Stephanie D Byrum, PhD

Research Program: Cancer Biology Faculty Rank: Associate Professor Campus: University of Arkansas for Medical Sciences College: College of Medicine Department: Biochemistry & Molecular Biology

Cancer Research Interest

• Disease Site Focus: Breast, Cutaneous/Melanoma
• Research Focus Area: Informatics, Carcinogenesis, Diagnosis/ Prognosis
• Type of Research: Basic
• Research Interest Statement: My research focus involves a translational approach for the identification of cancer systems biology, from the bench to the bedside. I have performed experiments ranging from collecting patient samples, to performing proteomic and genomic analyses, using bioinformatics to mine large complex data sets, and identify important clinical markers for metastatic breast cancer and melanoma. I have formal training in bioinformatics and mass spectrometry. Additionally, I direct the Arkansas Children’s Center for Translational Pediatric Research Systems Biology Bioinformatics Core. 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 chromatin remodelers), genomics (microarray, ChIP-seq, RNA-seq, miRNA-seq, DNA methylation), metagenomics, biostatistics and data mining, and pathway and functional analysis. My overall research goal is to discover therapeutic targets for breast cancer using a systems biology approach.

Contact Information

• Email Address: SBYRUM@UAMS.EDU
• Profiles Research Networking Software: View Profile

Active Grants

• NIH/Nat. Inst. of Diabetes & Digestive & Kidney Diseases – 1R01DK139476
  “Molecular mechanisms of pituitary plasticity”
  Co-Investigator
  9/18/2024 – 5/31/2029
• NIH/Nat. Inst. of General Medical Sciences – 1R01GM141040
  “Discovery and Characterization of Novel Sepsis Proteome Biomarkers”
  Co-Investigator
  9/10/2021 – 8/31/2025
• NIH/Nat. Inst. of Diabetes & Digestive & Kidney Diseases – 1R01DK127723
  “The Impact of Obesity on Somatotrope Function”
  Co-Investigator
  7/1/2021 – 6/30/2025

