Blood samples have traditionally been used as the main source of DNA for genetic analysis. How-ever, this source can be difficult in terms of collection, transportation, and long-term storage. In this study, we invest...Blood samples have traditionally been used as the main source of DNA for genetic analysis. How-ever, this source can be difficult in terms of collection, transportation, and long-term storage. In this study, we investigated whether human nail clippings could be used as a source of DNA for SNP genotyping, null-allele detection, and whole-genome amplification. From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for null-allele detection compared to DNA derived from matched blood sam-ples. For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and null-allele detection, respectively. Concordance was ~98% for both methods. When combined with OmniPlex whole-genome amplification, human nail clippings could potentially be used as an alternative to whole blood as a less invasive and more convenient source of DNA for genotyping studies.展开更多
Objective： Kaiso is upregulated in many cancers and proposed to bind with both methylated- and unmethylated-DNA in the nucleus as a transcriptional repressor. The objective is to define its subcellnlar localization i...Objective： Kaiso is upregulated in many cancers and proposed to bind with both methylated- and unmethylated-DNA in the nucleus as a transcriptional repressor. The objective is to define its subcellnlar localization in vivo and exact binding DNA sequences in cells. Methods： Compartmentalization of exogenous Kaiso in cells was tracked with enhanced green fluorescence protein （EGFP） tag. The endogenous Kaiso expression in gastric carcinoma tissue was examined with immunohistochemical staining. Kaiso-DNA binding was tested using electrophoretic mobility shift assay （EMSA） and chromatin immunoprecipitation assay （CHIP）. Results： Kaiso mainly localized in the nucleus of cancer and stromal cells in vivo, but remained in the cytoplasm of cultured cells. Most importantly, nuclear Kaiso can bind with the methylated-CGCG- containing sequence in the CDKN2A promoter, but not with the hydroxymethylated-CGCG sequence in HCT116 cells. Conclusions： Kaiso locates mainly in the nucleus in vivo where it binds with the methylated-CGCG sequences, but does not bind with the hydroxymethylated-CGCG sequences.展开更多
There are several kinds of epigenetic networks in the human body including the cell differentiation epigenetic network(DiEN) and the host adaptation epigenetic network(AdEN).DiEN networks are static and cell/tissue-sp...There are several kinds of epigenetic networks in the human body including the cell differentiation epigenetic network(DiEN) and the host adaptation epigenetic network(AdEN).DiEN networks are static and cell/tissue-specific.AdEN networks are variable and dependent upon environmental factors.DiEN and AdEN alterations can respectively serve as biomarkers for different kinds of diseases.Cancer is a consequence of accumulated pathophysiological adaptations of tissue stem cells to exposure of environmental carcinogens.Cancer cells are de-differentiated cells that obtain the capacity of unrestricted proliferation,local invasion,and distant migration/metastasis.Both DiEN and AdEN changes can be observed in cancer tissues.Alterations of DNA methylation are the most stable epigenetic modifications and can be sensitively detected in a small cell population.These advantages make DNA methylation the optimal biomarkers for detection of initiated cells in precancerous lesions and metastasis stem cells in cancer tissues.It has been proven that p16 methylation can be used as a diagnostic biomarker to determine malignant potential of epithelium dysplasia in many organs including the stomach.In a large-scale validation study on the DNA methylome of gastric carcinomas(GC),the methylation status of more than 90 CpG islands has been analyzed by DHPLC.Furthermore,GFRA1 demethylation and methylation of SRF and ZNF382 are frequent events during gastric carcinogenesis and consistently correlate to GC metastasis and overall survival of GC patients from China,Japan,and Korea,respectively.In a population study,it has been demonstrated that gradual increasing of plasma miR-211 and other miRNA levels may be an early risk predictor for GC development.展开更多
文摘Blood samples have traditionally been used as the main source of DNA for genetic analysis. How-ever, this source can be difficult in terms of collection, transportation, and long-term storage. In this study, we investigated whether human nail clippings could be used as a source of DNA for SNP genotyping, null-allele detection, and whole-genome amplification. From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for null-allele detection compared to DNA derived from matched blood sam-ples. For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and null-allele detection, respectively. Concordance was ~98% for both methods. When combined with OmniPlex whole-genome amplification, human nail clippings could potentially be used as an alternative to whole blood as a less invasive and more convenient source of DNA for genotyping studies.
基金supported by National Basic Research Program of China(Grant No.2011CB504201)
文摘Objective： Kaiso is upregulated in many cancers and proposed to bind with both methylated- and unmethylated-DNA in the nucleus as a transcriptional repressor. The objective is to define its subcellnlar localization in vivo and exact binding DNA sequences in cells. Methods： Compartmentalization of exogenous Kaiso in cells was tracked with enhanced green fluorescence protein （EGFP） tag. The endogenous Kaiso expression in gastric carcinoma tissue was examined with immunohistochemical staining. Kaiso-DNA binding was tested using electrophoretic mobility shift assay （EMSA） and chromatin immunoprecipitation assay （CHIP）. Results： Kaiso mainly localized in the nucleus of cancer and stromal cells in vivo, but remained in the cytoplasm of cultured cells. Most importantly, nuclear Kaiso can bind with the methylated-CGCG- containing sequence in the CDKN2A promoter, but not with the hydroxymethylated-CGCG sequence in HCT116 cells. Conclusions： Kaiso locates mainly in the nucleus in vivo where it binds with the methylated-CGCG sequences, but does not bind with the hydroxymethylated-CGCG sequences.
基金supported by National Natural Science Foundation of China (30921140311 and 90919015)National Key Basic Research Program of China (2010CB529300 and 2011CB-504201)
文摘There are several kinds of epigenetic networks in the human body including the cell differentiation epigenetic network(DiEN) and the host adaptation epigenetic network(AdEN).DiEN networks are static and cell/tissue-specific.AdEN networks are variable and dependent upon environmental factors.DiEN and AdEN alterations can respectively serve as biomarkers for different kinds of diseases.Cancer is a consequence of accumulated pathophysiological adaptations of tissue stem cells to exposure of environmental carcinogens.Cancer cells are de-differentiated cells that obtain the capacity of unrestricted proliferation,local invasion,and distant migration/metastasis.Both DiEN and AdEN changes can be observed in cancer tissues.Alterations of DNA methylation are the most stable epigenetic modifications and can be sensitively detected in a small cell population.These advantages make DNA methylation the optimal biomarkers for detection of initiated cells in precancerous lesions and metastasis stem cells in cancer tissues.It has been proven that p16 methylation can be used as a diagnostic biomarker to determine malignant potential of epithelium dysplasia in many organs including the stomach.In a large-scale validation study on the DNA methylome of gastric carcinomas(GC),the methylation status of more than 90 CpG islands has been analyzed by DHPLC.Furthermore,GFRA1 demethylation and methylation of SRF and ZNF382 are frequent events during gastric carcinogenesis and consistently correlate to GC metastasis and overall survival of GC patients from China,Japan,and Korea,respectively.In a population study,it has been demonstrated that gradual increasing of plasma miR-211 and other miRNA levels may be an early risk predictor for GC development.
