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Paul  Stewart

Paul Stewart, PhD

Program: Biostatistics and Bioinformatics

Research Program: Cancer Biology & Evolution Program


  • Overview

    Proteomics, Metabolomics, Multi-omics, Bioinformatics 


    • Biostatistics and Bioinformatics
    • Cancer Biology & Evolution Program
  • Research Interest

    Dr. Stewart has expertise in computational proteomics and metabolomics, integration of multi-omics datasets, and development of novel bioinformatics tools. He is broadly interested in cancer metabolism and how its dysregulation impacts the tumor microenvironment, host immune response, and therapeutic efficacy. 

  • Publications

    • Peak T, Tian Y, Patel A, Shaw T, Obermayer A, Laborde J, Kim Y, Johnson J, Stewart P, Fang B, Teer JK, Koomen J, Berglund A, Marchion D, Francis N, Echevarria PR, Dhillon J, Clark N, Chang A, Sexton W, Zemp L, Chahoud J, Wang L, Manley B. Pathogenic Roles for RNASET2 in Clear Cell Renal Cell Carcinoma. Lab Invest. 2024 May.104(5):102041. Pubmedid: 38431116.
    • Waqas A, Tripathi A, Mukund A, Stewart P, Naeini M, Rasool G. BIO24-031: Hierarchical Multimodal Learning on Pan-Squamous Cell Carcinomas for Improved Survival Outcomes. J Natl Compr Canc Ne. 2024 Apr.22(2.5). Pubmedid: 38579762.
    • Sasamoto N, Stewart PA, Wang T, Thompson ZJ, Yoder SJ, Hecht JL, Cleveland JL, Conejo-Garcia J, Fridley BL, Terry KL, Tworoger SS. Associations between prediagnostic aspirin use and ovarian tumor gene expression. Cancer Med. 2023 Sep.12(17):18405-18417. Pubmedid: 37525619. Pmcid: PMC10523980.
    • Soupir AC, Hayes MT, Peak TC, Ospina O, Chakiryan NH, Berglund AE, Stewart PA, Nguyen J, Segura CM, Francis NL, Echevarria PMR, Chahoud J, Li R, Tsai KY, Balasi JA, Peres YC, Dhillon J, Martinez LA, Gloria WE, Schurman N, Kim S, Gregory M, Mulé J, Fridley BL, Manley BJ. Increased spatial coupling of integrin and collagen IV in the immunoresistant clear cell renal cell carcinoma tumor microenvironment. bioRxiv. 2023 Nov. Pubmedid: 38014063. Pmcid: PMC10680839.
    • Stewart PA, Jaeger AM. Taking the temperature of lung cancer antigens. Nat Cancer. 2023 May.4(5):586-587. Pubmedid: 37237079.
    • Laborde J, Stewart PA, Chen Z, Chen YA, Brownstein NC. Sparse clusterability: testing for cluster structure in high dimensions. BMC Bioinformatics. 2023 Mar.24(1):125. Pubmedid: 37003995. Pmcid: PMC10064666.
    • Grass GD, Ercan D, Obermayer AN, Shaw T, Stewart PA, Chahoud J, Dhillon J, Lopez A, Johnstone PAS, Rogatto SR, Spiess PE, Eschrich SA. An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery. Cancers (Basel). 2023 Jul.15(14). Pubmedid: 37509297. Pmcid: PMC10377392.
    • Soupir AC, Tian Y, Stewart PA, Nunez-Lopez YO, Manley BJ, Pellini B, Bloomer AM, Zhang J, Mo Q, Marchion DC, Liu M, Koomen JM, Siegel EM, Wang L. Detectable Lipidomes and Metabolomes by Different Plasma Exosome Isolation Methods in Healthy Controls and Patients with Advanced Prostate and Lung Cancer. Int J Mol Sci. 2023 Jan.24(3). Pubmedid: 36768152. Pmcid: PMC9916336.
    • Adhikari E, Liu Q, Johnson J, Stewart P, Marusyk V, Fang B, Izumi V, Bowers K, Guzman KM, Koomen JM, Marusyk A, Lau EK. Brain metastasis-associated fibroblasts secrete fucosylated PVR/CD155 that induces breast cancer invasion. Cell Rep. 2023 Dec.42(12):113463. Pubmedid: 37995180.
    • Maurin M, Ranjouri M, Megino-Luque C, Newberg JY, Du D, Martin K, Miner RE, Prater MS, Wee DKB, Centeno B, Pruett-Miller SM, Stewart P, Fleming JB, Yu X, Bravo-Cordero JJ, Guccione E, Black MA, Mann KM. RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nat Commun. 2023 Dec.14(1):8444. Pubmedid: 38114498. Pmcid: PMC10730836.
    • Khaled ML, Ren Y, Kundalia R, Alhaddad H, Chen Z, Wallace GC, Evernden B, Ospina OE, Hall M, Liu M, Darville LNF, Izumi V, Chen YA, Pilon-Thomas S, Stewart PA, Koomen JM, Corallo SA, Jain MD, Robinson TJ, Locke FL, Forsyth PA, Smalley I. Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease. bioRxiv. 2023 Dec. Pubmedid: 38187773. Pmcid: PMC10769272.
    • Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol. 2022 Oct.82(4):354-362. Pubmedid: 35718636.
    • Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol. 2022 Nov.12:1051487. Pubmedid: 36505834. Pmcid: PMC9730332.
    • Sasamoto N, Stewart PA, Wang T, Yoder SJ, Chellappan S, Hecht JL, Fridley BL, Terry KL, Tworoger SS. Lifetime ovulatory years and ovarian cancer gene expression profiles. J Ovarian Res. 2022 May.15(1):59. Pubmedid: 35562768. Pmcid: PMC9102743.
