Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important informatio...Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid （AsA）, which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato （Solanum lycopersicum L.） fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty- four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.展开更多
Objective To explore the correlation between IT-GA6 gene ( rs12621278, G ) , MSMB gene ( rs10993994,T) ,chromosome 8q24 9 ( rs10086908, T) and prostate cancer ( PCa) in Beijing residents,and to explore the correlation...Objective To explore the correlation between IT-GA6 gene ( rs12621278, G ) , MSMB gene ( rs10993994,T) ,chromosome 8q24 9 ( rs10086908, T) and prostate cancer ( PCa) in Beijing residents,and to explore the correlation between genotype and pheno-展开更多
Objective To discuss the diagnosis and surgical management of multilocular cystic renal cell carcinoma ( MCRCC) and to evaluate the gene function of the mutation of von Hippel-Lindau ( VHL) gene in MCRCC. Methods Seve...Objective To discuss the diagnosis and surgical management of multilocular cystic renal cell carcinoma ( MCRCC) and to evaluate the gene function of the mutation of von Hippel-Lindau ( VHL) gene in MCRCC. Methods Seventeen MCRCC cases ( 11 men and展开更多
Objective To investigate the expression of human telomerase catalytic subunit,hTERT, in human non-small cell lung cancer (NSCLC) and its correlations to c-myc gene.Methods hTERT and c-myc mRNA expressions were detecte...Objective To investigate the expression of human telomerase catalytic subunit,hTERT, in human non-small cell lung cancer (NSCLC) and its correlations to c-myc gene.Methods hTERT and c-myc mRNA expressions were detected by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). Statistical correlation analysis was made to estimate whether there was interrelation between them.Results Positive rate of hTERT expression in 51 surgically resected lung cancer specimens was 86.3%,significantly higher than that in adjacent non-neoplastic lung tissues and benign lesions,which were 14.3% and 27.3% respectively. No statistical significance was observed between the frequency of hTERT expression and histologic types,degree of differentiation,TNM stages,tumor size or lymph nodes metastases. Correlation analysis revealed that the expression of c-myc gene was significantly related to that of hTERT (correlation coefficient,r =0.633,P <0.001).Conclusions hTERT may be a useful tumor marker in diagnosing lung cancer. Significant correlation between the expression of hTERT and c-myc mRNA indicates that the activation and up-regulation of hTERT might be conferred by over-expression of c-myc gene.展开更多
Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the cont...Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the contents of malondialdehyde(MDA),soluble sugar(SS),and proline(Pro)and the transcriptome of oat leaves under 0,12,24,36,and 48 h of drought treatment,revealing that the content of MDA increased with drought duration,whereas the contents of SS and Pro reached their maximum at 24 h of treatment,with a total between 0 h of treatment and the other groups.Differentially expressed genes(DEGs)presented significant enrichment in the phenylpropanoid biosynthetic pathway,flavonoid biosynthetic pathway,galactose metabolism,and glutathione metabolism.The biological changes caused by drought stress resulted in the obvious activation of antioxidase genes.The sugar and flavonoid biosynthetic genes were studied based on the detailed temporal patterns of expression of four major metabolic pathways.Additionally,14 candidate hub genes,such as the genes that encoded galactinol synthase,serine/threonineprotein kinase,and 1-aminocyclopropane-1-carboxylate oxidase,were identified by virtue of weighted gene co-expression network analysis.Differential transcription factor(TF)analysis showed that NAM,ATAF1/2,CUC2(NAC),Heat Shock(HS),Trihelix,TEOSINTE BRANCHED1/CYCLOIDEA/PCF(TCP),and other 11 TF families were closely related to drought stress.These findings help us understand the early responses of oat to drought stress from new perspectives and can guide further research.展开更多
