Publications

1.) Distal Immunization and Systemic Cytokines Establish a Transient Immune Alert State in the Intestine

»Yixuan Wu, Jessica Y. Huang, Michael T. Conlon, Meera K. Shenoy, Jaime L. Chao, Ming Yao Chooi, Meghan A. Koch, Michael Y. Gerner; Distal Immunization and Systemic Cytokines Establish a Transient Immune Alert State in the Intestine. J Immunol 1 August 2024; 213 (3): 373–383. https://doi.org/10.4049/jimmunol.2400209

2.)  Site-specific regulation of Th2 differentiation within lymph node microenvironments

»Lyons-Cohen MR, Shamskhou EA, Gerner MY. Journal of Experimental Medicine, vol. 221, no. 4, 4 Mar. 2024, https://doi.org/10.1084/jem.20231282.

3.) Information flow in the spatiotemporal organization of immune responses

» Huang JY, Lyons-Cohen MR, Gerner MY. Immunol Rev. 2022 Mar;306(1):93-107. doi: 10.1111/imr.13046. Epub 2021 Nov 29. PMID: 34845729; PMCID: PMC8837692

4.) Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated With Anti-Tumor Immunity

» Stoltzfus CR, Sivakumar R, Kunz L, Olin Pope BE, Menietti E, Speziale D, Adelfio R, Bacac M, Colombetti S, Perro M, Gerner MY. Front Immunol. 2021 Aug 5;12:726492. doi: 10.3389/fimmu.2021.726492. PMID: 34421928; PMCID: PMC8375665
» Di Pilato M, Kfuri-Rubens R, Pruessmann JN, Ozga AJ, Messemaker M, Cadilha BL, Sivakumar R, Cianciaruso C, Warner RD, Marangoni F, Carrizosa E, Lesch S, Billingsley J, Perez-Ramos D, Zavala F, Rheinbay E, Luster AD, Gerner MY, Kobold S, Pittet MJ, Mempel TR. Cell. 2021 Aug 19;184(17):4512-4530.e22. doi: 10.1016/j.cell.2021.07.015. Epub 2021 Aug 2. PMID: 34343496; PMCID: PMC8719451

6.) TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma.

» Benjamin H. Gern, Kristin N. Adams, Courtney R. Plumlee, Caleb R. Stoltzfus, Laila Shehata, Albanus O. Moguche, Kathleen Busman-Sahay, Scott G. Hansen, Michael K. Axthelm, Louis J. Picker, Jacob D. Estes, Kevin B. Urdahl, Michael Y. Gerner, 2021, Cell Host & Microbe, ISSN 1931-3128.

7.) Lymphoid stromal cells proGrem dendritic cell homeostasis

» Baptista AP, Gerner MY. Nat Immunol. 2021 May;22(5):541-543. doi: 10.1038/s41590-021-00924-2. PMID: 33903765

8.) Innate cell microenvironments in lymph nodes shape the generation of T cell responses during type I inflammation.

» Leal JM, Huang JY, Kohli K, Stoltzfus C, Lyons-Cohen MR, Olin BE, Gale M Jr, Gerner MY. Sci Immunol. 2021 Feb 12;6(56):eabb9435. doi: 10.1126/sciimmunol.abb9435. PMID: 33579750.

9.) Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis.

» Plumlee CR, Duffy FJ, Gern BH, Delahaye JL, Cohen SB, Stoltzfus CR, Rustad TR, Hansen SG, Axthelm MK, Picker LJ, Aitchison JD, Sherman DR, Ganusov VV, Gerner MY, Zak DE, Urdahl KB. Cell Host Microbe. 2021 Jan 13;29(1):68-82.e5. doi: 10.1016/j.chom.2020.10.003. Epub 2020 Nov 2. PMID: 33142108; PMCID: PMC7854984.

10.) CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues.

» Stoltzfus CR, Filipek J, Gern BH, Olin BE, Leal JM, Wu Y, Lyons-Cohen MR, Huang JY, Paz-Stoltzfus CL, Plumlee CR, Pöschinger T, Urdahl KB, Perro M, Gerner MY.  Cell Rep. 2020 Apr 21;31(3):107523. doi: 10.1016/j.celrep.2020.107523. PMID: 32320656; PMCID: PMC7233132.

11.) Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues.

» 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.  Nat Commun. 2019 Jul 4;10(1):2781. doi: 10.1038/s41467-019-10534-0. PMID: 31273194; PMCID: PMC6609674.

