University of California San Francisco

Gardnerjames
James
Gardner
MD, PhD

Assistant Professor of Surgery
Division of Transplant Surgery
Investigator, UCSF Diabetes Center
Director, UCSF VITAL Core

Address

505 Parnassus Avenue, #001
San Francisco, CA 94117
United States

Email: [email protected]
Phone: 415-514-7420

ORCID: 0000-0003-3470-9520

Biography

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.

Awards & Honors

Award Conferred By Date
PICI Investigator Parker Institute for Cancer Immunotherapy 2024
Burroughs Wellcome Next Gen Pregnancy Initiative Burroughs Wellcome Fund 2023/2027
Pew Biomedical Scholar The Pew Charitable Trusts 2023/2027
Sandler PSSP Grant UCSF Dean's Office 2019/2024
ASTS-Astellas Fellowship in Transplantation Grant American Society of Transplant Surgeons 2017/2019
Nusz Achievement Award UCSF Department of Surgery 2017/2017
Schecter Award for Senior Trauma Fellow UCSF Division of Trauma and Critical Care 2016/2016
ED Surgical Consultant of the Year UCSF Emergency Medicine 2016/2016

Education

Institution Degree Dept or School End Date
University of California San Francisco Clinical Instructor and Fellow Abdominal Transplant Surgery 08/2019
University of California San Francisco Chief Resident General Surgery 06/2017
University of California San Francisco Resident General Surgery 06/2016
University of California San Francisco MD/PhD Genetics 06/2012
Harvard University AB Biochemistry 06/2002

Board Certifications

American Board of Surgery, General Surgery

 

Clinical Expertise

Ascites
Bile Duct Cancer (Cholangiocarcinoma)
Bile Duct Injuries
Bile Duct Strictures
Bridging Therapies to Downstage HCC in Liver Transplant Setting
Choledochal Cysts
Deceased Donor Organ Utilization
Gallbladder Cancer
Hepatocellular Carcinoma (Primary Liver Cancer)
Kidney Transplantation
Laparoscopic Donor Nephrectomy
Liver Biopsy
Liver Cysts
Liver Metastases (Secondary Liver Cancer)
Liver Resection
Liver Transplantation
Living Donor Kidney Transplantation
Living Donor Liver Transplantation
Normothetic Machine Liver Perfusion
Organ Donation of Cardiovascular Death
Pancreas Transplantation
Pediatric Kidney Transplantation
Pediatric Liver Transplantation
Portal Hypertension

Foreign Languages Spoken

Spanish

Program Affiliations

UCSF Department of Surgery
UCSF Division of Transplant Surgery
UCSF Diabetes Center

Book Chapters

Gardner JM, Anderson MS. The Mouse Model of Autoimmune Polyglandular Syndrome Type I. Immunoendocrinology: Scientific and Clinical Aspects. 1st edition. Ed. Eisenbarth G. (New York: Humana Press, 2011.)

Gardner et al., American Transplant Congress, 2015. Outcomes in a new category of Pancreas-After-Islet Transplantation.
Gardner et al., UCSF Surgery Resident Research Symposium, 2013-2016. Extrathymic Aire-Expressing Cells in Immune Tolerance and Transplantation.
Gardner et al., International Pancreas and Islet Transplant Association 2013. Outcomes in a new category of Pancreas-After-Islet Transplantation.
Gardner et al., Children?s Diabetes Foundation of the North Bay Annual Retreat, 2010. Novel Approaches for Preventing and Treating Juvenile Diabetes: What?s on the Horizon?
Gardner et al., Kyoto T Cell Conference 2009. Extrathymic Aire-Expressing Cells and the Maintenance of Immunologic Tolerance.
Gardner et al., American Diabetes Association Tour de Cure Donors? Evening, 2008. New approaches to Preventing and Treating Autoimmune Diabetes.
Gardner et al., UCSF/UCB 2008 Immunology Retreat. Phenotypic and Functional Characterization of Extrathymic Aire-Expressing Cells.

In the News

UCSF Medical Student Eva Gillis-Buck Awarded UCSF 2020 Long-Term Dean's Prize in Research
May, 08, 2020 | UCSF General Surgery Residency Program
James M. Gardner, MD, PhD Awarded Appointment to Prestigious Physician-Scientist Scholar Program
July, 15, 2019 | UCSF Division of Transplant Surgery
James Gardner and Nicole Conkling Awarded 2017 ASTS Research Grants
July, 19, 2017 | UCSF Resident Research Program

Research Narrative

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.

