James Gardner, MD, PhD

Title(s)Assistant Professor, Surgery
SchoolSchool of Medicine
Address505 Parnassus Avenue, #M896E
San Francisco CA 94117
Phone415-514-7420
ORCID ORCID Icon0000-0003-3470-9520 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Harvard University, Cambridge, MAAB06/2002Biochemistry
    University of California San Francisco, San Francisco, CAMD/PhD06/2012Genetics
    University of California San Francisco, San Francisco, CAResident06/2016General Surgery
    University of California San Francisco, San Francisco, CAChief Resident06/2017General Surgery
    University of California San Francisco, San Francisco, CAClinical Instructor and Fellow08/2019Abdominal Transplant Surgery
    Collapse Awards and Honors
    The Pew Charitable Trusts2023  - 2027Pew Biomedical Scholar
    Burroughs Wellcome Fund2023  - 2027Burroughs Wellcome Next Gen Pregnancy Initiative
    UCSF Dean's Office2019  - 2024Sandler PSSP Grant
    American Society of Transplant Surgeons2017  - 2019ASTS-Astellas Fellowship in Transplantation Grant
    UCSF Department of Surgery2017  - 2017Nusz Achievement Award
    UCSF Division of Trauma and Critical Care2016  - 2016Schecter Award for Senior Trauma Fellow
    UCSF Emergency Medicine2016  - 2016ED Surgical Consultant of the Year
    Parker Institute for Cancer Immunotherapy2024PICI Investigator

    Collapse Overview 
    Collapse Overview
    The Gardner lab studies fundamental mechanisms of immune tolerance -- how the immune system learns to distinguish self from non-self -- and how this understanding can be applied in the context of autoimmunity, transplantation, maternal-fetal tolerance, and cancer immunology.

    We have a particular focus on the biology and function of a unique group of cells expressing the Autoimmune Regulator (Aire) gene. Previously the lab identified extra-Thymic Aire-expressing Cells (eTACs), a novel population that plays significant roles in immune homeostasis and immune tolerance. We have since described the fundamental biology and identity of eTACs, as well as defined potential roles for these populations in autoimmune diabetes and in maternal-fetal tolerance.

    We utilize multimodal approaches from transgenic engineering to single-cell multiomics to understand the biology and immunology of these unique populations, and more broadly of immune tolerance mechanisms.

    The Gardner lab also works closely with the UCSF Transplant community and with the VIable Tissue Acquisition Lab (VITAL) Core, which Dr. Gardner established and directs, to advance groundbreaking research in human immunology and human biology. We work collaboratively with a range of investigators locally and nationally in these efforts.
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Chimeric autoantibody-receptor T cells mediate depletion of autoantibody-producing B cells. Am J Transplant. 2024 May 01. Yin HS, Gillis-Buck EM, Gardner JM. PMID: 38701897.
      View in: PubMed   Mentions:
    2. Maternal-fetal microchimerism as a durable but finite and replaceable alloantigen reservoir. Am J Transplant. 2024 Apr; 24(4):512-513. Gillis-Buck EM, Gardner JM. PMID: 38556430.
      View in: PubMed   Mentions:    Fields:    
    3. Aire in Autoimmunity. Annu Rev Immunol. 2024 Feb 15. Miller CN, Waterfield MR, Gardner JM, Anderson MS. PMID: 38360547.
      View in: PubMed   Mentions:    Fields:    
    4. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nat Cell Biol. 2024 Feb; 26(2):250-262. Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. PMID: 38321203.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    5. Circadian clocks drive rhythmic antitumor immune responses mediated by migratory dendritic cells. Am J Transplant. 2024 Feb; 24(2):154-155. Chu SN, Gardner JM. PMID: 38159886.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    6. Dynamic encounters with red blood cells trigger splenic marginal zone B cell retention and function. Nat Immunol. 2024 Jan; 25(1):142-154. Liu D, Winer BY, Chou MY, Tam H, Xu Y, An J, Gardner JM, Cyster JG. PMID: 38049580; PMCID: PMC10761324.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    7. Successful cryopreservation of functional kidney allografts using vitrification and nanorewarming. Am J Transplant. 2023 Dec; 23(12):1822-1823. Rickert CG, Gardner JM. PMID: 37918481.
