Representative Publications



  • Ratiu JJ, Barclay WE, Wang Q, Wellford S, Mehta N, Harnois MJ, DiPalma D, Roy S, Conteras AV, Shinohara ML, Wiest D, Zhuang Y. 2022. Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection pre-T cells. Comm. Oct 6;13(1):5901. doi: 10.1038/s41467-022-33610-4.
  • Deerhake ME, Cardakli ED, Shinohara ML. Dectin-1 signaling in neutrophils upregulates PD-L1 and triggers a biphasic CD4+ T-cell suppressive phenotype. J. Leukoc Biol. 2022 Sep 8. doi: 10.1002/JLB.3A0322-152RR.
  • Whitson H, Colton C, El Khoury J, Gate D, Goate A, Heneka MT, Kaddurah-Daouk R, Klein RS, Shinohara ML, Sisodia S, Spudich SS, Stevens B, Tanzi R, Ting, JP, Garden G, the Symposium Planning Committee. 2022. Infection and Inflammation: New Perspectives on Alzheimer’s Disease. Brain Behav. Immun. Health. Apr 22;22:100462.
  • Reyes, EY, Shinohara ML. 2022. Host immune responses in the central nervous system during fungal infections. Immunol. Rev. DOI: 10.1111/imr.13101
  • Zhang Z, Ma Q, Velagapudi R, Barclay WE, Rodriguiz RM, Wetsel WC, Yang T, Shinohara ML, Terrando N. Annexin-A1 tripeptide attenuates surgery-induced neuroinflammation and memory deficits through regulation of the NLRP3 inflammasome. Frontiers Immunol. May 6;13:856254. doi: 10.3389/fimmu.2022.856254. eCollection 2022. PMID: 35603196. Available online:
  • Barclay WE, Deerhake ME, Inoue M, Nonaka T, Nozaki K, Luzum N, Aggarwal N, Miao EA, Shinohara ML. AIM2 inflammasome activation in astrocytes occurs during the late phase of EAE. 2022. JCI Insight. 7. Available online:



  • Khaw YM, Aggarwal N, Barclay WE, Kang E, Inoue M, Shinohara ML. Th1-dependent Cryptococcus-associated immune reconstitution inflammatory syndrome (C-IRIS) model with brain damage. 2020. Frontiers Immunol. 1:529219. doi:10.3389/fimmu.2020.529219.
  • Xu-Vanpala S, Deerhake ME, Wheaton JD, Parker ME, Juvvadi PR, MacIver N, Ciofani M, Shinohara ML. 2020. Functional heterogeneity of alveolar macrophage population based on expression of CXCL2. Sci. Immunol. Vol. 5, Issue 50,eaba7350
  • Liang J, Zhang JJ, Huang HI, Kanayama M, Youssef N, Jin YJ, Reyes EY, Abram CL, Yang S, Lowell CA, Wang D, Shao L, Shinohara ML, Zhang JY, Hammer GE. The ubiquitin-modifying enzyme A20 terminates C-type lectin receptor signals and is a suppressor of host defense against systemic fungal infection. Infect Immun. 2020 Jun 15:IAI.00048-20. doi: 10.1128/IAI.00048-20.
  • Thak EJ, Lee SB, Xu-Vanpala S, Lee DJ, Chung SY, Bahn YS, Oh DB, Shinohara ML, Kang HA. 2020. Core N-Glycan Structures Are Critical for the Pathogenicity of Cryptococcus neoformans by Modulating Host Cell Death. mBio. May 12;11(3):e00711-20. doi: 10.1128/mBio.00711-20.
  • Ide S, Yahara Y, Kobayashi Y, Strausser SA, Ide K, Watwe A, Xu-Vanpala S, Privratsky JR, Crowley SD, Shinohara ML, Alman BA, Souma T. 2020. Yolk-sac-derived macrophages progressively expand in the mouse kidney with age. Elife. 2020 Apr 17;9:e51756. doi: 10.7554/eLife.51756.
  • Deerhake ME,  Danzaki K, Inoue M, Cardakli ED, Nonaka T, Aggarwal A, Barclay WE, Ji RR, Shinohara ML. 2020. Dectin-1 limits central nervous system autoimmunity through a non-canonical pathway. bioRxiv.
  • Yahara Y, Barrientos T, Tang YJ, Puviindran V, Nadesan P, Zhang H, Gibson J, Gregory SG, Diao Y, Xiang Y, Qadri YJ, Souma T, Shinohara ML, Alman BA. 2020. Erythromyeloid progenitors give rise to a population of osteoclasts contributing to bone homeostasis and repair. Nat Cell Biol. Jan;22(1):49-59. doi: 10.1038/s41556-019-0437-8. Epub 2020 Jan 6.


