Joel Ernst, MD

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1001 Potrero Ave
San Francisco, CA 94110

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  • Professor, School of Medicine
  • Professor of Medicine, UCSF


Our laboratory studies the mechanisms of protective and pathological immunity to Mycobacterium tuberculosis, the bacteria that cause tuberculosis (TB). Even though TB can be treated and potentially cured, it still causes more human mortality than any other infectious disease, including HIV. Our goal is to inform development of effective TB vaccines, and for this we use mouse models and human translational immunology studies.

We use mouse models to discover and characterize mechanisms of immune evasion employed by M. tuberculosis to prevent immune responses from clearing the infection and establishing sterile immunity and memory.

Displaying 1 - 75 of 75

  1. Fossati A, Richards AL, Chen KH, Jaganath D, Cattamanchi A, Ernst JD, Swaney DL. Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion. J Proteome Res. 2021 08 06; 20(8):4031-4040. View on Pubmed
  2. Nathan A, Beynor JI, Baglaenko Y, Suliman S, Ishigaki K, Asgari S, Huang CC, Luo Y, Zhang Z, Lopez K, Lindestam Arlehamn CS, Ernst JD, Jimenez J, Calderón RI, Lecca L, Van Rhijn I, Moody DB, Murray MB, Raychaudhuri S. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nat Immunol. 2021 06; 22(6):781-793. View on Pubmed
  3. Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A. Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins. Cell Rep. 2021 May 11; 35(6):109105. View on Pubmed
  4. McLaughlin TA, Nizam A, Hayara FO, Ouma GS, Campbell A, Khayumbi J, Ongalo J, Ouma SG, Shah NS, Altman JD, Kaushal D, Rengarajan J, Ernst JD, Blumberg HM, Waller LA, Gandhi NR, Day CL, Benkeser D. Schistosoma mansoni Infection Is Associated With a Higher Probability of Tuberculosis Disease in HIV-Infected Adults in Kenya. J Acquir Immune Defic Syndr. 2021 02 01; 86(2):157-163. View on Pubmed
  5. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 10; 38(10):1174-1183. View on Pubmed
  6. Collins JM, Siddiqa A, Jones DP, Liu K, Kempker RR, Nizam A, Shah NS, Ismail N, Ouma SG, Tukvadze N, Li S, Day CL, Rengarajan J, Brust JC, Gandhi NR, Ernst JD, Blumberg HM, Ziegler TR. Tryptophan catabolism reflects disease activity in human tuberculosis. JCI Insight. 2020 05 21; 5(10). View on Pubmed
  7. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv. 2020 May 17. View on Pubmed
  8. Foreman TW, Bucsan AN, Mehra S, Peloquin C, Doyle LA, Russell-Lodrigue K, Gandhi NR, Altman J, Day CL, Ernst JD, Blumberg HM, Rengarajan J, Kaushal D. Isoniazid and Rifapentine Treatment Eradicates Persistent Mycobacterium tuberculosis in Macaques. Am J Respir Crit Care Med. 2020 02 15; 201(4):469-477. View on Pubmed
  9. Rivera-Correa J, de Siqueira IC, Mota S, do Rosário MS, Pereira de Jesus PA, Alcantara LCJ, Ernst JD, Rodriguez A. Anti-ganglioside antibodies in patients with Zika virus infection-associated Guillain-Barré Syndrome in Brazil. PLoS Negl Trop Dis. 2019 09; 13(9):e0007695. View on Pubmed
  10. Ernst JD, Cornelius A, Bolz M. Dynamics of Mycobacterium tuberculosis Ag85B Revealed by a Sensitive Enzyme-Linked Immunosorbent Assay. mBio. 2019 04 23; 10(2). View on Pubmed
