Mary Nakamura, MD


Mary Nakamura received her B.A. from Swarthmore College, her M.D. from Yale and trained in internal medicine at the University of California, San Francisco. She completed her rheumatology training at Johns Hopkins and UCSF. She did her post doctoral work at UCSF under the mentorship of Bill Seaman. She is a basic-translational researcher focused on studies in the field of osteoimmunology. She leads the Rheumatoid Arthritis Clinic at UCSF Parnassus and is a clinical attending at the SF VA HCS.

Research Statement
I am a clinical rheumatologist who has done basic research in the area of innate immune receptors for the past 29 years. I was a postdoctoral fellow with Bill Seaman focused studies of innate receptor regulation of Natural Killer cells. For the last 21 years I have focused much of our work on the role of innate immune receptors on osteoclasts and innate immune regulation of normal and pathological bone turnover. I led one of the early groups focusing research in the area of osteoimmunology and was one of the first to identify the role of innate receptors in osteoclast differentiation and function. Osteoimmunology, is defined as a cross disciplinary field to integrate studies of the immune system and bone and the interactions between these systems which is a topic integral to the clinical field of rheumatology and has furthered my goal of integrating my research with my clinical work. Recently we have also focused work on innate receptors, macrophages and tissue regeneration examining these cells and their function in bone, brain and cardiac injury. Our work has demonstrated roles for macrophages in tissue regeneration and we are examining effects of age and autoimmunity on macrophage phenotype and function which may contribute to defective tissue repair. I have worked with a number of young investigators to enhance their studies by providing key guidance and experiments to examine myeloid cells, bone and/or immune cells in the bone for a number of advanced trainee projects over the past few years.

I am also dedicated to promoting basic-translational work in rheumatologic and autoimmune disease at UCSF. I partnered with Lindsey Criswell to develop PREMIER, an NIH p30 Center for the Advancement of Precision Medicine in Rheumatology a number of years ago. Following her departure to NIAMS, I assumed directorship of the Center and I successfully applied to renew this center grant last year. I continue to lead this effort to integrate research focused on patient cohorts using clinical informatics and state of the art molecular phenotyping using patient samples to advance our understanding of rheumatologic disease heterogeneity, outcomes and therapeutic responses. As part of one of PREMIER's efforts, I led a study of SARS CoV2 vaccine response in autoimmune and autoinflammatory disease patients as soon as the vaccination effort rolled out and partnered with colleagues at Washington University in St. Louis to expand the cohort. We managed to publish this work about 8 months after vaccine administration began.
2018 - Diversity, Equity, and Inclusion Champion Training, University of California
Fellowship, 1994 - Rheumatology, University of California, San Francisco
Fellowship, 1991 - Rheumatology, Johns Hopkins University
Residency, 1989 - Internal Medicine, University of California, San Francisco
MD, 1986 - School of Medicine, Yale University
BA, 1981 - Biology, Swarthmore College
Honors and Awards
  • Director PREMIER: Precision Medicine in Rheumtology p30 Center, UCSF, 2020
  • Associate Director PREMIER: Precision Medicine in Rheumtology p30 Center, UCSF, 2016-2020
  • Excellence in Teaching Award in medical education, The Haile Debas Academy of Medical Educators, UCSF, 2015
  • Henry Kunkel Young Investigator Award, American College of Rheumatology, 2005
  • Ira M. Goldstein Award for Outstanding Teaching in Rheumatology, UCSF, 2004
  • Presidential Early Career Award, President of US, 2000
  • VA Career Development Award, VA, 1998
  • Physician Scientist Development Award, ACR, 1993
  • Jeffrey Weingarten Award for Housestaff, UCSF, 1989
  • J.M. Glasgow Memorial AMWA scholastic citation, Yale Medical School, 1986
  • Louis G. Welt Prize for medical school thesis, Yale Medical School, 1986
  1. Yang MM, Taylor KE, Paez D, Carividi A, Demissie E, Pawar N, El-Qunni AA, McMorrow LE, Schriefer RE, Huang K, Kinnett B, Klebert M, Haile A, O'Halloran JA, Presti RM, Kim W, Ellebedy AH, Ciorba MA, Paley MA, Deepak P, Kim AHJ, Katz P, Matloubian M, Nakamura M, Gensler LS. Reactogenicity of the mRNA SARS-CoV-2 Vaccines Associates with Immunogenicity in Patients with Autoimmune and Inflammatory Disease. 2022. PMID: 35412029