    • Lee BD, Gitter A, Greene CS, Raschka S, Maguire F, Titus AJ, Kessler MD, Lee AJ, Chevrette MG, Stewart PA, Britto-Borges T, Cofer EM, Yu KH, Carmona JJ, Fertig EJ, Kalinin AA, Signal B, Lengerich BJ, Triche TJ, Boca SM. Ten quick tips for deep learning in biology. PLoS Comput Biol. 2022 Mar.18(3):e1009803. Pubmedid: 35324884. Pmcid: PMC8946751.
    • Sarcar B, Fang B, Izumi V, Nunez-Lopez Y, Tassielli A, Pratley R, Jeong D, Permuth JB, Koomen JM, Fleming JB, Stewart PA. A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles. Mol Cell Proteomics. 2022 Dec.21(12):100438. Pubmedid: 36332889. Pmcid: PMC9792568.
    • Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. Acs Chem Biol. 2022 Apr.17(4):776-784. Pubmedid: 35311290.
    • Majumder A, Hosseinian S, Stroud M, Adhikari E, Saller JJ, Smith MA, Zhang G, Agarwal S, Creixell M, Meyer BS, Kinose F, Bowers K, Fang B, Stewart PA, Welsh EA, Boyle TA, Meyer AS, Koomen JM, Haura EB. Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Mol Cancer Res. 2022 Apr.20(4):542-555. Pubmedid: 35022314. Pmcid: PMC8983558.
    • Damaghi M, West J, Robertson-Tessi M, Xu L, Ferrall-Fairbanks MC, Stewart PA, Persi E, Fridley BL, Altrock PM, Gatenby RA, Sims PA, Anderson ARA, Gillies RJ. The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Proc Natl Acad Sci U S A. 2021 Jan.118(3). Pubmedid: 33452133. Pmcid: PMC7826394.
    • Stewart PA, Welsh EA, Fang B, Izumi V, Mesa T, Zhang C, Yoder S, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Avedon M, Wloch M, Fournier M, Fellows KM, Francis JM, Saller JJ, Boyle TA, Chen YA, Haura EB, Teer JK, Eschrich SA, Koomen JM. Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics. Methods Mol Biol. 2020 Sep.2194:187-221. Pubmedid: 32926368. Pmcid: PMC7771375.
    • Cook LM, Frieling JS, Nerlakanti N, McGuire JJ, Stewart PA, Burger KL, Cleveland JL, Lynch CC. Betaglycan drives the mesenchymal stromal cell osteogenic program and prostate cancer-induced osteogenesis. Oncogene. 2019 Oct.38(44):6959-6969. Pubmedid: 31409900. Pmcid: PMC7771554.
    • Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB. Proteogenomic landscape of squamous cell lung cancer. Nat Commun. 2019 Aug.10(1):3578. Pubmedid: 31395880. Pmcid: PMC6687710.
    • Stewart PA, Kuenzi BM, Mehta S, Kumar P, Johnson JE, Jagtap P, Griffin TJ, Haura EB. The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis. Methods Mol Biol. 2019 Apr.1977:249-261. Pubmedid: 30980333. Pmcid: PMC7787333.
    • Welsh EA, Stewart PA, Kuenzi BM, Eschrich JA. Escape Excel: A tool for preventing gene symbol and accession conversion errors. PLoS One. 2017 Sep.12(9):e0185207. Pubmedid: 28953918. Pmcid: PMC5617173.
    • Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. 2017 Mar.17(6). Pubmedid: 28195392. Pmcid: PMC5606153.
    • Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U. Polypharmacology-based ceritinib repurposing using integrated functional proteomics. Nat Chem Biol. 2017 Dec.13(12):1222-1231. Pubmedid: 28991240. Pmcid: PMC5909815.
    • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Jun.4(2):16. Pubmedid: 28154798. Pmcid: PMC5217344.
    • Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res. 2016 Dec.15(12):4747-4754. Pubmedid: 27680298. Pmcid: PMC5231908.
    • Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One. 2015 Nov.10(11):e0142162. Pubmedid: 26539827. Pmcid: PMC4634858.
    • Stewart PA, Luks J, Roycik MD, Sang QX, Zhang J. Differentially expressed transcripts and dysregulated signaling pathways and networks in African American breast cancer. PLoS One. 2013 Dec.8(12):e82460. Pubmedid: 24324792. Pmcid: PMC3853650.
    • Wang X, Stewart PA, Cao Q, Sang QX, Chung LW, Emmett MR, Marshall AG. Characterization of the phosphoproteome in androgen-repressed human prostate cancer cells by Fourier transform ion cyclotron resonance mass spectrometry. J Proteome Res. 2011 Sep.10(9):3920-3928. Pubmedid: 21786837.
  • Grants

    • Title: Multi-omic landscape of squamous cell lung cancer
      Sponsor: Moffitt Cancer Center
      PI: Stewart, P.
    • Title: Deep Phenotypic Characterization of Colorectal Cancer Patients to Identify Novel Predictors of Disease Recurrence
      Sponsor: Moffitt Cancer Center
      PI: Siegel, E., CO-PI: Kresovich, J., CO-PI: Stewart, P.
    • Title: Deep Phenotypic Characterization of Colorectal Cancer Patients to Identify Novel Predictors of Disease Recurrence
      Sponsor: Nat Institutes of Health
      PI: Siegel, E., CO-PI: Kresovich, J., CO-PI: Stewart, P.
    • Title: Innovative Proteogenomics to Investigate Tertiary Lymphoid Structures in Lung Cancer
      Sponsor: Cancer Research Institute
      PI: Stewart, P.

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