular adaptations to stress using a rat histiocytic tumor model, w...The p53 tumor suppressor gene is either non- functional or highly and frequently mutated in majority of cancers. In our study towards understanding cellular adaptations to stress using a rat histiocytic tumor model, we have identified mis-sense mutation in p53 that led to premature termination of translation at the carboxyl-termi- nus. Further, the cDNA isolated from heat stre- ssed cells producing two amplicons with cDNA specific primers (N-terminus) suggested occurrence of possible pseudogene(s). A comparative analysis between different tumor cell lines of rat origin and rat genomic DNA using p53 gene specific primers resulted in the amplification of a processed pseudogene and its positive interaction with wild type p53 probe on Southern blot analysis. The genomic DNA sequence analysis, and sequence comparison with cDNA discovered that the processed pseudogene lacks DNA binding domain and nuclear localization signal, however, contains the ribosomal entry and stop signals. Rat genome BLAST analysis of the pesudogene suggested chromosome-18 localization which was in addition to 14, 13, 10, 9 localization of the cDNA. In the interest of unraveling hidden dimensions of p53 tumor suppressor gene, our study explores the probability of p53 functional pseudogenes in rat histiocytoma.展开更多
基金the Wuhan University Medical Faculty Innovation Seed Fund Cultivation Project(No.TFZZ2018025)the Chen Xiao-ping Foundation for the Development of Science and Technology of Hubei Province(No.CXPJJH12000001-2020313)the National Natural Science Foundation of China(No.81670123 and No.81670144).
文摘Objective Pseudogenes are initially regarded as nonfunctional genomic sequences,but some pseudogenes regulate tumor initiation and progression by interacting with other genes to modulate their transcriptional activities.Olfactory receptor family 7 subfamily E member 47 pseudogene(OR7E47P)is expressed broadly in lung tissues and has been identified as a positive regulator in the tumor microenvironment(TME)of lung adenocarcinoma(LUAD).This study aimed to elucidate the correlation between OR7E47P and tumor immunity in lung squamous cell carcinoma(LUSC).Methods Clinical and molecular information from The Cancer Genome Atlas(TCGA)LUSC cohort was used to identify OR7E47P-related immune genes(ORIGs)by weighted gene correlation network analysis(WGCNA).Based on the ORIGs,2 OR7E47P clusters were identified using non-negative matrix factorization(NMF)clustering,and the stability of the clustering was tested by an extreme gradient boosting classifier(XGBoost).LASSO-Cox and stepwise regressions were applied to further select prognostic ORIGs and to construct a predictive model(ORPScore)for immunotherapy.The Botling cohorts and 8 immunotherapy cohorts(the Samstein,Braun,Jung,Gide,IMvigor210,Lauss,Van Allen,and Cho cohorts)were included as independent validation cohorts.Results OR7E47P expression was positively correlated with immune cell infiltration and enrichment of immune-related pathways in LUSC.A total of 57 ORIGs were identified to classify the patients into 2 OR7E47P clusters(Cluster 1 and Cluster 2)with distinct immune,mutation,and stromal programs.Compared to Cluster 1,Cluster 2 had more infiltration by immune and stromal cells,lower mutation rates of driver genes,and higher expression of immune-related proteins.The clustering performed well in the internal and 5 external validation cohorts.Based on the 7 ORIGs(HOPX,STX2,WFS,DUSP22,SLFN13,GGCT,and CCSER2),the ORPScore was constructed to predict the prognosis and the treatment response.In addition,the ORPScore was a better prognostic factor and correlated positively with the immunotherapeutic response in cancer patients.The area under the curve values ranged from 0.584 to 0.805 in the 6 independent immunotherapy cohorts.Conclusion Our study suggests a significant correlation between OR7E47P and TME modulation in LUSC.ORIGs can be applied to molecularly stratify patients,and the ORPScore may serve as a biomarker for clinical decision-making regarding individualized prognostication and immunotherapy.
