Medical Student Research Fellowship for Summer 2007

Mentor: David Euhus MD, Cheryl Lewis PhD
Department: Hamon Center for Therapeutic Oncology Research
Room number: NB8.220
Mail Code: 8593
Phone number: x84975
E-mail: david.euhus@utsouthwestern.edu, Cheryl.lewis@utsouthwestern.edu
Project title: Classification of DNA Methylation Patterns in Benign and Malignant Breast Epithelium

Human subjects IRB approved project number (where applicable): 072007-063

Animal subjects IRB approved project number (where applicable): N/A

Project Type (patient-based research, animal-based research, or basic research; this characterization is only to permit a general classification for grouping similar types of projects) patient-based research

Brief Description of Project:

The purpose of this study is to define and validate the optimal methylation marker panel for cell-based breast cancer risk stratification. There are three primary objectives that must be accomplished to achieve this goal.
Objective #1: Identify individual genes that are frequently methylated in benign breast epithelium from high risk women but rarely in benign breast epithelium from lower risk women.
Objective #2: Define the smallest possible panel of methylation markers that provides maximal discrimination between benign breast epithelium from high and lower risk women.
Objective #3: Validate the methylation panel defined in Objective #2 using an independent prospectively acquired sample set.

Techniques that will be learned by the summer student
1. Tissue culture of benign and malignant cells
2. Isolate of total RNA from cell lines
3. Isolation of total RNA from fine needle aspirations (FNA) of human breast cells
4. PAP staining
5. Use of a microscope
6. Exposure to cytological analysis of FNA samples
7. Experience with Microsoft Excel and Access databases
8. Primer design for PCR experiments
9. PCR
10. quantitative methylation specific PCR

Duties of the Summer Student
1. Isolate total RNA and genomic DNA from benign and malignant breast cell lines
2. Synthesize cDNA
3. Isolate total RNA from human FNA samples
4. PAP stain slides from FNA samples and
5. Count epithelial cells on PAP stained slides
6. Sodium bisulfite treatment of genomic DNA
7. Design and optimize a multiplex PCR reaction
8. Perform quantitative multiplex PCR reactions with clinical samples