AIM: To investigate the expression patterns of long non-coding RNAs (lncRNAs) in gastric cancer. METHODS: Two publicly available human exon arrays for gastric cancer and data for the corresponding normal tissue were d...AIM: To investigate the expression patterns of long non-coding RNAs (lncRNAs) in gastric cancer. METHODS: Two publicly available human exon arrays for gastric cancer and data for the corresponding normal tissue were downloaded from the Gene Expression Omnibus (GEO). We re-annotated the probes of the human exon arrays and retained the probes uniquely mapping to lncRNAs at the gene level. LncRNA expression profiles were generated by using robust multi-array average method in affymetrix power tools. The normalized data were then analyzed with a Bioconductor package linear models for microarray data and genes with adjusted P -values below 0.01 were considered differentially expressed. An independent data set was used to validate the results. RESULTS: With the computational pipeline established to re-annotate over 6.5 million probes of the Affymetrix Human Exon 1.0 ST array, we identified 136053 probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs, covering nearly 76% of the GENCODE lncRNA data set. By analyzing GSE27342 consisting of 80 paired gastric cancer and normal adjacent tissue samples, we identified 88 lncRNAs that were differentially expressed in gastric cancer, some of which have been reported to play a role in cancer, such as LINC00152, taurine upregulated 1, urothelial cancer associated 1, Pvt1 oncogene, small nucleolar RNA host gene 1 and LINC00261. In the validation data set GSE33335, 59% of these differentially expressed lncRNAs showed significant expression changes (adjusted P -value < 0.01) with the same direction. CONCLUSION: We identified a set of lncRNAs differentially expressed in gastric cancer, providing useful information for discovery of new biomarkers and therapeutic targets in gastric cancer.展开更多
AIM To identify circulating micro(mi)RNAs as biological markers for prediction of severe acute pancreatitis(SAP) with acute lung injury(ALI).METHODS Twenty-four serum samples were respectively collected and classified...AIM To identify circulating micro(mi)RNAs as biological markers for prediction of severe acute pancreatitis(SAP) with acute lung injury(ALI).METHODS Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the mi RNA expression profiles were determined by microarray analysis. These mi RNAs were validated by quantitative reverse transcriptionpolymerase chain reaction, and their putative targets were predicted by the online software Target Scan, mi Randa and Pic Tar database. Gene ontology(GO) and Kyoto encyclopedia of genes and genomes(commonly known as KEGG) were used to predict their possible functions and pathways involved.RESULTS We investigated 287 mi RNAs based on microarray data analysis. Twelve mi RNAs were differentially expressed in the patients with SAP with ALI and those with SAP without ALI. Hsa-mi R-1260 b, 762, 22-3 p, 23 b and 23 a were differently up-regulated and hsa-mi R-550 a*, 324-5 p, 484, 331-3 p, 140-3 p, 342-3 p and 150 were differently down-regulated in patients with SAP with ALI compared to those with SAP without ALI. In addition, 85 putative target genes of the significantly dysregulated mi RNAs were found by Target Scan, mi Randa and Pic Tar. Finally, GO and pathway network analysis showed that they were mainly enriched in signal transduction, metabolic processes, cytoplasm and cell membranes.CONCLUSION This is the first study to identify 12 circulating mi RNAs in patients with SAP with ALI, which may be biomarkers for prediction of ALI after SAP.展开更多
Sugar signaling is a mechanism that plants use to integrate various internal and external cues to achieve nutrient homeostasis, mediate developmental programs, and articulate stress responses. Many bZlP transcription ...Sugar signaling is a mechanism that plants use to integrate various internal and external cues to achieve nutrient homeostasis, mediate developmental programs, and articulate stress responses. Many bZlP transcription factors are known to be involved in nutrient and/or stress signaling. An Arabidopsis Sl-group bZlP gene, AtbZIP1, was identified as a sugar-sensitive gene in a previous gene expression profiling study （Plant Cell. 16, 2128-2150）. In this report, we show that the expression of AtbZIP1 is repressed by sugars in a fast, sensitive, and reversible way. The