文摘Novel pseudogenes homologous to the mitochondrial(mt) 16S rRNA gene were detected via different approaches. Eight pseudogenes were sequenced. Copynumber polymorphism of the mtDNA pseudogenes wasobserved among randomly chosen individuals, and evenamong siblings. A mtDNA pseudogene in the Ychromosome was observed in a YAC clone carrying onlyrepetitive sequence tag site (STS). PCR screening of human yeast artificial chromosome (YAC) libraries showedthat there were at least 5.7×105 hp of the mtDNA pseudogenes in each haploid nuclear genome. Possible involvement of the mtDNA pseudogenes in the variable part ofthe human nuclear genome is discussed.
基金funded by the National Natural Science Foundation of China(81372606 and 81072344)supported by the National Key Basic Research Program Grant(2013CB911400)+6 种基金the project supportedby the National Science Foundation for Distinguished Young Scholarsof China(81225020)Foundation of Jiangsu Province for Distinguished Young Scholars(BK2012042)Foundation for the Program for NewCentury Excellent Talents in University(NCET-10-0178)the Fok Ying-Tong Education Foundation for Young Teachers in the Higher Education Institutions(122031)Young Tip-top Talents Support Program by the Organization Department of the CPC Central Committee,the Author of National Excellent Doctoral Dissertation(201081)Jiangsu Province Clinical Science and Technology Projects(BL2012008)the Priority Academic Program for the Development of Jiangsu Higher Education Institutions(Public Health and PreventiveMedicine)
文摘Certain pseudogenes may regulate their protein-coding cousins by competing for miRNAs and play an active biological role in cancer. However, few studies have focused on the association of genetic variations in pseudogenes with cancer prognosis. We selected six potentially functional single nucleotide polymorphisms （SNPs） in cancerrelated pseudogenes, and performed a case-only study to assess the association between those SNPs and the prognosis of hepatocellular carcinoma （HCC） in 331 HBV-positive HCC patients without surgical treatment. Log-rank test and Cox proportional hazard models were used for survival analysis. We found that the A allele of rs9909601 in E2F3P1 was significantly associated with a better prognosis compared with the G allele [adjusted hazard ratio （HR） = 0.69, 95% confidence interval （CI） = 0.56-0.86, P = 0.001]. Additionally, this protective effect was more predominant for patients without chemotherapy and transcatheter hepatic arterial chemoembolization （TACE） treatment. Interestingly, we also detected a statistically significant multiplicative interaction between genotypes of rs9909601 and chemotherapy or TACE status on HCC survival （P for multiplicative interaction 〈 0.001）. These findings indicate that rs9909601 in the pseudogene E2F3P1 may be a genetic marker for HCC prognosis in Chinese.
基金funded by the Malaysian Ministry of Education(ERGS 203/PJJAUH/6730097)Universiti Sains Malaysia(RU grant 1001/PJJAUH/815095)
文摘Objective: To clone cytochrome P450 from Aedes aegypti(Ae. aegypti) and determine the characteristics using bioinformatics tools. Methods: Cytochrome P450 of Ae. aegypti was amplified using polymerase chain reaction, cloned and sequenced. Evolutionary relationship of the sequence was inferred and bioinformatics tools were used to predict subcellular localisation, signal peptide, transmembrane helix, phosphorylation, O-glycosylation, secondary and tertiary structures of the deduced protein. Results: Polymerase chain reaction rather amplified a cytochrome P450 pseudogene which was named CYP4H44P(Gen Bank accession number KF779932). The pseudogene has 1537 nucleotides and an open reading frame of 335 amino acids containing cytochrome P450 motifs except the Wxxx R motif. It is highly homologous to CYP4H28 and CYP4H28v2. Phylogenetic analysis and evolutionary divergence showed strong clustering with CYP4H28 alleles and least divergence from the alleles respectively. The deduced protein was predicted to be found in the cytoplasm and likely to be phosphorylated but devoid of signal peptide, transmembrane helix and O-glycosylated sites. The secondary and tertiary structures were also generated. Conclusions: A cytochrome P450 pseudogene, CYP4H44 P was cloned from Ae. aegypti. The pseudogene is homologous with CYP4H28 alleles and seems to have recently diverged from this group. Isolating this pseudogene is an important step for evaluating its biological role in the mosquito and for the evolutionary analysis of Ae. aegypti CYPs.
