1000 Chicago Cancer Genome Project

Cancer is, at it heart, a genetic disease, driven by the acquisition of mutations in important genes.  Although these mutations produce cancer, recent results in several tumors suggest that these mutations may also represent cancer’s Achilles heel. Over the last several years, several new successful chemotherapeutic drugs have been developed that directly target specific cancer mutations.  Thus, the identification of mutations that drive carcinogenesis will allow the development of new, more effective therapies for cancer. However, these drugs only work in a small percentage of cancers.  Cancer is extremely complex and heterogeneous, and the identification of which mutations are present in a tumor and should be targeted by chemotherapeutic therapy is not obvious.

The recent development of novel “next-generation” sequencing technologies now make it possible to identify every mutation in a cancer cell.  Over the last 18 months, the Institute for Genomics and Systems Biology at the University of Chicago has developed significant experience in this emerging technology.  Thus, the IGSB, in conjunction with the University of Chicago Medical Center, is proud to announce the launch of the 1000 Cancer Transcriptomes Project.  Over the next 2 years, the IGSB and UCMC will sequence the transcriptomes of 1000 tumors at the UCMC.  We combine this data with a series of sophisticated analyses and high throughput experiments to identify new targets for therapy, in some of the most common and deadly cancers.

Metabolic Diseases and Diabetes

In partnership with the IGSB, Mark Ratain, MD (Department of Medicine, Section of Hematology / Oncology) and colleagues are analyzing genome wide variation in DNA sequence and gene expression in a large collection of human livers to discover patterns of genomic variation and expression. This comprehensive study, never before conducted, will provide the basis for evaluating potential outcomes of drug therapy in individual cancer patients.

About 75% of the top 200 drugs prescribed are eliminated from the body through the metabolic enzymes in the liver. In addition to receiving seed funding as part of the IGSB Metabolic Diseases and Diabetes Initiative, Ratain and colleagues are using the resources of the High Throughput Genome Analysis Core (HGAC) to perform their study.

As part of the same Initiative, Chris Rhodes, PhD (Department of Medicine, Section of Endocrinology, Diabetes and Metabolism) is performing drug and genome screening of insulin-secreting cells in the Celluar Screening Center (CSC) to identify therapies which promote insulin production in diabetes patients.

Inflammatory Bowel Disease

Eugene Chang, MD (Department of Medicine, Section of Gastroenterology) has partnered with IGSB Core Member Dion Antonopoulos, PhD (IGSB, Argonne) to sequence patient gut contents, containing thousands of different bacterial species, to determine the relationship between specific bacteria and inflammatory bowel disease.

This metagenomics project has been supported by seed funding from the Institute’s Inflammatory Bowel Disease Initiative and takes advantage of the next generation sequencing technology within the High-Throughput Genome Analysis Core (HGAC), as well as the computational expertise at Argonne.