Professional Education


  • M.D./Ph.D., University of California, San Francisco
  • B.S., California Institute of Technology

All Publications


  • Acute Generalized Exanthematous Pustulosis JAMA DERMATOLOGY Lee, J., Endicott, A., Shinkai, K. 2021; 157 (5): 589
  • Test performance evaluation of SARS-CoV-2 serological assays. medRxiv : the preprint server for health sciences Whitman, J. D., Hiatt, J., Mowery, C. T., Shy, B. R., Yu, R., Yamamoto, T. N., Rathore, U., Goldgof, G. M., Whitty, C., Woo, J. M., Gallman, A. E., Miller, T. E., Levine, A. G., Nguyen, D. N., Bapat, S. P., Balcerek, J., Bylsma, S. A., Lyons, A. M., Li, S., Wong, A. W., Gillis-Buck, E. M., Steinhart, Z. B., Lee, Y., Apathy, R., Lipke, M. J., Smith, J. A., Zheng, T., Boothby, I. C., Isaza, E., Chan, J., Acenas, D. D., Lee, J., Macrae, T. A., Kyaw, T. S., Wu, D., Ng, D. L., Gu, W., York, V. A., Eskandarian, H. A., Callaway, P. C., Warrier, L., Moreno, M. E., Levan, J., Torres, L., Farrington, L. A., Loudermilk, R., Koshal, K., Zorn, K. C., Garcia-Beltran, W. F., Yang, D., Astudillo, M. G., Bernstein, B. E., Gelfand, J. A., Ryan, E. T., Charles, R. C., Iafrate, A. J., Lennerz, J. K., Miller, S., Chiu, C. Y., Stramer, S. L., Wilson, M. R., Manglik, A., Ye, C. J., Krogan, N. J., Anderson, M. S., Cyster, J. G., Ernst, J. D., Wu, A. H., Lynch, K. L., Bern, C., Hsu, P. D., Marson, A. 2020

    Abstract

    Background: Serological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use and interpretation require accurate assay performance data.Method: We conducted an evaluation of 10 lateral flow assays (LFAs) and two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic SARS-CoV-2 RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; and 52 recent samples from individuals who underwent respiratory viral testing but were not diagnosed with Coronavirus Disease 2019 (COVID-19). Samples were blinded and LFA results were interpreted by two independent readers, using a standardized intensity scoring system.Results: Among specimens from SARS-CoV-2 RT-PCR-positive individuals, the percent seropositive increased with time interval, peaking at 81.8-100.0% in samples taken >20 days after symptom onset. Test specificity ranged from 84.3-100.0% in pre-COVID-19 specimens. Specificity was higher when weak LFA bands were considered negative, but this decreased sensitivity. IgM detection was more variable than IgG, and detection was highest when IgM and IgG results were combined. Agreement between ELISAs and LFAs ranged from 75.7-94.8%. No consistent cross-reactivity was observed.Conclusion: Our evaluation showed heterogeneous assay performance. Reader training is key to reliable LFA performance, and can be tailored for survey goals. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.

    View details for DOI 10.1101/2020.04.25.20074856

    View details for PubMedID 32511497

  • Tissue-specific pathways extrude activated ILC2s to disseminate type 2 immunity JOURNAL OF EXPERIMENTAL MEDICINE Ricardo-Gonzalez, R. R., Schneider, C., Liao, C., Lee, J., Liang, H., Locksley, R. M. 2020; 217 (4)

    Abstract

    Group 2 innate lymphoid cells (ILC2s) are tissue-resident cells prominent at barrier sites. Although precursors are found in blood, mature ILC2s can enter the circulation after small intestinal perturbation by migratory helminths and move to distant tissues to influence the local reparative response. Using fate-mapping and methods to bypass the lung or intestinal phases of Nippostrongylus brasiliensis infection, we show that blood ILC2s comprise heterogeneous populations derived from distinct tissues that are dependent on alarmins matched to the receptor profile of the specific tissue ILC2s. Activation of local ILC2s by tissue-specific alarmins induced their proliferation, lymph node migration, and blood dissemination, thus systemically distributing type 2 cytokines. These studies uncover a possible mechanism by which local innate responses transition to systemic type 2 responses by extrusion of activated sentinel ILC2s from tissue into the circulation.

