Richard A Flavell PhD, FRS

Sterling Professor of Immunobiology; Investigator, Howard Hughes Medical Institute; Department Chair, Immunobiology

Research Interests

Animal Models; Autoimmunity; Diabetes; Gene Expression; Gene Transfer; Genes; Immune System; Lyme Borreliosis Or Lyme Disease; Molecular Cellular Entities; Recombinant DNA; Transgenic Animals; Autoimmunity; Knockout Mice; Lyme Disease; T Cell Lineages; Tolerance; Transgenic Mice

Current Projects

  • TGF-b in autoimmune diabetes
  • TGF-b in memory T cell development
  • The role of BCL2 in aging of the immune system
  • AMCase in lung inflammation
  • The role of TGF-b in the immune response to melanoma
  • Generation and analysis of mice with human immune systems
  • Developing immune therapies for Type 1 diabetes
  • Genetic approaches to immune function and tolerance

Research Summary

Richard Flavell is co-discoverer of introns in cellular genes: he showed DNA methylation correlates inversely with, and prevents, gene expression. He was the first to develop reverse genetics as a postdoc with Weissmann and in his own lab continued in this field throughout his career; he is a pioneer in the use of this approach in vivo to study function. Dr. Flavell’s laboratory studies the molecular and cellular basis of the immune response. He has been instrumental in discovering the molecular basis of T-cell differentiation from precursor cells into differentiated subsets. This work led to the discovery of GATA3 as a critical regulator of the Th2 response and the first example of such a molecule in Th cell differentiation. He went on to demonstrate the first case of regulation of gene expression in trans, via ”chromosome kissing.” Moreover his laboratory has elucidated the mechanisms of immunoregulation which prevent autoimmunity and overaggressive responses to pathogens. Specifically, Dr. Flavell's laboratory has elucidated the role of TGF-β in the regulation of immune response. This work is of relevance both to the control of autoimmune disease and the evasion of immune response by tumors.

Dr. Flavell’s laboratory has discovered the role of several receptor families in the innate immune response, including the role of several Toll-like receptors and intracellular Nod-like receptor families (NLRs). This has recently led to the elucidation of function of Nod2 in inflammatory bowel diseases and Nlrp proteins in the production of IL-1. Most recently he has established a fascinating connection between inflammasomes, microbial homeostasis and chronic diseases. He showed that inflammasome dysfunction causes dysbiosis of the microbiota which, in conjunction with a susceptible diet, leads to IBD and Metabolic Syndrome, including Obesity, Fatty Liver disease and Type 2 diabetes.

Extensive Research Description

The innate immune system contains genome-encoded receptors that provide a first line of defense to infection. Activation of innate immunity triggers adaptive immunity. There are three classes of innate immune receptors:

  • Toll-like receptors (TLRs), which sense agents in the extracellular/vesicular space;
  • Nod-like receptors (NLRs), which sense microorganisms that penetrate the cytoplasmic space; and
  • RIG-like receptors (RLRs), which recognize viral infection and trigger type 1 interferon production.
We identified the TLRs for double-strand RNA (TLR3), single-stranded RNA (TLR7), flagellar protein (TLR5), and lipoprotein (TLR1/2). Upon penetration of the cytoplasm, NLRs trigger NF?B activation, interleukin-1 (IL-1) production, or apoptosis. In humans, NLR mutation correlates with inflammatory disease. Nod2 carries a leucine-rich repeat region probably recognizing bacterial muramyl dipeptide, a nucleotide-binding domain mediating conformational change, thereby enabling oligomerization between CARD domains of Nod2 and downstream receptor-interacting protein (RIP) kinase, causing activation of NF?B and antimicrobial peptides. NOD2 is mutated in Crohn's disease (CD), an inflammatory bowel disease (IBD). Our Nod2-deficient mice were more susceptible to infection with pathogens delivered to the gut, because of reduced production of antimicrobial peptides. Thus, patients with CD may be unable to develop an effective antimicrobial response, causing enhanced infection and severe inflammation.

The Nalp proteins comprise a second arm of the NLR family. We study several of these, including Nalp3 (NLRP3), which senses infection or other stress that leads to K+ efflux and activates the "inflammasome" through oligomerization with the adaptor apoptosis-associated speck-like protein (ASC), enabling ASC to bind to and activate caspase-1 to process pro-IL-1ß and other substrates. We found that multiple stimuli activate the Nalp3 inflammasome, including Listeria infection. Jürg Tschopp (University of Lausanne) showed that this inflammasome recognizes uric acid crystals, explaining the inflammatory properties of uric acid in gout. We found that alum, a crystalline immune adjuvant and the only USA-approved human adjuvant, activates the NALP3 inflammasome, which triggers macrophage inflammatory cytokine production and adaptive immunity in vivo.