基金supported by Program for New Century Excellent Talents (NCET-07-0507)National Natural Science Foundation of China (30370218)+1 种基金Natural Science Foundation of Shandong Province (Z2008D01)Project of Science and Technology Development Plan of Shandong Province (2007GG2009011)
文摘Olfactory receptors（ORs）,the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation,constitute the largest gene family in vertebrates.Dogs and wolves,like many other mammals,have a highly developed capability to detect and identify odorant molecules,even at minimum concentrations.In this study,the olfactory receptor repertoire from domestic dog and its closest relative,the wolf,were sequenced to estimate the fraction of pseudogenes in each subspecies.The fraction of disrupted olfactory receptor genes in dog was 17.78%,whereas,that in wolf was 12.08%.As expected the dog was less dependent on olfaction than the wolf,and the dog had more olfactory receptor pseudogenes.However,the observed difference between the two subspecies was not at the significant level（χ2 = 1.388,p = 0.239 0.05）.The values indicated that although domestication might play a role in the reduction of OR genes,it could not be concluded that the living environment provided by domestication lead to a significant reduction of the functional olfactory receptor repertoire.Furthermore,the purpose of domestication may also have influence on the ratio of functional olfactory receptor genes reduction.
基金supported by the National Natural Science Foundation of China Grants 81872127,81602289(FQ)81872694,81673267,81473040(JL)+3 种基金81402753,81672303,81871876(LY)Guangzhou Science Research Program General Project Grant 201707010123(FQ)Guangzhou Municipal Scientific Research Project Grant 1201630073(FQ)Guangdong High School Young Innovative Talents Project Grant 2015KQNCX136(FQ).
文摘The outcomes of ovarian cancer are complicated and usually unfavorable due to their diagnoses at a late stage.Identifying the efficient prognostic biomarkers to improve the survival of ovarian cancer is urgently warranted.The survival-related pseudogenes retrieved from the Cancer Genome Atlas database were screened by univariate Cox regression analysis and further assessed by least absolute shrinkage and selection operator(LASSO)method.A risk score model based on the prognostic pseudogenes was also constructed.The pseudogene-mRNA regulatory networks were established using correlation analysis,and their potent roles in the ovarian cancer progression were uncovered by functional enrichment analysis.Lastly,ssGSEA and ESTIMATE algorithms was used to evaluate the levels of immune cell infiltrations in cancer tissues and explore their relationship with risk signature.A prediction model of 10-pseudogenes including RPL10P6,AC026688.1,FAR2P4,AL391840.2,AC068647.2,FAM35BP,GBP1P1,ARL4AP5,RPS3AP2,and AMD1P1 was established.The 10-pseudogenes signature was demonstrated to be an independent prognostic factor in patient with ovarian cancer in the random set(hazard ratio[HR]=2.512,95%confidence interval[CI]=2.03–3.11,P<0.001)and total set(HR=1.71,95%CI=1.472–1.988,P<0.001).When models integrating with age,grade,stage,and risk signature,the Area Under Curve(AUC)of the 1-year,3-year,5-year and 10-year Receiver Operating Characteristic curve in the random set and total set were 0.854,0.824,0.855,0.805 and 0.679,0.697,0.739,0.790,respectively.The results of functional enrichment analysis indicated that the underlying mechanisms by which these pseudogenes influence cancer prognosis may involve the immune-related biological processes and signaling pathways.Correlation analysis showed that risk signature was significantly correlated with immune cell infiltration and immune score.We identified a novel 10-pseudogenes signature to predict the survival of patients with ovarian cancer,and that may serve as novel possible prognostic biomarkers and therapeutic targets for ovarian cancer.
基金This work was supported by National Natural Science Foundation of China[81901957]China Postdoctoral Science Foundation[2018M633723].