    View details for DOI 10.1084/jem.20191172

    View details for Web of Science ID 000531027000013

    View details for PubMedID 32031571

    View details for PubMedCentralID PMC7144525

  • Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nature biotechnology Whitman, J. D., Hiatt, J. n., Mowery, C. T., Shy, B. R., Yu, R. n., Yamamoto, T. N., Rathore, U. n., Goldgof, G. M., Whitty, C. n., Woo, J. M., Gallman, A. E., Miller, T. E., Levine, A. G., Nguyen, D. N., Bapat, S. P., Balcerek, J. n., Bylsma, S. A., Lyons, A. M., Li, S. n., Wong, A. W., Gillis-Buck, E. M., Steinhart, Z. B., Lee, Y. n., Apathy, R. n., Lipke, M. J., Smith, J. A., Zheng, T. n., Boothby, I. C., Isaza, E. n., Chan, J. n., Acenas, D. D., Lee, J. n., Macrae, T. A., Kyaw, T. S., Wu, D. n., Ng, D. L., Gu, W. n., York, V. A., Eskandarian, H. A., Callaway, P. C., Warrier, L. n., Moreno, M. E., Levan, J. n., Torres, L. n., Farrington, L. A., Loudermilk, R. P., Koshal, K. n., Zorn, K. C., Garcia-Beltran, W. F., Yang, D. n., Astudillo, M. G., Bernstein, B. E., Gelfand, J. A., Ryan, E. T., Charles, R. C., Iafrate, A. J., Lennerz, J. K., Miller, S. n., Chiu, C. Y., Stramer, S. L., Wilson, M. R., Manglik, A. n., Ye, C. J., Krogan, N. J., Anderson, M. S., Cyster, J. G., Ernst, J. D., Wu, A. H., Lynch, K. L., Bern, C. n., Hsu, P. D., Marson, A. n. 2020

    Abstract

    Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay performance. We conducted a head-to-head evaluation of ten point-of-care-style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays to detect anti-SARS-CoV-2 IgM and IgG antibodies in 5-d time intervals from symptom onset and studied the specificity of each assay in pre-coronavirus disease 2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 d after symptom onset). Test specificity ranged from 84.3% to 100.0% and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies (sensitivity) in a subset of SARS-CoV-2 real-time PCR-positive cases. Our results underline the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Although there was no standout serological assay, four tests achieved more than 80% positivity at later time points tested and more than 95% specificity.

    View details for DOI 10.1038/s41587-020-0659-0

    View details for PubMedID 32855547

  • Tissue-Resident Group 2 Innate Lymphoid Cells Differentiate by Layered Ontogeny and In Situ Perinatal Priming IMMUNITY Schneider, C., Lee, J., Koga, S., Ricardo-Gonzalez, R. R., Nussbaum, J. C., Smith, L. K., Villeda, S. A., Liang, H., Locksley, R. M. 2019; 50 (6): 1425-+

    Abstract

    The perinatal period is a critical window for distribution of innate tissue-resident immune cells within developing organs. Despite epidemiologic evidence implicating the early-life environment in the risk for allergy, temporally controlled lineage tracing of group 2 innate lymphoid cells (ILC2s) during this period remains unstudied. Using complementary fate-mapping approaches and reporters for ILC2 activation, we show that ILC2s appeared in multiple organs during late gestation like tissue macrophages, but, unlike the latter, a majority of peripheral ILC2 pools were generated de novo during the postnatal window. This period was accompanied by systemic ILC2 priming and acquisition of tissue-specific transcriptomes. Although perinatal ILC2s were variably replaced across tissues with age, the dramatic increases in tissue ILC2s following helminth infection were mediated through local expansion independent of de novo generation by bone marrow hematopoiesis. We provide comprehensive temporally controlled fate mapping of an innate lymphocyte subset with notable nuances as compared to tissue macrophage ontogeny.

