Department of Immunology

Michael Gerner, PhD


Dr. Gerner graduated with a Bachelor’s degree in Biochemistry from the University of Wisconsin – Madison. He went on to receive his Ph.D. in Immunology in 2009 from the University of Minnesota – Twin Cities. He completed his postdoctoral training at the National Institutes of Health and joined the University of Washington Department of Immunology as an Assistant Professor in 2015.



Department of Immunology
UW Box 358059
750 Republican St.
Seattle, WA 98109-8059



Microscopy, Vaccines,
Tissue structure-function
relationships, Immune Cell Crosstalk


Graduate Students:
Jessica Huang,
Joey Leal,
Miranda Lyons-Cohen,
Michael Conlon,

Postdoctoral Fellows:
Ramya Sivakumar,
Yixuan Wu,

Laboratory Staff:
Brandy Olin,
Caleb Stoltzfus,


Lab Website



Dr. Michael Gerner


The immune system is composed of a highly heterogeneous network of innate and adaptive cell populations with unique phenotypic and functional properties. These diverse cells are differentially distributed within tissues, creating specialized microenvironments with select roles and functions. Furthermore, these localized cells are in constant communication with one another and coordinate their activities to generate immune responses specifically tailored to distinct challenges. In the Gerner lab, we investigate these processes directly in situ by studying micro-anatomical tissue organization on cellular and molecular levels, cell-cell communication events that generate immune responses, as well as localized effector responses in inflamed peripheral sites that allow for protective immunity. We utilize cutting-edge microscopy tools, such as 2-photon intra-vital microscopy, multi-parameter whole-organ confocal microscopy and analytical Histo-Cytometry. Investigating such cell-cell crosstalk and coordinated activity, as well as the broader structure-function relationships for whole organs and inflamed sites is critical for understanding the underpinnings of immune processes. These studies will lead to improved design of vaccines and immuno-modulatory therapeutics and will allow for tight and regionalized regulation of select cells and functions.