Recent Publications

• Richardson KK, Adam GO, Ling W, [et al., including Byrum SD]. Mitochondrial protein deacetylation by SIRT3 in osteoclasts promotes bone resorption with aging in female mice. Molecular metabolism. 2024 88:102012. PMID: 39154858. PMCID: PMC11399565.
• O'Connell KA, Kopchick B, Carlson T, [et al., including Byrum SD]. Understanding proteome quantification in an interactive learning module on Google Cloud Platform. Briefings in bioinformatics. 2024 25(Supplement_1). PMID: 39041914. PMCID: PMC11264296.
• Hong A, Piva M, Liu S, [et al., including Byrum SD]. Expression of Concern: Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Antitumor T-cell Immunity. Cancer discovery. 2024 14(7):1357. PMID: 38946326.
• Choudhury SR, Byrum SD, Blossom SJ. Trichloroethylene metabolite modulates DNA methylation-dependent gene expression in Th1 polarized CD4+ T cells from autoimmune-prone mice. Toxicological sciences : an official journal of the Society of Toxicology. 2024. PMID: 38518092. PMCID: PMC11131021.
• Chappell K, Byrum SD. Understanding PTM Cross Talk Through a Visualization Tool, PTMViz. Methods in molecular biology (Clifton, N.J.). 2024 2836:57-65. PMID: 38995535.
• Miles TK, Odle AK, Byrum SD, [et al.]. Anterior Pituitary Transcriptomics Following a High-Fat Diet: Impact of Oxidative Stress on Cell Metabolism. Endocrinology. 2023 165(2). PMID: 38103263. PMCID: PMC10771268.
• Zhao S, Lu J, Pan B, [et al., including Byrum SD]. TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons. Nature. 2023 623(7987):633-642. PMID: 37938770. PMCID: PMC11000523.
• McCrury M, Swafford K, Shuttleworth SL, [et al., including Byrum SD]. Bifunctional inhibitor reveals NEK2 as a therapeutic target and regulator of oncogenic pathways in lymphoma. Molecular cancer therapeutics. 2023. PMID: 37816504. PMCID: PMC10932871.
• Garg S, Morehead LC, Bird JT, [et al., including Byrum SD]. Characterization of methionine dependence in melanoma cells. Molecular omics. 2023. PMID: 37782107. PMCID: PMC10903584.
• Todorova VK, Byrum SD, Mackintosh SG, [et al.]. Exosomal MicroRNA and Protein Profiles of Hepatitis B Virus-Related Hepatocellular Carcinoma Cells. International journal of molecular sciences. 2023 24(17). PMID: 37685904. PMCID: PMC10487651.
• Chen M, Li J, Zhang L, [et al., including Byrum SD]. CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins. Nucleic acids research. 2023 51(14):7288-7313. PMID: 37378433. PMCID: PMC10415139.
• Moreira ARS, Lim J, Urbaniak A, [et al., including Byrum SD]. Musashi Exerts Control of Gonadotrope Target mRNA Translation During the Mouse Estrous Cycle. Endocrinology. 2023 164(9). PMID: 37477898. PMCID: PMC10402870.
• Seman A, Chandra PK, Byrum SD, [et al.]. Targeting mitochondria in the aged cerebral vasculature with SS-31, a proteomic study of brain microvessels. GeroScience. 2023. PMID: 37458933. PMCID: PMC10643806.
• Venugopal G, Bird JT, Roys H, [et al., including Byrum SD]. BOTH THE INFECTION STATUS AND INFLAMMATORY MICROENVIRONMENT INDUCE TRANSCRIPTIONAL REMODELING IN MACROPHAGES IN MURINE LEISHMANIAL LESIONS. The Journal of parasitology. 2023 109(3):200-210. PMID: 37270767.
• Sun RW, Zhang H, Mehdi SJ, [et al., including Byrum SD]. Upregulated MicroRNA-21 Drives the Proliferation of Lymphatic Malformation Endothelial Cells by Inhibiting PDCD4. The Journal of investigative dermatology. 2023. PMID: 37088278. PMCID: PMC10524134.
• Wong L, Randolph C, Kanwischer E, [et al., including Byrum SD]. Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced. Microbiology resource announcements. 2023 12(3):e0000723. PMID: 36779742. PMCID: PMC10019291.
• Avaritt NL, Byrum SD. Cutting-Edge Technologies Driving Quantitative Mass Spectrometry. Journal of visualized experiments : JoVE. 2023(193). PMID: 37602860.
• Choudhury S, Byrum SD, Alkam D, [et al.]. Expression of integrin β-7 is epigenetically enhanced in multiple myeloma subgroups with high-risk cytogenetics. Clinical epigenetics. 2023 15(1):18. PMID: 36737807. PMCID: PMC9898982.
• Flores VV, Hernandez Gifford JA, Soto-Navarro SA, [et al., including Byrum SD]. Calves severely affected by bovine respiratory disease have reduced protection against histone toxicity and exhibit lower complement activity. Journal of animal science. 2023 101. PMID: 37410397. PMCID: PMC10347967.