sugar repression of Atb- ZIP1 is affected by a conserved sugar signaling component, hexokinase. Besides being a sugar-regulated gene, AtbZIP1 can mediate sugar signaling and affect gene expression, plant growth, and development. When carbon nutrients are limited, gain or loss of function of AtbZlP1 causes changes in the rates of early seedling establishment. Results of phenotypic analyses indicate that AtbZlP1 acts as a negative regulator of early seedling growth. Using gain- and loss-of-function plants in a microarray analysis, two sets of putative AtbZIP1-regulated genes have been identified. Among them, sugar-responsive genes are highly over-represented, implicating a role of AtbZlP1 in sugar-mediated gene expression. Using yeast two-hybrid （Y-2-H） screens and bimolecular fluorescence complementation （BiFC） analyses, we are able to recapitulate extensive C/S1 AtbZlP protein interacting network in living cells. Finally, we show that AtbZIP1 can bind ACGT-based motifs in vitro and that the binding characteristics appear to be affected by the heterodimerization between AtbZlP1 and the C-group AtbZIPs, including AtbZlP10 and AtbZlP63.展开更多
Background Hepatocellular carcinoma （HCC） is a common primary cancer frequently associated with hepatitis B virus （HBV） infection. However, whether these identified genes are particularly associated with HBV-relat...Background Hepatocellular carcinoma （HCC） is a common primary cancer frequently associated with hepatitis B virus （HBV） infection. However, whether these identified genes are particularly associated with HBV-related HCC remains unknown. The aim of this study was to investigate the differential gene expression between HBV-related HCC tissues and adjacent noncancerous tissues. Methods cDNA microarray was used to detect the differential gene expression profile in the HBV-related HCC tissues and adjacent noncancerous tissues, and reverse transcription-polymerase chain reaction （RT-PCR） was performed to verify the differential expression of candidate genes obtained from cDNA microarray experiment. Results In this study, 1369 genes or expressed sequence tags （ESTs） including 121 genes or ESTs with at least two-fold expression alterations between cancerous and noncancerous tissues were identified. Special AT-rich sequence binding protein 1 （SATB-1） expression was positive in 73% （16/22） of cancerous tissues and negative （0/22） in all noncancerous tissues of HBV-related HCC patients. Transmembrane 4 superfamily member 1 （TM4SF-1） expression was positive in 86% （19/22） of cancerous tissues and negative （0/22） in all noncancerous tissues. Suppression of tumorigenicity 14 （ST-14） expression was positive in 73% （16/22） of noncancerous tissues in patients with HBV-related HCC and negative in all HCC tissues （0/22）. Conclusion This study provided the gene expression profile of HBV-related HCC and presented differential expression patterns of SATB-1, TM4SF-1 and ST-14 between cancerous and noncancerous tissues in patients with HBV-related HCC.展开更多
Early screening for colorectal cancer(CRC) holds the key to combat and control the increasing global burden of CRC morbidity and mortality. However, the current available screening modalities are severely inadequate b...Early screening for colorectal cancer(CRC) holds the key to combat and control the increasing global burden of CRC morbidity and mortality. However, the current available screening modalities are severely inadequate because of their high cost and cumbersome preparatory procedures that ultimately lead to a low participation rate. People simply do not like to have colonoscopies. It would be ideal, therefore, to develop an alternative modality based on blood biomarkers as the first line screening test. This will allow for the differentiation of the general population from high risk individuals. Colonoscopy would then become the secondary test, to further screen the high risk segment of the population. This will encourage participation and therefore help to reach the goal of early detection and thereby reduce the anticipated increasing global CRC incidence rate. A blood-based screening test is anappealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher participation rate. This review surveys various blood-based test strategies currently under investigation, discusses the potency of what is available, and assesses how new technology may contribute to future test design.展开更多