  2. Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M. Physical Activity Associates with Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis. 2022. PMID: 35777820

  3. Matsuo K, Lepinski A, Chavez RD, Barruet E, Pereira A, Moody TA, Ton AN, Sharma A, Hellman J, Tomoda K, Nakamura MC, Hsiao EC. Corrigendum to "ACVR1R206H extends inflammatory responses in human induced pluripotent stem cell-derived macrophages" [Bone. 153 2021 Dec; 116129. doi:10.1016/j.bone.2021.116129. Epub 2021 Jul 24. PMID: 34311122]. 2022. PMID: 35241401

  4. Kim AHJ, Nakamura MC. COVID-19 Breakthrough Infection Among Immunocompromised Persons. 2021. PMID: 34962552

  5. Somebang K, Rudolph J, Imhof I, Li L, Niemi EC, Shigenaga J, Tran H, Gill TM, Lo I, Zabel BA, Schmajuk G, Wipke BT, Gyoneva S, Jandreski L, Craft M, Benedetto G, Plowey ED, Charo I, Campbell J, Ye CJ, Panter SS, Nakamura MC, Eckalbar W, Hsieh CL. CCR2 deficiency alters activation of microglia subsets in traumatic brain injury. 2021. PMID: 34551293

  6. Deepak P, Kim W, Paley MA, Yang M, Carvidi AB, Demissie EG, El-Qunni AA, Haile A, Huang K, Kinnett B, Liebeskind MJ, Liu Z, McMorrow LE, Paez D, Pawar N, Perantie DC, Schriefer RE, Sides SE, Thapa M, Gergely M, Abushamma S, Akuse S, Klebert M, Mitchell L, Nix D, Graf J, Taylor KE, Chahin S, Ciorba MA, Katz P, Matloubian M, O'Halloran JA, Presti RM, Wu GF, Whelan SPJ, Buchser WJ, Gensler LS, Nakamura MC, Ellebedy AH, Kim AHJ. Effect of Immunosuppression on the Immunogenicity of mRNA Vaccines to SARS-CoV-2 : A Prospective Cohort Study. 2021. PMID: 34461029

  7. Matsuo K, Lepinski A, Chavez RD, Barruet E, Pereira A, Moody TA, Ton AN, Sharma A, Hellman J, Tomoda K, Nakamura MC, Hsiao EC. ACVR1R206H extends inflammatory responses in human induced pluripotent stem cell-derived macrophages. 2021. PMID: 34311122

  8. Fraenkel L, Bathon JM, England BR, St Clair EW, Arayssi T, Carandang K, Deane KD, Genovese M, Huston KK, Kerr G, Kremer J, Nakamura MC, Russell LA, Singh JA, Smith BJ, Sparks JA, Venkatachalam S, Weinblatt ME, Al-Gibbawi M, Baker JF, Barbour KE, Barton JL, Cappelli L, Chamseddine F, George M, Johnson SR, Kahale L, Karam BS, Khamis AM, Navarro-Millán I, Mirza R, Schwab P, Singh N, Turgunbaev M, Turner AS, Yaacoub S, Akl EA. 2021 American College of Rheumatology Guideline for the Treatment of Rheumatoid Arthritis. 2021. PMID: 34101387