Disruption of the pathway eliminates alum's adjuvant capacity. Likewise, particulate environmental pollutants, including silica and asbestos, also activate the Nalp3 inflammasome to cause devastating chronic inflammatory disease. Thus, inflammasomes mediate anti-infective immunity, immunopathology to environmental pollutants, and adaptive immunity. The immune response sometimes reacts to self-tissues, causing autoimmunity. How can antigenic stimulation of a lymphocyte lead to such different outcomes? During an immune response or in autoimmunity, the lymphocytes divide and differentiate into effector cells. However, when immune tolerance occurs, the cell is either inactivated or dies.

How are the decisions made to proliferate, differentiate, be tolerized, or die, and how is this controlled?
Regulatory cells producing inhibitory cytokines are critical to prevent autoimmunity. Of these, the CD4+CD25+Foxp3+Treg is the most studied. The functioning, generation, and maintenance of regulatory T cells (Treg) are controlled by cytokines. Both transforming growth factor-ß (TGFß) and IL-10-family cytokines are important. Mice lacking TGFß develop autoimmunity to several tissues. To elucidate upon which cells TGFß acts, we expressed a dominant-negative TGFß receptor (dnTGFßRII) on either T cells or antigen-presenting cells (APCs). Mice displaying the dnTGFßRII on T cells recapitulate the diseases of TGFß-knockout mice: autoimmunity and IBD. In addition to autoimmunity, such animals have an enhanced anti-infective response, better resistance to infection. Finally, mice carrying the dnTGFßRII on their T cells are resistant to tumors. Thus, tumors use TGFß to inhibit the antitumor T cell response; but if TGFß cannot act, immune clearance of tumors occurs. To determine whether TGFß controls innate immunity, we expressed dnTGFßRII using the CD11c promoter, which expresses in dendritic (DC) and natural killer (NK) cells, both key mediators of innate immunity. When innate immune cells cannot be inhibited by TGFß, both NK and DC innate, as well as adaptive, immune responses are enhanced. CD11c dnTGFßRII mice are also more susceptible to autoimmunity, because TGFß fails to control APC function. Thus, TGFß controls T cells, APCs, and NK cells. We revealed additional mechanisms of TGFß function by studying conditional-knockout mice lacking TGFßRII on T cells. TGFß is required for Treg homeostasis and function and TGFßRII must be present on a target cell for a Treg to be suppressed. We also found that TGFß controls the magnitude of T helper 1 cell (Th1) response by setting the level of CD122 ß chain of the IL-15 receptor, which controls the pool size of Th1 cells. Many cells make TGFß. To determine which TGFß source is important, we first eliminated TGFß on T cells, using conditional targeting. Mice with T cells that cannot make TGFß also developed autoimmune disease and IBD, albeit slower than mice lacking the receptor on all T cells. Thus, T cell–produced TGFß is important in immune response, but other sources must play a role. Regulatory T cells that cannot produce TGFß poorly control IBD, and T cell–produced TGFß is essential to generate Th17 cells, which mediate disease in experimental autoimmune encephalomyelitis. T cells are activated and differentiate into specialized effector cells.