  • Deerhake ME, Biswas DD, Barclay WE, Shinohara ML. Pattern Recognition Receptors in Multiple Sclerosis and Its Animal Models. Front. Immunol. 12 November 2019.


  • Aggarwal N, Barclay W, Shinohara ML. 2018. Understanding Mechanisms Underlying the Pathology of Immune Reconstitution Inflammatory Syndrome (IRIS) by Using Animal Models. Curr Clin Microbiol Rep. 5:201–209.
  • Deerhake ME, Barclay WE, Shinohara ML. 2018. Are Neuropeptide-Reactive T Cells behind Narcolepsy? Immunity. 49(5):796-798.


  • Barclay W, Shinohara ML 2017. Inflammasome activation in multiple sclerosis and experimental autoimmune encephalomyelitis (EAE). Brain Pathol. 27(2):213-219.
  • Schmidt EA, Fee BE, Henry SC, Nichols AG, Shinohara ML, Rathmell JC, MacIver NJ, Coers J, Ilkayeva OR, Koves TR, Taylor GA. 2017. Metabolic alterations contribute to enhanced inflammatory cytokine production in Irgm1-deficient macrophages. J Biol Chem. 292(11):4651-4662.
  • Singh N, Inoue M, Osawa R, Wagener MM, Shinohara ML. 2017. Inflammasome expression and cytomegalovirus viremia in critically ill patients with sepsis. J. Clin. Virol. 93:8-14.
  • Kanayama M, Xu S, Danzaki K, Gibson JR, Inoue M, Gregory SG, Shinohara ML. 2017. Skewing of the population balance of lymphoid and myeloid cells by secreted and intracellular osteopontin. Nat Immunol. 18:973-984.

Featured in:

    • Research Highlights in Nature Reviews Immunology by Minton K. (2017) 17:466
    • News and Views in Nature Immunology by Gerlic M and Croker BA (2017) 17:953-954
  • Shinohara ML. Yes, research matters. PLoS Pathog. 2017 Aug 10;13(8):e1006420.
  • Xu S, Shinohara ML. 2017. Tissue-resident macrophages in fungal infection 2017. Front. Immunol. 2017 Dec 12;8:1798.


  • Inoue M, Chen PH, Siecinski S, Li QJ, Liu C, Steinman L, Gregory SG Benner E, Shinohara ML. 2016. An interferon-β-resistant and NLRP3 inflammasome-independent subtype of EAE with neuronal damage.   Nat Neurosci. 19(12):1599-1609.

Featured in:

    • MedicalNewsToday
    • ScienceDaily
    • Neuroscience News
  • Kanayama M, Shinohara ML. Roles of autophagy and autophagy-related proteins in antifungal immunity. Front Immunol. 7:47. doi: 10.3389/fimmu.2016.00047.
  • Kanayama M, Shinohara ML. Lung inflammation regulates autoimmunity in the central nervous system. J  Neurol & Neuromedicine. 1(5): 34-37
  • Kanayama M, Danzaki K, He YW, Shinohara ML. 2016. Lung inflammation stalls Th17-cell migration en route to the central nervous system during the development of experimental autoimmune encephalomyelitis. Int. Immunol. 28:463-9.
  • Gerriets VA, Danzaki K, Kishton RJ, Eisner W, Nichols AG, Saucillo DC, Shinohara ML, MacIver NJ. 2016. Leptin directly promotes T-cell glycolytic metabolism to drive effector T-cell differentiation in a mouse model of autoimmunity. Eur J Immunol. 46:1970-83.
  • Danzaki K, Kanayama M, Alcazar O, Cantor H, Shinohara ML. Osteopontin has a protective role in prostate tumor development in mice. Eur J Immunol. 46:2669-78. 