  1. Delahaye JL, Gern BH, Cohen SB, Plumlee CR, Shafiani S, Gerner MY, Urdahl KB.Cutting Edge: Bacillus Calmette-Guérin-Induced T Cells Shape Mycobacterium tuberculosis Infection before Reducing the Bacterial Burden. J Immunol. 2019 Aug 15;203(4):807-812. doi: 10.4049/jimmunol.1900108. Epub 2019 Jul 15. PubMed PMID: 31308091; PubMed Central PMCID: PMC6684453.
  2. Glaser AK, Reder NP, Chen Y, Yin C, Wei L, Kang S, Barner LA, Xie W, McCarty EF, Mao C, Halpern AR, Stoltzfus CR, Daniels JS, Gerner MY, Nicovich PR, Vaughan JC, True LD, Liu JTC. Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. Nat Commun. 2019 Jul 4;10(1):2781. doi: 10.1038/s41467-019-10534-0. PubMed PMID: 31273194; PubMed Central PMCID: PMC6609674.
  3. Li W, Germain RN, Gerner MY. High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging. Nat Protoc. 2019 Jun;14(6):1708-1733. doi: 10.1038/s41596-019-0156-4. Epub 2019 Apr 26. PubMed PMID: 31028373.
  4. Baptista AP, Gola A, Huang Y, Milanez-Almeida P, Torabi-Parizi P, Urban JF Jr, Shapiro VS, Gerner MY, Germain RN. The Chemoattractant Receptor Ebi2 Drives Intranodal Naive CD4+ T Cell Peripheralization to Promote Effective Adaptive Immunity.Immunity. 2019 May 21;50(5):1188-1201.e6. doi: 10.1016/j.immuni.2019.04.001. Epub 2019 Apr 30. PubMed PMID: 31053504.
  5. Cabeza-Cabrerizo M, van Blijswijk J, Wienert S, Heim D, Jenkins RP, Chakravarty P, Rogers N, Frederico B, Acton S, Beerling E, van Rheenen J, Clevers H, Schraml BU, Bajénoff M, Gerner M, Germain RN, Sahai E, Klauschen F, Reis E Sousa C. Tissue clonality of dendritic cell subsets and emergency DCpoiesis revealed by multicolor fate mapping of DC progenitors. Sci Immunol. 2019 Mar 1;4(33). doi: 10.1126/sciimmunol.aaw1941. PubMed PMID: 30824528; PubMed Central PMCID: PMC6420147.
  6. Lynn GM, Chytil P, Francica JR, Lagová A, Kueberuwa G, Ishizuka AS, Zaidi N, Ramirez-Valdez RA, Blobel NJ, Baharom F, Leal J, Wang AQ, Gerner MY, Etrych T, Ulbrich K, Seymour LW, Seder RA, Laga R. Impact of Polymer-TLR-7/8 Agonist (Adjuvant) Morphology on the Potency and Mechanism of CD8 T Cell Induction.Biomacromolecules. 2019 Feb 11;20(2):854-870. doi: 10.1021/acs.biomac.8b01473. Epub 2019 Jan 22. PubMed PMID: 30608149.
  7. Cohen SB, Gern BH, Delahaye JL, Adams KN, Plumlee CR, Winkler JK, Sherman DR, Gerner MY, Urdahl KB. Alveolar Macrophages Provide an Early Mycobacterium tuberculosis Niche and Initiate Dissemination. Cell Host Microbe. 2018 Sep 12;24(3):439-446.e4. doi: 10.1016/j.chom.2018.08.001. Epub 2018 Aug 23. PubMed PMID: 30146391; PubMed Central PMCID: PMC6152889.
  8. Mao K, Baptista AP, Tamoutounour S, Zhuang L, Bouladoux N, Martins AJ, Huang Y, Gerner MY, Belkaid Y, Germain RN. Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism. Nature. 2018 Feb 8;554(7691):255-259. doi: 10.1038/nature25437. Epub 2018 Jan 22. PubMed PMID: 29364878.
  9. Gerner MY, Casey KA, Kastenmuller W, Germain RN. Dendritic cell and antigen dispersal landscapes regulate T cell immunity. J Exp Med. 2017 Oct 2;214(10):3105-3122. doi: 10.1084/jem.20170335. Epub 2017 Aug 28. PubMed PMID: 28847868; PubMed Central PMCID: PMC5626399.
  10. Lynn GM, Laga R, Darrah PA, Ishizuka AS, Balaci AJ, Dulcey AE, Pechar M, Pola R, Gerner MY, Yamomoto A Buechler CR, Quinn KM, Smelkinson MG, Vanek O, Cawood R, Hills T, Vasalatiy O, Kastenmuller K, Francica JR, Stutts L, Tom JK, Ryu KA, Esser-Kahn AP, Etrych T, Fisher KD, Seymour LW, Seder RA. 2015. Particle formation by polymer-bound TLR agonists is the principal physiochemical determinant for enhancing vaccine immunogenicity. Nat. Biotech. In press.
  11. Da Fonseca DM, Hand TW, Han SJ, Gerner MY, Zaretsky AG, Byrd AL, Harrison OJ, Ortiz AM, Quinones M, Trinchieri G, Brenchley JM, Brodsky IE, Germain RN, Randolph GJ, Belkaid Y. 2015. Microbiota-dependent sequelae of acute infection compromise tissue-specific immunity. Cell. 163(2):354-66
  12. Eickhoff S, Brewitz A, Gerner MY, Klauschen F, Komander K, Hemmi H, Garbi N, Kaisho T, Germain RN, Kastenmüller W. 2015. Robust Anti-viral Immunity Requires Multiple Distinct T Cell-Dendritic Cell Interactions. Cell. doi: 10.1016
  13. Gerner MY, Torabi-Parizi P and Germain RN. 2015. Strategically localized dendritic cells promote rapid T cell responses to lymph-borne particulate antigens. Immunity. 42(1):172-85