Sara Cooper Lab
Using genomic technologies for better care
The Sara Cooper Lab uses metabolomics and genomics to explore and understand human disease with an emphasis on cancer. We apply functional genomics, including statistical analysis, with the ultimate goal of identifying signatures associated with human disease pathology, progression, and therapeutic response and then implementing those signatures in a clinical setting. We analyze human samples, such as tumor tissue or blood, to identify signatures associated with disease, and then we transition to cell-based models to further refine and understand the signatures. We partner with clinicians, including close collaborators at the University of Alabama Birmingham, to identify the most important clinical problems and aim to develop clinically useful signatures using various technologies including RNA-sequencing, DNA methylation measurements, small RNA sequencing and metabolomics. Examples of ongoing and recent work include the identification of gene expression signatures associated with patient survival in pancreatic cancer (Kirby 2016), identification of gene expression signatures of cellular proliferation and development of an analytical approach to understanding the role for that signature in predicting patient survival across cancer (Ramaker 2016), and an integrated metabolomic and genomic study of post-mortem brain tissue to understand molecular changes in neuropsychiatric disease (Ramaker 2017).
Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM. RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4. Molecular Oncology October 2016:1160-1182. PMID: 27282075.
Ramaker RC, Lasseigne BN, Hardigan AA, Palacio L, Gunther DS, Myers RM, Cooper SJ. RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature. Oncotarget. 2017 Jun 13;8(24):38668-38681. PMID: 28454104.
Ramaker RC, Bowling KM, Lasseigne BN, Hagenauer MH, Hardigan AA, Davis NS, Gertz J, Cartagena PM, Walsh DM, Vawter MP, Jones EG, Schatzberg AF, Barchas JD, Watson SJ, Bunney BG, Akil H, Bunney WE, Li JZ, Cooper SJ, Myers RM. Post-mortem molecular profiling of three psychiatric disorders reveals widespread dysregulation of cell-type associated transcripts and refined disease-related transcription changes. Genome Medicine 2017 9:72. PMID: 28754123.
The Cooper Lab is supported in part by the National Institutes of Health under Award Number UL1TR001417, the Breast Cancer Research Foundation of Alabama, and the UAB-HudsonAlpha Center for Genomic Medicine. The content of this website is solely the responsibility of the authors and does not necessarily represent the official views of the sponsors.