  • Heneka MT, Carson MJ, El Khoury J, Landreth GE, Brosseron F, Feinstein DL, Jacobs AH, Wyss-Coray T, Vitorica J, Ransohoff RM, Herrup K, Frautschy SA, Finsen B, Brown GC, Verkhratsky A, Yamanaka K, Koistinaho J, Latz E, Halle A, Petzold GC, Town T, Morgan D, Shinohara ML, Perry VH, Holmes C,  . Bazan NG, Brooks DJ, Hunot S, Joseph B, Deigendesch N, Garaschuk O, Boddeke E, Dinarello CA, Breitner JC, Cole GM, Golenbock DT, Kummer MP.   Neuroinflammation in Alzheimer’s Disease.  Lancet Neurol.  14: 388-405.
  • Kanayama M, Inoue M, Danzaki K, Hammer G, He YW, Shinohara ML. Autophagy enhances NFκB activity in tissue specific macrophages by sequestering A20 to boost early anti-fungal immunity.  Nat Comm.   Jan 22;6:5779.  PMC4304414.

Featured in:

    • F1000 Prime
    • Duke University News
  • Kanayama M, He YW, Shinohara ML.  Lung is protected from spontaneous inflammation by autophagy in myeloid cells.  J. Immunol. 194:5465-71.

Featured in:

    • “In This Issue,” The Journal of Immunology
  • Lee SC, Li A, Calo S, Inoue M, Thonthat NK, Bain JM, Louw J, Shinohara ML, Erwig LP, Schumacher MA, Ko DC, Heitman J. 2015. Calcineurin orchestrates dimorphic transitions, antifungal drug responses, and host-pathogen interactions of the pathogenic mucoralean fungus Mucor circinelloides. Molecular Microbiology.  97(5):844-65.
  • Inoue M, Shinohara ML. 2015. Cutting Edge: Role of Osteopontin and Integrin αv in T Cell-Mediated Anti-Inflammatory Responses in Endotoxemia. J Immunol.  194(12):5595-8.
  • Inoue M, Shinohara ML. New mechanism to inhibit hyperinflammation triggered by macrophages and the involvement of T cells in the inhibition during endotoxemia and sepsis.  Oncotarget.  6:23040-1.
  • Inoue M, Shinohara ML [NLRP3 inflammasome and multiple sclerosis/EAE]. Nihon Rinsho. 2015 Sep;73 Suppl 7:835-41. (Book Chapter)


  • Inoue M, Shinohara ML. 2014. Clustering of pattern recognition receptors for fungal detection. PLoS Pathogens. 10(2):e1003873. 
  • Wang B, Rao YH, Inoue M, Hao R, Lai CH, Chen D, McDonald SL, Choi MC, Wang Q, Shinohara ML, Tso-Pang Yao. 2014. Microtubule acetylation amplifies p38 kinase signaling and anti-inflammatory IL-10 production. Nat Comm.  Mar 17;5:3479.  PMC4000527.
  • Inoue M, Arikawa T, Chen YH, Moriwaki Y, Price M, Brown M, Perfect J, Shinohara ML. T cells downregulate macrophage TNF production by IRAK1-mediated IL-10 expression and control innate hyperinflammation.  Proc. Natl. Acad. Sci. USA. 111: 5295-300.  PMC3986140.
  • Gerriets VA, Kishton RJ, Nichols AG, Macintyre AN, Inoue M, Ilkayeva O, Winter PS, Wood KC, Liu X, Priyadharshini B, Slawinska ME, Haeberli L, Huck C, Turka LA, Hale LP, Smith PA, Schneider MA, MacIver NJ, Locasale JW, Newgard CB, Shinohara ML, Rathmell JC. Metabolic Programming and PDHK Control CD4 T-Cell Subsets and Inflammation. J. Clin. Invest.  125: 194-207.  PMC4382238.

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  • Gorentla BK, Krishna S, Shin J, Inoue M, Shinohara ML, Grayson JM, Fukunaga R, Zhong XP. Mnk1 and 2 are dispensable for T cell development and activation but important for the pathogenesis of experimental autoimmune encephalomyelitis.  J. Immunol. 190(3):1026-37. PMC3552100.
  • Inoue M, Shinohara ML 2013. The role of interferon-β in the treatment of multiple sclerosis and experimental autoimmune encephalomyelitis – in the perspective of inflammasomes.  Immunology.  139(1):11-8. PMC3634535.
  • Inoue M, Shinohara ML. NLRP3 inflammasome and MS/EAE.  Autoimmune Dis. 2013:859145. PMC3556409.
  • Inoue M, Kanayama M, Shinohara ML. 2013. Encyclopedia of Inflammatory Diseases. Springer Basel. DOI 10.1007/978-3-0348-0620-6_77-1.