      View in: PubMed   Mentions:    Fields:    
    8. Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance. Sci Immunol. 2023 10 27; 8(88):eabq3109. Sin JH, Sucharov J, Kashyap S, Wang Y, Proekt I, Liu X, Parent AV, Gupta A, Kastner P, Chan S, Gardner JM, Ntranos V, Miller CN, Anderson MS, Schjerven H, Waterfield MR. PMID: 37889983.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    9. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis. J Clin Invest. 2023 10 16; 133(20). Reyes EA, Castillo-Azofeifa D, Rispal J, Wald T, Zwick RK, Palikuqi B, Mujukian A, Rabizadeh S, Gupta AR, Gardner JM, Boffelli D, Gartner ZJ, Klein OD. PMID: 37643009; PMCID: PMC10575728.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    10. RORγt-lineage APCs: The Aire apparent. Sci Immunol. 2022 Dec 23; 7(78):eade9240. Gardner JM, Liston A. PMID: 36525506.
      View in: PubMed   Mentions: 2     Fields:    
    11. Tissue-specific mitochondrial HIGD1C promotes oxygen sensitivity in carotid body chemoreceptors. Elife. 2022 10 18; 11. Timón-Gómez A, Scharr AL, Wong NY, Ni E, Roy A, Liu M, Chau J, Lampert JL, Hireed H, Kim NS, Jan M, Gupta AR, Day RW, Gardner JM, Wilson RJA, Barrientos A, Chang AJ. PMID: 36255054; PMCID: PMC9635879.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    12. A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation. Nature. 2022 10; 610(7933):737-743. Kedmi R, Najar TA, Mesa KR, Grayson A, Kroehling L, Hao Y, Hao S, Pokrovskii M, Xu M, Talbot J, Wang J, Germino J, Lareau CA, Satpathy AT, Anderson MS, Laufer TM, Aifantis I, Bartleson JM, Allen PM, Paidassi H, Gardner JM, Stoeckius M, Littman DR. PMID: 36071167; PMCID: PMC9908423.
      View in: PubMed   Mentions: 48     Fields:    Translation:Cells
    13. A novel microsurgical reconstruction technique in a living-related liver donor hepatic artery dissection using the native hepatic artery. Am J Transplant. 2022 10; 22(10):2467-2469. Sitta R, Roberts J, Gardner J, Ascher N, Piper M. PMID: 35612995.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. Nodular Regenerative Hyperplasia After Liver Transplant; It's All in the Presentation. Front Surg. 2022; 9:876818. Chen AK, Lunow-Luke T, Yamaguchi S, Praglin C, Agudelo E, Mehta N, Dirks R, Braun HJ, Gardner JM, Roberts JP, Syed SM, Roll GR. PMID: 35656084; PMCID: PMC9152168.
      View in: PubMed   Mentions: 1  
    15. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science. 2022 05 13; 376(6594):eabl4896. Tabula Sapiens Consortium*, Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, Aaron KA, Concepcion W, Gardner JM, Kelly B, Neidlinger N, Wang Z, Crasta S, Kolluru S, Morri M, Tan SY, Travaglini KJ, Xu C, Alcántara-Hernández M, Almanzar N, Antony J, Beyersdorf B, Burhan D, Calcuttawala K, Carter MM, Chan CKF, Chang CA, Chang S, Colville A, Culver RN, Cvijovic I, D'Amato G, Ezran C, Galdos FX, Gillich A, Goodyer WR, Hang Y, Hayashi A, Houshdaran S, Huang X, Irwin JC, Jang S, Juanico JV, Kershner AM, Kim S, Kiss B, Kong W, Kumar ME, Kuo AH, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Puluca N, Qi Z, Rao P, Raquer-McKay H, Schaum N, Scott B, Seddighzadeh B, Segal J, Sen S, Sikandar S, Spencer SP, Steffes LC, Subramaniam VR, Swarup A, Swift M, Van Treuren W, Trimm E, Veizades S, Vijayakumar S, Vo KC, Vorperian SK, Wang W, Weinstein HNW, Winkler J, Wu TTH, Xie J, Yung AR, Zhang Y, Detweiler AM, Mekonen H, Neff NF, Sit RV, Tan M, Yan J, Bean GR, Charu V, Forgó E, Martin BA, Ozawa MG, Silva O, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, Olivieri JE, Park M, Ravikumar N, Stanley G, Tan W, Tarashansky AJ, Vanheusden R, Wang P, Wang S, Xing G, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Leylek R, Liu S, Maltzman JS, Metzger RJ, Phansalkar R, Sasagawa K, Sinha R, Song H, Swarup A, Trimm E, Veizades S, Wang B, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Kuo CS, Nguyen P, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wu A, Wu SM, Wyss-Coray T. PMID: 35549404; PMCID: PMC9812260.