  11. Norris BA, Ernst JD. Mononuclear cell dynamics in M. tuberculosis infection provide opportunities for therapeutic intervention. PLoS Pathog. 2018 10; 14(10):e1007154. View on Pubmed
  12. Ernst JD, Cornelius A, Desvignes L, Tavs J, Norris BA. Limited Antimycobacterial Efficacy of Epitope Peptide Administration Despite Enhanced Antigen-Specific CD4 T-Cell Activation. J Infect Dis. 2018 10 05; 218(10):1653-1662. View on Pubmed
  13. Ernst JD. Mechanisms of M. tuberculosis Immune Evasion as Challenges to TB Vaccine Design. Cell Host Microbe. 2018 07 11; 24(1):34-42. View on Pubmed
  14. Ernst JD. Float Like Bacilli, STING Like a B: Type I Interferons in Tuberculosis. Am J Respir Crit Care Med. 2018 03 15; 197(6):706-707. View on Pubmed
  15. Whatney WE, Gandhi NR, Lindestam Arlehamn CS, Nizam A, Wu H, Quezada MJ, Campbell A, Allana S, Kabongo MM, Khayumbi J, Muchiri B, Ongalo J, Tonui J, Sasser LE, Fergus TJ, Ouma GS, Ouma SG, Beck AA, Mulligan MJ, Oladele A, Kaushal D, Cain KP, Waller L, Blumberg HM, Altman JD, Ernst JD, Rengarajan J, Day CL, TBRU-ASTRa Study Group . A High Throughput Whole Blood Assay for Analysis of Multiple Antigen-Specific T Cell Responses in Human Mycobacterium tuberculosis Infection. J Immunol. 2018 04 15; 200(8):3008-3019. View on Pubmed
  16. Bolz M, Ernst JD. Fishing for Answers in Human Mycobacterial Infections. Immunity. 2017 09 19; 47(3):395-397. View on Pubmed
  17. Boggiano C, Eichelberg K, Ramachandra L, Shea J, Ramakrishnan L, Behar S, Ernst JD, Porcelli SA, Maeurer M, Kornfeld H. "The Impact of Mycobacterium tuberculosis Immune Evasion on Protective Immunity: Implications for TB Vaccine Design" - Meeting report. Vaccine. 2017 06 14; 35(27):3433-3440. View on Pubmed
  18. Arlehamn CS, Copin R, Leary S, Mack SJ, Phillips E, Mallal S, Sette A, Blatner G, Siefers H, Ernst JD, TBRU-ASTRa Study Team . Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 100 Luo infants from the Boro area of Nyanza Province, Kenya. Hum Immunol. 2017 Apr; 78(4):325-326. View on Pubmed
  19. Ernst JD. Antigenic Variation and Immune Escape in the MTBC. Adv Exp Med Biol. 2017; 1019:171-190. View on Pubmed
  20. Copin R, Wang X, Louie E, Escuyer V, Coscolla M, Gagneux S, Palmer GH, Ernst JD. Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity. PLoS Pathog. 2016 Dec; 12(12):e1006111. View on Pubmed
  21. Portal-Celhay C, Tufariello JM, Srivastava S, Zahra A, Klevorn T, Grace PS, Mehra A, Park HS, Ernst JD, Jacobs WR, Philips JA. Mycobacterium tuberculosis EsxH inhibits ESCRT-dependent CD4+ T-cell activation. Nat Microbiol. 2016 Dec 05; 2:16232. View on Pubmed
  22. Wiens KE, Ernst JD. Type I Interferon is Pathogenic During Chronic Mycobacterium africanum Infection. J Infect Dis. 2016 Dec 15; 214(12):1893-1896. View on Pubmed
  23. Blumberg HM, Ernst JD. The Challenge of Latent TB Infection. JAMA. 2016 Sep 06; 316(9):931-3. View on Pubmed
  24. Wiens KE, Ernst JD. The Mechanism for Type I Interferon Induction by Mycobacterium tuberculosis is Bacterial Strain-Dependent. PLoS Pathog. 2016 08; 12(8):e1005809. View on Pubmed
  25. Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, Ernst JD, Hatherill M, Hanekom WA, Peters B, Scriba TJ, Sette A. A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans. PLoS Pathog. 2016 07; 12(7):e1005760. View on Pubmed
