Stephanie ByrumAssistant Professor

Member Arkansas Children’s Research Institute
Associate Member Winthrop P. Rockefeller Cancer Institute

Ph.D., University of Arkansas at Little Rock/University of Arkansas for Medical Sciences
MSc, University of Arkansas at Little Rock/University of Arkansas for Medical Sciences
B.S., Ouachita Baptist University

E-mail:  SByrum@uams.edu
Office:  (501) 686-5783 – Biomedical Research Center 1 B402
Lab: (501) 686-5194 – Biomedical Research Center 1 B410
FAX:  (501) 686-8169

 

Bioinformatics of breast cancer

Breast cancer is the most common malignancy in women and the second most common cause of cancer-related death in women. Breast cancers are subdivided into types based on the expression of three receptors that respond to estrogen, progesterone, and human epidermal growth factor. Targeted therapies are used clinically for treatment of cancers expressing one or more of these receptors. Breast cancers which lack expression of all three receptors are classified as triple-negative breast cancers (TNBC). Targeted therapies for TNBC do not currently exist, making these tumors the most difficult to treat. My research focus involves using a multi-omics approach to understand the mechanisms of TNBC.

My bioinformatics skill set includes: proteomics (label-free, stable isotope tags, SILAC, TMT-labeling, intensity-based analysis, metaproteomics), epigenetics (quantitation of histone posttranslational modifications and ATAC-seq), genomics (microarray, ChIP-seq, RNA-seq, miRNA-seq, DNA methylation), metagenomics, biostatistics and data mining, and pathway and functional analysis.

 

Selected Publications

 Washam CL, Byrum SD, Leitzel K, Ali SM, Tackett AJ, Gaddy D, Sundermann SE, Lipton A, Suva LJ. (2013). Identification of PTHrP(12-48) as a plasma biomarker associated with breast cancer bone metastasis. Cancer Epidemiol Biomarkers Prev. 22(5):972-83. PMID: 23462923. This work presents the first validated, plasma biomarker signature for diagnosis of breast cancer bone metastasis that may improve the early diagnosis of high-risk individuals.

Byrum SD, Raman A, Taverna SD, Tackett AJ. (2012). ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep. 2(1):198-205. PMID: 22840409. [Commentary in Nature 491:143-147. Highlighted in FASEB annual review of NIH funding in Arkansas.] In this first generation ChAP-MS (Chromatin Affinity Purification with Mass Spectrometry) approach, my group isolated a native 1 kb section of promoter chromatin and used mass spectrometry to unbiasedly identify bound proteins and histone posttranslational modifications. This was the first approach to perform such an analysis. The ChAP-MS approach is extremely powerful as one can now identify the proteins and histone posttranslational modifications at a specific section of chromatin.

Byrum SD, Taverna SD, Tackett AJ. (2013). Purification of a specific native genomic locus for proteomic analysis. Nucleic Acids Res. 41(20):e195. PMID: 24030711. In this second generation ChAP-MS approach, we circumvented the need for genomic engineering of a LexA DNA binding site by using PrA-tagged TALE proteins for enrichment. This TAL-ChAP-MS approach is applicable to any cellular system.

Byrum SD, Larson SK, Avaritt NL, Moreland LE, Mackintosh SG, Cheung WL, Tackett AJ. (2013). Quantitative proteomics identifies activation of hallmark pathways of cancer in patient melanoma. J Proteomics Bioinform. 6(3):43-50. PMID: 23976835. [Commentary in Genetic Engineering and Biotechnology News, March 1, 2013.] In this work we report the most comprehensive analysis of formalin-fixed paraffin-embedded human melanoma tissues using quantitative proteomics. Our results reveal that molecular pathways involved with tumor cell proliferation, motility, and apoptosis are mis-regulated in melanoma.

Pubmed link to additional publications

Systems Biology Bioinformatics Core