Alex Soupir, PhD

My research focuses on developing computational frameworks that transform spatially-resolved molecular and imaging data into actionable insights for cancer diagnosis, prognosis, and therapy. By integrating spatial transcriptomics, multiplex immunofluorescence, spatial metabolomics, and digital pathology, I investigate the spatial organization of the tumor microenvironment—particularly immune-tumor interactions—at single-cell resolution. This interdisciplinary work bridges bioinformatics, biostatistics, and systems immunology, with an emphasis on algorithm development and spatial statistics to identify spatial biomarkers that inform treatment strategies. A central goal of my research is to build clinically adaptable tools and workflows that prioritize interpretability, reproducibility, and translational utility across cancer types.

Associations

• Biostatistics and Bioinformatics
• Genitourinary Oncology
• Molecular Medicine Program

I am broadly interested in computational methods for spatial biology, with a focus on understanding how the spatial organization of cells and molecules within the tumor microenvironment contributes to cancer progression and response to therapy. My research integrates spatial transcriptomics, multiplex immunofluorescence, and spatial metabolomics with statistical modeling, machine learning, and deep learning to uncover spatial biomarkers and functional tissue architecture. A central focus of my work is the development of open-source software that simplifies the analysis and interpretation of spatial omics data. These tools are designed to enable researchers to explore tumor architecture, benchmark spatial methods, and apply new analyses to their own datasets. I am particularly interested in optimizing algorithms for real-time performance on large-scale, single-cell multiplex imaging data and in developing methods that are accessible and reproducible across research settings. My current applications are anchored in kidney and ovarian cancer. In kidney cancer, I work with patient tumor samples to study how the tumor microenvironment changes in response to immunotherapy. In ovarian cancer, I analyze tissues from large epidemiologic cohorts to explore immune-tumor dynamics across diverse populations. These projects serve as key platforms for method development and evaluation. Ultimately, my research aims to bridge high-resolution spatial discovery with clinical and translational relevance, using spatially-informed computational tools to guide therapeutic insights and improve patient outcomes.