  • Inoue M, Williams KL, Oliver T, Vandenabeele P, Rajan JV, Miao EA, Shinohara ML. Interferon-β therapy against EAE is effective only when development of the disease depends on the NLRP3 inflammasome. Sci. Signaling. 5, ra38.

Featured in:

    • Research Highlight in Nature Reviews Immunology (2012. 12: 477)
    • Science Signaling Podcast: 22 May 2012,
    • F1000 Prime
    • Signals by International Society for Interferon and Cytokine Research (ISICR)(September 2012 issue).
  • Inoue M, Williams K, Gunn MD, Shinohara ML.  2012.NLRP3 inflammasome enhances T helper cell migration to the CNS during EAE progression.  Proc. Natl. Acad. Sci. USA. 109:10480-5.    PMC3387125.
  • Lin YY, Jones-Mason ME, Inoue M, Lasorella A, Iavarone A, Li QJ, Shinohara ML, Zhuang Y. 2012.

    Transcriptional Regulator Id2 Is Required for the CD4 T Cell Immune Response in the Development of Experimental Autoimmune Encephalomyelitis.  J. Immunol. 189(3):1400-5.  PMC3401239.


  • Baliga S, Merrill GF, Shinohara ML, Denhardt DT.Intracellular osteopontin is differentially expressed in cortical brain tissue and is an early marker of stroke-induced cell death.  PLoS One. Jan 21;6(1):e14568. PMC3024983.
  • Inoue M, Moriwaki Y, Arikawa T, Chen YH, Oh YJ, Oliver T, Shinohara ML. Cutting edge: Critical role of intracellular osteopontin in anti-fungal innate immune responses.    J Immunol. 186:19-23. PMC3538145.
  • Michalek RD, Gerriets VA, Nichols AG, Inoue M, Kazmin D, Chang C, Dwyer M, Nelson ER, Ilkayeva O, Giguere V, Zuercher WJ, Shinohara ML, McDonnell DP, Rathmell JC. Estrogen related receptor-α is a metabolic regulator of effector T cell activation and differentiation.   Proc. Natl. Acad. Sci. USA.  108: 18348-53PMC3215012.

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  • Inoue M, Shinohara ML. Intracellular osteopontin (iOPN) and immunity.    Immunol Res. 49:160-72. PMC3509172.
  • Alvarez Arias DA, McCarty N, Lu L, Maldonado RA, Shinohara ML, Cantor H. Unexpected role of clathrin adaptor AP-1 in MHC-dependent positive selection of T cells.

    Proc. Natl. Acad. Sci. USA. 107:2556-61. PMC2823916.


2009 and before (Selected publications)

  • Cantor H, Shinohara ML.Regulation of T helper-cell lineage development by osteopontin: the inside story.  Nat. Rev. Immunol. 9:137-41.    PMC2696694.
  • Shinohara ML, Kim JH, Garcia VA, Cantor H. Engagement of the type I interferon receptor on dendritic cells inhibits T helper 17 cell development: role of intracellular osteopontin. Immunity. 29:68-78.    PMC2625293.
  • Shinohara ML, Kim HJ, Kim JH, Garcia VA, Cantor H. Alternative translation of Osteopontin generates intracellular and secreted isoforms that mediate distinct biological activities in dendritic cells.  Proc. Natl. Acad. Sci. USA, 105:7235-9.  PMC2438233.
  • Shinohara ML, Jansson M, Hwang ES, Werneck MBF, Glimcher LH, Cantor H.   T-bet dependent expression of Osteopontin contributes to T cell polarization.  Proc. Natl. Acad. Sci. USA, 102:17101-6.
  • Shinohara ML, Lu L, Bu J, Werneck MBF, Kobayashi KS, Glimcher LH, Cantor H. 2006. Osteopontin expression is essential for production of IFN-α by plasmacytoid dendritic cells.  Nat. Immunol.7, 498- 506.

Featured in:

    • F1000 Prime
    • News and Views in Nature Immunology
  • Shinohara ML, Correa A, Bell-Pedersen D, Dunlap JC, Loros JJ.Neurospora clock-controlled gene 9 (ccg-9) encodes trehalose synthase: circadian regulation of stress responses and development. Eukaryotic Cell, 1:33-43.
  • Shinohara ML, Loros JJ, Dunlap JC. 1998. Glyceraldehyde 3-phosphate dehydrogenase is regulated on a daily basis by the circadian clock. J Biol Chem. 273:446-52.