• Batts TL, Sasaki E, Miller M, [et al., including Byrum SD]. Neoplastic signatures: Comparative proteomics of canine hepatobiliary neuroendocrine tumors to normal niche tissue. PloS one. 2023 18(1):e0280928. PMID: 36696389. PMCID: PMC9876354.
• Liu S, Wu J, Stolarz A, [et al., including Byrum SD]. PCSK9 attenuates efferocytosis in endothelial cells and promotes vascular aging. Theranostics. 2023 13(9):2914-2929. PMID: 37284459. PMCID: PMC10240829.
• Miles TK, Allensworth-James ML, Odle AK, [et al., including Byrum SD]. Maternal undernutrition results in transcript changes in male offspring that may promote resistance to high fat diet induced weight gain. Frontiers in endocrinology. 2023 14:1332959. PMID: 38720938. PMCID: PMC11077627.
• Scieszka D, Byrum SD, Mackintosh SG, [et al.]. Subchronic Electronic Cigarette Exposures Have Overlapping Protein Biomarkers with Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. American journal of respiratory cell and molecular biology. 2022 67(4):503-506. PMID: 36178855. PMCID: PMC9564931.
• Venugopal G, Bird JT, Washam CL, [et al., including Byrum SD]. In vivo transcriptional analysis of mice infected with Leishmania major unveils cellular heterogeneity and altered transcriptomic profiling at single-cell resolution. PLoS neglected tropical diseases. 2022 16(7):e0010518. PMID: 35789215. PMCID: PMC9286232.
• Barbosa P, Landes RD, Graw S, [et al., including Byrum SD]. Effect of excess weight and insulin resistance on DNA methylation in prepubertal children. Scientific reports. 2022 12(1):8430. PMID: 35589784. PMCID: PMC9120504.
• Li D, Yu X, Kottur J, [et al., including Byrum SD]. Discovery of a dual WDR5 and Ikaros PROTAC degrader as an anti-cancer therapeutic. Oncogene. 2022. PMID: 35525905. PMCID: PMC9189076.
• Kaufmann Y, Byrum SD, Acott AA, [et al.]. Proteomic profiling of tear fluid as a promising non-invasive screening test for colon cancer. American journal of surgery. 2022. PMID: 35354531.
• Lin VJT, Hu J, Zolekar A, [et al., including Byrum SD]. Deficiency of N-glycanase 1 perturbs neurogenesis and cerebral development modeled by human organoids. Cell death & disease. 2022 13(3):262. PMID: 35322011. PMCID: PMC8942998.
• Vazquez JH, Kennon-McGill S, Byrum SD, [et al.]. Proteomics Indicates Lactate Dehydrogenase Is Prognostic in Acetaminophen-Induced Acute Liver Failure Patients and Reveals Altered Signaling Pathways. Toxicological sciences : an official journal of the Society of Toxicology. 2022. PMID: 35172013. PMCID: PMC9216044.
• Todorova VK, Byrum SD, Gies AJ, [et al.]. Circulating Exosomal microRNAs as Predictive Biomarkers of Neoadjuvant Chemotherapy Response in Breast Cancer. Current oncology (Toronto, Ont.). 2022 29(2):613-630. PMID: 35200555. PMCID: PMC8870357.
• Richardson KK, Ling W, Krager K, [et al., including Byrum SD]. Ionizing Radiation Activates Mitochondrial Function in Osteoclasts and Causes Bone Loss in Young Adult Male Mice. International journal of molecular sciences. 2022 23(2). PMID: 35054859. PMCID: PMC8775597.
• Robeson MS 2nd, Manna K, Randolph C, [et al., including Byrum S]. Short-Term Metformin Treatment Enriches Bacteroides dorei in an Obese Liver Steatosis Zucker Rat Model. Frontiers in microbiology. 2022 13:834776. PMID: 35432282. PMCID: PMC9006818.
• Zhang Y, Gabere M, Taylor MA, [et al., including Byrum SD]. Repurposing live attenuated trivalent MMR vaccine as cost-effective cancer immunotherapy. Frontiers in oncology. 2022 12:1042250. PMID: 36457491. PMCID: PMC9706410.
• Zuniga O, Byrum S, Wolfe AR. Discovery of the inhibitor of DNA binding 1 as a novel marker for radioresistance in pancreatic cancer using genome-wide RNA-seq. Cancer drug resistance (Alhambra, Calif.). 2022 5(4):926-938. PMID: 36627902. PMCID: PMC9771737.
• Chau MJ, Quintero JE, Blalock E, [et al., including Byrum S]. Transection injury differentially alters the proteome of the human sural nerve. PloS one. 2022 17(11):e0260998. PMID: 36417411. PMCID: PMC9683555.
• Bettadapura M, Roys H, Bowlin A, [et al., including Byrum SD]. HIF-α Activation Impacts Macrophage Function during Murine Leishmania major Infection. Pathogens (Basel, Switzerland). 2021 10(12). PMID: 34959539. PMCID: PMC8706659.