• Soupir A, Ospina OE, Hampton O, Churchman M, Radmacher M, Hedges D, McKean D, Agius P, Zeeshan S, Seligson ND, Pollock R, Liebner D, Chen JL, Tinoco G, Salhia B, McCarter M, Wilky BA, Miller BJ, Cavnar MJ, Groundland JS, Schneider BP, Riedlinger G, Edge SB, Moskaluk CA, Cardona K, Naqash AR, Gonzalez RJ, Mullinax JE, Joyce DM, Binitie O, Douglas Letson G, Naghavi AO, Druta M, Reed DR, Siegel EM, Teer JK, Fridley BL, Brohl AS. Genomic, transcriptomic, and immunogenomic landscape of over 1300 sarcomas of diverse histology subtypes. Nat Commun. 2025 May.16(1):4206. Pubmedid: 40328759. Pmcid: PMC12055966.
• Ospina OE, Manjarres-Betancur R, Gonzalez-Calderon G, Soupir AC, Smalley I, Tsai KY, Markowitz J, Vallebuona E, Berglund AE, Eschrich SA, Yu X, Fridley BL. spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis. Cancer Res. 2025 Mar.85(5):848-858. Pubmedid: 39636739. Pmcid: PMC11873723.
• May AM, Kadomoto S, Williams C, Soupir AC, The S, McGue JJ, Robinson T, Shelley G, Hayes MT, Fridley BL, Balasi JA, Ramos Echevarria PM, Dhillon J, Nallandhighal S, Acharyya S, Chen L, Aldous J, Schurman N, Baladandayuthapani V, Frankel TL, Salami SS, Manley BJ, Mehra R, Udager AM, Keller ET. Spatial analysis reveals a novel inflammatory tumor transition state which promotes a macrophage-driven induction of sarcomatoid renal cell carcinoma. bioRxiv. 2025 Jun. Pubmedid: 40661608. Pmcid: PMC12259133.
• Fenlon J, Van Bibber N, Mahlow J, Yamoah K, Soupir AC, Nguyen JV, Moran Segura C, Spivak AM, Knudsen BS, Zhou Q, Hu-Lieskovan S, Puri S, Zhang W, DeRose YS, Suneja G, Coghill AE. Human Immunodeficiency Virus-Associated Differences in the Tumor Immune Microenvironment of Lung, Breast, and Prostate Cancers. Cancer Epidemiol Biomarkers Prev. 2025 Jun.34(6):860-867. Pubmedid: 40183760. Pmcid: PMC12133412.
• Davis JT, Obermayer AN, Soupir AC, Hesterberg RS, Duong T, Yang CY, Dao KP, Manley BJ, Grass GD, Avram D, Rodriguez PC, Fridley BL, Yu X, Teng M, Wang X, Shaw TI. BatchFLEX: feature-level equalization of X-batch. Bioinformatics. 2024 Oct.40(10). Pubmedid: 39360977. Pmcid: PMC11486499.
• Wrobel J, Soupir AC, Hayes MT, Peres LC, Vu T, Leroux A, Fridley BL. mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data. Bioinform Adv. 2024 Nov.4(1):vbae155. Pubmedid: 39552929. Pmcid: PMC11568348.
• Ospina OE, Soupir AC, Manjarres-Betancur R, Gonzalez-Calderon G, Yu X, Fridley BL. Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models. Sci Rep. 2024 May.14(1):10967. Pubmedid: 38744956. Pmcid: PMC11094014.
• Huelster HL, Gould B, Schiftan EA, Camperlengo L, Davaro F, Rose KM, Soupir AC, Jia S, Zheng T, Sexton WJ, Pow-Sang J, Spiess PE, Daniel Grass G, Wang L, Wang X, Vosoughi A, Necchi A, Meeks JJ, Faltas BM, Du P, Li R. Novel Use of Circulating Tumor DNA to Identify Muscle-invasive and Non-organ-confined Upper Tract Urothelial Carcinoma. Eur Urol. 2024 Mar.85(3):283-292. Pubmedid: 37802683.
• Ospina OE, Manjarres-Betancur R, Gonzalez-Calderon G, Soupir AC, Smalley I, Tsai K, Markowitz J, Vallebuona E, Berglund A, Eschrich S, Yu X, Fridley BL. spatialGE: A user-friendly web application to democratize spatial transcriptomics analysis. bioRxiv. 2024 Jul. Pubmedid: 39005315. Pmcid: PMC11244876.
• 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. Genome Biol. 2024 Dec.25(1):308. Pubmedid: 39639369. Pmcid: PMC11622564.
• 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.
• Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol. 2023 Mar.2629:115-140. Pubmedid: 36929076.
• Laajala TD, Sreekanth V, Soupir AC, Creed JH, Halkola AS, Calboli FCF, Singaravelu K, Orman MV, Colin-Leitzinger C, Gerke T, Fridley BL, Tyekucheva S, Costello JC. A harmonized resource of integrated prostate cancer clinical, -omic, and signature features. Sci Data. 2023 Jul.10(1):430. Pubmedid: 37407670. Pmcid: PMC10322899.
• 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.
• Laajala TD, Sreekanth V, Soupir A, Creed J, Calboli FC, Singaravelu K, Orman M, Colin-Leitzinger C, Gerke T, Fridley BL, Tyekucheva S, Costello JC. curatedPCaData: Integration of clinical, genomic, and signature features in a curated and harmonized prostate cancer data resource. bioRxiv. 2023 Jan. Pubmedid: 36711769. Pmcid: PMC9882125.
• Huang J, Du M, Soupir A, Wang L, Tan W, Kalari KR, Kilari D, Park J, Huang CC, Kohli M, Wang L. Plasma Copy Number Alteration-Based Prognostic and Predictive Multi-Gene Risk Score in Metastatic Castration-Resistant Prostate Cancer. Cancers (Basel). 2022 Sep.14(19). Pubmedid: 36230636. Pmcid: PMC9562906.
• 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.
• Tian Y, Soupir A, Liu Q, Wu L, Huang CC, Park JY, Wang L. Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation. Hum Mol Genet. 2022 May.31(10):1610-1621. Pubmedid: 34849858. Pmcid: PMC9122641.
• Huang J, Soupir AC, Wang L. Cell-free DNA methylome profiling by MBD-seq with ultra-low input. Epigenetics. 2022 Mar.17(3):239-252. Pubmedid: 33724157. Pmcid: PMC8920199.
• Wilson C, Soupir AC, Thapa R, Creed J, Nguyen J, Segura CM, Gerke T, Schildkraut JM, Peres LC, Fridley BL. Tumor immune cell clustering and its association with survival in African American women with ovarian cancer. PLoS Comput Biol. 2022 Mar.18(3):e1009900. Pubmedid: 35235563. Pmcid: PMC8920290.
• Ospina OE, Wilson CM, Soupir AC, Berglund A, Smalley I, Tsai KY, Fridley B. spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics. Bioinformatics. 2022 Apr.38(9):2645-2647. Pubmedid: 35258565.
• Huang J, Soupir AC, Schlick BD, Teng M, Sahin IH, Permuth JB, Siegel EM, Manley BJ, Pellini B, Wang L. Cancer Detection and Classification by CpG Island Hypermethylation Signatures in Plasma Cell-Free DNA. Cancers (Basel). 2021 Nov.13(22). Pubmedid: 34830765. Pmcid: PMC8616264.
• Creed JH, Wilson CM, Soupir AC, Colin-Leitzinger CM, Kimmel GJ, Ospina OE, Chakiryan NH, Markowitz J, Peres LC, Coghill A, Fridley BL. spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data. Bioinformatics. 2021 Dec.37(23):4584-4586. Pubmedid: 34734969. Pmcid: PMC8652029.