DNA Damage Mediated S and G2 Checkpoints in Human Embryonal Carcinoma Cells

For mouse embryonic stem (ES) cells, the importance of the S and G2 cell cycle checkpoints for genomic integrity is increased by the absence of the G1 checkpoint. We have investigated ionizing radiation (IR)-mediated cell cycle checkpoints in undifferentiated and retinoic acid-differentiated human embryonal carcinoma (EC) cells. Like mouse ES cells, human EC cells did not undergo G1 arrest after IR but displayed a prominent S-phase delay followed by a G2-phase delay. In contrast, although differentiated EC cells also failed to arrest at G1-phase after IR, they quickly exited S-phase and arrested in G2-phase. In differentiated EC cells, the G2-M-phase cyclin B1/CDC2 complex was upregulated after IR, but the G1-S-phase cyclin E and the cyclin E/CDK2 complex were expressed at constitutively low levels, which could be an important factor distinguishing DNA damage responses between undifferentiated and differentiated EC cells. S-phase arrest and expression of p21 could be inhibited by 7-hydroxystaurosporine, suggesting that the ataxia-telangiectasia and Rad-3-related-checkpoint kinase 1 (ATR-CHK1), and p21 pathways might play a role in the IR-mediated S-phase checkpoint in EC cells. IR-mediated phosphorylation of ataxia-telangiectasia mutated, (CHK1), and checkpoint kinase 2 were distinctly higher in undifferentiated EC cells compared with differentiated EC cells. Combined with the prominent S and G2 checkpoints and a more efficient DNA damage repair system, these mechanisms operate together in the maintenance of genome stability for EC cells. Stem Cells 2009;27:568–57

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival

Additional file 12: Table S11. of Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

Primers for expression analysis in zebrafish. (XLSX 9 kb

Additional file 11: Table S10. of Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

gRNA and primers for zebrafish knockout and T7E1 assay. (XLSX 9 kb

Additional file 11: Table S10. of Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

gRNA and primers for zebrafish knockout and T7E1 assay. (XLSX 9 kb