Identification of Tumor viruses using DTS and Proteomics
EMSL Project ID
47765
Abstract
The Chang/Moore laboratory, in collaboration with PNNL, was awarded new funding to pursue the discovery of novel cancer viruses in hematologic malignancies using a combination of genomic and proteomic approaches for both directed and unbiased data generation and comparison. The directed approach will survey a large panel of hematologic malignancies for the presence of the new human polymaviruses. The unbiased approach will use DTS to examine highly-selected gold-standard cases of EBV-negative post-transplant lymphoproliferative disorder (EN-PTLD) for presence of novel viral transcripts. High PHRED-equivalent sequencing of EN-PTLD tumors will be performed to identify novel viral transcripts. These data will be compared to DTS results on EBV-positive PTLD to confirm virus transcript detection and determine differential cellular gene expression patterns between EBV-negative and positive disease. Specific to PNNL’s contribution to this collaborative project, application of advanced LC-MS/MS proteomics capabilities at EMSL will be applied to whole EN-PTLD tissue samples with comparison of DTS transcripts and detected peptide sequence data from the same tissue samples that will allow a more precise subtraction of human sequence data in the identification of novel viruses present in tumors. In addition to EN-PTLD we will examine additional hematologic samples which have epidemiologic features suggestive of viral association. These including various AIDS associated lymphomas, EBV negative Hodgkin lymphomas, and malignant histiocytosis, This collaborative project expands on the initial LC-MS/MS centric proteomic application with the application of additional advanced separations and informatics approaches beyond the scope of the driving biomedical collaboration, and which are anticipated to provide novel and complementary data to the ongoing study.
Project Details
Start Date
2013-01-31
End Date
2013-09-30
Status
Closed
Released Data Link
Team
Principal Investigator