The calcium/ calcineurin/ NFAT pathway is essential for the adaptive immune response, a point underscored by the clinical efficacy of the calcineurin inhibitors cyclosporin A (CsA) and FK506. NFAT also plays an important role in the development and function of many other organs and cell types - neurons, heart, skeletal and smooth muscle, bone, skin, pancreas, and the vasculature. Surprisingly, however, there has not yet been a detailed examination, at a genome-wide level, of how NFAT transcription factors bind cis-regulatory DNA elements and change the transcriptional profiles of cells. In this application, we address this point for CD4+ Th1 and CD8+ cytolytic T cells (CTL). A striking feature of NFAT proteins is their ability to form tight complexes with unrelated transcription factors such as AP-1 (Fos-Jun) on composite elements in DNA. We have shown that NFAT in the absence of its partner AP-1 induces a negative regulatory programme of gene expression (T cell 'anergy' or 'exhaustion') that is distinct from the programme of T cell activation induced by NFAT: AP-1 complexes. Indeed, our preliminary data suggest that in the absence of AP-1, NFAT potentially functions as a 'master regulator' of CD8+ T cell exhaustion, a hypothesis that will be tested here.
In Aim 1 of the application, we will examine the binding of the three immune-related NFAT proteins - NFAT1, NFAT2 and NFAT4 - to regulatory regions in genomic DNA of Th1 cells and CTL, under conditions of cooperation or lack of cooperation with AP-1. We will perform chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq), and a variant procedure known as ChIP-exo that more closely defines the binding sites for these transcription factors in DNA. We will also define the gene expression patterns regulated by these wild type and mutant NFAT proteins, by performing RNA-sequencing (RNA-seq) for steady-state or 'nascent' (chromatin-associated) RNA-sequencing on cells expressing the proteins.
In Aim 2, we will repeat these experiments in human T cells.
In Aim 3, we will implement a novel high-throughput screen to identify compounds that block the NFAT: AP-1 interaction without affecting the binding of NFAT to DNA or the formation of NFAT complexes with other partners such as FOXP3.
In Aim 4, we will relate the patterns of gene expression defined in vitro in Aims 1 and 2 to the patterns obtained during immune responses in vivo, and ask whether T cells expressing mutant NFAT proteins that cannot cooperate with AP-1 induce a more profound phenotype of T cell anergy/ exhaustion during viral infections. From a clinical perspective, our project is very relevant to cancer immunotherapy and the treatment of viral infections, since CD8+ T cell exhaustion limits T cell responses in tumour-infiltrating CTL and during chronic viral infections.

Public Health Relevance

In this project we will investigate the functions of a protein known as NFAT, which is present in all cells including those of the brain, heart, muscle and immune system, and controls a huge diversity of cellular functions. When calcium enters cells, NFAT enters the nucleus, binds to DNA, and turns on genes important for the proper functioning of the cell. Here we propose to use cutting-edge approaches, including next- generation sequencing, to investigate the role of NFAT in T cells of the immune system. We will ask which regions of DNA are bound by NFAT and which genes it turns on during different phases of the T cell immune response. We expect to identify new regulatory mechanisms that will provide novel therapies for autoimmunity and other immune diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI109842-30
Application #
9315767
Study Section
Cellular and Molecular Immunology - A Study Section (CMIA)
Program Officer
Mallia, Conrad M
Project Start
2014-08-01
Project End
2019-07-31
Budget Start
2017-08-01
Budget End
2018-07-31
Support Year
30
Fiscal Year
2017
Total Cost
Indirect Cost
Name
La Jolla Institute
Department
Type
DUNS #
603880287
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Pereira, Renata M; Hogan, Patrick G; Rao, Anjana et al. (2017) Transcriptional and epigenetic regulation of T cell hyporesponsiveness. J Leukoc Biol 102:601-615
Yu, Bingfei; Zhang, Kai; Milner, J Justin et al. (2017) Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation. Nat Immunol 18:573-582
Mognol, Giuliana P; Spreafico, Roberto; Wong, Victor et al. (2017) Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells. Proc Natl Acad Sci U S A 114:E2776-E2785
Hogan, Patrick G (2017) Calcium-NFAT transcriptional signalling in T cell activation and T cell exhaustion. Cell Calcium 63:66-69
Martinez, Gustavo J; Hu, Joyce K; Pereira, Renata M et al. (2016) Cutting Edge: NFAT Transcription Factors Promote the Generation of Follicular Helper T Cells in Response to Acute Viral Infection. J Immunol 196:2015-9
Scott-Browne, James P; López-Moyado, Isaac F; Trifari, Sara et al. (2016) Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection. Immunity 45:1327-1340
Hogan, Patrick G (2015) Sphingomyelin, ORAI1 channels, and cellular Ca2+ signaling. J Gen Physiol 146:195-200
Chang, Xing; Li, Bin; Rao, Anjana (2015) RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation. Proc Natl Acad Sci U S A 112:E1888-97
Martinez, Gustavo J; Pereira, Renata M; Äijö, Tarmo et al. (2015) The transcription factor NFAT promotes exhaustion of activated CD8? T cells. Immunity 42:265-278
Chen, Runqiang; Bélanger, Simon; Frederick, Megan A et al. (2014) In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation. Immunity 41:325-38

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