Team #1: Genetics

Identifying Genetic Susceptibilities and the Genetic Profile of Therapy-Related Leukemias

Overview

Team 1 is developing a genetic profile of t-AML. Researchers are profiling the genetic signatures of both healthy and malignant cells from a large group of t-AML patients treated at the University of Chicago Medical Center and other institutions throughout the world. Their work will identify both the inherited genetic risk factors that make some cancer patients susceptible to t-AML, and the genetic mutations acquired during the development of t-AML. This information can be used to discover the altered cellular pathways responsible for producing malignant bloods cells in myeloid leukemia and to identify the subset of cancer patients at greatest risk for t-AML.

The Project In Detail

There is currently no effective treatment for t-AML. Much of what is known about t-AML is based on large-scale genetic abnormalities that have been found in the cancer genome. In this project, University of Chicago researchers are using cutting-edge technology to study DNA abnormalities that are specific to t-AML. The overall goal of this work, accomplished by profiling the DNA of both healthy and t-AML cells, is to understand the genetics of t-AML and, subsequently, identify the cause and treatments for this disease.

Profiling Genetic Susceptibility Factors
To identify genetic risk factors for t-AML, researchers are performing a genome-wide association study (GWAS), which is a research approach that involves scanning the entire human genome for genetic markers. These markers may include single nucleotide polymorphisms (SNPs), which are variations found at a single site in DNA sequence, and changes in gene copy number. Variations such as these may produce abnormal biological effects and be associated with an increased susceptibility to disease.

Team 1 is profiling healthy DNA from approximately 400 cases (t-AML patients) and 400 controls (patients with the same primary cancer but who did not develop t-AML). They are looking for genetic factors that differ between these two groups of patients. Any differences they find are likely to be associated with t-AML susceptibility. To accomplish this task, they are using microarray technology, specifically the Affymetrix Genome-Wide Human SNP Array, which is a glass slide that has been spotted with over 900,000 pieces of DNA containing unique SNPs. Samples from each patient are processed, tagged with fluorescent probes, and allowed to react with the slide. If the samples contain DNA sequence with SNPs, they will bind to the same SNP on the slide. Researchers can precisely measure the level of fluorescence at each SNP and generate a profile of SNPs contained in each sample. In the same manner, researchers can determine if variations in gene copy number exist.

SNPs or copy number variants that are associated with disease risk, i.e., those that are found in patients with t-AML but not control patients, will be used to develop a diagnostic panel to identify individuals who are at increased risk for developing t-AML. The information gathered from this project will also allow researchers to identify the specific therapeutic agents that put patients with these genetic factors at risk for the development of t-AML. Thus, these SNPs can additionally be used to guide the selection of an appropriate therapy to minimize disease risk.

Profiling New Mutations that are Acquired in t-AML
Scientists hypothesize that t-AML cells have genetic mutations in their DNA that cause leukemia and can serve as targets for new therapies. Team 1 is testing this hypothesis by using next-generation genome sequencing technology that enables rapid identification of genetic abnormalities. T-AMLs are excellent candidates for sequencing analysis because they are thought to arise as a direct result of DNA changes caused by the toxic effects of chemotherapy and radiation.

Next-generation sequencing is a cutting-edge technology that has revolutionized the ability of scientists to characterize the human (or cancer) genome. It has enabled researchers to read the genetic code significantly faster and cheaper than previous technologies. University of Chicago researchers are using Illumina technology, which involves the isolation of the 1% of DNA from leukemia cells that encodes for proteins. This portion of the genome is most likely to contribute to cancer. From this material, researchers build a library containing millions of pieces of DNA. These individual DNA molecules are bound to a small slide, generating a lawn of individual pieces of DNA. These pieces are amplified directly on the slide to create millions of clusters, each cluster containing about 1000 copies of the original DNA. To sequence them, fluorescently labeled nucleotides (the letters in the genetic code) are added sequentially, and a picture is taken for each letter. Each nucleotide has a unique color, so the colors are translated into the genetic code, allowing researchers to determine if genetic mutations exist.

Team 1 is profiling DNA mutations acquired during the development of leukemia by sequencing 50 t-AML patient samples. These mutations are thought to be responsible for the development of t-AML. Once a candidate group of mutations has been discovered, researchers will confirm their findings in a larger group of 100 t-AML patients. This information will allow scientists to identify pathways that are altered in t-AML, correlate DNA mutations with clinical outcome, identify clinical markers for the disease, and generate targets for new therapies.

Milestones

How does this Work Relate to the Work of Other Research Teams?

Members of Team 1 will work closely with Team 3 to identify SNPs that can predict response to therapy and be used as a guide to individualize treatment. Team 1 will also work with Team 4 to test the importance of newly-discovered mutations in the development of t-AML and with Team 5 to design new clinical trials.

Project-Related Activities & Publications

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