# Defining regulators of immunity to acute infection using CRISPR screens

> **NIH NIH U19** · HARVARD MEDICAL SCHOOL · 2021 · $2,292,456

## Abstract

The overarching goal of this U19 Program is to use forward genetic screens in mice to advance our
understanding of immune responses to pathogens. This U19 Program is driven by our recent
development of a genetic screening platform that uses pooled, in vivo CRISPR-mediated loss-of-
function genetic screens to identify genes that positively or negatively regulate the fate and function of
immune cells. We will couple this novel approach with single-cell gene profiling and systems-level
computational modeling of innate and adaptive cells during acute infection to nominate candidates to
perturb functionally in genetic screens. We will then test thousands of potential regulators in pooled
CRISPR-Cas9 based forward genetic screens in mice, and validate novel candidate regulators in
mouse infection models and human cells. Our proposed U19 Program consists of 2 highly interactive
Projects, supported by 4 Cores. Project 1 (Haining/Kuchroo/Sharpe) will conduct forward genetic
screens to identify genes that regulate the fate and function of CD8+ and CD4+ T cells responding to
acute infection. Project 2 (Hacohen/Kagan) will conduct screens to identify genes that control DC
activation in response to pathogens, pathogen components and T cells. Administrative Core A
(Sharpe/Haining) will provide administrative and scientific coordination, and implement our Pilot Project
program. Data Management and Bioinformatics Core B (Regev) will develop, apply and disseminate
cutting-edge methods and tools for single cell RNA-seq analysis of immune cell responses and for
selecting and ranking candidate genes for genetic manipulation in CRISPR screens. Core B will also
establish and maintain a public portal and software pipelines for sharing data, analyses and methods.
CRISPR Library Core C (Doench) will design and generate custom single guide RNA (sgRNA) libraries
needed to conduct forward genetic screens and to validate candidate regulators. Core C will also
analyze genomic DNA from cells obtained pooled screens, performing sequencing and sequence
deconvolution to identify sgRNAs that caused the phenotype of interest. Mouse Perturbation Core D
(Sharpe/Haining) will provide a uniform platform to execute CRISPR-Cas9 screens and validation
experiments in mouse infection models. The use of standardized experimental methods and
computational tools by the cores will make it possible to compare and integrate results in different
settings and disease models. We expect that our in vivo forward genetic screens and systems level
single-cell genomic analyses will identify the central molecules, pathways and mechanism that guide
innate and adaptive immune responses to infection. These findings will lay the foundation for new
vaccination strategies for infectious diseases and therapies for allergy and autoimmunity.

## Key facts

- **NIH application ID:** 10207344
- **Project number:** 5U19AI133524-05
- **Recipient organization:** HARVARD MEDICAL SCHOOL
- **Principal Investigator:** Arlene H. Sharpe
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $2,292,456
- **Award type:** 5
- **Project period:** 2017-07-05 → 2023-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10207344

## Citation

> US National Institutes of Health, RePORTER application 10207344, Defining regulators of immunity to acute infection using CRISPR screens (5U19AI133524-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10207344. Licensed CC0.

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