Pauken Laboratory
Kristen E. Pauken, Ph.D.
Principal Investigator
- Departments, Labs and Institutes
- Labs
- Pauken Laboratory
Areas of Research
- Immunology
- Immunotherapy
- Cancer Biology
- Systems Biology
The Pauken lab seeks to understand how perturbing immune regulation by administering PD-1-based immunotherapy impacts CD8+ T cell fate and function both in the setting of protective anti-cancer responses, as well as pathogenic immune-driven toxicities. Our long-term goal is to develop strategies to uncouple the protective benefits of PD-1 immunotherapy from the pathogenic side effects, making immunotherapy safer and more effective for patients.
Our Research
The Pauken lab utilizes mouse models of cancer and autoimmunity to interrogate: 1) the cellular and molecular drivers of CD8+ T cell fate and functional potential in the settings of cancer and autoimmunity, 2) how anatomical location interfaces with CD8+ T cell differentiation, and how these two factors impact sensitivity to immunotherapy agents such as PD-1 inhibitors, and 3) how the presence of one chronic disease state (e.g. cancer) influences T cell differentiation and function in other chronic disease states (e.g. autoimmunity), and how this ultimately impacts response to immunotherapy.
Our lab uses high dimensional flow cytometry, immunofluorescence microscopy, and single cell RNA seq to interrogate CD8+ T cell differentiation state and function in cancer and autoimmunity. Moreover, the lab utilizes the T cell receptor (TCR) sequence as a molecular barcode to enable focusing of analyses to the populations of highest interest to each disease setting. Projects in the Pauken lab can: exclusively focus on cancer, exclusively focus on autoimmunity, or combine the two to interrogate how multiple disease states in the same individual impact the ensuing immune response.
Join Our Lab
Contact Dr. Pauken for more information or inquiries.
Selected Publications
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Mahuron KM+, Shahid O+, Sao P+, Wu C+, Haugh AM, Huppert LA, Levine LS, Lowe MM, Alvarado M, Micu M, Tsai KK, Chow M, Singer M, Schenkel JM, Sharpe AH, Rosenblum MD*, Pauken KE*, Daud AI*.
Single-Cell Analyses Reveal a Functionally Heterogeneous Exhausted CD8+ T-cell Subpopulation That Is Correlated with Response to Checkpoint Therapy in Melanoma Opens a new window
Cancer Res. 2025 Apr 15;85(8):1424-1440. PMID: 40042995. +Co-first authors, *Co-corresponding authors
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Pauken KE, Alhalabi O, Goswami S, Sharma P.
Neoadjuvant immune checkpoint therapy: Enabling insights into fundamental human immunology and clinical benefit. Opens a new window
Cancer Cell. 2025 Apr 14;43(4):623-640. PMID: 40118048.
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Schenkel JM*, Pauken KE*.
Localization, tissue biology and T cell state – implications for cancer immunotherapy. Opens a new window
Nat Rev Immunol. 2023 Dec;23(12):807-823. PMID 37253877. (*Co-corresponding, equal contribution)
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Pauken KE*, Lagattuta KA, Lu BY, Lucca LE, Daud AI, Hafler DA, Kluger HM, Raychaudhuri S, Sharpe AH*. *co-corresponding authors.
TCR-sequencing in cancer and autoimmunity: barcodes and beyond. Opens a new window
Trends in Immunology. 43(3):180-194. PMID: 35090787; PMCID: PMC8882139. 2022.
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Pauken KE*, Shahid O*, Lagattuta KA*, Mahuron KM*, Luber JM*, Lowe MM, Huang L, Delaney C, Long JM, Fung ME, Newcomer K, Tsai KK, Chow M, Guinn S, Kuchroo JR, Burke KP, Schenkel JM, Rosenblum MD, Daud AI, Sharpe AH, Singer M. *equal contribution.
Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment Opens a new window
Journal of Experimental Medicine. 218(4):e20200920. PMID: 33651880; PMCID: PMC7933992; 2021.
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Pauken KE, Sammons MA, Odorizzi PM, Manne S, Godec J, Khan O, Drake AM, Chen Z, Sen D, Kurachi M, Barnitz RA, Bartman C, Bengsch B, Huang AC, Schenkel JM, Vahedi G, Haining WN, Berger SL, and Wherry EJ.
Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Opens a new window
Science. 354(6316): 1160-1165. PMID: 27789795; PMCID: PMC5484795; 2016.