# Orthogonal CRISPR GEMMs

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $669,251

## Abstract

PROJECT SUMMARY
The heart of this proposal is to overturn the existing one-gene-at-a-time paradigm for studying human
genes in organismal model studies, and to push the envelope for studying genetic interactions in vivo.
We have developed a technology to study gene interactions in mouse models using a high-throughput
CRISPR technology suitable for interrogating specific genes implicated in a given pathway or disease.
An in vivo high-throughput targeted multi-mutation approach has never been accomplished in any
organismal model and this will revolutionize the study of complex gene interaction in physiologically
relevant organismal model systems. Our preliminary data have addressed the major feasibility gaps but
we need to further develop the platform and apply rigor/reproducibility.
Multimer technology will help bridge the gap between the enormous volumes of data generated by
genome sequencing studies and the ability to use these data for the understanding of biology and
disease. Our end goal is to benchmark the proposed technology, illustrating its application in a use-case
setting—targeting a set of CD antigens with orthogonal gene activation and gene editing CRISPR
machinery to reveal underlying genetic interactions and pathway directionality. Our general strategy is to
take advantage of novel tools and methodologies that we have developed during the past two years–
using innovative high throughput CRISPR screening methods. Our end goal is to develop a modular
toolset that advances functional genomics approaches. All this will be done in vivo in an animal model.
Our goal is to pilot an orthogonal Multimer platform to investigate up to 900 combinations of
perturbations in vivo in a single animal. We will benchmark our technology using CD antigens as
reporter genes that are easy to quantitate using commercially available monoclonal antibodies.
Targeted edits and transcript abundance will be analyzed by flow cytometry and via single-cell
sequencing on subpopulations of B and T cells.
The future for bioinformatically dissecting mechanisms of complex diseases is promising but
challenging. Multiple large-scale reference data sets of human sequences are rapidly becoming
available and are expected to increase over the coming decades. Millions of human genome
sequencing data sets will constitute an incredible resource for interpretation of DNA mutations.
Unfortunately, there are no feasible approaches for interrogating the thousands of combinations of
genes in animal models. This proposal aims to further a new technology that would advance complex
genetics problems relevant to organismal biology and human disease and will showcase promising new
technologies for studying genetic interaction in vivo.

## Key facts

- **NIH application ID:** 10639698
- **Project number:** 1R01CA279801-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** MICHAEL T MCMANUS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $669,251
- **Award type:** 1
- **Project period:** 2023-03-01 → 2027-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10639698

## Citation

> US National Institutes of Health, RePORTER application 10639698, Orthogonal CRISPR GEMMs (1R01CA279801-01). Retrieved via AI Analytics 2026-06-12 from https://api.ai-analytics.org/grant/nih/10639698. Licensed CC0.

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