James Gardner, MD, PhD

Asst Professor In Residence
Surgery
+1 415 514-7420

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.

Publications: 

Impact of short-term vegan versus ketogenic diets on human immunity and microbiome.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Horner NK, Gillis-Buck EM, Gardner JM

Aire in Autoimmunity.

Annual review of immunology

Miller CN, Waterfield MR, Gardner JM, Anderson MS

Dual α-globin and truncated EPO receptor knockin restores hemoglobin production in α-thalassemia-derived red blood cells.

bioRxiv : the preprint server for biology

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

Chimeric autoantibody-receptor T cells mediate depletion of autoantibody-producing B cells.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Yin HS, Gillis-Buck EM, Gardner JM

Maternal-fetal microchimerism as a durable but finite and replaceable alloantigen reservoir.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Gillis-Buck EM, Gardner JM

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains.

Nature cell biology

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

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

Chu SN, Gardner JM

Dynamic encounters with red blood cells trigger splenic marginal zone B cell retention and function.

Nature immunology

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

Rickert CG, Gardner JM

Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance.

Science immunology

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

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

ROR?t-lineage APCs: The Aire apparent.

Science immunology

Gardner JM, Liston A

Tissue-specific mitochondrial HIGD1C promotes oxygen sensitivity in carotid body chemoreceptors.

eLife

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 RORγt+ cell instructs gut microbiota-specific Treg cell differentiation.

Nature

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

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

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

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.)

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, Pisco AO, 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, Crasta S, 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, Kolluru S, Kong W, Kumar ME, Kuo AH, Leylek R, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Morri M, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Phansalkar R, Pisco AO, 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, Travaglini KJ, 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, Tan SY, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Detweiler AM, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, de Morree A, Olivieri JE, Park M, Pisco AO, Ravikumar N, Salzman J, Stanley G, Swift M, Tan M, Tan W, Tarashansky AJ, Vanheusden R, Vorperian SK, Wang P, Wang S, Xing G, Xu C, Yosef N, Alcántara-Hernández M, Antony J, Chan CKF, Chang CA, Colville A, Crasta S, Culver R, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Kershner AM, Kong W, Kumar ME, Kuo AH, Leylek R, Liu S, Loeb GB, Lu WJ, Maltzman JS, Metzger RJ, de Morree A, Neuhöfer P, Perez K, Phansalkar R, Qi Z, Rao P, Raquer-McKay H, Sasagawa K, Scott B, Sinha R, Song H, Spencer SP, Swarup A, Swift M, Travaglini KJ, Trimm E, Veizades S, Vijayakumar S, Wang B, Wang W, Winkler J, Xie J, Yung AR, Artandi SE, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Krasnow M, Kuo CS, Nguyen P, Quake SR, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wang B, Wu A, Wu SM, Wyss-Coray T

Thymic and extrathymic Aire-expressing cells in maternal-fetal tolerance.

Immunological reviews

Sun IH, Gillis-Buck E, Mackenzie TC, Gardner JM

Procurement of Deceased Donor Parathyroid Glands With the Aid of Near-infrared Autofluorescence Imaging.

Transplantation direct

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

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

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

Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium.

Science immunology

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

RNA splicing programs define tissue compartments and cell types at single-cell resolution.

eLife

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

Extrathymic Aire-expressing cells support maternal-fetal tolerance.

Science immunology

Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC

A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance.

The Journal of experimental medicine

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

Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla.

Nature communications

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

Lin JA, Gardner JM, Kolli KP, Cook AC

CON: Portal Vein Thrombosis Does Not Impact Liver Transplantation Outcomes.

Clinical liver disease

Sherman C, Syed S, Gardner J, Yao FY

COVID-19 and Abdominal Transplant: A Stepwise Approach to Practice During Pandemic Conditions.

Transplantation

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.

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

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

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

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

Metzger TC, Khan IS, Gardner JM, Mouchess ML, Johannes KP, Krawisz AK, Skrzypczynska KM, Anderson MS

Extrathymic Aire-expressing cells are a distinct bone marrow-derived population that induce functional inactivation of CD4⁺ T cells.

Immunity

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

Neuropilin-1 distinguishes natural and inducible regulatory T cells among regulatory T cell subsets in vivo.

The Journal of experimental medicine

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

Gardner JM, Anderson MA

AIRE in the thymus and beyond.

Current opinion in immunology

Gardner JM, Fletcher AL, Anderson MS, Turley SJ

The sickness unto Deaf.

Nature immunology

Gardner JM, Anderson MS

Deletional tolerance mediated by extrathymic Aire-expressing cells.

Science (New York, N.Y.)

Gardner JM, Devoss JJ, Friedman RS, Wong DJ, Tan YX, Zhou X, Johannes KP, Su MA, Chang HY, Krummel MF, Anderson MS

Mycobacterium tuberculosis-specific CD8+ T cells preferentially recognize heavily infected cells.

American journal of respiratory and critical care medicine

Lewinsohn DA, Heinzel AS, Gardner JM, Zhu L, Alderson MR, Lewinsohn DM

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