• Rosa F, Zybailov BL, Glazko GV, [et al., including Byrum S]. Milk Formula Diet Alters Bacterial and Host Protein Profile in Comparison to Human Milk Diet in Neonatal Piglet Model. Nutrients. 2021 13(11). PMID: 34835974. PMCID: PMC8618976.
• Paidi SK, Troncoso JR, Raj P, [et al., including Byrum SD]. Raman Spectroscopy and Machine Learning Reveals Early Tumor Microenvironmental Changes Induced by Immunotherapy. Cancer research. 2021. PMID: 34645610. PMCID: PMC8841097.
• Delgado M, Washam CL, Urbaniak A, [et al., including Byrum SD]. Phosphoproteomics Provides Novel Insights into the Response of Primary Acute Lymphoblastic Leukemia Cells to Microtubule Depolymerization in G1 Phase of the Cell Cycle. ACS omega. 2021 6(38):24949-24959. PMID: 34604676. PMCID: PMC8482483.
• Xu C, Meng F, Park KS, [et al., including Byrum SD]. A NSD3-targeted PROTAC suppresses NSD3 and cMyc oncogenic nodes in cancer cells. Cell chemical biology. 2021. PMID: 34469831. PMCID: PMC8882712.
• Wang Y, Liu S, Yang Z, [et al., including Byrum SD]. Anti-PD-1/L1 lead-in before MAPK inhibitor combination maximizes antitumor immunity and efficacy. Cancer cell. 2021. PMID: 34416167. PMCID: PMC9126729.
• Ahn JH, Davis ES, Daugird TA, [et al., including Byrum SD]. Phase separation drives aberrant chromatin looping and cancer development. Nature. 2021. PMID: 34163069. PMCID: PMC8647409.
• Chappell K, Tackett A, Manna K, [et al., including Byrum SD]. Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer. Molecular omics. 2021. PMID: 34142686. PMCID: PMC8504614.
• Brown T, Boerma M, McElroy T, [et al., including Byrum SD]. Cognitive impairment resulting from treatment with docetaxel, doxorubicin, and cyclophosphamide. Brain research. 2021 1760:147397. PMID: 33705788. PMCID: PMC9179831.
• Reed MR, Maddukuri L, Ketkar A, [et al., including Byrum SD]. Inhibition of tryptophan 2,3-dioxygenase impairs DNA damage tolerance and repair in glioma cells. NAR cancer. 2021 3(2):zcab014. PMID: 33870196. PMCID: PMC8034706.
• Chappell K, Graw S, Washam CL, [et al., including Byrum SD]. PTMViz: a tool for analyzing and visualizing histone post translational modification data. BMC bioinformatics. 2021 22(1):275. PMID: 34039258. PMCID: PMC8157737.
• Fan H, Guo Y, Tsai YH, [et al., including Byrum SD]. A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. Nucleic acids research. 2021 49(8):4441-4455. PMID: 33823544. PMCID: PMC8096256.
• Schinke CD, Boerma M, Bird JT, [et al., including Byrum SD]. PHF19 inhibition as a therapeutic target in multiple myeloma. Current research in translational medicine. 2021 69(3):103290. PMID: 33894670. PMCID: PMC8316274.
• Xu C, Tsai YH, Galbo PM, [et al., including Byrum SD]. Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer. Nucleic acids research. 2021. PMID: 33849067. PMCID: PMC8136773.
• Allensworth-James M, Banik J, Odle A, [et al., including Byrum SD]. Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi. Endocrinology. 2021 162(3). PMID: 33570120.
• Allensworth-James M, Banik J, Odle A, [et al., including Byrum SD]. Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi. Endocrinology. 2021 162(3). PMID: 33373440. PMCID: PMC7814296.
• Jenkins SV, Alimohammadi M, Terry AS, [et al., including Byrum SD]. Dysbiotic stress increases the sensitivity of the tumor vasculature to radiotherapy and c-Met inhibitors. Angiogenesis. 2021. PMID: 33629198. PMCID: PMC8295215.
• Wallis KF, Morehead LC, Bird JT, [et al., including Byrum S]. Differences in cell death in methionine versus cysteine depletion. Environmental and molecular mutagenesis. 2021. PMID: 33615565. PMCID: PMC8130902.
• Li J, Galbo PM Jr, Gong W, [et al., including Byrum SD]. ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism. Nature communications. 2021 12(1):1045. PMID: 33594072. PMCID: PMC7886901.
• Groves T, Corley C, Byrum SD, Allen AR. The Effects of 5-Fluorouracil/Leucovorin Chemotherapy on Cognitive Function in Male Mice. Frontiers in molecular biosciences. 2021 8:762116. PMID: 34778377. PMCID: PMC8581634.
• Graw S, Tackett A, Chappell K, [et al., including Byrum SD]. Multi-omics data integration considerations and study design for biological systems and disease. Molecular omics. 2020. PMID: 33347526. PMCID: PMC8058243.
• Hong A, Piva M, Liu S, [et al., including Byrum SD]. Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Antitumor T-cell Immunity. Cancer discovery. 2020. PMID: 33318037. PMCID: PMC7933113.