Aim:This study aimed to translate a known drug-resistance mechanism of long-term CSFIR inhibition into multicellu-lar biomarkers that can serve as potential therapeutic targets as well as predictive markers for the su...Aim:This study aimed to translate a known drug-resistance mechanism of long-term CSFIR inhibition into multicellu-lar biomarkers that can serve as potential therapeutic targets as well as predictive markers for the survival of glioma patients.Methods:Using existing data from a published mouse study of drug resistance in immunotherapy for glioma,we identified mulicellular differentially expressed genes(DEGs)between drug-sensitive and drug-resistant mice and translated the DEGs in mouse genome to human homolog.We constructed correlation gene networks for drug re-sistance in mice and glioma patients and selected candidate genes via concordance analysis of human with mouse gene networks.Markers of drug resistance and an associated predictive signature for patient survival were developed using regularized Cox models with data of glioma patients from The Cancer Genome Atlas(TCGA)database.Predic-tive performance of the identified predictive signature was evaluated using an independent human dataset from the Chinese Glioma Genome Atlas(CGGA)database.Results:Fourteen genes(CCL22,ADCY2,PDK1,ZFP36,CP,CD2,PLAUR,ACAPI,COL5A1,FAM83D,PBK,FANCA,ANXA7,and TACC3)were identified as genetic biomarkers that were all associated with pathways in glioma progression and drug resistance.Five of the 14 genes(CCL22,ADCY2,PDK1,CD2,and COL5A1)were used to construct a signature that is predictive of patient survival in the proneural subtype GBM patients with an AUC under the time-dependent receiver operating characteristic(ROC)of 2-year survival equal to 0.89.This signature also shows promising predic-tive accuracy for the survival of LGG patients but not for non-proneural type GBMs.Conclusion:Our translational approach can utilize gene correlation networks from multiple types of cells in the tu-mor microenvironment of an imals.The identified biomarkers of drug resistance have good power to predict patient survival in some major subtypes of gliomas(the proneural subtype of GBM and LGG).The expression levels of the biomarkers of drug resistance may be modified for the development of personalized immunotherapies to prolong survival for a large portion of glioma patients.展开更多
We investigated the androgen receptor(AR) gene mutation profiles of Chinese patients exhibiting severe androgen insensitivity syndrome(AIS) phenotypes. The present study enrolled 28 patients with genetically diagnosed...We investigated the androgen receptor(AR) gene mutation profiles of Chinese patients exhibiting severe androgen insensitivity syndrome(AIS) phenotypes. The present study enrolled 28 patients with genetically diagnosed AIS, who presented with severe phenotypes(Prader grade 0–3). Patients and some family members were screened via amplification and sequencing of their AR exons 1–8, including the corresponding intronic flanking regions. Luteinizing(LH), follicle-stimulating(FSH), and testosterone(T) hormone levels were found to be slightly, but not significantly, higher in patients with complete androgen insensitivity syndrome(CAIS) than in patients with partial androgen insensitivity syndrome(PAIS)(P>0.05). We identified 24 different AR mutations, including 12 that were novel. Ten patients(cases 2, 3, 10, 28, 11, 12, 19, 20, 24, and 25) were found to carry five recurrent mutations(p.Y572 S, p.P914 S, p.S176 R, p.Y782 N, and p.R841H); of these, p.Y572 S, p.S176 R, and p.Y782 N were novel. Among the mutations identified in patients with CAIS, six(66.7%) were characterized as single-nucleotide missense mutations, and six(66.7%) were found to be located in the AR ligand-binding domain(LBD). Among the mutations identified in patients with PAIS, 15(93.8%) were found to be missense, and 11(68.8%) were found to be located in the LBD. Patients 10 and 28 were determined to harbor the same missense mutation(p.P914S), but were diagnosed with CAIS and PAIS, respectively.Sex hormone levels were slightly, but not significantly, elevated in patients with CAIS compared to those with PAIS. Missense mutations spanning AR exons 1–8 were the predominant form of identified mutations, and these were mostly located in the AR LBD. Approximately 50% of the identified mutations were novel, and have enriched the AR gene-mutation database. Patients harboring identical mutations were in some instances found to exhibit divergent phenotypes.展开更多
基金supported by the National Natural Science Foundation of China (31271959)National Basic Research Program (2011CB100604) of China
文摘Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid （AsA）, which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato （Solanum lycopersicum L.） fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty- four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.