    View details for DOI 10.1016/j.immuni.2019.04.019

    View details for Web of Science ID 000471876100014

    View details for PubMedID 31128962

    View details for PubMedCentralID PMC6645687

  • Tissue signals imprint ILC2 identity with anticipatory function NATURE IMMUNOLOGY Ricardo-Gonzalez, R. R., Van Dyken, S. J., Schneider, C., Lee, J., Nussbaum, J. C., Liang, H., Vaka, D., Eckalbar, W. L., Molofsky, A. B., Erle, D. J., Locksley, R. M. 2018; 19 (10): 1093-+

    Abstract

    Group 2 innate lymphoid cells (ILC2s) are distributed systemically and produce type 2 cytokines in response to a variety of stimuli, including the epithelial cytokines interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP). Transcriptional profiling of ILC2s from different tissues, however, grouped ILC2s according to their tissue of origin, even in the setting of combined IL-25-, IL-33-receptor-, and TSLP-receptor-deficiency. Single-cell profiling confirmed a tissue-organizing transcriptome and identified ILC2 subsets expressing distinct activating receptors, including the major subset of skin ILC2s, which were activated preferentially by IL-18. Tissue ILC2 subsets were unaltered in number and expression in germ-free mice, suggesting that endogenous, tissue-derived signals drive the maturation of ILC2 subsets by controlling expression of distinct patterns of activating receptors, thus anticipating tissue-specific perturbations occurring later in life.

    View details for DOI 10.1038/s41590-018-0201-4

    View details for Web of Science ID 000445968600015

    View details for PubMedID 30201992

    View details for PubMedCentralID PMC6202223

  • Pulmonary neuroendocrine cells amplify allergic asthma responses SCIENCE Sui, P., Wiesner, D. L., Xu, J., Zhang, Y., Lee, J., Van Dyken, S., Lashua, A., Yu, C., Klein, B. S., Locksley, R. M., Deutsch, G., Sun, X. 2018; 360 (6393): 1086-+

    Abstract

    Pulmonary neuroendocrine cells (PNECs) are rare airway epithelial cells whose function is poorly understood. Here we show that Ascl1-mutant mice that have no PNECs exhibit severely blunted mucosal type 2 response in models of allergic asthma. PNECs reside in close proximity to group 2 innate lymphoid cells (ILC2s) near airway branch points. PNECs act through calcitonin gene-related peptide (CGRP) to stimulate ILC2s and elicit downstream immune responses. In addition, PNECs act through the neurotransmitter γ-aminobutyric acid (GABA) to induce goblet cell hyperplasia. The instillation of a mixture of CGRP and GABA in Ascl1-mutant airways restores both immune and goblet cell responses. In accordance, lungs from human asthmatics show increased PNECs. These findings demonstrate that the PNEC-ILC2 neuroimmunological modules function at airway branch points to amplify allergic asthma responses.

    View details for DOI 10.1126/science.aan8546

    View details for Web of Science ID 000434635500037

    View details for PubMedID 29599193

    View details for PubMedCentralID PMC6387886

  • Recruited Monocytes and Type 2 Immunity Promote Lung Regeneration following Pneumonectomy CELL STEM CELL Lechner, A. J., Driver, I. H., Lee, J., Conroy, C. M., Nagle, A., Locksley, R. M., Rock, J. R. 2017; 21 (1): 120-+

    Abstract

    To investigate the role of immune cells in lung regeneration, we used a unilateral pneumonectomy model that promotes the formation of new alveoli in the remaining lobes. Immunofluorescence and single-cell RNA sequencing found CD115+ and CCR2+ monocytes and M2-like macrophages accumulating in the lung during the peak of type 2 alveolar epithelial stem cell (AEC2) proliferation. Genetic loss of function in mice and adoptive transfer studies revealed that bone marrow-derived macrophages (BMDMs) traffic to the lung through a CCL2-CCR2 chemokine axis and are required for optimal lung regeneration, along with Il4ra-expressing leukocytes. Our data suggest that these cells modulate AEC2 proliferation and differentiation. Finally, we provide evidence that group 2 innate lymphoid cells are a source of IL-13, which promotes lung regeneration. Together, our data highlight the potential for immunomodulatory therapies to stimulate alveologenesis in adults.

