Functionally dissecting the transcriptional regulatory network of the innate immune response using CRISPR-effectors

Univ Of Massachusetts Med Sch Worcester, Worcester MA

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Abstract

? DESCRIPTION (provided by applicant): The dendritic cell (DC) is a cornerstone for a proper adaptive immune response. When a DC detects a pathogen it launches a specific transcriptional program that leads to DC maturation and an ensuing adaptive immune response. To this day, we still do not understand how the underlying transcriptional regulatory networks regulate DC maturation in response to specific stimuli including pathogen detection. Without detailed knowledge of these regulatory networks it is impossible to predict the impact of genomic variations on the capacity of DCs to mount a proper response. More generally, a better understanding of how specific gene regulatory networks operate during DC maturation can be used to control DCs and has the potential for a broad-spectrum of applications reaching from improved vaccination efforts to controlling autoimmunity. We have previously mapped the epigenetic cis-regulatory landscape of mouse dendritic cells by using a combination of transcriptional profiling (RNA-Seq) and annotation of chromatin occupancy of over 30 different transcription factors and modified histones (ChIP-Seq). The regulatory network models we built from these datasets are the basis for this proposal. Until recently, a thorough functional characterization of these regulatory networks was out of reach. The proposal outlined here describes the use a CRISPR-effector technology we recently developed, to functionally dissect the transcriptional network operating during DC maturation. This innovative technology not only allows for a rapid functional annotation of individual regulatory elements but also allows for combinatorial inactivation of gene coding and non-coding genomic regions. Here we propose to probe both cis- and trans- effectors that regulate the maturation of primary DCs derived from CRISPR-effector mice in response to lipopolysaccharide (LPS). We propose a network perturbation approach that targets network nodes with distinct regulatory patterns to test and refine previously identified regulatory network models. In the first Aim we repress key trans activators by delivering a KRAB domain to key transcription factors. We have previously shown that this repressor is extremely effective in silencing transcription when delivered to gene promoters. We will also explore network molarity by dissecting Tumor Necrosis Factor (TNF) signaling, a network component critical for the late phase of DC maturation after LPS stimulation. In the second aim we deliver an enhancer specific CRISPR-effector (LSD1) to key cis- regulatory regions to perturb specific enhancers activity. Here, we will test whether differential enhancer activity affects their targets and the regulatory network. The latter will hae important implications for genomic variation in cis-regulatory elements, a feature under active investigation in the context of genome wide association studies.