How is the effector pathway triggered that is appropriate to the class of infection? We found the Th2 response is activated when parasite antigen induces Notch ligand expression on dendritic cells. This activates Notch in naïve T cells, which in turn induces GATA3, the key Th2 transcription factor, by a Notch-responsive promoter. Thus is a pathogenic signal converted to a signal for T cell differentiation through Notch. We identified cis-regulatory elements that are the targets of transcription factors, such as GATA3. In the interleukin-4 (IL-4) locus, the IL-4, IL-13, and IL-5 genes are clustered, and several DNA elements within that region are important for gene expression. IL-4 gene regulation occurs through epigenetic mechanisms that target regulatory elements distal from the IL-4 gene. One of these elements is a previously unrecognized locus control region (LCR) that is found embedded in the introns of the RAD50 gene in the cluster. This LCR, together with these respective promoters and other cis elements of the locus, is in a preassembled complex in naïve T cells that serves as a hub from which epigenetic changes in histone acetylation and DNA methylation occur and enables rapid response of the loci. When naïve T cells are activated, both the IL-4 locus on chromosome 11 and the interferon-? (IFN-?) locus on chromosome 10 are expressed almost immediately, despite the fact that following differentiation these loci are never coexpressed but instead are alternatively expressed in the Th2 and Th1 lineages, respectively. To investigate this rapid coexpression, we examined the physical relationship between these two loci on the different chromosomes. The LCR of the IL-4 locus on chromosome 11 and the IFN-? gene region on chromosome 10 are associated in the interphase nucleus of the precursor cells but separate upon differentiation into effector cells. Mutation in the LCR on chromosome 11 delays expression of the IFN-? gene on chromosome 10. We find other such associations and further evidence for their functional roles. Thus, regulatory sequences on one chromosome likely control "in trans" gene expression on other chromosomes. Our laboratory retains a long-standing interest in the underlying mechanisms of apoptosis. The program of cell death is triggered through the activation of cysteine proteases called caspases. Caspase-3 and -7 cleave similar substrates. Caspase-7–knockout mice have only a mild phenotype, but the combination with caspase-3 deficiency results in embryonic lethality. Caspase-3 and -7 are also required for upstream mitochondrial functions in apoptosis, via a positive-feedback loop, in addition to their roles as effector caspases.

Selected Publications

  • Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, Degnan PH, Hu J, Peter I, Zhang W, Ruggiero E, Cho JH, Goodman AL and Flavell RA: Immunoglobulin a coating identifies colitogenic bacteria in inflammatory bowel disease. Cell. 2014 Aug 28;158 (5) :1000-10. PMID: 25171403
  • Wlodarska M, Thaiss CA, Nowarski R, Henao-Mejia J, Zhang JP, Brown EM, Frankel G, Levy M, Katz MN, Philbrick WM, Elinav E, Finlay BB and Flavell RA: NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion. Cell. 2014 Feb 27;156 (5) :1045-59. PMID: 24581500
  • Rongvaux A, Willinger T, Martinek J, Strowig T, Gearty SV, Teichmann LL, Saito Y, Marches F, Halene S, Palucka AK, Manz MG and Flavell RA: Development and function of human innate immune cells in a humanized mouse model. Nat Biotechnol. 2014 Apr;32 (4) :364-72. Epub 2014 Mar 16. PMID: 24633240
  • Gagliani N, Palm NW, de Zoete MR and Flavell RA: Inflammasomes and intestinal homeostasis: regulating and connecting infection, inflammation and the microbiota. Int Immunol. 2014 Sep;26 (9) :495-499. Epub 2014 Jun 19. PMID: 24948595
  • Henao-Mejia J.*, Williams A*, Goff L.A., Staron M, Licona-Limón P, Kaech S.M., Nakayama M, Rinn J.L., Flavell R.A. miR-181 is a cellular metabolic rheostat essential for NKT cell development. Immunity. (2013). PMC3738211
  • Huber S, Gagliani N, Zenewicz LA, Huber FJ, Hedl W, O’Connor W, Murphy AJ, Valenzuela DM, Yancopoulos GD, Booth CJ, Cho JH, Ouyang W, Abraham C, Flavell RA IL-22BP axis is regulated by the inflammasome and modulates tumorogenesis in the intestine. Nature Nov 8;491(7423):259-63. (2012). PMC3493690.
  • Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss CA, Kau AL, Eisenbarth SC, Jurczak MJ, Camporez J-P, Shulman GI, Gordon JI, Hoffman HM, Flavell RA. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482:179-185 (2012) Feb 1. PMC3276682
  • Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Eisenbarth SC, Gordon JI, Flavell RA. NLRP6 inflammasome is a regulator of the colonic microbial ecology and risk for colitis. Cell 145:745-757 (2011) May 27. PMC3140910
  • Esplugues E, Huber S, Gagliani N, Hauser AE, Town T, Wan YY, O’Connor W, Rongvaux A, Van Rooijen N, Haberman AM, Iwakura Y, Kuchroo VK, Kolls JK, Bluestone JA, Herold, K, Flavell RA. Control of Th17 cells occurs in the small intestine. Nature 475:514-518 (2011) PMC3148838
  • Zenewicz LA, Abraham C, Flavell RA, Cho JH. Unraveling the genetics of autoimmunity. Cell 140:791-797 (2010).


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