  26. Srivastava S, Grace PS, Ernst JD. Antigen Export Reduces Antigen Presentation and Limits T Cell Control of M. tuberculosis. . 2016 Jan 13; 19(1):44-54. View on Pubmed
  27. Gaur RL, Ren K, Blumenthal A, Bhamidi S, Gibbs S, Jackson M, Zare RN, Ehrt S, Ernst JD, Banaei N. Correction: LprG-Mediated Surface Expression of Lipoarabinomannan Is Essential for Virulence of Mycobacterium tuberculosis. PLoS Pathog. 2015 Dec; 11(12):e1005336. View on Pubmed
  28. Grace PS, Ernst JD. Suboptimal Antigen Presentation Contributes to Virulence of Mycobacterium tuberculosis In Vivo. J Immunol. 2016 Jan 01; 196(1):357-64. View on Pubmed
  29. Coscolla M, Copin R, Sutherland J, Gehre F, de Jong B, Owolabi O, Mbayo G, Giardina F, Ernst JD, Gagneux S. M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens. . 2015 Nov 11; 18(5):538-48. View on Pubmed
  30. Desvignes L, Weidinger C, Shaw P, Vaeth M, Ribierre T, Liu M, Fergus T, Kozhaya L, McVoy L, Unutmaz D, Ernst JD, Feske S. STIM1 controls T cell-mediated immune regulation and inflammation in chronic infection. J Clin Invest. 2015 Jun; 125(6):2347-62. View on Pubmed
  31. Young DC, Layre E, Pan SJ, Tapley A, Adamson J, Seshadri C, Wu Z, Buter J, Minnaard AJ, Coscolla M, Gagneux S, Copin R, Ernst JD, Bishai WR, Snider BB, Moody DB. In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. Chem Biol. 2015 Apr 23; 22(4):516-526. View on Pubmed
  32. Srivastava S, Ernst JD, Desvignes L. Beyond macrophages: the diversity of mononuclear cells in tuberculosis. Immunol Rev. 2014 Nov; 262(1):179-92. View on Pubmed
  33. Gaur RL, Ren K, Blumenthal A, Bhamidi S, González-Nilo FD, Gibbs S, Jackson M, Zare RN, Ehrt S, Ernst JD, Banaei N. LprG-mediated surface expression of lipoarabinomannan is essential for virulence of Mycobacterium tuberculosis. PLoS Pathog. 2014 Sep; 10(9):e1004376. View on Pubmed
  34. Copin R, Coscollá M, Efstathiadis E, Gagneux S, Ernst JD. Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG). Vaccine. 2014 Oct 14; 32(45):5998-6004. View on Pubmed
  35. Srivastava S, Ernst JD. Cell-to-cell transfer of M. tuberculosis antigens optimizes CD4 T cell priming. . 2014 Jun 11; 15(6):741-52. View on Pubmed
  36. Copin R, Coscollá M, Seiffert SN, Bothamley G, Sutherland J, Mbayo G, Gagneux S, Ernst JD. Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. mBio. 2014 Jan 14; 5(1):e00960-13. View on Pubmed
  37. Wiens KE, Swaminathan H, Copin R, Lun DS, Ernst JD. Equivalent T cell epitope promiscuity in ecologically diverse human pathogens. PLoS One. 2013; 8(8):e73124. View on Pubmed
  38. Srivastava S, Ernst JD. Cutting edge: Direct recognition of infected cells by CD4 T cells is required for control of intracellular Mycobacterium tuberculosis in vivo. J Immunol. 2013 Aug 01; 191(3):1016-20. View on Pubmed
  39. Desvignes LP, Ernst JD. Taking sides: interferons in leprosy. . 2013 Apr 17; 13(4):377-8. View on Pubmed
  40. Fan L, Xiao HP, Hu ZY, Ernst JD. Variation of Mycobacterium tuberculosis antigen-specific IFN-γ and IL-17 responses in healthy tuberculin skin test (TST)-positive human subjects. PLoS One. 2012; 7(8):e42716. View on Pubmed
  41. Bold TD, Ernst JD. CD4+ T cell-dependent IFN-γ production by CD8+ effector T cells in Mycobacterium tuberculosis infection. J Immunol. 2012 Sep 01; 189(5):2530-6. View on Pubmed
  42. Ernst JD. The immunological life cycle of tuberculosis. Nat Rev Immunol. 2012 Jul 13; 12(8):581-91. View on Pubmed