文摘Objective To explore the correlation between IT-GA6 gene ( rs12621278, G ) , MSMB gene ( rs10993994,T) ,chromosome 8q24 9 ( rs10086908, T) and prostate cancer ( PCa) in Beijing residents,and to explore the correlation between genotype and pheno-
文摘Objective To discuss the diagnosis and surgical management of multilocular cystic renal cell carcinoma ( MCRCC) and to evaluate the gene function of the mutation of von Hippel-Lindau ( VHL) gene in MCRCC. Methods Seventeen MCRCC cases ( 11 men and
文摘Objective To investigate the expression of human telomerase catalytic subunit,hTERT, in human non-small cell lung cancer (NSCLC) and its correlations to c-myc gene.Methods hTERT and c-myc mRNA expressions were detected by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). Statistical correlation analysis was made to estimate whether there was interrelation between them.Results Positive rate of hTERT expression in 51 surgically resected lung cancer specimens was 86.3%,significantly higher than that in adjacent non-neoplastic lung tissues and benign lesions,which were 14.3% and 27.3% respectively. No statistical significance was observed between the frequency of hTERT expression and histologic types,degree of differentiation,TNM stages,tumor size or lymph nodes metastases. Correlation analysis revealed that the expression of c-myc gene was significantly related to that of hTERT (correlation coefficient,r =0.633,P <0.001).Conclusions hTERT may be a useful tumor marker in diagnosing lung cancer. Significant correlation between the expression of hTERT and c-myc mRNA indicates that the activation and up-regulation of hTERT might be conferred by over-expression of c-myc gene.
基金conducted with the funds from the Oat Whole Industry Chain Technology Innovation Teamthe National Key Research and Development Program of China(No.2018YFE0107900)+2 种基金the National Modern Agricultural Industry Technology System(No.CARS-07)the Inner Mongolia Autonomous Region Oat Engineering Laboratory Capacity Building Project(No.BR221023)the Inner Mongolia University Oat Engineering Research Center,the Oat Engineering Laboratory of Inner Mongolia Autonomous Region,and the Inner Mongolia Agricultural University Coarse-grain Industry Collaborative Innovation Center,China.
文摘Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the contents of malondialdehyde(MDA),soluble sugar(SS),and proline(Pro)and the transcriptome of oat leaves under 0,12,24,36,and 48 h of drought treatment,revealing that the content of MDA increased with drought duration,whereas the contents of SS and Pro reached their maximum at 24 h of treatment,with a total between 0 h of treatment and the other groups.Differentially expressed genes(DEGs)presented significant enrichment in the phenylpropanoid biosynthetic pathway,flavonoid biosynthetic pathway,galactose metabolism,and glutathione metabolism.The biological changes caused by drought stress resulted in the obvious activation of antioxidase genes.The sugar and flavonoid biosynthetic genes were studied based on the detailed temporal patterns of expression of four major metabolic pathways.Additionally,14 candidate hub genes,such as the genes that encoded galactinol synthase,serine/threonineprotein kinase,and 1-aminocyclopropane-1-carboxylate oxidase,were identified by virtue of weighted gene co-expression network analysis.Differential transcription factor(TF)analysis showed that NAM,ATAF1/2,CUC2(NAC),Heat Shock(HS),Trihelix,TEOSINTE BRANCHED1/CYCLOIDEA/PCF(TCP),and other 11 TF families were closely related to drought stress.These findings help us understand the early responses of oat to drought stress from new perspectives and can guide further research.
基金supported by research grants P30CA016087,P50CA225450,P30AG066512 from the National Institute of Health(NIH).
