We are using systematic experimental and computational approaches to map the molecular networks induced by DNA damage. Since DNA damage response pathways are conserved across eukaryotes, our studies are focused on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe-impacting our basic knowledge of the DNA damage response while keeping within species for which systems data are easily obtained. In our past five years of funding (NIH grant R01-ES14811), significant progress was made in mapping the architecture of transcriptional networks responding to DNA damage and in perturbing these networks to reveal their key state transitions. In the present proposal, we turn our attention to the global networks of DNA-damage-induced kinases and other signaling proteins.
Specific Aim 1 will use Epistatic MiniArray Profiling (E-MAP) to develop dynamic genetic interaction maps of signaling across a panel of ten diverse DNA damaging agents. Genetic interaction screens will be conducted among a core set of ~500 genes including all kinases, phosphatases, and transcription factors (TFs) in budding and fission yeast.
Specific Aim 2 will use expression profiling to identify functional interactions between kinases and TFs in response to DNA damage. Kinase/TF pairs that regulate similar damage-responsive genes will be investigated for functional association by seeking specific phosphorylation sites on the TF and exploring the functional consequences of TF phosphorylation on DNA repair.
Specific Aim 3 will seek to computationally integrate the interaction data to identify conserved network modules and to experimentally categorize these modules by their specific functions related to DNA repair. Network maps will be visualized and processed using Cytoscape and deposited in the CellCircuits database. Developing a comprehensive map of DNA-damage-induced genetic interactions will be critical for understanding the genetic polymorphisms that confer susceptibility to DNA damage. Such networks are also a predictive tool for synthetic lethality and epistasis in human cancer.

Public Health Relevance

We propose to develop a comprehensive genetic and physical interaction map of signal transduction in response to DNA damage. This map is a major biomedical resource which will be used to identify and target chemotherapeutic agents and their modulators.

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Research Project (R01)
Project #
5R01ES014811-09
Application #
8610920
Study Section
Special Emphasis Panel (ZRG1-BST-N (02))
Program Officer
Balshaw, David M
Project Start
2005-09-26
Project End
2016-01-31
Budget Start
2014-02-01
Budget End
2015-01-31
Support Year
9
Fiscal Year
2014
Total Cost
$545,162
Indirect Cost
$133,996
Name
University of California San Diego
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Srivas, Rohith; Shen, John Paul; Yang, Chih Cheng et al. (2016) A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol Cell 63:514-25
Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz et al. (2016) Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Syst 2:77-88
Hofree, Matan; Carter, Hannah; Kreisberg, Jason F et al. (2016) Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun 7:12096
Jaeger, Philipp A; McElfresh, Cameron; Wong, Lily R et al. (2015) Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments. Appl Environ Microbiol 81:5639-49
Han, Yixing; Gao, Shouguo; Muegge, Kathrin et al. (2015) Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights 9:29-46
Shen, John Paul; Srivas, Rohith; Gross, Andrew et al. (2015) Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget 6:35755-69
Choueiri, Michel B; Shen, John Paul; Gross, Andrew M et al. (2015) ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLoS One 10:e0126898
Raju, Sharat C; Hauff, Samantha J; Lemieux, Aaron J et al. (2015) Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma. Oral Oncol 51:470-5
Yan, Julia Fangfei; Kim, Hoguen; Jeong, Seul-Ki et al. (2015) Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. J Proteome Res 14:4995-5006
Lee, KiYoung; Sung, Min-Kyung; Kim, Jihyun et al. (2014) Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A 111:E3157-66

Showing the most recent 10 out of 34 publications