Principal Investigator

John O’Shea, M.D.

Dr. O’Shea is Scientific Director of the NIAMS and Director of the Intramural Research Program. He is Chief of the Molecular Immunology and Inflammation Branch and studies cytokine signaling transduction.

Cytokines are critical for host defense but are also key factors in immune and inflammatory diseases. Innate and adaptive lymphocytes, including T cells, are important selective producers of cytokines, and it is through the production of these that immune responses work together to eliminate microbial pathogens. Host defense against pathogenic microorganisms requires this elegant means of communication between innate and adaptive arms of the immune system. Indeed, cytokines produced by various types of lymphocytes exquisitely tailor immune responses that effectively eliminate intracellular and extracellular pathogens when regulated properly. On the other hand, hyper-active lymphocytes can drive allergic and autoimmune diseases. Conversely, loss-of-function mutations of lymphocyte genes can cause primary immunodeficiencies.

The goal of the Molecular Immunology and Inflammation Branch (MIIB) is to understand how lymphocytes differentiate to selectively produce key immunoregulatory cytokines and to better define the molecular basis of cytokine action.

Discovery of JAK3 and Development of Jakinibs

We now know that a plethora of cytokines is produced by innate immune cells and that these cytokines are critical for the development and specification of CD4 subsets. A substantial portion of cytokines (more than 60) binds to receptors that associate with a class of protein tyrosine kinases termed Janus Kinases or JAKs (illustrated in Figure 2). The MIIB first cloned human JAK3, a kinase predominantly expressed in immune and hematopoietic cells; in partnership with NIH colleagues, the branch went on to demonstrate that JAK3 associates with the common γ chain (γc). This shared cytokine receptor is used by interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21, and we found that mutations of JAK3 underlie autosomal recessive severe combined immunodeficiency (SCID). Because of the critical functions of JAKs in cytokine signaling, pharmacological JAK inhibitors (jakinibs) were developed as a new class of immunomodulatory drugs. The NIH holds patents pertaining to Janus Kinases and identification of immune modulators (United States patents 7,070,972 and 7,488,808). The NIAMS partnered with Pfizer in a Cooperative Research and Development Agreement (CRADA), leading to the development of multiple jakinibs. At present, there are nine approved jakinibs for indications ranging from rheumatoid arthritis, psoriatic arthritis, juvenile arthritis, ulcerative colitis, atopic dermatitis, graft-vs-host disease, and myeloproliferative neoplasms to COVID-19. The MIIB, in collaboration with other investigators, is studying the efficacy of jakinibs in lupus, Sjogren’s syndrome, and other disorders.

Helper T cell differentiation (O'Shea and Paul. 2010.
Figure 1 - Targeting JAKs in human diseases by Jakinibs (Spinelli FR et al. Eur J Immunol 2021. PubMed: 33930196)

Cytokine Signaling via STATs

JAK-STAT Pathway
Figure 2 - JAK-STAT pathway (Gadina et al. Rheumatology (Oxford). 2019.  PubMed: 30806710)


The MIIB demonstrated that IL-12 activates STAT4, a key factor that initiates the development of Th1 cells that produce the signature cytokine interferon-γ (IFN-γ). The branch has continued its interest in dissecting the function of STAT4 over the last 16 years since this initial discovery. Most recently, we have used second-generation, deep sequencing technology to define the genome-wide targets of STAT4 and relate this knowledge to the roles of STAT4 in regulating gene expression and changes in the epigenome of differentiating CD4+ T cells. Capitalizing on the opportunities provided by deep sequencing technology and computational biology tools, defining the genome-wide functions of STAT4 and other STATs is a focal point of research in the lab.


Th17 cell differentiation is dependent upon this transcription factor. Importantly, the Job's syndrome or Hyper IgE syndrome (HIES) disorder is due to mutations of STAT3. The MIIB, in collaboration with other NIH scientists, showed that a major defect in this disorder is impairment of Th17 cell generation. We used Chip-seq methodology to identify STAT3 target genes in developing Th17 cells. Dissecting the functions of STAT3 in this intriguing subset of cells is an ongoing interest of the lab.

Helper T cell differentiation (O'Shea and Paul. 2010.
Figure 3 - Helper T cell differentiation (O'Shea et al. Science 2010. PubMed: 20185720)


Patients with STAT1 gain-of-function mutations have clinical presentations similar in many respects to patients with HIES. We are currently studying mouse models to increase our understanding of the pathophysiology of the rare Mendelian disease, which may provide insights into more common diseases.


