Research Focus Area:
Informatics, Carcinogenesis, Diagnosis/ Prognosis
Type of Research:
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.
NIH/Nat. Inst. of General Medical Sciences – 2P20GM103429
“Partnerships for Biomedical Research in Arkansas”
05/01/20 – 04/30/25
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.
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.
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.
Bettadapura M, Roys H, Bowlin A, [et al., including Byrum SD]. HIF-? 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.
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.
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.
Ahn JH, Davis ES, Daugird TA, [et al., including Byrum SD]. Phase separation drives aberrant chromatin looping and cancer development. Nature. 2021. PMID: 34163069.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 Anti-Tumor T-cell Immunity. Cancer discovery. 2020. PMID: 33318037.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Cragle CE, MacNicol MC, Byrum SD, [et al.]. Musashi interaction with poly(A)-binding protein is required for activation of target mRNA translation. The Journal of biological chemistry. 2019 294(28):10969-10986. PMID: 31152063. PMCID: PMC6635449.
Chiang TC, Koss B, Su L, [et al., including Byrum SD]. Effect of Sulforaphane and 5-Aza-2'-Deoxycytidine on Melanoma Cell Growth. Medicines (Basel, Switzerland). 2019 6(3). PMID: 31252639. PMCID: PMC6789461.
Mao XW, Nishiyama NC, Byrum SD, [et al.]. Characterization of mouse ocular response to a 35-day spaceflight mission: Evidence of blood-retinal barrier disruption and ocular adaptations. Scientific reports. 2019 9(1):8215. PMID: 31160660. PMCID: PMC6547757.
Lo S, Byrum SD, Tackett AJ, Parajuli N. Cold Storage Increases Albumin and Advanced Glycation-End Product-Albumin Levels in Kidney Transplants: A Possible Cause for Exacerbated Renal Damage. Transplantation direct. 2019 5(6):e454. PMID: 31723591. PMCID: PMC6791592.
Garcia-Rill E, Tackett AJ, Byrum SD, [et al.]. Local and Relayed Effects of Deep Brain Stimulation of the Pedunculopontine Nucleus. Brain sciences. 2019 9(3). PMID: 30889866. PMCID: PMC6468768.
Shields BD, Koss B, Taylor EM, [et al., including Byrum SD]. Loss of E-Cadherin Inhibits CD103 Antitumor Activity and Reduces Checkpoint Blockade Responsiveness in Melanoma. Cancer research. 2019 79(6):1113-1123. PMID: 30674537. PMCID: PMC6420873.
West KL, Byrum SD, Mackintosh SG, [et al.]. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics. 2019 14(2):130-145. PMID: 30739529. PMCID: PMC6557609.
Byrum SD, Tackett A, Washam CL, [et al.]. Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells. Frontiers in immunology. 2019 10:2016. PMID: 31555266. PMCID: PMC6724578.
Zybailov BL, Glazko GV, Rahmatallah Y, [et al., including Byrum SD]. Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats. PloS one. 2019 14(1):e0199274. PMID: 30699108. PMCID: PMC6353070.
Cheema AK, Byrum SD, Sharma NK, [et al.]. Proteomic Changes in Mouse Spleen after Radiation-Induced Injury and its Modulation by Gamma-Tocotrienol. Radiation research. 2018 190(5):449-463. PMID: 30070965. PMCID: PMC6297072.
Byrum SD, Loughran AJ, Beenken KE, [et al.]. Label-Free Proteomic Approach to Characterize Protease-Dependent and -Independent Effects of sarA Inactivation on the Staphylococcus aureus Exoproteome. Journal of proteome research. 2018 17(10):3384-3395. PMID: 30209945. PMCID: PMC6209314.
Barham C, Fil D, Byrum SD, [et al.]. RNA-Seq Analysis of Spinal Cord Tissues from hPFN1G118V Transgenic Mouse Model of ALS at Pre-symptomatic and End-Stages of Disease. Scientific reports. 2018 8(1):13737. PMID: 30213953. PMCID: PMC6137178.
Mao XW, Byrum S, Nishiyama NC, [et al.]. Impact of Spaceflight and Artificial Gravity on the Mouse Retina: Biochemical and Proteomic Analysis. International journal of molecular sciences. 2018 19(9). PMID: 30154332. PMCID: PMC6165321.
Wang P, Byrum S, Fowler FC, [et al.]. Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break. Nucleic acids research. 2017 45(19):10923-10940. PMID: 29036368. PMCID: PMC5737490.
Shields BD, Mahmoud F, Taylor EM, [et al., including Byrum SD]. Indicators of responsiveness to immune checkpoint inhibitors. Scientific reports. 2017 7(1):807. PMID: 28400597. PMCID: PMC5429745.
Hartman JH, Miller GP, Caro AA, [et al., including Byrum SD]. 1,3-Butadiene-induced mitochondrial dysfunction is correlated with mitochondrial CYP2E1 activity in Collaborative Cross mice. Toxicology. 2017 378:114-124. PMID: 28082109. PMCID: PMC5319481.
Holthoff ER, Byrum SD, Mackintosh SG, [et al.]. Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1. Clinical proteomics. 2017 14:40. PMID: 29225558. PMCID: PMC5717999.
Byrum SD, Burdine MS, Orr L, [et al.]. Time- and radiation-dose dependent changes in the plasma proteome after total body irradiation of non-human primates: Implications for biomarker selection. PloS one. 2017 12(3):e0174771. PMID: 28350824. PMCID: PMC5370149.
Loughran AJ, Gaddy D, Beenken KE, [et al., including Byrum SD]. Impact of sarA and Phenol-Soluble Modulins on the Pathogenesis of Osteomyelitis in Diverse Clinical Isolates of Staphylococcus aureus. Infection and immunity. 2016 84(9):2586-94. PMID: 27354444. PMCID: PMC4995912.
Atanassov BS, Mohan RD, Lan X, [et al., including Byrum SD]. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Molecular cell. 2016 62(4):558-71. PMID: 27132940. PMCID: PMC4874879.
Wu TP, Wang T, Seetin MG, [et al., including Byrum SD]. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature. 2016 532(7599):329-33. PMID: 27027282. PMCID: PMC4977844.
Salinas E, Byrum SD, Moreland LE, [et al.]. Identification of Viral and Host Proteins That Interact with Murine Gammaherpesvirus 68 Latency-Associated Nuclear Antigen during Lytic Replication: a Role for Hsc70 in Viral Replication. Journal of virology. 2016 90(3):1397-413. PMID: 26581985. PMCID: PMC4719591.
Byrum SD, Burdine MS, Orr L, [et al.]. A Quantitative Proteomic Analysis of Urine from Gamma-Irradiated Non-Human Primates. Journal of proteomics & bioinformatics. 2016 9(Suppl 10). PMID: 26962295. PMCID: PMC4780756.