  43. Ernst JD, Hanekom W, Hawn T, Kampmann B, Rengarajan J. Meeting report: The International Conference on Human Immunity to Tuberculosis. Tuberculosis (Edinb). 2012 Sep; 92(5):440-4. View on Pubmed
  44. Desvignes L, Wolf AJ, Ernst JD. Dynamic roles of type I and type II IFNs in early infection with Mycobacterium tuberculosis. J Immunol. 2012 Jun 15; 188(12):6205-15. View on Pubmed
  45. Bold TD, Davis DC, Penberthy KK, Cox LM, Ernst JD, de Jong BC. Impaired fitness of Mycobacterium africanum despite secretion of ESAT-6. J Infect Dis. 2012 Mar 15; 205(6):984-90. View on Pubmed
  46. Blomgran R, Desvignes L, Briken V, Ernst JD. Mycobacterium tuberculosis inhibits neutrophil apoptosis, leading to delayed activation of naive CD4 T cells. . 2012 Jan 19; 11(1):81-90. View on Pubmed
  47. Philips JA, Ernst JD. Tuberculosis pathogenesis and immunity. Annu Rev Pathol. 2012; 7:353-84. View on Pubmed
  48. Bold TD, Banaei N, Wolf AJ, Ernst JD. Suboptimal activation of antigen-specific CD4+ effector cells enables persistence of M. tuberculosis in vivo. PLoS Pathog. 2011 May; 7(5):e1002063. View on Pubmed
  49. Blomgran R, Ernst JD. Lung neutrophils facilitate activation of naive antigen-specific CD4+ T cells during Mycobacterium tuberculosis infection. J Immunol. 2011 Jun 15; 186(12):7110-9. View on Pubmed
  50. Philips JA, Ernst JD. Directly observing therapy: a new view of drug tolerance in tuberculosis. Cell. 2011 Apr 01; 145(1):13-4. View on Pubmed
  51. Kwan CK, Ernst JD. HIV and tuberculosis: a deadly human syndemic. Clin Microbiol Rev. 2011 Apr; 24(2):351-76. View on Pubmed
  52. Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD, Gagneux S. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet. 2010 Jun; 42(6):498-503. View on Pubmed
  53. Desvignes L, Ernst JD. Interferon-gamma-responsive nonhematopoietic cells regulate the immune response to Mycobacterium tuberculosis. Immunity. 2009 Dec 18; 31(6):974-85. View on Pubmed
  54. Olmos S, Stukes S, Ernst JD. Ectopic activation of Mycobacterium tuberculosis-specific CD4+ T cells in lungs of CCR7-/- mice. J Immunol. 2010 Jan 15; 184(2):895-901. View on Pubmed
  55. Benson SA, Ernst JD. TLR2-dependent inhibition of macrophage responses to IFN-gamma is mediated by distinct, gene-specific mechanisms. PLoS One. 2009 Jul 24; 4(7):e6329. View on Pubmed
  56. Banaei N, Kincaid EZ, Lin SY, Desmond E, Jacobs WR, Ernst JD. Lipoprotein processing is essential for resistance of Mycobacterium tuberculosis to malachite green. Antimicrob Agents Chemother. 2009 Sep; 53(9):3799-802. View on Pubmed
  57. Miller EA, Ernst JD. Anti-TNF immunotherapy and tuberculosis reactivation: another mechanism revealed. J Clin Invest. 2009 May; 119(5):1079-82. View on Pubmed
  58. Blumenthal A, Kobayashi T, Pierini LM, Banaei N, Ernst JD, Miyake K, Ehrt S. RP105 facilitates macrophage activation by Mycobacterium tuberculosis lipoproteins. . 2009 Jan 22; 5(1):35-46. View on Pubmed
  59. Bold TD, Ernst JD. Who benefits from granulomas, mycobacteria or host? Cell. 2009 Jan 09; 136(1):17-9. View on Pubmed
  60. Miller EA, Ernst JD. Illuminating the black box of TNF action in tuberculous granulomas. Immunity. 2008 Aug 15; 29(2):175-7. View on Pubmed
  61. Sinnis P, Ernst JD. CO-opting the host HO-1 pathway in tuberculosis and malaria. Cell Host Microbe. 2008 May 15; 3(5):277-9. View on Pubmed