      View in: PubMed   Mentions: 185     Fields:    Translation:HumansCells
    16. Thymic and extrathymic Aire-expressing cells in maternal-fetal tolerance. Immunol Rev. 2022 07; 308(1):93-104. Sun IH, Gillis-Buck E, Mackenzie TC, Gardner JM. PMID: 35535447.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    17. Internal hernia involving the transplant ureter after simultaneous pancreas and kidney transplant - and the atypical management of a consequent transplant ureteral injury. Clin Transplant. 2022 07; 36(7):e14675. Gupta AR, Kelly YM, Syed SM, Gardner JM. PMID: 35430751.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    18. Procurement of Deceased Donor Parathyroid Glands With the Aid of Near-infrared Autofluorescence Imaging. Transplant Direct. 2022 Apr; 8(4):e1306. Ward CJ, Kelly YM, Syed SM, Meier RPH, Ando T, Wisel SA, Gardner JM, Stock PG, Duh QY. PMID: 35310601; PMCID: PMC8923582.
      View in: PubMed   Mentions:
    19. Cell types of origin of the cell-free transcriptome. Nat Biotechnol. 2022 06; 40(6):855-861. Vorperian SK, Moufarrej MN, Tabula Sapiens Consortium, Quake SR. PMID: 35132263; PMCID: PMC9200634.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    20. Advantages and Limitations of Clinical Scores for Donation After Circulatory Death Liver Transplantation. Front Surg. 2021; 8:808733. Meier RPH, Kelly Y, Yamaguchi S, Braun HJ, Lunow-Luke T, Adelmann D, Niemann C, Maluf DG, Dietch ZC, Stock PG, Kang SM, Feng S, Posselt AM, Gardner JM, Syed SM, Hirose R, Freise CE, Ascher NL, Roberts JP, Roll GR. PMID: 35071316; PMCID: PMC8766343.
      View in: PubMed   Mentions: 4  
    21. Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. Sci Immunol. 2021 Nov 12; 6(65):eabl5053. Wang J, Lareau CA, Bautista JL, Gupta AR, Sandor K, Germino J, Yin Y, Arvedson MP, Reeder GC, Cramer NT, Xie F, Ntranos V, Satpathy AT, Anderson MS, Gardner JM. PMID: 34767455; PMCID: PMC8855935.
      View in: PubMed   Mentions: 23     Fields:    Translation:Animals
    22. RNA splicing programs define tissue compartments and cell types at single-cell resolution. Elife. 2021 09 13; 10. Olivieri JE, Dehghannasiri R, Wang PL, Jang S, de Morree A, Tan SY, Ming J, Ruohao Wu A, Tabula Sapiens Consortium, Quake SR, Krasnow MA, Salzman J. PMID: 34515025; PMCID: PMC8563012.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    23. Extrathymic Aire-expressing cells support maternal-fetal tolerance. Sci Immunol. 2021 07 16; 6(61). Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC. PMID: 34272228; PMCID: PMC9363019.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    24. A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance. J Exp Med. 2021 08 02; 218(8). Warshauer JT, Belk JA, Chan AY, Wang J, Gupta AR, Shi Q, Skartsis N, Peng Y, Phipps JD, Acenas D, Smith JA, Tamaki SJ, Tang Q, Gardner JM, Satpathy AT, Anderson MS. PMID: 34115115; PMCID: PMC8203485.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    25. Transplantation From Older Donors: Can Senolytics Turn Back the Clock? Transplantation. 2021 04 01; 105(4):681-682. Dixon W, Feng S, Gardner J. PMID: 33760787.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    26. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nat Commun. 2021 02 17; 12(1):1096. Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV. PMID: 33597545; PMCID: PMC7889611.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    27. Surgical, Interventional, and Medical Palliation of Portal Hypertension. Am Surg. 2020 Nov; 86(11):1467-1472. Lin JA, Gardner JM, Kolli KP, Cook AC. PMID: 33153284.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    28. CON: Portal Vein Thrombosis Does Not Impact Liver Transplantation Outcomes. Clin Liver Dis (Hoboken). 2020 Oct; 16(4):132. Sherman C, Syed S, Gardner J, Yao FY. PMID: 33163163; PMCID: PMC7609708.
