Joanna Halkias, MD

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.
Education
2019 - Diversity, Equity, and Inclusion Champion Training, University of California
Postdoc, 2013 - Immunology, University of California, Berkeley
Fellowship, 2007 - Neonatal-Perinatal Medicine, Children’s Hospital Los Angeles/University of Southern California
Residency, 2004 - Pediatric, Children’s Hospital Los Angeles
MD, 2001 - Medicine, Albert Einstein College of Medicine
BA, 1995 - Biology, University of Pennsylvania

  1. Dhariwala MO, DeRogatis AM, Okoro JN, Weckel A, Tran VM, Habrylo I, Ojewumi OT, Tammen AE, Leech JM, Merana GR, Carale RO, Barrere-Cain R, Hiam-Galvez KJ, Spitzer MH, Scharschmidt TC. Commensal myeloid crosstalk in neonatal skin regulates long-term cutaneous type 17 inflammation. bioRxiv : the preprint server for biology 2023. PMID: 37873143


  2. Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J. Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans. JCI insight 2023. PMID: 37856221


  3. 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. Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy. Cell reports. Medicine 2022. PMID: 35932762


  4. Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Corroborating evidence refutes batch effect as explanation for fetal bacteria. Volume 9 of Issue 1. Microbiome 2021. PMID: 33436079


  5. Rackaityte E, Halkias J. Mechanisms of Fetal T Cell Tolerance and Immune Regulation. Volume 11. Frontiers in immunology 2020. PMID: 32328065


  6. Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Viable bacterial colonization is highly limited in the human intestine in utero. Volume 26 of Issue 4. Nature medicine 2020. PMID: 32094926


  7. Halkias J, Rackaityte E, Hillman SL, Aran D, Mendoza VF, Marshall LR, MacKenzie TC, Burt TD. CD161 contributes to prenatal immune suppression of IFNγ-producing PLZF+ T cells. Volume 129 of Issue 9. The Journal of clinical investigation 2019. PMID: 31145102


  8. Ross JO, Melichar HJ, Halkias J, Robey EA. Studying T Cell Development in Thymic Slices. Volume 1323. Methods in molecular biology (Clifton, N.J.) 2016. PMID: 26294404


  9. Halkias J, Yen B, Taylor KT, Reinhartz O, Winoto A, Robey EA, Melichar HJ. Conserved and divergent aspects of human T-cell development and migration in humanized mice. Volume 93 of Issue 8. Immunology and cell biology 2015. PMID: 25744551


  10. Halkias J, Melichar HJ, Taylor KT, Robey EA. Tracking migration during human T cell development. Volume 71 of Issue 16. Cellular and molecular life sciences : CMLS 2014. PMID: 24682469


  11. Coombes JL, Charsar BA, Han SJ, Halkias J, Chan SW, Koshy AA, Striepen B, Robey EA. Motile invaded neutrophils in the small intestine of Toxoplasma gondii-infected mice reveal a potential mechanism for parasite spread. Volume 110 of Issue 21. Proceedings of the National Academy of Sciences of the United States of America 2013. PMID: 23650399


  12. Halkias J, Melichar HJ, Taylor KT, Ross JO, Yen B, Cooper SB, Winoto A, Robey EA. Opposing chemokine gradients control human thymocyte migration in situ. Volume 123 of Issue 5. The Journal of clinical investigation 2013. PMID: 23585474


  13. Podd BS, Thoits J, Whitley N, Cheng HY, Kudla KL, Taniguchi H, Halkias J, Goth K, Camerini V. T cells in cryptopatch aggregates share TCR gamma variable region junctional sequences with gamma delta T cells in the small intestinal epithelium of mice. Volume 176 of Issue 11. Journal of immunology (Baltimore, Md. : 1950) 2006. PMID: 16709810