• Xu YZ, Jenjaroenpun P, Wongsurawat T, [et al., including Byrum SD]. Activation-induced cytidine deaminase localizes to G-quadruplex motifs at mutation hotspots in lymphoma. NAR cancer. 2020 2(4):zcaa029. PMID: 33094287. PMCID: PMC7556405.
• Ramirez AM, Beenken KE, Byrum SD, [et al.]. SarA plays a predominant role in controlling the production of extracellular proteases in the diverse clinical isolates of Staphylococcus aureus LAC and UAMS-1. Virulence. 2020 11(1):1738-1762. PMID: 33258416. PMCID: PMC7738309.
• Garcia M, Salazar R, Wilson T, [et al., including Byrum S]. Early Gestational Exposure to Inhaled Ozone Impairs Maternal Uterine Artery and Cardiac Function. Toxicological sciences : an official journal of the Society of Toxicology. 2020. PMID: 33146391. PMCID: PMC8453811.
• Graw S, Tang J, Zafar MK, [et al., including Byrum SD]. proteiNorm - A User-Friendly Tool for Normalization and Analysis of TMT and Label-Free Protein Quantification. ACS omega. 2020 5(40):25625-25633. PMID: 33073088. PMCID: PMC7557219.
• Koss B, Boerma M, Shields BD, [et al., including Byrum SD]. Epigenetic Control of Cdkn2a.Arf Protects Tumor-Infiltrating Lymphocytes from Metabolic Exhaustion. Cancer research. 2020. PMID: 33004350. PMCID: PMC7642172.
• Mao XW, Nishiyama NC, Byrum SD, [et al.]. Spaceflight induces oxidative damage to blood-brain barrier integrity in a mouse model. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2020. PMID: 32981077. PMCID: PMC8191453.
• Batteiger TA, Spencer N, Washam CL, [et al., including Byrum S]. Endocervical miRNA Expression Profiles in Women Positive for Chlamydia trachomatis with Clinical Signs and/or Symptoms Are Distinct from Those in Women Positive for Chlamydia trachomatis without Signs and Symptoms. Infection and immunity. 2020 88(10). PMID: 32690634. PMCID: PMC7504953.
• Newton J, Brown T, Corley C, [et al., including Byrum SD]. Cranial irradiation impairs juvenile social memory and modulates hippocampal physiology. Brain research. 2020 1748:147095. PMID: 32896524. PMCID: PMC7602883.
• Taylor EM, Byrum SD, Edmondson JL, [et al.]. Proteogenomic analysis of melanoma brain metastases from distinct anatomical sites identifies pathways of metastatic progression. Acta neuropathologica communications. 2020 8(1):157. PMID: 32891176. PMCID: PMC7487560.
• Elolimy AA, Washam C, Byrum S, [et al.]. Formula Diet Alters the Ileal Metagenome and Transcriptome at Weaning and during the Postweaning Period in a Porcine Model. mSystems. 2020 5(4). PMID: 32753508. PMCID: PMC7406227.
• Storey AJ, Naceanceno KS, Lan RS, [et al., including Byrum SD]. ProteoViz: a tool for the analysis and interactive visualization of phosphoproteomics data. Molecular omics. 2020. PMID: 32347222. PMCID: PMC7423749.
• Dimori M, Heard-Lipsmeyer ME, Byrum SD, [et al.]. Respiratory defects in the CrtapKO mouse model of osteogenesis imperfecta. American journal of physiology. Lung cellular and molecular physiology. 2020 318(4):L592-L605. PMID: 32022592. PMCID: PMC7191481.
• McElroy T, Brown T, Kiffer F, [et al., including Byrum SD]. Assessing the Effects of Redox Modifier MnTnBuOE-2-PyP 5+ on Cognition and Hippocampal Physiology Following Doxorubicin, Cyclophosphamide, and Paclitaxel Treatment. International journal of molecular sciences. 2020 21(5). PMID: 32182883. PMCID: PMC7084440.
• Storey AJ, Hardman RE, Byrum SD, [et al.]. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. Journal of proteome research. 2020 19(3):1183-1195. PMID: 32027144. PMCID: PMC7241437.
• Ramirez AM, Byrum SD, Beenken KE, [et al.]. Exploiting Correlations between Protein Abundance and the Functional Status of saeRS and sarA To Identify Virulence Factors of Potential Importance in the Pathogenesis of Staphylococcus aureus Osteomyelitis. ACS infectious diseases. 2020 6(2):237-249. PMID: 31722523. PMCID: PMC7294808.
• Carr LE, Bowlin AK, Elolimy AA, [et al., including Byrum SD]. Neonatal Diet Impacts Circulatory miRNA Profile in a Porcine Model. Frontiers in immunology. 2020 11:1240. PMID: 32655560. PMCID: PMC7324749.
• Martinez Barrera S, Byrum S, Mackintosh SG, Kozubowski L. Registered report protocol: Quantitative analysis of septin Cdc10-associated proteome in Cryptococcus neoformans. PloS one. 2020 15(12):e0242381. PMID: 33315917. PMCID: PMC7735571.