    View details for DOI 10.1016/j.stem.2017.03.024

    View details for Web of Science ID 000404888100015

    View details for PubMedID 28506464

    View details for PubMedCentralID PMC5501755

  • A tissue checkpoint regulates type 2 immunity. Nature immunology Van Dyken, S. J., Nussbaum, J. C., Lee, J., Molofsky, A. B., Liang, H., Pollack, J. L., Gate, R. E., Haliburton, G. E., Ye, C. J., Marson, A., Erle, D. J., Locksley, R. M. 2016

    Abstract

    Group 2 innate lymphoid cells (ILC2s) and CD4(+) type 2 helper T cells (TH2 cells) are defined by their similar effector cytokines, which together mediate the features of allergic immunity. We found that tissue ILC2s and TH2 cells differentiated independently but shared overlapping effector function programs that were mediated by exposure to the tissue-derived cytokines interleukin 25 (IL-25), IL-33 and thymic stromal lymphopoietin (TSLP). Loss of these three tissue signals did not affect lymph node priming, but abrogated the terminal differentiation of effector TH2 cells and adaptive lung inflammation in a T cell-intrinsic manner. Our findings suggest a mechanism by which diverse perturbations can activate type 2 immunity and reveal a shared local-tissue-elicited checkpoint that can be exploited to control both innate and adaptive allergic inflammation.

    View details for DOI 10.1038/ni.3582

    View details for PubMedID 27749840

    View details for PubMedCentralID PMC5275767

  • Interleukin-33 and Interferon-gamma Counter-Regulate Group 2 Innate Lymphoid Cell Activation during Immune Perturbation IMMUNITY Molofsky, A. B., Van Gool, F., Liang, H., Van Dyken, S. J., Nussbaum, J. C., Lee, J., Bluestone, J. A., Locksley, R. M. 2015; 43 (1): 161-174

    Abstract

    Group 2 innate lymphoid cells (ILC2s) and regulatory T (Treg) cells are systemically induced by helminth infection but also sustain metabolic homeostasis in adipose tissue and contribute to tissue repair during injury. Here we show that interleukin-33 (IL-33) mediates activation of ILC2s and Treg cells in resting adipose tissue, but also after helminth infection or treatment with IL-2. Unexpectedly, ILC2-intrinsic IL-33 activation was required for Treg cell accumulation in vivo and was independent of ILC2 type 2 cytokines but partially dependent on direct co-stimulatory interactions via ICOSL-ICOS. IFN-γ inhibited ILC2 activation and Treg cell accumulation by IL-33 in infected tissue, as well as adipose tissue, where repression increased with aging and high-fat diet-induced obesity. IL-33 and ILC2s are central mediators of type 2 immune responses that promote tissue and metabolic homeostasis, and IFN-γ suppresses this pathway, likely to promote inflammatory responses and divert metabolic resources necessary to protect the host.

    View details for DOI 10.1016/j.immuni.2015.05.019

    View details for Web of Science ID 000360101100018

    View details for PubMedID 26092469

    View details for PubMedCentralID PMC4512852

  • The kinase LRRK2 is a regulator of the transcription factor NFAT that modulates the severity of inflammatory bowel disease NATURE IMMUNOLOGY Liu, Z., Lee, J., Krummey, S., Lu, W., Cai, H., Lenardo, M. J. 2011; 12 (11): 1063-U65

    Abstract

    Leucine-rich repeat kinase 2 (LRRK2) has been identified by genome-wide association studies as being encoded by a major susceptibility gene for Crohn's disease. Here we found that LRRK2 deficiency conferred enhanced susceptibility to experimental colitis in mice. Mechanistic studies showed that LRRK2 was a potent negative regulator of the transcription factor NFAT and was a component of a complex that included the large noncoding RNA NRON (an NFAT repressor). Furthermore, the risk-associated allele encoding LRRK2 Met2397 identified by a genome-wide association study for Crohn's disease resulted in less LRRK2 protein post-translationally. Severe colitis in LRRK2-deficient mice was associated with enhanced nuclear localization of NFAT1. Thus, our study defines a new step in the control of NFAT activation that involves an immunoregulatory function of LRRK2 and has important implications for inflammatory bowel disease.

    View details for DOI 10.1038/ni.2113

    View details for Web of Science ID 000296500100011

    View details for PubMedID 21983832

    View details for PubMedCentralID PMC4140245