In addition to Th cells, regulatory T (Treg) cells represent another important immunoregulatory subset of CD4+ T cells. The MIIB showed that STAT5 is critical for Treg cell differentiation, binding to the gene encoding the transcription factor Foxp3. Conversely, we showed that STAT5, in response to IL-2 stimulation, also inhibits Th17 differentiation. We further showed STAT5 and STAT3 compete in the Il7a-Il17f locus and that this is an important mechanism underlying the ability of IL-2 to limit Th17 differentiation.

Latest Research into Transcriptome and Epigenome

Flexibility in lymphocyte epigenomes
Figure 4 - Flexibility in lymphocyte epigenomes (Sciumè et al. Immunity 2020. PubMed: 33010223)

A major ongoing issue in lymphocyte biology is the extent to which different subsets behave as terminally differentiated lineages or retain flexibility in their differentiation programs. By assessing the epigenomes of the different helper cell subsets, we have identified mechanisms through which flexibility is retained, even in polarized "lineages." We have explored the issue of plasticity and heterogeneity of helper T cells and their relationship to innate lymphocytes. We have also explored in detail the structure of key cytokine loci including the Ifng/Il22 and Il4/Il13/Il5 super-enhancer loci.

Furthermore, we study how long noncoding RNAs and microRNAs regulate immune responses, how activation globally impacts chromatin accessibility and architecture, and how these concepts relate to lymphocyte function.

Future Directions

By studying how the engagement of cytokine receptors transduces signals that, in turn, regulate transcription factors and epigenetic events to modulate gene expression, we hope to understand in detail how lymphocytes participate in host defense and contribute to the pathogenesis of immune-mediated diseases. The insights gained from these studies facilitate the development of new therapeutic approaches.

Contact Us

Iris Pratt

Staff Assistant
9000 Rockville Pike
Building: 10, Room: 13C103
Bethesda MD 20892

Core Research Facilities

Labs at the NIAMS are supported by the following state-of-the-art facilities and services:


NIAMS Scientific Director
Research Fellow (Visiting)
Independent Research Scholar
Graduate Student
Staff Scientist
Independent Research Scholar
Postdoctoral Fellow
Postdoctoral Fellow
Postbaccalaureate Fellow

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Scientific Publications

Selected Recent Publications

MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23.

Mikami Y, Philips RL, Sciumè G, Petermann F, Meylan F, Nagashima H, Yao C, Davis FP, Brooks SR, Sun HW, Takahashi H, Poholek AC, Shih HY, Afzali B, Muljo SA, Hafner M, Kanno Y, O'Shea JJ
2021 Mar 9;
doi: 10.1016/j.immuni.2021.02.015
PMID: 33657395

Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells.

Sciumè G, Mikami Y, Jankovic D, Nagashima H, Villarino AV, Morrison T, Yao C, Signorella S, Sun HW, Brooks SR, Fang D, Sartorelli V, Nakayamada S, Hirahara K, Zitti B, Davis FP, Kanno Y, O'Shea JJ, Shih HY
2020 Oct 13;
doi: 10.1016/j.immuni.2020.09.008
PMID: 33010223

Translating JAKs to Jakinibs.

Gadina M, Chisolm DA, Philips RL, McInness IB, Changelian PS, O'Shea JJ
J Immunol.
2020 Apr 15;
doi: 10.4049/jimmunol.1901477
PMID: 32253269

The Magnitude of IFN-γ Responses Is Fine-Tuned by DNA Architecture and the Non-coding Transcript of Ifng-as1.

Petermann F, Pękowska A, Johnson CA, Jankovic D, Shih HY, Jiang K, Hudson WH, Brooks SR, Sun HW, Villarino AV, Yao C, Singleton K, Akondy RS, Kanno Y, Sher A, Casellas R, Ahmed R, O'Shea JJ
Mol Cell.
2019 Sep 19;
doi: 10.1016/j.molcel.2019.06.025
PMID: 31377117

Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation.

Nagashima H, Mahlakõiv T, Shih HY, Davis FP, Meylan F, Huang Y, Harrison OJ, Yao C, Mikami Y, Urban JF Jr, Caron KM, Belkaid Y, Kanno Y, Artis D, O'Shea JJ
2019 Oct 15;
doi: 10.1016/j.immuni.2019.06.009
PMID: 31353223

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection.

Yao C, Sun HW, Lacey NE, Ji Y, Moseman EA, Shih HY, Heuston EF, Kirby M, Anderson S, Cheng J, Khan O, Handon R, Reilley J, Fioravanti J, Hu J, Gossa S, Wherry EJ, Gattinoni L, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T
Nat Immunol.
2019 Jul;
doi: 10.1038/s41590-019-0403-4
PMID: 31209400

Janus kinases to jakinibs: from basic insights to clinical practice.

