Institute for Refractory Cancer Research (IRCR) Data Access Committee

Dac ID Contact Person Email Access Information
EGAC00001000272 Jason Kyungha Sa js2dark [at] gmail [dot] com No additional information is available

This DAC controls 6 datasets:

Dataset ID Description Technology Samples
EGAD00001001424 We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases). Illumina HiSeq 2000,Illumina HiSeq 2500 141
EGAD00001002143 We expanded our previous collection of longitudinal GBM patients (EGAS00001001041) by recruiting 21 additional patients. Tumor specimens were subjected to whole-exome sequencing (16 of 21 cases, with the matched normal/blood) and transcriptome sequencing (16 of 21 cases). Illumina HiSeq 2500 86
EGAD00001002248 Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors. Illumina HiSeq 2500 104
EGAD00001002249 Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA). Illumina HiSeq 2500 355
EGAD00001003441 Total of 584 tumor specimens and/or patient-derived cells across 14 cancer types were subjected for whole-exome/targeted-exome and/or whole-transcriptome sequencing. Illumina HiSeq 2500 584
EGAD00001004862 Glioblastoma multiforme (GBM) is clinically highly aggressive as a result of evolutionary dynamics induced by cross-talk between cancer cells and a heterogeneous group of immune cells in tumor microenvironment. The brain harbors limited numbers of immune cells with few lymphocytes and macrophages; thus, innate‐like lymphocytes, such as γδ T cells, have important roles in antitumor immunity. Here, we characterized GBM‐infiltrating γδ T cells, which may have roles in regulating the GBM tumor microenvironment and cancer cell gene expression. V(D)J repertoires of tumor‐infiltrating and blood‐circulating γδ T cells from four patients were analyzed by next-generation sequencing-based T-cell receptor (TCR) sequencing in addition to mutation and immune profiles in four GBM cases. In all tumor tissues, abundant innate and effector/memory lymphocytes were detected, accompanied by large numbers of tumor‐associated macrophages and closely located tumor‐infiltrating γδ T cells, which appear to have anti-tumor activity. The immune-related gene expression analysis using the TCGA database showed that the signature gene expression extent of γδ T cells were more associated with those of cytotoxic T and Th1 cells and M1 macrophages than those of Th2 cells and M2 macrophages. Although the most abundant γδ T cells were Vγ9Vδ2 T cells in both tumor tissues and blood, the repertoire of intratumoral Vγ9Vδ2 T cells was distinct from that of peripheral blood Vγ9Vδ2 T cells and was dominated by Vγ9Jγ2 sequences, not by canonical Vγ9JγP sequences that are mostly commonly found in blood γδ T cells. Collectively, unique GBM‐specific TCR clonotypes were identified by comparing TCR repertoires of peripheral blood and intra‐tumoral γδ T cells. These findings will be helpful for the elucidation of tumor-specific antigens and development of anticancer immunotherapies using tumor-infiltrating γδ T cells. Illumina HiSeq 2500 18