James Gardner, MD, PhD
Assistant Professor
Surgery
School of Medicine

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.

• Aire in Autoimmunity.
  Annual review of immunology 2024 Miller CN, Waterfield MR, Gardner JM, Anderson MS
• Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains.
  Nature cell biology 2024 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 …
• Circadian clocks drive rhythmic antitumor immune responses mediated by migratory dendritic cells.
  American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2023 Chu SN, Gardner JM
• Dynamic encounters with red blood cells trigger splenic marginal zone B cell retention and function.
  Nature immunology 2023 Liu D, Winer BY, Chou MY, Tam H, Xu Y, An J, Gardner JM, Cyster JG
• Successful cryopreservation of functional kidney allografts using vitrification and nanorewarming.
  American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2023 Rickert CG, Gardner JM
• Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance.
  Science immunology 2023 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
• Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis.
  The Journal of clinical investigation 2023 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
• RORγt-lineage APCs: The Aire apparent.
  Science immunology 2022 Gardner JM, Liston A
• Tissue-specific mitochondrial HIGD1C promotes oxygen sensitivity in carotid body chemoreceptors.
  eLife 2022 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
• A novel microsurgical reconstruction technique in a living-related liver donor hepatic artery dissection using the native hepatic artery.
  American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2022 Sitta R, Roberts J, Gardner J, Ascher N, Piper M
• Nodular Regenerative Hyperplasia After Liver Transplant; It's All in the Presentation.
  Frontiers in surgery 2022 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
• The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.
  Science (New York, N.Y.) 2022 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, …
• Thymic and extrathymic Aire-expressing cells in maternal-fetal tolerance.
  Immunological reviews 2022 Sun IH, Gillis-Buck E, Mackenzie TC, Gardner JM
• Internal hernia involving the transplant ureter after simultaneous pancreas and kidney transplant - and the atypical management of a consequent transplant ureteral injury.
  Clinical transplantation 2022 Gupta AR, Kelly YM, Syed SM, Gardner JM
• Procurement of Deceased Donor Parathyroid Glands With the Aid of Near-infrared Autofluorescence Imaging.
  Transplantation direct 2022 Ward CJ, Kelly YM, Syed SM, Meier RPH, Ando T, Wisel SA, Gardner JM, Stock PG, Duh QY
• Cell types of origin of the cell-free transcriptome.
  Nature biotechnology 2022 Vorperian SK, Moufarrej MN, Tabula Sapiens Consortium, Quake SR
• Advantages and Limitations of Clinical Scores for Donation After Circulatory Death Liver Transplantation.
  Frontiers in surgery 2022 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…
• RNA splicing programs define tissue compartments and cell types at single-cell resolution.
  eLife 2021 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
• A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance.
  The Journal of experimental medicine 2021 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
• Transplantation From Older Donors: Can Senolytics Turn Back the Clock?
  Transplantation 2021 Dixon W, Feng S, Gardner J
• Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla.
  Nature communications 2021 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
• Surgical, Interventional, and Medical Palliation of Portal Hypertension.
  The American surgeon 2020 Lin JA, Gardner JM, Kolli KP, Cook AC
• CON: Portal Vein Thrombosis Does Not Impact Liver Transplantation Outcomes.
  Clinical liver disease 2020 Sherman C, Syed S, Gardner J, Yao FY
• COVID-19 and Abdominal Transplant: A Stepwise Approach to Practice During Pandemic Conditions.
  Transplantation 2020 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
• Curr Hepatology Rep
  Non-selective Beta-Blockers in Decompensated Cirrhosis. 2020 Huang, A.C., Gardner, J.M. & Hameed, B.
• Ethical Issues in the COVID Era: Doing the Right Thing Depends on Location, Resources, and Disease Burden.
  Transplantation 2020 Stock PG, Wall A, Gardner J, Domínguez-Gil B, Chadban S, Muller E, Dittmer I, Tullius SG, TTS Ethics Committee
• Pancreas-After-Islet Transplantation in Nonuremic Type 1 Diabetes: A Strategy for Restoring Durable Insulin Independence.
  American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2017 Wisel SA, Gardner JM, Roll GR, Harbell J, Freise CE, Feng S, Kang SM, Hirose R, Kaufman DB, Posselt AM, Stock PG
• Effect of intratonsillar injection of steroids on the palatine tonsils of rabbits.
  The Laryngoscope 2014 Cho DY, Sinha SR, Gardner JM, Schaller MP, Pamnani RD, Felt SA, Barral JK, Messner AH
• Lineage tracing and cell ablation identify a post-Aire-expressing thymic epithelial cell population.
  Cell reports 2013 Metzger TC, Khan IS, Gardner JM, Mouchess ML, Johannes KP, Krawisz AK, Skrzypczynska KM, Anderson MS
• Neuropilin-1 distinguishes natural and inducible regulatory T cells among regulatory T cell subsets in vivo.
  The Journal of experimental medicine 2012 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
• Immunoendocrinology: Scientific and Clinical Aspects. Eisenbarth, GS (Ed.)
  The Mouse Model of Autoimmune Polyglandular Syndrome Type I 2011 Gardner JM, Anderson MA
• AIRE in the thymus and beyond.
  Current opinion in immunology 2009 Gardner JM, Fletcher AL, Anderson MS, Turley SJ
• The sickness unto Deaf.
  Nature immunology 2009 Gardner JM, Anderson MS
• Mycobacterium tuberculosis-specific CD8+ T cells preferentially recognize heavily infected cells.
  American journal of respiratory and critical care medicine 2003 Lewinsohn DA, Heinzel AS, Gardner JM, Zhu L, Alderson MR, Lewinsohn DM