Gadina M, Le MT, Schwartz DM, Silvennoinen O, Nakayamada S, Yamaoka K, O'Shea JJ
Rheumatology (Oxford).
2019 Feb 1;
58(Suppl 1).
doi: 10.1093/rheumatology/key432
PMID: 30806710

Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology.

Schwartz DM, Farley TK, Richoz N, Yao C, Shih HY, Petermann F, Zhang Y, Sun HW, Hayes E, Mikami Y, Jiang K, Davis FP, Kanno Y, Milner JD, Siegel R, Laurence A, Meylan F, O'Shea JJ
2019 Jan 15;
doi: 10.1016/j.immuni.2018.12.014
PMID: 30650370

Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury.

Harrison OJ, Linehan JL, Shih HY, Bouladoux N, Han SJ, Smelkinson M, Sen SK, Byrd AL, Enamorado M, Yao C, Tamoutounour S, Van Laethem F, Hurabielle C, Collins N, Paun A, Salcedo R, O'Shea JJ, Belkaid Y
2019 Jan 4;
pii: eaat6280. doi: 10.1126/science.aat6280
PMID: 30523076

The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells.

Iwata S, Mikami Y, Sun HW, Brooks SR, Jankovic D, Hirahara K, Onodera A, Shih HY, Kawabe T, Jiang K, Nakayama T, Sher A, O'Shea JJ, Davis FP, Kanno Y
2017 Jun 20;
doi: 10.1016/j.immuni.2017.05.005
PMID: 28623086

BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency.

Afzali B, Grönholm J, Vandrovcova J, O'Brien C, Sun HW, Vanderleyden I, Davis FP, Khoder A, Zhang Y, Hegazy AN, Villarino AV, Palmer IW, Kaufman J, Watts NR, Kazemian M, Kamenyeva O, Keith J, Sayed A, Kasperaviciute D, Mueller M, Hughes JD, Fuss IJ, Sadiyah MF, Montgomery-Recht K, McElwee J, Restifo NP, Strober W, Linterman MA, Wingfield PT, Uhlig HH, Roychoudhuri R, Aitman TJ, Kelleher P, Lenardo MJ, O'Shea JJ, Cooper N, Laurence ADJ
Nat Immunol.
2017 Jul;
doi: 10.1038/ni.3753
PMID: 28530713

Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality.

Shih HY, Sciumè G, Mikami Y, Guo L, Sun HW, Brooks SR, Urban JF Jr, Davis FP, Kanno Y, O'Shea JJ
2016 May 19;
doi: 10.1016/j.cell.2016.04.029
PMID: 27156451

Type I/II cytokines, JAKs, and new strategies for treating autoimmune diseases.

Schwartz DM, Bonelli M, Gadina M, O'Shea JJ
Nat Rev Rheumatol.
2016 Jan;
doi: 10.1038/nrrheum.2015.167
PMID: 26633291

Super-enhancers delineate disease-associated regulatory nodes in T cells.

Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SC, Erdos MR, Davis SR, Roychoudhuri R, Restifo NP, Gadina M, Tang Z, Ruan Y, Collins FS, Sartorelli V, O'Shea JJ
2015 Apr 23;
doi: 10.1038/nature14154
PMID: 25686607

News & Highlights

Announcement | March 24, 2021

NIAMS’ John O’Shea Awarded 2021 Harrington Prize for Innovation in Medicine

For his groundbreaking work in immunology, John J. O’Shea, M.D., will receive the eighth annual Harrington Prize for Innovation in Medicine.
Featured | March 22, 2021

Research: MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23

In a recent study in the journal Immunity, NIAMS investigators provide new insight into mechanisms of disease by the adaptive immune system.
Spotlight on Research | October 22, 2019

Molecule Identified as Potential Treatment Target for Worm Infections, Inflammatory Disorders

Researchers from the NIH and Weill Cornell Medicine have identified a molecule in lymphocytes that could potentially lead to treatments for inflammatory disorders, such as atopic dermatitis, food allergies and asthma.
Press Release | May 5, 2016

Rapid-Response Immune Cells are Fully Prepared Before Invasion Strikes

Through the use of powerful genomic techniques, researchers at the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) have found that the development of immune cells, called innate lymphoid cells (ILCs), gradually prepares these cells for rapid response to infection.
Announcement | December 8, 2015

NIAMS’ O’Shea Delivers Research Lecture at Nobel Forum

John O’Shea, M.D., NIAMS Scientific Director and Chief of the Molecular Immunology and Inflammation Branch, was an in

Press Release | February 17, 2015

NIH researchers reveal link between powerful gene regulatory elements and autoimmune diseases

Investigators with the National Institutes of Health have discovered the genomic switches of a blood cell key to regulating the human immune system.
Last Updated: July 2021 Back to Top