Research Interests

Immune tolerance
Transplant surgery
Autoimmmune diabetes

Research Pathways

Basic Biomedical & Translational Research

Publications

MOST RECENT PUBLICATIONS FROM A TOTAL OF 43
  1. Impact of short-term vegan versus ketogenic diets on human immunity and microbiome.
    Horner NK, Gillis-Buck EM, Gardner JM| | PubMed
  2. Aire in Autoimmunity.
    Miller CN, Waterfield MR, Gardner JM, Anderson MS| | PubMed
  3. Dual α-globin and truncated EPO receptor knockin restores hemoglobin production in α-thalassemia-derived red blood cells.
    Chu SN, Soupene E, Wienert B, Yin H, Sharma D, McCreary T, Jia K, Homma S, Hampton JP, Gardner JM, Conklin BR, MacKenzie TC, Porteus MH, Cromer MK| | PubMed
  4. Chimeric autoantibody-receptor T cells mediate depletion of autoantibody-producing B cells.
    Yin HS, Gillis-Buck EM, Gardner JM| | PubMed
  5. Maternal-fetal microchimerism as a durable but finite and replaceable alloantigen reservoir.
    Gillis-Buck EM, Gardner JM| | PubMed
  6. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains.
    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| | PubMed
  7. Circadian clocks drive rhythmic antitumor immune responses mediated by migratory dendritic cells.
    Chu SN, Gardner JM| | PubMed
  8. Dynamic encounters with red blood cells trigger splenic marginal zone B cell retention and function.
    Liu D, Winer BY, Chou MY, Tam H, Xu Y, An J, Gardner JM, Cyster JG| | PubMed
  9. Successful cryopreservation of functional kidney allografts using vitrification and nanorewarming.
    Rickert CG, Gardner JM| | PubMed
  10. Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance.
    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| | PubMed
  11. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis.
    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| | PubMed
  12. RORγt-lineage APCs: The Aire apparent.
    Gardner JM, Liston A| | PubMed
  13. Tissue-specific mitochondrial HIGD1C promotes oxygen sensitivity in carotid body chemoreceptors.
    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| | PubMed
  14. A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation.
    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| | PubMed
  15. A novel microsurgical reconstruction technique in a living-related liver donor hepatic artery dissection using the native hepatic artery.
    Sitta R, Roberts J, Gardner J, Ascher N, Piper M| | PubMed
  16. Nodular Regenerative Hyperplasia After Liver Transplant; It's All in the Presentation.
    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| | PubMed
  17. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.
    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| | PubMed
  18. Thymic and extrathymic Aire-expressing cells in maternal-fetal tolerance.
    Sun IH, Gillis-Buck E, Mackenzie TC, Gardner JM| | PubMed
  19. Internal hernia involving the transplant ureter after simultaneous pancreas and kidney transplant - and the atypical management of a consequent transplant ureteral injury.
    Gupta AR, Kelly YM, Syed SM, Gardner JM| | PubMed
  20. Procurement of Deceased Donor Parathyroid Glands With the Aid of Near-infrared Autofluorescence Imaging.
    Ward CJ, Kelly YM, Syed SM, Meier RPH, Ando T, Wisel SA, Gardner JM, Stock PG, Duh QY| | PubMed
  21. Cell types of origin of the cell-free transcriptome.
    Vorperian SK, Moufarrej MN, Tabula Sapiens Consortium, Quake SR| | PubMed
  22. Advantages and Limitations of Clinical Scores for Donation After Circulatory Death Liver Transplantation.
    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| | PubMed
  23. Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium.
    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| | PubMed
  24. RNA splicing programs define tissue compartments and cell types at single-cell resolution.
    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| | PubMed
  25. Extrathymic Aire-expressing cells support maternal-fetal tolerance.
    Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC| | PubMed
  26. A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance.
    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| | PubMed
  27. Transplantation From Older Donors: Can Senolytics Turn Back the Clock?
    Dixon W, Feng S, Gardner J| | PubMed
  28. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla.
    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| | PubMed
  29. Surgical, Interventional, and Medical Palliation of Portal Hypertension.
    Lin JA, Gardner JM, Kolli KP, Cook AC| | PubMed
  30. CON: Portal Vein Thrombosis Does Not Impact Liver Transplantation Outcomes.
    Sherman C, Syed S, Gardner J, Yao FY| | PubMed
  31. COVID-19 and Abdominal Transplant: A Stepwise Approach to Practice During Pandemic Conditions.
    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| | PubMed
  32. Curr Hepatology Rep
    Huang, A.C., Gardner, J.M. & Hameed, B.| | UCSF Research Profile
  33. Ethical Issues in the COVID Era: Doing the Right Thing Depends on Location, Resources, and Disease Burden.
    Stock PG, Wall A, Gardner J, Domínguez-Gil B, Chadban S, Muller E, Dittmer I, Tullius SG, TTS Ethics Committee| | PubMed
  34. Pancreas-After-Islet Transplantation in Nonuremic Type 1 Diabetes: A Strategy for Restoring Durable Insulin Independence.
    Wisel SA, Gardner JM, Roll GR, Harbell J, Freise CE, Feng S, Kang SM, Hirose R, Kaufman DB, Posselt AM, Stock PG| | PubMed
  35. Effect of intratonsillar injection of steroids on the palatine tonsils of rabbits.
    Cho DY, Sinha SR, Gardner JM, Schaller MP, Pamnani RD, Felt SA, Barral JK, Messner AH| | PubMed
  36. Lineage tracing and cell ablation identify a post-Aire-expressing thymic epithelial cell population.
    Metzger TC, Khan IS, Gardner JM, Mouchess ML, Johannes KP, Krawisz AK, Skrzypczynska KM, Anderson MS| | PubMed
  37. Extrathymic Aire-expressing cells are a distinct bone marrow-derived population that induce functional inactivation of CD4⁺ T cells.
    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| | PubMed
  38. Neuropilin-1 distinguishes natural and inducible regulatory T cells among regulatory T cell subsets in vivo.
    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| | PubMed
  39. Immunoendocrinology: Scientific and Clinical Aspects. Eisenbarth, GS (Ed.)
    Gardner JM, Anderson MA| | UCSF Research Profile
  40. AIRE in the thymus and beyond.
    Gardner JM, Fletcher AL, Anderson MS, Turley SJ| | PubMed
  41. The sickness unto Deaf.
    Gardner JM, Anderson MS| | PubMed
  42. Deletional tolerance mediated by extrathymic Aire-expressing cells.
    Gardner JM, Devoss JJ, Friedman RS, Wong DJ, Tan YX, Zhou X, Johannes KP, Su MA, Chang HY, Krummel MF, Anderson MS| | PubMed
  43. Mycobacterium tuberculosis-specific CD8+ T cells preferentially recognize heavily infected cells.
    Lewinsohn DA, Heinzel AS, Gardner JM, Zhu L, Alderson MR, Lewinsohn DM| | PubMed