  9. Fraenkel L, Bathon JM, England BR, St Clair EW, Arayssi T, Carandang K, Deane KD, Genovese M, Huston KK, Kerr G, Kremer J, Nakamura MC, Russell LA, Singh JA, Smith BJ, Sparks JA, Venkatachalam S, Weinblatt ME, Al-Gibbawi M, Baker JF, Barbour KE, Barton JL, Cappelli L, Chamseddine F, George M, Johnson SR, Kahale L, Karam BS, Khamis AM, Navarro-Millán I, Mirza R, Schwab P, Singh N, Turgunbaev M, Turner AS, Yaacoub S, Akl EA. 2021 American College of Rheumatology Guideline for the Treatment of Rheumatoid Arthritis. 2021. PMID: 34101376

  10. Vallania F, Zisman L, Macaubas C, Hung SC, Rajasekaran N, Mason S, Graf J, Nakamura M, Mellins ED, Khatri P. Multicohort Analysis Identifies Monocyte Gene Signatures to Accurately Monitor Subset-Specific Changes in Human Diseases. 2021. PMID: 34054824

  11. Clark D, Halpern B, Miclau T, Nakamura M, Kapila Y, Marcucio R. The Contribution of Macrophages in Old Mice to Periodontal Disease. 2021. PMID: 33906501

  12. Calabrese DR, Aminian E, Mallavia B, Liu F, Cleary SJ, Aguilar OA, Wang P, Hoover J, Singer JP, Hays SR, Golden JA, Kukreja J, Dugger DT, Nakamura M, Lanier LL, Looney MR, Greenland JR. Natural killer cells activated through NKG2D mediate lung ischemia-reperfusion injury. 2020. PMID: 33290276

  13. Vasudevan S, Vásquez JJ, Chen W, Aguilar-Rodriguez B, Niemi EC, Zeng S, Tamaki W, Nakamura MC, Arjomandi M. Lower PDL1/2 and AXL Expression on Lung Myeloid Cells Suggests Inflammatory Bias in Smoking and COPD. 2020. PMID: 32915645

  14. Wilfong EM, Croze R, Fang X, Schwede M, Niemi E, López GY, Lee JW, Nakamura MC, Matthay MA. Proinflammatory cytokines and ARDS pulmonary edema fluid induce CD40 on human mesenchymal stromal cells-A potential mechanism for immune modulation. 2020. PMID: 33021986

  15. Razani B, Whang MI, Kim FS, Nakamura MC, Sun X, Advincula R, Turnbaugh JA, Pendse M, Tanbun P, Achacoso P, Turnbaugh PJ, Malynn BA, Ma A. Non-catalytic ubiquitin binding by A20 prevents psoriatic arthritis-like disease and inflammation. 2020. PMID: 32205880

  16. Clark D, Brazina S, Yang F, Hu D, Hsieh CL, Niemi EC, Miclau T, Nakamura MC, Marcucio R. Age-related changes to macrophages are detrimental to fracture healing in mice. 2020. PMID: 32096907

  17. Wang L, Roth T, Nakamura MC, Nissenson RA. Female-Specific Role of Progranulin to Suppress Bone Formation. 2019. PMID: 31237618

  18. Barruet E, Morales BM, Cain CJ, Ton AN, Wentworth KL, Chan TV, Moody TA, Haks MC, Ottenhoff TH, Hellman J, Nakamura MC, Hsiao EC. NF-?B/MAPK activation underlies ACVR1-mediated inflammation in human heterotopic ossification. 2018. PMID: 30429363

  19. Clark D, Nakamura M, Miclau T, Marcucio R. Effects of Aging on Fracture Healing. Volume 15 of Issue 6. 2017. PMID: 29143915

  20. Humphrey MB, Nakamura MC. A Comprehensive Review of Immunoreceptor Regulation of Osteoclasts. Volume 51 of Issue 1. 2016. PMID: 26573914

  21. Kim CC, Nakamura MC, Hsieh CL. Brain trauma elicits non-canonical macrophage activation states. Volume 13 of Issue 1. 2016. PMID: 27220367

  22. Kawabori M, Kacimi R, Kauppinen T, Calosing C, Kim JY, Hsieh CL, Nakamura MC, Yenari MA. Triggering receptor expressed on myeloid cells 2 (TREM2) deficiency attenuates phagocytic activities of microglia and exacerbates ischemic damage in experimental stroke. Volume 35 of Issue 8. 2015. PMID: 25716838