12.) The Chemoattractant Receptor Ebi2 Drives Intranodal Naive CD4+ T Cell Peripheralization to Promote Effective Adaptive Immunity.

» Baptista AP, Gola A, Huang Y, Milanez-Almeida P, Torabi-Parizi P, Urban JF Jr, Shapiro VS, Gerner MY, Germain RN.  Immunity. 2019 May 21;50(5):1188-1201.e6. doi: 10.1016/j.immuni.2019.04.001. Epub 2019 Apr 30. PMID: 31053504.

13.) High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging.

» Li W, Germain RN, Gerner MY.  Nat Protoc. 2019 Jun;14(6):1708-1733. doi: 10.1038/s41596-019-0156-4. Epub 2019 Apr 26. PMID: 31028373.

14.) Impact of Polymer-TLR-7/8 Agonist (Adjuvant) Morphology on the Potency and Mechanism of CD8 T Cell Induction. 

» 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. Biomacromolecules. 2019 Feb 11;20(2):854-870. doi: 10.1021/acs.biomac.8b01473. Epub 2019 Jan 22. PMID: 30608149.

15.) Alveolar Macrophages Provide an Early Mycobacterium tuberculosis Niche and Initiate Dissemination. 

» Cohen SB, Gern BH, Delahaye JL, Adams KN, Plumlee CR, Winkler JK, Sherman DR, Gerner MY, Urdahl KB.  Cell Host Microbe. 2018 Sep 12;24(3):439-446.e4. doi: 10.1016/j.chom.2018.08.001. Epub 2018 Aug 23. PMID: 30146391; PMCID: PMC6152889.

16.) 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 Feb 8;554(7691):255-259. doi: 10.1038/nature25437. Epub 2018 Jan 22. PMID: 29364878.

17.) Dendritic cell and antigen dispersal landscapes regulate T cell immunity.

» Gerner MY, Casey KA, Kastenmuller W, Germain RN.  J Exp Med. 2017 Oct 2;214(10):3105-3122. doi: 10.1084/jem.20170335. Epub 2017 Aug 28. PMID: 28847868; PMCID: PMC5626399.

18.) Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D).

» Li W, Germain RN, Gerner MY.  Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7321-E7330. doi: 10.1073/pnas.1708981114. Epub 2017 Aug 14. PMID: 28808033; PMCID: PMC5584454.

19.) Follicular CD8 T cells accumulate in HIV infection and can kill infected cells in vitro via bispecific antibodies.

» Petrovas C, Ferrando-Martinez S, Gerner MY, Casazza JP, Pegu A, Deleage C, Cooper A, Hataye J, Andrews S, Ambrozak D, Del Río Estrada PM, Boritz E, Paris R, Moysi E, Boswell KL, Ruiz-Mateos E, Vagios I, Leal M, Ablanedo-Terrazas Y, Rivero A, Gonzalez-Hernandez LA, McDermott AB, Moir S, Reyes-Terán G, Docobo F, Pantaleo G, Douek DC, Betts MR, Estes JD, Germain RN, Mascola JR, Koup RA. Sci Transl Med. 2017 Jan 18;9(373). pii: eaag2285. doi: 10.1126/scitranslmed.aag2285.

20.) Allergen-Induced CD4+ T Cell Cytokine Production within Airway Mucosal Dendritic Cell-T Cell Clusters Drives the Local Recruitment of Myeloid Effector Cells.

» Veres TZ, Kopcsányi T, van Panhuys N, Gerner MY, Liu Z, Rantakari P, Dunkel J, Miyasaka M, Salmi M, Jalkanen S, Germain RN. J Immunol. 2017 Jan 15;198(2):895-907. doi: 10.4049/jimmunol.1601448. Epub 2016 Nov 30.

21.) Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy.

» Im SJ, Hashimoto M, Gerner MY, Lee J, Kissick HT, Burger MC, Shan Q, Hale JS, Lee J, Nasti TH, Sharpe AH, Freeman GJ, Germain RN, Nakaya HI, Xue HH, Ahmed R. Nature. 2016 Sep 15;537(7620):417-421. doi: 10.1038/nature19330. Epub 2016 Aug 2.

22.) Immune homeostasis enforced by co-localized effector and regulatory T cells.

» Liu Z, Gerner MY, Van Panhuys N, Levine AG, Rudensky AY, Germain RN. Nature. 2015 Dec 10;528(7581):225-30. doi: 10.1038/nature16169. Epub 2015 Nov 25.

23.) In vivo characterization of the physicochemical properties of polymer-linked TLR agonists that enhance vaccine immunogenicity.

