Joanna Halkias, MD

Title(s)Assistant Professor, Pediatrics
SchoolSchool of Medicine
Address550 16th Street, #5578
San Francisco CA 94158
ORCID ORCID Icon0000-0003-0721-8961 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of PennsylvaniaBA1995Biology
    Albert Einstein College of MedicineMD2001Medicine
    Children’s Hospital Los AngelesResidency2004Pediatric
    Children’s Hospital Los Angeles/University of Southern CaliforniaFellowship2007Neonatal-Perinatal Medicine
    University of California, BerkeleyPostdoc2013Immunology
    University of California, San Francisco, CA2019Diversity, Equity, and Inclusion Champion Training

    Collapse Overview 
    Collapse Overview
    The Halkias lab studies the cellular and molecular signals that drive human immune development with a focus on understanding how early life host-microbe interactions influence adaptive immune responses to perinatal inflammatory disorders such as preterm birth. Early life is a critical time in immune development marked by rapid exposure to environmental antigens. Microbial colonization of mucosal tissues plays a key role in the development and education of the host immune system and influences the susceptibility to immune-mediated disease later in life. Infants born preterm are predisposed to prenatal immune activation and inflammation, critical risk factors underlying much of the pathophysiology in this vulnerable population. In utero infection is the most frequently identified cause of spontaneous preterm birth and fetal T cell activation is associated with severe neonatal disease, yet the signals that drive the activation, differentiation, and regulation of fetal adaptive immunity are not known. We utilize immune and microbial transcriptomics, high parameter flow and mass cytometry, and humanized mouse models to understand the cellular and molecular interactions that instruct human immune cells during this critical window of development.

    Collapse Research 
    Collapse Research Activities and Funding
    Harnessing immune regulatory mechanisms to target the fetal inflammatory response in preterm birth
    Burroughs Wellcome Fund 1019828Jun 1, 2019 - Apr 1, 2023
    Role: PI
    Intrauterine sex steroids and fetal T cell development.
    NIH/NIAID 5 K08 AI128007 02Jul 1, 2017 - Jun 30, 2022
    Role: PI
    Intrauterine sex steroids and human fetal T cell development
    NIH K08AI128007Jul 1, 2017 - Jun 30, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans. JCI Insight. 2023 Nov 22; 8(22). Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J. PMID: 37856221; PMCID: PMC10721317.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy. Cell Rep Med. 2022 08 16; 3(8):100713. McCauley KE, Rackaityte E, LaMere B, Fadrosh DW, Fujimura KE, Panzer AR, Lin DL, Lynch KV, Halkias J, Mendoza VF, Burt TD, Bendixsen C, Barnes K, Kim H, Jones K, Ownby DR, Johnson CC, Seroogy CM, Gern JE, Boushey HA, Lynch SV, ECHO Children’s Respiratory and Environmental Workgroup. PMID: 35932762; PMCID: PMC9418802.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    3. Corroborating evidence refutes batch effect as explanation for fetal bacteria. Microbiome. 2021 01 12; 9(1):10. Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. PMID: 33436079; PMCID: PMC7805121.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    4. Mechanisms of Fetal T Cell Tolerance and Immune Regulation. Front Immunol. 2020; 11:588. Rackaityte E, Halkias J. PMID: 32328065; PMCID: PMC7160249.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    5. Viable bacterial colonization is highly limited in the human intestine in utero. Nat Med. 2020 04; 26(4):599-607. Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. PMID: 32094926; PMCID: PMC8110246.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansCells
    6. CD161 contributes to prenatal immune suppression of IFNγ-producing PLZF+ T cells. J Clin Invest. 2019 05 30; 129(9):3562-3577. Halkias J, Rackaityte E, Hillman SL, Aran D, Mendoza VF, Marshall LR, MacKenzie TC, Burt TD. PMID: 31145102; PMCID: PMC6715406.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    7. Studying T Cell Development in Thymic Slices. Methods Mol Biol. 2016; 1323:131-40. Ross JO, Melichar HJ, Halkias J, Robey EA. PMID: 26294404.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    8. Conserved and divergent aspects of human T-cell development and migration in humanized mice. Immunol Cell Biol. 2015 Sep; 93(8):716-26. Halkias J, Yen B, Taylor KT, Reinhartz O, Winoto A, Robey EA, Melichar HJ. PMID: 25744551; PMCID: PMC4575952.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    9. Tracking migration during human T cell development. Cell Mol Life Sci. 2014 Aug; 71(16):3101-17. Halkias J, Melichar HJ, Taylor KT, Robey EA. PMID: 24682469.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    10. Motile invaded neutrophils in the small intestine of Toxoplasma gondii-infected mice reveal a potential mechanism for parasite spread. Proc Natl Acad Sci U S A. 2013 May 21; 110(21):E1913-22. Coombes JL, Charsar BA, Han SJ, Halkias J, Chan SW, Koshy AA, Striepen B, Robey EA. PMID: 23650399; PMCID: PMC3666704.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    11. Opposing chemokine gradients control human thymocyte migration in situ. J Clin Invest. 2013 May; 123(5):2131-42. Halkias J, Melichar HJ, Taylor KT, Ross JO, Yen B, Cooper SB, Winoto A, Robey EA. PMID: 23585474; PMCID: PMC3635739.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    12. T cells in cryptopatch aggregates share TCR gamma variable region junctional sequences with gamma delta T cells in the small intestinal epithelium of mice. J Immunol. 2006 Jun 01; 176(11):6532-42. Podd BS, Thoits J, Whitley N, Cheng HY, Kudla KL, Taniguchi H, Halkias J, Goth K, Camerini V. PMID: 16709810.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
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