  23. Hsieh CL, Niemi EC, Wang SH, Lee CC, Bingham D, Zhang J, Cozen ML, Charo I, Huang EJ, Liu J, Nakamura MC. CCR2 deficiency impairs macrophage infiltration and improves cognitive function after traumatic brain injury. Volume 31 of Issue 20. 2014. PMID: 24806994

  24. Charles JF, Nakamura MC. Bone and the innate immune system. Volume 12 of Issue 1. 2014. PMID: 24500569

  25. Nakamura MC. CIITA: a master regulator of adaptive immunity shows its innate side in the bone. Volume 29 of Issue 2. 2014. PMID: 24343972

  26. Kawabori M, Hokari M, Zheng Z, Kim JY, Calosing C, Hsieh CL, Nakamura MC, Yenari MA. Triggering Receptor Expressed on Myeloid Cells-2 Correlates to Hypothermic Neuroprotection in Ischemic Stroke. Volume 3 of Issue 4. 2013. PMID: 24380032

  27. Hsieh CL, Kim CC, Ryba BE, Niemi EC, Bando JK, Locksley RM, Liu J, Nakamura MC, Seaman WE. Traumatic brain injury induces macrophage subsets in the brain. Volume 43 of Issue 8. 2013. PMID: 23630120

  28. Charles JF, Hsu LY, Niemi EC, Weiss A, Aliprantis AO, Nakamura MC. Inflammatory arthritis increases mouse osteoclast precursors with myeloid suppressor function. Volume 122 of Issue 12. 2012. PMID: 23114597

  29. Chitu V, Nacu V, Charles JF, Henne WM, McMahon HT, Nandi S, Ketchum H, Harris R, Nakamura MC, Stanley ER. PSTPIP2 deficiency in mice causes osteopenia and increased differentiation of multipotent myeloid precursors into osteoclasts. Volume 120 of Issue 15. 2012. PMID: 22923495

  30. Hammer GE, Turer EE, Taylor KE, Fang CJ, Advincula R, Oshima S, Barrera J, Huang EJ, Hou B, Malynn BA, Reizis B, DeFranco A, Criswell LA, Nakamura MC, Ma A. Expression of A20 by dendritic cells preserves immune homeostasis and prevents colitis and spondyloarthritis. Volume 12 of Issue 12. 2011. PMID: 22019834

  31. Baker-LePain JC, Nakamura MC, Lane NE. Effects of inflammation on bone: an update. Volume 23 of Issue 4. 2011. PMID: 21532485

  32. Baker-LePain JC, Nakamura MC, Shepherd J, von Scheven E. Assessment of bone remodelling in childhood-onset systemic lupus erythematosus. Volume 50 of Issue 3. 2010. PMID: 21098573

  33. Adapala NS, Barbe MF, Langdon WY, Nakamura MC, Tsygankov AY, Sanjay A. The loss of Cbl-phosphatidylinositol 3-kinase interaction perturbs RANKL-mediated signaling, inhibiting bone resorption and promoting osteoclast survival. Volume 285 of Issue 47. 2010. PMID: 20851882

  34. Baker-LePain JC, Stone DH, Mattis AN, Nakamura MC, Fye KH. Clinical diagnosis of segmental arterial mediolysis: differentiation from vasculitis and other mimics. Volume 62 of Issue 11. 2010. PMID: 20662047

  35. Xing Z, Lu C, Hu D, Yu YY, Wang X, Colnot C, Nakamura M, Wu Y, Miclau T, Marcucio RS. Multiple roles for CCR2 during fracture healing. Volume 3 of Issue 7-8. 2010. PMID: 20354109

  36. Li L, Fang CJ, Ryan JC, Niemi EC, Lebrón JA, Björkman PJ, Arase H, Torti FM, Torti SV, Nakamura MC, Seaman WE. Binding and uptake of H-ferritin are mediated by human transferrin receptor-1. Volume 107 of Issue 8. 2010. PMID: 20133674

