# Editing to Create and Correct Gene Variants

> **NIH NIH P01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $445,243

## Abstract

Mutations in over 350 genes have been implicated as drivers of primary immunodeficiency (PID), but the genes
that are mutated to cause many of these rare, but clinically serious conditions remain unknown, even despite
whole exome sequencing. The use of whole genome sequencing promises to reveal coding and non-coding
mutations for cases of T lymphocyte deficiency that cannot be solved by whole exome sequencing. However,
confidently distinguishing pathogenic PID mutations from the exceedingly large number of benign variants across
the entire genome is daunting, due to the rare incidence of each PID, incomplete knowledge of the genes
required for T cell development, and our lack sequence-based rules to predict which non-coding variants may
be pathogenic. CRISPR-Cas9 genome editing combined with our in vitro T cell differentiation platform offers
unprecedented opportunities to test directly how human genetic sequences control immune cell development
from hematopoietic stem progenitor cells (HSPCs) and ultimately to arrive at new therapies consisting of rewriting
mutations that cause human immune diseases in patient blood-forming cells. Progress in pinpointing each
patient’s causal mutation will open the next frontier: precise non-viral correction of endogenous disease-causing
mutations for autologous gene therapy in HSPCs, avoiding the necessity to use imperfectly matched allogeneic
donor transplants, for which graft rejection and graft vs. host disease are potentially devastating complications.
This project will develop high-efficiency, high-throughput CRISPR-based technologies for identification of
essential genes T for cell development, rapid functional testing of candidate mutations, and therapeutic genetic
correction of a patient’s own HSPCs. We have developed CRISPR-Cas9 as a molecular scalpel to edit specific
genome sequences in primary human cells and recently improved this technology for therapeutically-relevant
editing in HPSCs. We will further apply CRISPR-based technologies for high-throughput mapping of coding and
non-coding mutations in genes related to SCID and other forms of T-cell deficient PID, and we will develop new
technologies for therapeutic gene editing in primary human HSPCs. Thus this project’s three central aims
address fundamental challenges to achieving cures for PID through gene editing: 1) Discovery of all gene
perturbations that could result in T cell deficiency, 2) Rapid identification of causal mutations for PID cases with
unsolved genetic basis, and 3) Improvement in technology to introduce efficient and specific gene corrections
into primary HPSCs as a forerunner to personalized autologous gene correction to restore immune function.

## Key facts

- **NIH application ID:** 10691245
- **Project number:** 5P01AI138962-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Alexander Marson
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $445,243
- **Award type:** 5
- **Project period:** 2020-09-08 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10691245

## Citation

> US National Institutes of Health, RePORTER application 10691245, Editing to Create and Correct Gene Variants (5P01AI138962-04). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10691245. Licensed CC0.

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