目的:探讨荧光原位杂交技术(fluorescence in situ hybridization,FISH)在产前诊断染色体嵌合体中的应用。方法:22例行绒毛/羊水细胞体外培养染色体核型结果提示可能存在染色体嵌合现象的病例,进一步用染色体微阵列比较基因组杂交检测(c...目的:探讨荧光原位杂交技术(fluorescence in situ hybridization,FISH)在产前诊断染色体嵌合体中的应用。方法:22例行绒毛/羊水细胞体外培养染色体核型结果提示可能存在染色体嵌合现象的病例,进一步用染色体微阵列比较基因组杂交检测(chromosomal microarray analaysis,CMA)和FISH技术分析确定其异常核型及嵌合比例。结果:22例核型结果提示嵌合体的病例中,性染色体数目嵌合13例,常染色体三体嵌合6例,性染色体结构异常嵌合3例。近50%病例CMA结果未检测到嵌合现象,可能与CMA技术仅能检测基因拷贝数变化且无法检测低比例嵌合有关。因常染色体数目异常对胎儿生长发育影响较大,常染色体数目异常嵌合病例中,除1例病例外其余均选择终止妊娠。3例结构异常嵌合病例经核型分析结合CMA及FISH结果确定均为性染色体双着丝粒染色体复杂结构嵌合。结论:对于产前诊断提示可能存在染色体嵌合的病例,不应急于终止妊娠,需采用多种方法加以验证,应充分应用CMA技术和FISH技术结合G显带核型结果进行综合分析,并需要对胎儿形态进行细致的超声评估,从而更加准确地确定嵌合类型以及异常核型的嵌合比例,为临床医师指导遗传咨询提供更加可靠的依据。展开更多
文摘AIM: To investigate the expression patterns of long non-coding RNAs (lncRNAs) in gastric cancer. METHODS: Two publicly available human exon arrays for gastric cancer and data for the corresponding normal tissue were downloaded from the Gene Expression Omnibus (GEO). We re-annotated the probes of the human exon arrays and retained the probes uniquely mapping to lncRNAs at the gene level. LncRNA expression profiles were generated by using robust multi-array average method in affymetrix power tools. The normalized data were then analyzed with a Bioconductor package linear models for microarray data and genes with adjusted P -values below 0.01 were considered differentially expressed. An independent data set was used to validate the results. RESULTS: With the computational pipeline established to re-annotate over 6.5 million probes of the Affymetrix Human Exon 1.0 ST array, we identified 136053 probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs, covering nearly 76% of the GENCODE lncRNA data set. By analyzing GSE27342 consisting of 80 paired gastric cancer and normal adjacent tissue samples, we identified 88 lncRNAs that were differentially expressed in gastric cancer, some of which have been reported to play a role in cancer, such as LINC00152, taurine upregulated 1, urothelial cancer associated 1, Pvt1 oncogene, small nucleolar RNA host gene 1 and LINC00261. In the validation data set GSE33335, 59% of these differentially expressed lncRNAs showed significant expression changes (adjusted P -value < 0.01) with the same direction. CONCLUSION: We identified a set of lncRNAs differentially expressed in gastric cancer, providing useful information for discovery of new biomarkers and therapeutic targets in gastric cancer.
基金Supported by the National Natural Science Foundation of China,No.30971626 and No.81473512
文摘AIM To identify circulating micro(mi)RNAs as biological markers for prediction of severe acute pancreatitis(SAP) with acute lung injury(ALI).METHODS Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the mi RNA expression profiles were determined by microarray analysis. These mi RNAs were validated by quantitative reverse transcriptionpolymerase chain reaction, and their putative targets were predicted by the online software Target Scan, mi Randa and Pic Tar database. Gene ontology(GO) and Kyoto encyclopedia of genes and genomes(commonly known as KEGG) were used to predict their possible functions and pathways involved.RESULTS We investigated 287 mi RNAs based on microarray data analysis. Twelve mi RNAs were differentially expressed in the patients with SAP with ALI and those with SAP without ALI. Hsa-mi R-1260 b, 762, 22-3 p, 23 b and 23 a were differently up-regulated and hsa-mi R-550 a*, 324-5 p, 484, 331-3 p, 140-3 p, 342-3 p and 150 were differently down-regulated in patients with SAP with ALI compared to those with SAP without ALI. In addition, 85 putative target genes of the significantly dysregulated mi RNAs were found by Target Scan, mi Randa and Pic Tar. Finally, GO and pathway network analysis showed that they were mainly enriched in signal transduction, metabolic processes, cytoplasm and cell membranes.CONCLUSION This is the first study to identify 12 circulating mi RNAs in patients with SAP with ALI, which may be biomarkers for prediction of ALI after SAP.
基金This work was supported by The National Science Foundation （IOB- 0543751 to J.C.J.）.We thank the Arabidopsis Biological Resource Center （Columbus, Ohio） for providing DNA clones and seeds, Dr Biao Ding formicroscopy facility, Dr Steven St Martin for microarray design and data analysis, Cyrus Hah for protoplast transient expression analysis, Drs John Finer and Michelle Jones for critical reading of the manuscript, and Joe Takayama for greenhouse support. No conflict of interest declared.