» Lynn GM, Laga R, Darrah PA, Ishizuka AS, Balaci AJ, Dulcey AE, Pechar M, Pola R, Gerner MY, Yamamoto A, Buechler CR, Quinn KM, Smelkinson MG, Vanek O, Cawood R, Hills T, Vasalatiy O, Kastenmüller K, Francica JR, Stutts L, Tom JK, Ryu KA, Esser-Kahn AP, Etrych T, Fisher KD, Seymour LW, Seder RA. Nat Biotechnol. 2015 Nov;33(11):1201-10. doi: 10.1038/nbt.3371. Epub 2015 Oct 26.

24.) Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity.

» Fonseca DM, Hand TW, Han SJ, Gerner MY, Glatman Zaretsky A, Byrd AL, Harrison OJ, Ortiz AM, Quinones M, Trinchieri G, Brenchley JM, Brodsky IE, Germain RN, Randolph GJ, Belkaid Y. Cell. 2015 Oct 8;163(2):354-66. doi: 10.1016/j.cell.2015.08.030.

25.) Robust Anti-viral Immunity Requires Multiple Distinct T Cell-Dendritic Cell Interactions.

» Eickhoff S, Brewitz A, Gerner MY, Klauschen F, Komander K, Hemmi H, Garbi N, Kaisho T, Germain RN, Kastenmüller W. Cell. 2015 Sep 10;162(6):1322-37. doi: 10.1016/j.cell.2015.08.004. Epub 2015 Aug 18.

26.) Lymph-node resident CD8α+ dendritic cells capture antigens from migratory malaria sporozoites and induce CD8+ T cell responses.

» Radtke AJ, Kastenmüller W, Espinosa DA, Gerner MY, Tse SW, Sinnis P, Germain RN, Zavala FP, Cockburn IA. PLoS Pathog. 2015 Feb 6;11(2):e1004637. doi: 10.1371/journal.ppat.1004637. eCollection 2015 Feb.

27.) Strategically localized dendritic cells promote rapid T cell responses to lymph-borne particulate antigens.

» Gerner MY, Torabi-Parizi P, Germain RN. Immunity. 2015 Jan 20;42(1):172-85. doi: 10.1016/j.immuni.2014.12.024. Epub 2014 Dec 27.

28.) Pathogen-related differences in the abundance of presented antigen are reflected in CD4+ T cell dynamic behavior and effector function in the lung.

» Torabi-Parizi P, Vrisekoop N, Kastenmuller W, Gerner MY, Egen JG, Germain RN. J Immunol. 2014 Feb 15;192(4):1651-60. doi: 10.4049/jimmunol.1301743. Epub 2014 Jan 15.

29.) Cutting edge: IL-12 and type I IFN differentially program CD8 T cells for programmed death 1 re-expression levels and tumor control.

» Gerner MY, Heltemes-Harris LM, Fife BT, Mescher MF. J Immunol. 2013 Aug 1;191(3):1011-5. doi: 10.4049/jimmunol.1300652. Epub 2013 Jun 26.

30.) CD4 T follicular helper cell dynamics during SIV infection.

» 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. J Clin Invest. 2012 Sep;122(9):3281-94. doi: 10.1172/JCI63039. Epub 2012 Aug 27.

31.) Histo-cytometry: a method for highly multiplex quantitative tissue imaging analysis applied to dendritic cell subset microanatomy in lymph nodes.

» Gerner MY, Kastenmuller W, Ifrim I, Kabat J, Germain RN. Immunity. 2012 Aug 24;37(2):364-76. doi: 10.1016/j.immuni.2012.07.011. Epub 2012 Aug 2.

32.) The in situ dynamics of dendritic cell interactions.

» Kastenmüller W, Gerner MY, Germain RN. Eur J Immunol. 2010 Aug;40(8):2103-6. doi: 10.1002/eji.201040482.

33.) Antigen processing and MHC-II presentation by dermal and tumor-infiltrating dendritic cells.

» Gerner MY, Mescher MF. J Immunol. 2009 Mar 1;182(5):2726-37. doi: 10.4049/jimmunol.0803479.

34.) Defective MHC class II presentation by dendritic cells limits CD4 T cell help for antitumor CD8 T cell responses.

» Gerner MY, Casey KA, Mescher MF. J Immunol. 2008 Jul 1;181(1):155-64.

35.) Signal 3 availability limits the CD8 T cell response to a solid tumor.

» Curtsinger JM, Gerner MY, Lins DC, Mescher MF. J Immunol. 2007 Jun 1;178(11):6752-60.