      View in: PubMed   Mentions:
    29. COVID-19 and Abdominal Transplant: A Stepwise Approach to Practice During Pandemic Conditions. Transplantation. 2020 11; 104(11):2215-2220. Syed SM, Gardner J, Roll G, Webber A, Mehta N, Shoji J, Adelmann D, Niemann C, Braun HJ, Mello A, Yao F, Posselt A, Kang SM, Hirose R, Roberts J, Feng S, Ascher N, Stock P, Freise C. PMID: 32639408; PMCID: PMC7363383.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCellsPHPublic Health
    30. Curr Hepatology Rep. Non-selective Beta-Blockers in Decompensated Cirrhosis. 2020. Huang, A.C., Gardner, J.M. & Hameed, B. View Publication.
    31. Ethical Issues in the COVID Era: Doing the Right Thing Depends on Location, Resources, and Disease Burden. Transplantation. 2020 07; 104(7):1316-1320. Stock PG, Wall A, Gardner J, Domínguez-Gil B, Chadban S, Muller E, Dittmer I, Tullius SG, TTS Ethics Committee. PMID: 32569002; PMCID: PMC7340125.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCellsPHPublic Health
    32. Pancreas-After-Islet Transplantation in Nonuremic Type 1 Diabetes: A Strategy for Restoring Durable Insulin Independence. Am J Transplant. 2017 Sep; 17(9):2444-2450. Wisel SA, Gardner JM, Roll GR, Harbell J, Freise CE, Feng S, Kang SM, Hirose R, Kaufman DB, Posselt AM, Stock PG. PMID: 28489277; PMCID: PMC5573612.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    33. Effect of intratonsillar injection of steroids on the palatine tonsils of rabbits. Laryngoscope. 2014 Dec; 124(12):2811-7. Cho DY, Sinha SR, Gardner JM, Schaller MP, Pamnani RD, Felt SA, Barral JK, Messner AH. PMID: 24114886.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    34. Lineage tracing and cell ablation identify a post-Aire-expressing thymic epithelial cell population. Cell Rep. 2013 Oct 17; 5(1):166-79. Metzger TC, Khan IS, Gardner JM, Mouchess ML, Johannes KP, Krawisz AK, Skrzypczynska KM, Anderson MS. PMID: 24095736; PMCID: PMC3820422.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    35. Extrathymic Aire-expressing cells are a distinct bone marrow-derived population that induce functional inactivation of CD4⁺ T cells. Immunity. 2013 Sep 19; 39(3):560-72. Gardner JM, Metzger TC, McMahon EJ, Au-Yeung BB, Krawisz AK, Lu W, Price JD, Johannes KP, Satpathy AT, Murphy KM, Tarbell KV, Weiss A, Anderson MS. PMID: 23993652; PMCID: PMC3804105.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    36. Neuropilin-1 distinguishes natural and inducible regulatory T cells among regulatory T cell subsets in vivo. J Exp Med. 2012 Sep 24; 209(10):1713-22, S1-19. Yadav M, Louvet C, Davini D, Gardner JM, Martinez-Llordella M, Bailey-Bucktrout S, Anthony BA, Sverdrup FM, Head R, Kuster DJ, Ruminski P, Weiss D, Von Schack D, Bluestone JA. PMID: 22966003; PMCID: PMC3457729.
      View in: PubMed   Mentions: 359     Fields:    Translation:AnimalsCells
    37. Immunoendocrinology: Scientific and Clinical Aspects. Eisenbarth, GS (Ed.). The Mouse Model of Autoimmune Polyglandular Syndrome Type I. 2011; 1(1):95-113. Gardner JM, Anderson MA.
    38. AIRE in the thymus and beyond. Curr Opin Immunol. 2009 Dec; 21(6):582-9. Gardner JM, Fletcher AL, Anderson MS, Turley SJ. PMID: 19833494; PMCID: PMC2787634.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    39. The sickness unto Deaf. Nat Immunol. 2009 Sep; 10(9):934-6. Gardner JM, Anderson MS. PMID: 19692991; PMCID: PMC2773699.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    40. Deletional tolerance mediated by extrathymic Aire-expressing cells. Science. 2008 Aug 08; 321(5890):843-7. Gardner JM, Devoss JJ, Friedman RS, Wong DJ, Tan YX, Zhou X, Johannes KP, Su MA, Chang HY, Krummel MF, Anderson MS. PMID: 18687966; PMCID: PMC2532844.
      View in: PubMed   Mentions: 242     Fields:    Translation:AnimalsCells
    41. Mycobacterium tuberculosis-specific CD8+ T cells preferentially recognize heavily infected cells. Am J Respir Crit Care Med. 2003 Dec 01; 168(11):1346-52. Lewinsohn DA, Heinzel AS, Gardner JM, Zhu L, Alderson MR, Lewinsohn DM. PMID: 12969871.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
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