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Rajat Varma, Ph.D.

Photo of Rajat Varma, Ph.D. 

Chief, T-Cell Biophysics Unit

Laboratory of Systems Biology

Major Areas of Research

  • Translating ligand engagement to immune response
  • Diversity in T-cell receptor (TCR) proximal signals dictated by receptor-ligand interaction affinity
  • Connecting proximal TCR signaling to transcription factor activation
  • Positive and negative regulation of TCR signaling via atypical Rho GTPase, RhoH
  • Biology of the common gamma chain family of cytokine receptors

Program Description

The complexity of cellular signaling networks in many cases makes it difficult, if not impossible, to anticipate the result of receptor stimulation. When T cells engage peptide-major histocompatibility complex (MHC) proteins on the surface of antigen-presenting cells through the TCR, a wide variety of signals are generated. These include calcium signals, small G-protein activation, and the activation of the three principal transcription factors: NFAT, NF-κB, and AP-1. Each T cell expresses a unique TCR, which can potentially interact with a continuum of affinities, with diverse peptides presented on MHC molecules in vivo.

To study cellular responses following TCR engagement by ligands of varying affinity, we use a model system consisting of a transgenic TCR interacting with altered peptide ligands of known potency for the receptor. In this model system, we are investigating how the balance between calcium signals and small G-protein activation is modulated by these ligands. The relative balance of these two types of signals at a given signal strength, in turn, will modulate transcription factor activation downstream of the TCR. These experiments are being conducted at two different levels: 1) investigation of the assembly of signaling molecules proximal to the engaged TCR and 2) monitoring the induction of immediate early genes such as cFos. Understanding the characteristics of TCR signaling across a spectrum of ligand affinity is important in uncovering how the immune response is initiated and autoimmunity is kept in check.

Several signaling molecules can play multiple and often opposite roles in a signaling pathway. An example of such a signaling molecule is RhoH, an atypical Rho GTPase that has no intrinsic GTPase activity and is indispensable for T-cell development. RhoH can act as a positive regulator of TCR signaling by potentially recruiting Lck and Zap70 to the immunological synapse. At the same time, it can act as a negative regulator by facilitating the inactive state of Lck and negatively regulating actin polymerization. To fully understand the mechanisms by which such multiple roles of a protein are orchestrated, computational modeling provides us with insightful paradigms. We are collaborating with the group of Martin Meier-Schellersheim to model such signaling pathways.

The common gamma chain family of cytokine receptors regulates a wide variety of immune processes, such as T-cell clonal expansion, T-cell development and survival, class switching, and T-helper differentiation. The family consists of IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21 cytokine receptors, all of which use the gamma chain for signaling. How these receptors use the common gamma chain is not clear. Two competing models suggest either a pre-association of the receptors with the gamma chain or a cytokine driven association of the receptors with the gamma chain. We are exploring the conditions under which the gamma chain becomes limiting for signaling. Is there a possibility of cross-talk between the cytokine signaling as a result of signaling through the shared gamma chain?

Our lab has a cross-disciplinary approach utilizing a variety of techniques in all the projects described. We extensively use and develop quantitative live cell fluorescence microscopy and spectroscopic tools for our research. Current technologies in the lab are total internal reflection fluorescence microscopy (TIRFM), spinning disc confocal microscopy, and fluorescence correlation spectroscopy. Other techniques include molecular biology and biochemical tools, flow cytometry, gene array experiments, and computational modeling.

Future projects in the lab will include study of TCR specificity, T-cell tuning, cross-talk between TCR and cytokine signaling pathways, cell biology of MHC molecules, and cell-cell communication networks.

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Dr. Varma received his Ph.D. in cell biology from the National Center for Biological Sciences, India, where he studied the organization of GPI-anchored proteins in living cells using FRET microscopy. His postdoctoral training took place at the Skirball Institute for Biomolecular Medicine, New York University, where he described TCR microclusters as sites of signaling. He joined the NIAID Laboratory of Cellular and Molecular Immunology in the winter of 2007 and transitioned to the Laboratory of Systems Biology in the spring of 2012.

Research Group

Rajat Varma's research group
From left to right: Travis Crites, Kaitlyn Sadtler, James Muller, Pauline Gonnord, Kartika Padhan, Lirong Chen, and Rajat Varma.

Selected Publications

Crites TJ, Chen L, Varma R. A TIRF microscopy technique for real-time, simultaneous imaging of the TCR and its associated signaling proteins. J Vis Exp. 2012 Mar 22;(61). pii: 3892.

Padhan K, Varma R. Immunological synapse: a multi-protein signaling cellular apparatus for controlling gene expression. Immunology. 2010 Mar;129(3):322-8.

Crites TJ, Varma R. On the issue of peptide recognition in T-cell development. Self Nonself. 2010 Jan;1(1):55-61.

Varma R. Diffusion and signaling revisited. Immunity. 2009 Sep 18:31(3):452-4.

Varma R. TCR triggering by the pMHC complex: valency, affinity, and dynamics. Sci Signal. 2008 May 13;1(19):pe21.

Skokos D, Shakhar G, Varma R, Waite JC, Cameron TO, Lindquist RL, Schwickert T, Nussenzweig MC, Dustin ML. Peptide-MHC potency governs dynamic interactions between T cells and dendritic cells in lymph nodes. Nat Immunol. 2007 Aug;8(8):835-44.

Visit PubMed for a complete publication list.

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Last Updated October 19, 2012

Last Reviewed October 19, 2012