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:
Michelle Messmer,
Ramya Sivakumar,

Laboratory Staff:
Brandy Olin,
Caleb Stoltzfus,


Lab Website

Postdoctoral Position Available


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. Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism. Mao K, Baptista AP, Tamoutounour S, Zhuang L, Bouladoux N, Martins AJ, Huang Y, Gerner MY, Belkaid Y, Germain RN. Nature. 2018; 554(7691):255-259. PMID: 29364878
  2. Dendritic cell and antigen dispersal landscapes regulate T cell immunity. Gerner MY, Casey KA, Kastenmuller W, Germain RN.The Journal of experimental medicine. 2017; 214(10):3105-3122. PMID:28847868
  3. 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.
  4. 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
  5. 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
  6. 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
  7. Radtke AJ, Kastenmuller W, Espinosa DA, Gerner MY, Tse S, Sinnis P, Germain RN, Zavala FP, Ian A. Cockburn IA. 2015. Lymph-node Resident CD8α+ Dendritic Cells Capture Antigens from Migratory Malaria Sporozoites and Induce CD8+ T Cell Responses. Plos Pathog. 11(2)
  8. Torabi-Parizi P, Vrisekoop N, Kastenmuller W, Gerner MY, Egen J.G., Germain RN. 2014. Pathogen-related differences in the abundance of presented antigen are reflected in CD4+ T cell dynamic behavior and effector function in the lung. J Immunol 192(4):1651-60
  9. Gerner MY*, Heltemes-Harris LM*, Fife BT, Mescher MF. 2013. Cutting Edge: IL-12 and Type I IFN Differentially Program CD8 T Cells for Programmed Death 1 Re-expression Levels and Tumor Control. J Immunol 191(3):1011-5
  10. Petrovas C, Yamamoto T, Gerner MY, Boswell KL, Wloka K, Smith EC, Ambrozak DR, Sandler NG, Timmer KJ, Sun X, Pan L, Poholek A, Rao SS, Brenchley JM, Alam SM, Tomaras GD, Roederer M, Douek DC, Seder RA, Germain RN, Haddad EK, Koup RA. 2012. CD4 T follicular helper cell dynamics during SIV infection. J Clin Invest. 122(9):3281-94
  11. Gerner MY, Kastenmuller W, Ifrim I, Kabat J, Germain RN. 2012. Histo-cytometry: a method for highly multiplex quantitative tissue imaging analysis applied to dendritic cell subset microanatomy in lymph nodes. Immunity. 37(2):364-76
  12. Kastenmuller W, Gerner MY, Germain RN. 2010. The In Situ Dynamics of Dendritic Cell Interactions. Eur J Immunol 40:2103-6
  13. Gerner MY, Mescher MF 2009. Antigen processing and MHC-II presentation by dermal and tumor-infiltrating DC. J Immunol 182:2726-37
  14. Gerner MY, Casey KA, Mescher MF. 2008. Defective MHC-II presentation by DC limits CD4 T cell help for anti-tumor CD8 T cell responses. J Immunol 181:155-64.
  15. Curtsinger JM, Gerner MY, Lins DC, Mescher MF. 2007. Signal 3 availability limits the CD8 T cell response to a solid tumor. J Immunol 178:6752-6760.
  16. Mescher MF, Popescu FE, Gerner M, Hammerbeck CD, and Curtsinger JM. 2007. Activation-induced non-responsiveness (anergy) limits CD8 T cell responses to tumors. Semin Cancer Biol 17:299-308.
  17. Mescher MF, Curtsinger JM, Agarwal P, Casey KA, Gerner M, Hammerbeck CD, Popescu F, and Z. Xiao Z . 2006. Signals required for programming effector and memory development by CD8+ T cells. Immunol Rev 211:81-92