Joanna Halkias, MD

Asst Professor In Residence

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.


Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans.

JCI insight

Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J

Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy.

Cell reports. Medicine

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

Corroborating evidence refutes batch effect as explanation for fetal bacteria.


Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV

Mechanisms of Fetal T Cell Tolerance and Immune Regulation.

Frontiers in immunology

Rackaityte E, Halkias J

Viable bacterial colonization is highly limited in the human intestine in utero.

Nature medicine

Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV

CD161 contributes to prenatal immune suppression of IFN?-producing PLZF+ T cells.

The Journal of clinical investigation

Halkias J, Rackaityte E, Hillman SL, Aran D, Mendoza VF, Marshall LR, MacKenzie TC, Burt TD

Studying T Cell Development in Thymic Slices.

Methods in molecular biology (Clifton, N.J.)

Ross JO, Melichar HJ, Halkias J, Robey EA

Conserved and divergent aspects of human T-cell development and migration in humanized mice.

Immunology and cell biology

Halkias J, Yen B, Taylor KT, Reinhartz O, Winoto A, Robey EA, Melichar HJ

Tracking migration during human T cell development.

Cellular and molecular life sciences : CMLS

Halkias J, Melichar HJ, Taylor KT, Robey EA

Motile invaded neutrophils in the small intestine of Toxoplasma gondii-infected mice reveal a potential mechanism for parasite spread.

Proceedings of the National Academy of Sciences of the United States of America

Coombes JL, Charsar BA, Han SJ, Halkias J, Chan SW, Koshy AA, Striepen B, Robey EA

Opposing chemokine gradients control human thymocyte migration in situ.

The Journal of clinical investigation

Halkias J, Melichar HJ, Taylor KT, Ross JO, Yen B, Cooper SB, Winoto A, Robey EA

T cells in cryptopatch aggregates share TCR gamma variable region junctional sequences with gamma delta T cells in the small intestinal epithelium of mice.

Journal of immunology (Baltimore, Md. : 1950)

Podd BS, Thoits J, Whitley N, Cheng HY, Kudla KL, Taniguchi H, Halkias J, Goth K, Camerini V