STRUCTURAL AND FUNCTIONAL GENOMICS ABSTRACT The goals of the Structural and Functional Genomics Program (SFG) are aligned and integrated with the vision and strategies of Moores Cancer Center (MCC) and the UC San Diego School of Medicine. They use the SFG members? interdisciplinary strength and expertise in computational biology and genomics to employ a full range of both structural and functional genomic data to elucidate complex signaling pathways and identify candidate targets and compounds that can be translated into novel diagnostic and therapeutic targets and clinical interventions. Approved by the NCI in 1997, the Cancer Genetics Program has evolved to SFG to reflect how, during the past project period, members have expanded use of multi-omic data types, moved analysis methods to molecular tumor boards, and elucidated context-dependent molecular states for more targeted treatments. SFG has 36 members from 14 academic departments with $19.2M of peer-reviewed research grant funding (annual direct costs), $6.3M (33%) of which is from the NCI. SFG members published 714 programmatically aligned articles since 2013, 11% were the result of intra-programmatic collaborations, 20% were inter-programmatic, and 34% were inter-NCI Cancer Center. SFG?s specific aims are to: 1) develop innovative, integrative computational genomic methods that synthesize multi-omic patient and clinical data to drive fundamental and translational cancer research and to disseminate them to the broader cancer research community; 2) analyze genetic, transcriptomic, epigenetic, proteomic, immunologic, and metabolomic data to elucidate the underlying biological pathways and mechanisms of cancer development and progression; and 3) characterize context dependent, functional states of tumor cells and understand the dynamics of resistance in order to identify novel diagnostic, prognostic, and therapeutic strategies, including combination therapies. SFG themes are data science and machine learning, signature and network approaches, and precision therapy. SFG is co-led by Joseph Califano, a head and neck surgeon and translational researcher who applies genomics to develop novel prognostic indicators and therapies and Jill Mesirov, a computational biologist who analyzes complex genome-scale cancer datasets to better understand the underlying mechanisms of cancer, stratify patients, and identify candidate therapies. Their complementary expertise and highly integrated efforts foster collaboration among the outstanding SFG investigators who are leaders in their fields with track records of extraordinary productivity and inter- programmatic collaborations among the MCC research programs. As a result, SFG members have conducted paradigm-shifting studies defining the broad role of extrachromosomal DNA in human cancers, developed carcinogen-based mutational signatures across cancer types, demonstrated the role of the microbiome in hepatocellular cancer development, and produced and maintained key computational methods and tools used by hundreds of thousands of scientists worldwide.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
2P30CA023100-33
Application #
9703597
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
2019-05-01
Budget End
2020-04-30
Support Year
33
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of California, San Diego
Department
Type
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Singh, Siddharth; Loomba, Rohit (2018) Role of two-dimensional shear wave elastography in the assessment of chronic liver diseases. Hepatology 67:13-15
Hartman, Sheri J; Nelson, Sandahl H; Myers, Emily et al. (2018) Randomized controlled trial of increasing physical activity on objectively measured and self-reported cognitive functioning among breast cancer survivors: The memory & motion study. Cancer 124:192-202
Hoffmann, Hanne M; Gong, Ping; Tamrazian, Anika et al. (2018) Transcriptional interaction between cFOS and the homeodomain-binding transcription factor VAX1 on the GnRH promoter controls Gnrh1 expression levels in a GnRH neuron maturation specific manner. Mol Cell Endocrinol 461:143-154
Liu, Xuxiang; Cao, Minghui; Palomares, Melanie et al. (2018) Metastatic breast cancer cells overexpress and secrete miR-218 to regulate type I collagen deposition by osteoblasts. Breast Cancer Res 20:127
Huang, Justin K; Carlin, Daniel E; Yu, Michael Ku et al. (2018) Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst 6:484-495.e5
Kalyanaraman, Hema; Schwaerzer, Gerburg; Ramdani, Ghania et al. (2018) Protein Kinase G Activation Reverses Oxidative Stress and Restores Osteoblast Function and Bone Formation in Male Mice With Type 1 Diabetes. Diabetes 67:607-623
Hartman, Sheri J; Marinac, Catherine R; Cadmus-Bertram, Lisa et al. (2018) Sedentary Behaviors and Biomarkers Among Breast Cancer Survivors. J Phys Act Health 15:1-6
Wu, Yan; Tamayo, Pablo; Zhang, Kun (2018) Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. Cell Syst 7:656-666.e4
Dow, Michelle; Pyke, Rachel M; Tsui, Brian Y et al. (2018) Integrative genomic analysis of mouse and human hepatocellular carcinoma. Proc Natl Acad Sci U S A 115:E9879-E9888
Que, Xuchu; Hung, Ming-Yow; Yeang, Calvin et al. (2018) Oxidized phospholipids are proinflammatory and proatherogenic in hypercholesterolaemic mice. Nature 558:301-306

Showing the most recent 10 out of 862 publications