The overall goal of this PPG application is to compare and contrast the mechanisms by which the inhibitory receptors PD1 and LAG3 operate on T cells in the context of tolerance and autoimmunity, cancer, and chronic infection. One major approach to be used throughout the studies is the application of genome-wide transcriptional profiling. The purpose of the Functional Genomics and Computational Biology Core (Core C) is to provide essential and centralized sequencing-based genomics services for all three Projects in this Program. In addition, this Core will operate provide the service of a retroviral (RV)-enforced expression and knockdown platform that can directly test in vivo individual genes and pathways identified from computational analyses. Thus, Core C will provide integrated bioinformatic and computational analytical platforms and data integration services coupled to downstream RV-enforced expression and knockdown as well as in vivo CRISPR/Cas9-focused genetic screening.
The Aims are:
AIM 1 : To provide initial data hosting, normalization, preprocessing, and analysis as well as perform cross-Project data integration and computational network modeling for bulk and single-cell transcriptomic and epigenetic datasets. Core C will (i) provide raw data QC, data cleaning, pre-processing, and generation of files for downstream analyses as well as operate a web portal interface for user exploration of the data; (ii) perform primary and secondary genomics data analyses; and (iii) perform network and integrated analyses including. The Core also will support and/or develop new analytical tools as technologies become available (as for scRNA-seq in the last cycle).
AIM 2 : To enable in vivo CRISPR/Cas9 screening and provide an RV-enforced expression and knowckdown platform for downstream in vivo interrogation of genes and pathways regulated by PD-1 and/or LAG3. Core C will aid in design of CRISPR screening libraries for in vivo CRISPR screening platforms by the Projects as well as downstream data analysis. Core C will also provide an in vivo retroviral platform to enforce expression or shRNA knock-down of high-priority GOIs. By its nature, Core C is highly interactive with other components of this PPG. Samples from Projects 1, 2, and 3 will enter Core C, which will analyze samples with input from the Projects and integrate results among the three Projects. Core C will interact heavily with Cores A, B, and D for administrative support and to identify gene targets for novel mouse strains and immunostaining analysis.
Chronic infections with viruses such as HIV, HCV and HBV affect half a billion people and are significant causes of morbidity and mortality. T cell dysfunction or ?exhaustion? is a major immunological defect during these infections and can be modeled with LCMV infection in mice. The studies proposed will define the role of the inhibitory receptors PD-1 and LAG-3 in CD8+ and CD4+ T cell exhaustion and provide new insights into how to reverse and avoid T cell exhaustion and improve immunity during these and other chronic infections.
| Stelekati, Erietta; Chen, Zeyu; Manne, Sasikanth et al. (2018) Long-Term Persistence of Exhausted CD8 T Cells in Chronic Infection Is Regulated by MicroRNA-155. Cell Rep 23:2142-2156 |
| Bengsch, Bertram; Ohtani, Takuya; Khan, Omar et al. (2018) Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity 48:1029-1045.e5 |
| Overacre-Delgoffe, Abigail E; Vignali, Dario A A (2018) Treg Fragility: A Prerequisite for Effective Antitumor Immunity? Cancer Immunol Res 6:882-887 |
| Ratay, Michelle L; Glowacki, Andrew J; Balmert, Stephen C et al. (2017) Treg-recruiting microspheres prevent inflammation in a murine model of dry eye disease. J Control Release 258:208-217 |
| Huang, Alexander C; Postow, Michael A; Orlowski, Robert J et al. (2017) T-cell invigoration to tumour burden ratio associated with anti-PD-1 response. Nature 545:60-65 |
| Hope, Jennifer L; Stairiker, Christopher J; Spantidea, Panagiota I et al. (2017) The Transcription Factor T-Bet Is Regulated by MicroRNA-155 in Murine Anti-Viral CD8+ T Cells via SHIP-1. Front Immunol 8:1696 |
| Andrews, Lawrence P; Marciscano, Ariel E; Drake, Charles G et al. (2017) LAG3 (CD223) as a cancer immunotherapy target. Immunol Rev 276:80-96 |
| Chen, Zeyu; Stelekati, Erietta; Kurachi, Makoto et al. (2017) miR-150 Regulates Memory CD8 T Cell Differentiation via c-Myb. Cell Rep 20:2584-2597 |
| Zhang, Qianxia; Chikina, Maria; Szymczak-Workman, Andrea L et al. (2017) LAG3 limits regulatory T cell proliferation and function in autoimmune diabetes. Sci Immunol 2: |
| Kurachi, Makoto; Kurachi, Junko; Chen, Zeyu et al. (2017) Optimized retroviral transduction of mouse T cells for in vivo assessment of gene function. Nat Protoc 12:1980-1998 |
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