文摘Aim:This study aimed to translate a known drug-resistance mechanism of long-term CSFIR inhibition into multicellu-lar biomarkers that can serve as potential therapeutic targets as well as predictive markers for the survival of glioma patients.Methods:Using existing data from a published mouse study of drug resistance in immunotherapy for glioma,we identified mulicellular differentially expressed genes(DEGs)between drug-sensitive and drug-resistant mice and translated the DEGs in mouse genome to human homolog.We constructed correlation gene networks for drug re-sistance in mice and glioma patients and selected candidate genes via concordance analysis of human with mouse gene networks.Markers of drug resistance and an associated predictive signature for patient survival were developed using regularized Cox models with data of glioma patients from The Cancer Genome Atlas(TCGA)database.Predic-tive performance of the identified predictive signature was evaluated using an independent human dataset from the Chinese Glioma Genome Atlas(CGGA)database.Results:Fourteen genes(CCL22,ADCY2,PDK1,ZFP36,CP,CD2,PLAUR,ACAPI,COL5A1,FAM83D,PBK,FANCA,ANXA7,and TACC3)were identified as genetic biomarkers that were all associated with pathways in glioma progression and drug resistance.Five of the 14 genes(CCL22,ADCY2,PDK1,CD2,and COL5A1)were used to construct a signature that is predictive of patient survival in the proneural subtype GBM patients with an AUC under the time-dependent receiver operating characteristic(ROC)of 2-year survival equal to 0.89.This signature also shows promising predic-tive accuracy for the survival of LGG patients but not for non-proneural type GBMs.Conclusion:Our translational approach can utilize gene correlation networks from multiple types of cells in the tu-mor microenvironment of an imals.The identified biomarkers of drug resistance have good power to predict patient survival in some major subtypes of gliomas(the proneural subtype of GBM and LGG).The expression levels of the biomarkers of drug resistance may be modified for the development of personalized immunotherapies to prolong survival for a large portion of glioma patients.
基金supported by the Public Health Project for Residents in Beijing (Z151100003915103)the National Key Research and Development Program of China (2016YFC0901505)
文摘We investigated the androgen receptor(AR) gene mutation profiles of Chinese patients exhibiting severe androgen insensitivity syndrome(AIS) phenotypes. The present study enrolled 28 patients with genetically diagnosed AIS, who presented with severe phenotypes(Prader grade 0–3). Patients and some family members were screened via amplification and sequencing of their AR exons 1–8, including the corresponding intronic flanking regions. Luteinizing(LH), follicle-stimulating(FSH), and testosterone(T) hormone levels were found to be slightly, but not significantly, higher in patients with complete androgen insensitivity syndrome(CAIS) than in patients with partial androgen insensitivity syndrome(PAIS)(P>0.05). We identified 24 different AR mutations, including 12 that were novel. Ten patients(cases 2, 3, 10, 28, 11, 12, 19, 20, 24, and 25) were found to carry five recurrent mutations(p.Y572 S, p.P914 S, p.S176 R, p.Y782 N, and p.R841H); of these, p.Y572 S, p.S176 R, and p.Y782 N were novel. Among the mutations identified in patients with CAIS, six(66.7%) were characterized as single-nucleotide missense mutations, and six(66.7%) were found to be located in the AR ligand-binding domain(LBD). Among the mutations identified in patients with PAIS, 15(93.8%) were found to be missense, and 11(68.8%) were found to be located in the LBD. Patients 10 and 28 were determined to harbor the same missense mutation(p.P914S), but were diagnosed with CAIS and PAIS, respectively.Sex hormone levels were slightly, but not significantly, elevated in patients with CAIS compared to those with PAIS. Missense mutations spanning AR exons 1–8 were the predominant form of identified mutations, and these were mostly located in the AR LBD. Approximately 50% of the identified mutations were novel, and have enriched the AR gene-mutation database. Patients harboring identical mutations were in some instances found to exhibit divergent phenotypes.