  37. Park-Min KH, Ji JD, Antoniv T, Reid AC, Silver RB, Humphrey MB, Nakamura M, Ivashkiv LB. IL-10 suppresses calcium-mediated costimulation of receptor activator NF-kappa B signaling during human osteoclast differentiation by inhibiting TREM-2 expression. Volume 183 of Issue 4. 2009. PMID: 19625651

  38. Hsieh CL, Koike M, Spusta SC, Niemi EC, Yenari M, Nakamura MC, Seaman WE. A role for TREM2 ligands in the phagocytosis of apoptotic neuronal cells by microglia. Volume 109 of Issue 4. 2009. PMID: 19302484

  39. Charles JF, Humphrey MB, Zhao X, Quarles E, Nakamura MC, Aderem A, Seaman WE, Smith KD. The innate immune response to Salmonella enterica serovar Typhimurium by macrophages is dependent on TREM2-DAP12. Volume 76 of Issue 6. 2008. PMID: 18391000

  40. Wu Y, Humphrey MB, Nakamura MC. Osteoclasts - the innate immune cells of the bone. Volume 41 of Issue 3. 2008. PMID: 18365831

  41. Wu Y, Torchia J, Yao W, Lane NE, Lanier LL, Nakamura MC, Humphrey MB. Bone microenvironment specific roles of ITAM adapter signaling during bone remodeling induced by acute estrogen-deficiency. Volume 2 of Issue 7. 2007. PMID: 17611621

  42. Hamerman JA, Jarjoura JR, Humphrey MB, Nakamura MC, Seaman WE, Lanier LL. Cutting edge: inhibition of TLR and FcR responses in macrophages by triggering receptor expressed on myeloid cells (TREM)-2 and DAP12. Volume 177 of Issue 4. 2006. PMID: 16887962

  43. Humphrey MB, Lanier LL, Nakamura MC. Role of ITAM-containing adapter proteins and their receptors in the immune system and bone. Volume 208. 2005. PMID: 16313340

  44. Humphrey MB, Daws MR, Spusta SC, Niemi EC, Torchia JA, Lanier LL, Seaman WE, Nakamura MC. TREM2, a DAP12-associated receptor, regulates osteoclast differentiation and function. Volume 21 of Issue 2. 2005. PMID: 16418779

  45. Chen TT, Li L, Chung DH, Allen CD, Torti SV, Torti FM, Cyster JG, Chen CY, Brodsky FM, Niemi EC, Nakamura MC, Seaman WE, Daws MR. TIM-2 is expressed on B cells and in liver and kidney and is a receptor for H-ferritin endocytosis. Volume 202 of Issue 7. 2005. PMID: 16203866

  46. Lane NE, Yao W, Nakamura MC, Humphrey MB, Kimmel D, Huang X, Sheppard D, Ross FP, Teitelbaum SL. Mice lacking the integrin beta5 subunit have accelerated osteoclast maturation and increased activity in the estrogen-deficient state. Volume 20 of Issue 1. 2004. PMID: 15619670

  47. Mócsai A, Humphrey MB, Van Ziffle JA, Hu Y, Burghardt A, Spusta SC, Majumdar S, Lanier LL, Lowell CA, Nakamura MC. The immunomodulatory adapter proteins DAP12 and Fc receptor gamma-chain (FcRgamma) regulate development of functional osteoclasts through the Syk tyrosine kinase. Volume 101 of Issue 16. 2004. PMID: 15073337

  48. Humphrey MB, Ogasawara K, Yao W, Spusta SC, Daws MR, Lane NE, Lanier LL, Nakamura MC. The signaling adapter protein DAP12 regulates multinucleation during osteoclast development. Volume 19 of Issue 2. 2003. PMID: 14969392

  49. Chung DH, Humphrey MB, Nakamura MC, Ginzinger DG, Seaman WE, Daws MR. CMRF-35-like molecule-1, a novel mouse myeloid receptor, can inhibit osteoclast formation. Volume 171 of Issue 12. 2003. PMID: 14662855