  62. Wolf AJ, Desvignes L, Linas B, Banaiee N, Tamura T, Takatsu K, Ernst JD. Initiation of the adaptive immune response to Mycobacterium tuberculosis depends on antigen production in the local lymph node, not the lungs. J Exp Med. 2008 Jan 21; 205(1):105-15. View on Pubmed
  63. Ernst JD, Lewinsohn DM, Behar S, Blythe M, Schlesinger LS, Kornfeld H, Sette A. Meeting Report: NIH Workshop on the Tuberculosis Immune Epitope Database. Tuberculosis (Edinb). 2008 Jul; 88(4):366-70. View on Pubmed
  64. Blythe MJ, Zhang Q, Vaughan K, de Castro R, Salimi N, Bui HH, Lewinsohn DM, Ernst JD, Peters B, Sette A. An analysis of the epitope knowledge related to Mycobacteria. Immunome Res. 2007 Dec 14; 3:10. View on Pubmed
  65. Kincaid EZ, Wolf AJ, Desvignes L, Mahapatra S, Crick DC, Brennan PJ, Pavelka MS, Ernst JD. Codominance of TLR2-dependent and TLR2-independent modulation of MHC class II in Mycobacterium tuberculosis infection in vivo. J Immunol. 2007 Sep 01; 179(5):3187-95. View on Pubmed
  66. Wolf AJ, Linas B, Trevejo-Nuñez GJ, Kincaid E, Tamura T, Takatsu K, Ernst JD. Mycobacterium tuberculosis infects dendritic cells with high frequency and impairs their function in vivo. J Immunol. 2007 Aug 15; 179(4):2509-19. View on Pubmed
  67. Ernst JD, Trevejo-Nuñez G, Banaiee N. Genomics and the evolution, pathogenesis, and diagnosis of tuberculosis. J Clin Invest. 2007 Jul; 117(7):1738-45. View on Pubmed
  68. Banaiee N, Jacobs WR, Ernst JD. LspA-independent action of globomycin on Mycobacterium tuberculosis. J Antimicrob Chemother. 2007 Aug; 60(2):414-6. View on Pubmed
  69. Banaiee N, Kincaid EZ, Buchwald U, Jacobs WR, Ernst JD. Potent inhibition of macrophage responses to IFN-gamma by live virulent Mycobacterium tuberculosis is independent of mature mycobacterial lipoproteins but dependent on TLR2. J Immunol. 2006 Mar 01; 176(5):3019-27. View on Pubmed
  70. Rosales JL, Ernst JD, Hallows J, Lee KY. GTP-dependent secretion from neutrophils is regulated by Cdk5. J Biol Chem. 2004 Dec 24; 279(52):53932-6. View on Pubmed
  71. Peters W, Cyster JG, Mack M, Schlöndorff D, Wolf AJ, Ernst JD, Charo IF. CCR2-dependent trafficking of F4/80dim macrophages and CD11cdim/intermediate dendritic cells is crucial for T cell recruitment to lungs infected with Mycobacterium tuberculosis. J Immunol. 2004 Jun 15; 172(12):7647-53. View on Pubmed
  72. Fortune SM, Solache A, Jaeger A, Hill PJ, Belisle JT, Bloom BR, Rubin EJ, Ernst JD. Mycobacterium tuberculosis inhibits macrophage responses to IFN-gamma through myeloid differentiation factor 88-dependent and -independent mechanisms. J Immunol. 2004 May 15; 172(10):6272-80. View on Pubmed
  73. Nagabhushanam V, Solache A, Ting LM, Escaron CJ, Zhang JY, Ernst JD. Innate inhibition of adaptive immunity: Mycobacterium tuberculosis-induced IL-6 inhibits macrophage responses to IFN-gamma. J Immunol. 2003 Nov 01; 171(9):4750-7. View on Pubmed
  74. Kincaid EZ, Ernst JD. Mycobacterium tuberculosis exerts gene-selective inhibition of transcriptional responses to IFN-gamma without inhibiting STAT1 function. J Immunol. 2003 Aug 15; 171(4):2042-9. View on Pubmed
  75. Peters W, Ernst JD. Mechanisms of cell recruitment in the immune response to Mycobacterium tuberculosis. Microbes Infect. 2003 Feb; 5(2):151-8. View on Pubmed