文摘Sugar signaling is a mechanism that plants use to integrate various internal and external cues to achieve nutrient homeostasis, mediate developmental programs, and articulate stress responses. Many bZlP transcription factors are known to be involved in nutrient and/or stress signaling. An Arabidopsis Sl-group bZlP gene, AtbZIP1, was identified as a sugar-sensitive gene in a previous gene expression profiling study （Plant Cell. 16, 2128-2150）. In this report, we show that the expression of AtbZIP1 is repressed by sugars in a fast, sensitive, and reversible way. The sugar repression of Atb- ZIP1 is affected by a conserved sugar signaling component, hexokinase. Besides being a sugar-regulated gene, AtbZIP1 can mediate sugar signaling and affect gene expression, plant growth, and development. When carbon nutrients are limited, gain or loss of function of AtbZlP1 causes changes in the rates of early seedling establishment. Results of phenotypic analyses indicate that AtbZlP1 acts as a negative regulator of early seedling growth. Using gain- and loss-of-function plants in a microarray analysis, two sets of putative AtbZIP1-regulated genes have been identified. Among them, sugar-responsive genes are highly over-represented, implicating a role of AtbZlP1 in sugar-mediated gene expression. Using yeast two-hybrid （Y-2-H） screens and bimolecular fluorescence complementation （BiFC） analyses, we are able to recapitulate extensive C/S1 AtbZlP protein interacting network in living cells. Finally, we show that AtbZIP1 can bind ACGT-based motifs in vitro and that the binding characteristics appear to be affected by the heterodimerization between AtbZlP1 and the C-group AtbZIPs, including AtbZlP10 and AtbZlP63.
文摘Background Hepatocellular carcinoma （HCC） is a common primary cancer frequently associated with hepatitis B virus （HBV） infection. However, whether these identified genes are particularly associated with HBV-related HCC remains unknown. The aim of this study was to investigate the differential gene expression between HBV-related HCC tissues and adjacent noncancerous tissues. Methods cDNA microarray was used to detect the differential gene expression profile in the HBV-related HCC tissues and adjacent noncancerous tissues, and reverse transcription-polymerase chain reaction （RT-PCR） was performed to verify the differential expression of candidate genes obtained from cDNA microarray experiment. Results In this study, 1369 genes or expressed sequence tags （ESTs） including 121 genes or ESTs with at least two-fold expression alterations between cancerous and noncancerous tissues were identified. Special AT-rich sequence binding protein 1 （SATB-1） expression was positive in 73% （16/22） of cancerous tissues and negative （0/22） in all noncancerous tissues of HBV-related HCC patients. Transmembrane 4 superfamily member 1 （TM4SF-1） expression was positive in 86% （19/22） of cancerous tissues and negative （0/22） in all noncancerous tissues. Suppression of tumorigenicity 14 （ST-14） expression was positive in 73% （16/22） of noncancerous tissues in patients with HBV-related HCC and negative in all HCC tissues （0/22）. Conclusion This study provided the gene expression profile of HBV-related HCC and presented differential expression patterns of SATB-1, TM4SF-1 and ST-14 between cancerous and noncancerous tissues in patients with HBV-related HCC.
基金Supported by The Valley Hospital Foundation Research FundThe community of The Valley Hospital in Ridgewood,NJ,especially Ms.Audrey Meyers,CEO,Mr.Anastasios Kozaitis,president of the Valley Hospital Foundation
文摘Early screening for colorectal cancer(CRC) holds the key to combat and control the increasing global burden of CRC morbidity and mortality. However, the current available screening modalities are severely inadequate because of their high cost and cumbersome preparatory procedures that ultimately lead to a low participation rate. People simply do not like to have colonoscopies. It would be ideal, therefore, to develop an alternative modality based on blood biomarkers as the first line screening test. This will allow for the differentiation of the general population from high risk individuals. Colonoscopy would then become the secondary test, to further screen the high risk segment of the population. This will encourage participation and therefore help to reach the goal of early detection and thereby reduce the anticipated increasing global CRC incidence rate. A blood-based screening test is anappealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher participation rate. This review surveys various blood-based test strategies currently under investigation, discusses the potency of what is available, and assesses how new technology may contribute to future test design.