文摘HMGN2 have functions in inflammatory response.However,the role of HMGN2 in severe acute pancreatitis(SAP)remains unclear.Here,our study was to discuss the role and regulatory mechanism ofHMGN2 in SAP.In this study,the SAP cell model of AR42J was used to study the function and mechanism of HMGN2 in SAP.The protein expression in cells and serums were examined by western blot and ELISA assay.qPCR was used to test the transcriptional RNA level.Cell viability were examined by MTT assay.Luciferase assay was used to evaluate the interaction between gene and gene.Our results showed that HMGN2 was significantly upregulated in SAP patients.The database predicted and luciferase assay data indicated the HMGN2 was directly binding with miR-590-3p.ELISA,MTT and western blot experiments showed that the HMGN2 were promoted the cell proliferation,reduced the inflammation,and repressed the cell autophagy.Mechanism studies showed that the pseudogene HMGN2P46 level was positively correlated with HMGN2 and upregulated HMGN2 expression by competing for miR-590-3p in SAP.Taken together,all over these results showed upregulation of HMGN2 alleviates SAP,this process was regulated by HMGN2P46 competitively binding with miR-590-3p,which may provide a new insight for the treatment and intervention in SAP.Pseudogene HMGN2P46 was a miRNA sponge to regulate HMGN2 level by competing for miR-590-3p to alleviate the process of SAP.It provided a novel strategy for the diagnosis and treatment of severe acute pancreatitis.
文摘GAPDH is a conserved enzyme that binds diverse proteins, such as Siah during apoptotic nuclear translocation. There is one somatic GAPDH gene, but over 60 pseudogenes, the expression of which is nebulous. A single nucleotide polymorphism (SNP) in the GAPDHP44 pseudogene exhibits a beneficial allele in AD. The objective of this study was to examine the P44 gene and to propose a mechanism for the putative protein and its impact on AD. We examined the sequences in the putative coding region of the human GAPDHP44 gene and the upstream genetic elements usinga bioinformatics approach. We compared the amino acid sequences of the putative gene product with that of the parent GAPDH protein. There is a TATA box 24 nt upstream from, and a Kozak sequence at, putative transcription and translation start sites, respecttively. The upstream region also has sequences (7 - 16 nt) paralogous to those in parent gene introns;one shows homology to a known enhancer element. The resulting protein would contain 139 aa due to a stop codon, roughly the same size as the dinucleotide domain (151 aa) of the parent protein. The SNP is in a region (residues 80 - 120) that binds to the protein GOSPEL. We propose that the beneficial SNP may cause a glutamine to glutamate substitution. NMDA-stmulated neurons undergo GAPDH nitrosylation, Siah translocation, but can be rescued by GOSPEL binding to GAPDH. Our model suggests that the putative P44 protein may regulate GAPDH-GO-SPEL interaction and the beneficial SNPmay ameliorate AD.
文摘The p53 tumor suppressor gene is either non- functional or highly and frequently mutated in majority of cancers. In our study towards understanding cellular adaptations to stress using a rat histiocytic tumor model, we have identified mis-sense mutation in p53 that led to premature termination of translation at the carboxyl-termi- nus. Further, the cDNA isolated from heat stre- ssed cells producing two amplicons with cDNA specific primers (N-terminus) suggested occurrence of possible pseudogene(s). A comparative analysis between different tumor cell lines of rat origin and rat genomic DNA using p53 gene specific primers resulted in the amplification of a processed pseudogene and its positive interaction with wild type p53 probe on Southern blot analysis. The genomic DNA sequence analysis, and sequence comparison with cDNA discovered that the processed pseudogene lacks DNA binding domain and nuclear localization signal, however, contains the ribosomal entry and stop signals. Rat genome BLAST analysis of the pesudogene suggested chromosome-18 localization which was in addition to 14, 13, 10, 9 localization of the cDNA. In the interest of unraveling hidden dimensions of p53 tumor suppressor gene, our study explores the probability of p53 functional pseudogenes in rat histiocytoma.
