Project description:With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number alterations (CNAs) and uniparental disomies (UPDs) . Here we identified somatic mutations by whole-exome sequencing in 25 NKTCL patients and extended validation through targeted sequencing in an additional 80 cases.
Project description:Natural killer/T-cell lymphoma (NKTCL) is a malignant proliferation of CD56+/cytoCD3+ lymphocytes and constitutes a heterogeneous group of aggressive lymphomas prevalent in Asian and South American populations. Molecular pathogenesis of NKTCL remains largely elusive. Here we identified somatic mutations in RNA helicase gene DDX3X. Gene expression profiling revealed an association of DDX3X mutations with activation of NF-kB and MAPK pathways. Together, our work suggests the heterogeneity of gene mutational spectrum in NKTCL.
Project description:Through whole-exome sequencing we identified somatic missense mutations in DICER1 and DROSHA in Wilms tumor, a childhood kidney cancer. DICER1 and DROSHA are key enzymes in the microRNA biogenesis pathway. To determine the effect of these mutations on microRNA expression, we prepared small RNAs from Wilms tumors and used next-generation sequencing to determine the expression levels of microRNAs in the tumors. Comparison of miRNA expression in tumors with and without mutations in DICER1 or DROSHA.
Project description:Through whole-exome sequencing we identified somatic missense mutations in DICER1 and DROSHA in Wilms tumor, a childhood kidney cancer. DICER1 and DROSHA are key enzymes in the microRNA biogenesis pathway. To determine the effect of these mutations on microRNA expression, we prepared small RNAs from Wilms tumors and used next-generation sequencing to determine the expression levels of microRNAs in the tumors.
Project description:Background The identification and characterization of somatic cancer driver mutations in the noncoding genome remains challenging.
Objective To broadly characterize noncoding driver mutations for pancreatic ductal adenocarcinoma (PDAC).
Design Using mutation calls from whole-genome sequence (WGS) data in PDACs and genome-scale maps of accessible gene regulatory regions in normal- and tumor-derived pancreatic samples, we analyzed enrichment of noncoding mutations in gene regulatory regions relevant to normal- and tumor-derived pancreatic contexts. Functional follow up of potential driver mutations was performed using chromatin interaction analyses, massively parallel reporter assays (MPRA) and targeted analysis of selected noncoding somatic mutations.
Results We first created genome-scale maps of accessible chromatin regions (ACRs) and histone modification marks (HMMs) in pancreatic cell lines and purified pancreatic acinar and duct cells. Integration with whole-genome mutation calls from 506 PDACs revealed 314 ACRs/HMMs significantly enriched with 3,614 noncoding somatic mutations (NCSMs). Chromatin interaction analysis identified 416 potential target genes and MPRA revealed 178 NCSMs impacting reporter activity (19.45% of those tested). Targeted luciferase validation confirmed negative effects on gene regulatory activity for NCSMs near ZFP36L2 and CDKN2A. For the former, CRISPR interference (CRISPRi) identified ZFP36L2 as a target gene (16.0 - 24.0% reduced expression, P = 0.023-0.0047), and growth inhibition after overexpression of ZFP36L2 (4.1 - 14.1-fold reduction, P = 6.0x10-4 - 3.2x10-3) implicates a possible tumor suppressor function.
Conclusion Our integrative approach provides a catalog of potential noncoding driver mutations and nominates ZFP36L2 as a novel PDAC driver gene with a likely tumor suppressor function.
Project description:We report a novel approach to identify genome-wide somatic hypermutation hotspots from short Illumina H3K4me3 ChIPseq reads in diffuse large B-cell lymphoma cells (DLBCL). Abberant somatic hypermation are known to occur at the promoters of several proto-oncogenes in DLBCL. To identify such events genome-wide, we performed H3K4me3 ChIPseq experiments (as to enrich promoter sequences of actively transcribed genes) in 2 DLBCL cells lines (OCI-Ly1 and OCI-Ly8) and their normal B-cell counterparts, Naive B cells (NBC) and Germinal Center B cells (GCBs). We discover new genes that harbor mutations in their promoter regions that are potentially introduced by the aberrant activation-induced cytosine deaminase activity in lymphoma cell lines, and many of these genes are important for the B cell biology. Moreover, we show that these mutations can affect the activities of these promoters. Our study provides a feasible approach for the detection of promoter mutations and broadens our knowledge on promoter mutations in lymphomas.
Project description:We report a novel approach to identify genome-wide somatic hypermutation hotspots from short Illumina H3K4me3 ChIPseq reads in diffuse large B-cell lymphoma cells (DLBCL). Abberant somatic hypermation are known to occur at the promoters of several proto-oncogenes in DLBCL. To identify such events genome-wide, we performed H3K4me3 ChIPseq experiments (as to enrich promoter sequences of actively transcribed genes) in 2 DLBCL cells lines (OCI-Ly1 and OCI-Ly8) and their normal B-cell counterparts, Naive B cells (NBC) and Germinal Center B cells (GCBs). We discover new genes that harbor mutations in their promoter regions that are potentially introduced by the aberrant activation-induced cytosine deaminase activity in lymphoma cell lines, and many of these genes are important for the B cell biology. Moreover, we show that these mutations can affect the activities of these promoters. Our study provides a feasible approach for the detection of promoter mutations and broadens our knowledge on promoter mutations in lymphomas. Examination of 1 histone mark (H3K4me3) in 4 different cell types.