Possible Rotation Projects:
- Construct gene regulatory networks underlying immune cell function
- Build a spatial communication networks of immune cells in the lung
- Evaluate new spatial transcriptomics algorithms
Training Technologies Used:
- Mouse models of disease
- Immunology and cell biology techniques
- Next-generation sequencing
- Single-cell genomics
- Spatial transcriptomics
- Epigenomics
- Multi-omic profiling
- Bioinformatics
- Machine learning and computational analysis including cell-cell communication and gene regulatory network analysis.
- B.S. Biological Sciences, Fordham University, Bronx, NY 2002
- PhD. Cell Biology, Yale University, New Haven, CT 2009
- Post-doctoral fellow, NIAMS, NIH 2015
Zheng Y, Giri S, Zhang J, Chen Y, Yang A, Kale SL, Beeravolu H, Pannucci A, Marinov AD, Tilstra JS, He K, Creech A, Schwartz DM, Gottschalk RA, Bouladoux N, Belkaid Y, Cillo AR, Ray A, Poholek AC. IL-9 and Blimp-1 protect the transcriptional identity of group 2 innate lymphocytes in allergic asthma. Nat Immunol. 2026 Jun;27(6):1197-1211. PubMed Central PMCID: PMC13226057.
He K, Xiao H, MacDonald WA, Mehta I, Kishore A, Vincent A, Xu Z, Ray A, Chen W, Weaver CT, Lambrecht BN, Das J, Poholek AC. Spatial microniches of IL-2 combine with IL-10 to drive lung migratory T(H)2 cells in response to inhaled allergen. Nat Immunol. 2024 Nov;25(11):2124-2139. PubMed Central PMCID: PMC11934206.
He K, Hettinga A, Kale SL, Hu S, Xie MM, Dent AL, Ray A, Poholek AC. Blimp-1 is essential for allergen-induced asthma and Th2 cell development in the lung. J Exp Med. 2020 Jul 6;217(7) PubMed Central PMCID: PMC7336314.
Poholek AC, Jankovic D, Villarino AV, Petermann F, Hettinga A, Shouval DS, Snapper SB, Kaech SM, Brooks SR, Vahedi G, Sher A, Kanno Y, O'Shea JJ. IL-10 induces a STAT3-dependent autoregulatory loop in T(H)2 cells that promotes Blimp-1 restriction of cell expansion via antagonism of STAT5 target genes. Sci Immunol. 2016 Oct;1(5) PubMed Central PMCID: PMC5509416.
Ramjattun K, Wang A, Lee H, Giri S, Chen Y, MacDonald WA, Lord ND, Poholek AC, Lee Y, Das J. Characterizing spatial functional microniches with SpaceTravLR. bioRxiv. 2025 Nov 14; PubMed Central PMCID: PMC12642522.
The Poholek Laboratory studies how tissue microenvironments shape immune cell differentiation, function, and fate during health and disease. Our research seeks to understand how local environmental signals—including cytokines, cell-cell interactions, and tissue architecture—are integrated through transcriptional, epigenetic, and gene regulatory networks to establish immune cell identity. We are particularly interested in how these mechanisms control immune responses within barrier tissues and tumors, where the surrounding tissue environment profoundly influences whether immune cells promote protective immunity, chronic inflammation, or immune dysfunction.
Our laboratory combines experimental immunology with systems biology to investigate these questions across multiple scales of biology. We develop and apply cutting-edge approaches including single-cell and spatial transcriptomics, epigenomics, advanced mouse genetics, and computational approaches to understand how immune cells communicate within complex tissues. Current research focuses on defining the molecular mechanisms that regulate tissue-resident lymphocytes in allergic inflammation, understanding how the tumor microenvironment drives T cell exhaustion and immune suppression, and identifying the spatial organization and cellular interactions that govern effective immune responses. Increasingly, our work integrates machine learning and computational approaches to reconstruct gene regulatory networks and model cell-cell communication directly from high-dimensional genomic data.
