The heterogeneity within the CD4+ effector/memory T-cell compartment is critical for our ability to deal with diverse pathogens. For example, dedicated populations of CD4+ T helper cells are required for promoting immune defense against intracellular infections (Th1 cells), helminth infections (Th2 cells), and fungal infection (Th17 cells). On the other hand, each of these differentiated states is associated with human disease: Th1 and Th17 cells can promote autoimmunity, while Th2 cells can promote allergy and asthma. Thus, understanding and learning to exploit the mechanisms that underlie lineage choice is vital for understanding and treatment of immunological and infectious diseases. We are interested in epigenetic regulation of T-cell lineage commitment and T-cell memory. Here, we propose a novel strategy to target the Th cell epigenome in order to modify their phenotype and promote or inhibit inflammatory immune response. The cellular epigenome, represented by DNA methylation, histone modifications and ncRNA, is believed to reflect the differentiation history of the cell and determine its phenotype. Working with human helper T cells, we have found that the ability of memory CD4 T cells to quickly induce key cytokines (rapid recall ability) is correlated with epigenetic gene poising: the presence of positive histone modifications at several regulatory elements in the resting memory cells. Based on this observation, we hypothesize that memory T-cell lineage commitment is encoded in the epigenome. As a first step toward proving this hypothesis (and to T-cell reprogramming), we will attempt to modify T cell phenotype by changing chromatin marks at several key elements that we and others have previously identified. To do so, we are using TALEMs - fusion proteins of TAL-based engineered DNA binding domains (DBDs) with Epigenetic Modifier enzymes. We will use TALEMs to remove positive chromatin marks (e.g., H3K4 methylation) from the previously identified regulatory elements in the IL4/13 locus to test whether the presence of such marks is indeed required for the maintenance of Th2 phenotype and IL4/13 gene inducibility. We will also test whether deposition of negative marks (e.g., K9me2 and DNA methylation) there will be sufficient to reverse Th2 differentiation. Similarly, we will test whether deposition of the positie marks at these elements is sufficient to force Th2 cytokine inducibility in nave T cells. Finallywe will test, whether such epigenetic reprogramming can affect disease phenotype in a mouse model of experimental asthma. If successful, this strategy may potentially lead to creation of therapies for immunological diseases and immunotherapy of cancer. In one hypothetical scenario, for asthma, allergen- specific inflammatory Th2 cells could be purified from patient's blood using tetramers, propagated and reprogrammed into immunosuppressive Tregs. These Treg cells could then be returned back to patient to restore tolerance and, potentially, to provide a cure. Importantly, the ability of allergen-specific Tregs to cure experimental asthma has already been demonstrated in a murine model. Similarly, tumor antigen-specific Treg cells could be purified from tumors and reprogrammed into Th1 effectors for immunotherapy. Knowledge gained through this study would enable similar applications in other biomedical areas.
This project aims to develop tools for the direct epigenetic reprogramming of T cells. If successful, this technology may potentially lead to novel treatments for immunological diseases, cancer immunotherapy and wider applications allowed by epigenetic reprogramming.
| Vallabh, Sushmitha; Kartashov, Andrey V; Barski, Artem (2018) Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe. Methods Mol Biol 1783:343-360 |
| Harley, John B; Chen, Xiaoting; Pujato, Mario et al. (2018) Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nat Genet 50:699-707 |
| Kelly, Daniel; Kotliar, Michael; Woo, Vivienne et al. (2018) Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. JCI Insight 3: |
| Bouffi, Carine; Barski, Artem; Fulkerson, Patricia C (2018) Chromatin Preparation from Murine Eosinophils for Genome-Wide Analyses. Methods Mol Biol 1799:265-274 |
| Maezawa, So; Hasegawa, Kazuteru; Yukawa, Masashi et al. (2018) Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline. Proc Natl Acad Sci U S A 115:4957-4962 |
| Maezawa, So; Hasegawa, Kazuteru; Alavattam, Kris G et al. (2018) SCML2 promotes heterochromatin organization in late spermatogenesis. J Cell Sci 131: |
| Rochman, Yrina; Dienger-Stambaugh, Krista; Richgels, Phoebe K et al. (2018) TSLP signaling in CD4+ T cells programs a pathogenic T helper 2 cell state. Sci Signal 11: |
| Grace, Jillian O; Malik, Astha; Reichman, Hadar et al. (2018) Reuse of public, genome-wide, murine eosinophil expression data for hypotheses development. J Leukoc Biol 104:185-193 |
| Stevens, Mariana L; Chaturvedi, Praneet; Rankin, Scott A et al. (2017) Genomic integration of Wnt/?-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional programs. Development 144:1283-1295 |
| Barski, Artem; Cuddapah, Suresh; Kartashov, Andrey V et al. (2017) Rapid Recall Ability of Memory T cells is Encoded in their Epigenome. Sci Rep 7:39785 |
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