Genome-wide analysis of histone H3 lysine 27 trimethylation by ChIP-chip in gastric cancer patients
JOURNAL OF GASTROENTEROLOGY
Authors: Zhang, Li; Zhong, Keli; Dai, Yong; Zhou, Hanxin
Abstract
Trimethylation of histone H3 lysine 27 (H3K27me3) is a posttranslational modification that is highly correlated with genomic silencing. In gastric cancer (GC), global and gene-specific DNA methylation changes have been demonstrated to occur. However, to date, our understanding of the alterations in H3K27me3 in GC is incomplete. This study aimed to investigate the variations in H3K27me3 in CpG island regions between gastric cancerous and matched non-cancerous tissues. H3K27me3 variations were analyzed in eight pairs of GC and adjacent normal tissues, from eight GC patients, using a chromatin immunoprecipitation linked to the microarray (ChIP-chip) approach. ChIP-real time PCR was used to validate the microrray results. In addition, DNA methylation status also was further analyzed by methyl-DNA immunoprecipitation quantitative PCR. One hundred twenty-eight (119 increased and 9 decreased H3K27me3) genes displaying significant H3K27me3 differences were found between GC and adjacent normal tissues. The results of ChIP-real time PCR coincided well with those of microarray. Aberrant DNA methylation can also be found on selected randomly positive genes (MMP15, UNC5B, SHH, AFF3, and RB1). Our study indicates that there are significant alterations of H3K27me3 in gastric cancerous tissues, which may help clarify the molecular mechanisms involved in the pathogenesis of GC. Such novel findings show the significance of H3K27me3 as a potential biomarker or promising target for epigenetic-based GC therapies.
Detection of genes responsible for cetuximab sensitization in colorectal cancer cells using CRISPR-Cas9
BIOSCIENCE REPORTS
Authors: Hu, Ting-ting; Yang, Jia-wen; Yan, Ye; Chen, Ying-ying; Xue, Hai-bo; Xiang, You-qun; Ye, Le-chi
Abstract
Colorectal cancer (CRC) is a common malignant tumor in digestive tract with highly invasive and metastatic capacity. Drug sensitivity remains a significant obstacle to successful chemotherapy in CRC patients. The present study aimed to explore genes related to cetuximab (CTX) sensitivity in CRC by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Celigo image cytometer was used to detect suitable cells and optimal dosage of CTX. Inhibition rate of CTX on Caco-2 cells was evaluated by cell counting kit-8 (CCK-8) method before and after transfection. 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl tetrazolium bromide (MTT) was performed to explore suitable concentration of puromycin and multiplicity of infection (MOI). CRISPR-Cas9, sequencing data quality analysis and cell viability test were used for the selection of genes related to CTX sensitivity in CRC cells. Finally, the selected genes associated with CTX sensitivity in CRC cells were further validated by colony formation and CCK-8 assays. In the present study, Caco-2 cells had a better prolificacy, and CTX 100 mu g/ml exhibited a good inhibition trend on the 7th and 14th days of infection. MTT assay indicated that the minimum lethal concentration of puromycin was 2.5 mu g/ml. Forty-six candidate genes were preliminarily screened via sequencing data quality analysis. Subsequently, we found that knockout of any of the four genes (MMP15, MRPL48, CALN1 and HADHB) could enhance CTX sensitivity in Caco-2 cells, which was further confirmed by colony formation assay. In summary, MMP15, MRPL48, CALN1 and HADHB genes are related to the mediation of CTX sensitivity in CRC.