# Harnessing multiplexed Cas9 genome editing for sequential genetic manipulations and recording activities in cell lineages

> **NIH NIH R01** · UNIVERSITY OF ILLINOIS AT CHICAGO · 2023 · $302,288

## Abstract

SUMMARY
Time is a problem for biologists, especially for those interested in cancer, stem cell, and developmental
biology. Whereas cellular processes occur in real time, we most often try to understand biology by piecing
together information obtained with static end-point experiments. The goal of this proposal is to expand a novel
technology to provide innovative of dealing with problems posed by time in biology. The technology records a
ledger of events within the cell’s own genome with CRISPR/Cas9 gene editing tools, which have been
developed to execute machine-like instructions in cells. The ledger can be “read” by next generation DNA
sequencing, allowing the reading many ledger entries at one time at once. The presence of multiple ledger
entries on a contiguous DNA strand enables all the entries from many cells to be read at the individual cell
level. The system of recording is based on combining multiple modular activities in series to develop a
cascading process through sequentially activated steps; each step is encoded by a single module. We have
developed and validated the essential components of individual modules, and here we propose to build and
optimize series of modules linked together in pre-programmed orders. The proposed research is organized by
three Specific Aims of 1) expanding the duration of stem cell lineage tracking with a 10-module long cascade,
2) record the history of Wnt signaling in individual cells in a lineage using our technology, and 3) control a
ratcheting progression of cellular recording such that cellular events can be identified with a cell division
number tracker. Completion of the proposal will provide a substantial new capability for biologists in
interrogating the functions of biological systems.

## Key facts

- **NIH application ID:** 10528482
- **Project number:** 5R01GM139894-03
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT CHICAGO
- **Principal Investigator:** Bradley J Merrill
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $302,288
- **Award type:** 5
- **Project period:** 2021-02-01 → 2024-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10528482

## Citation

> US National Institutes of Health, RePORTER application 10528482, Harnessing multiplexed Cas9 genome editing for sequential genetic manipulations and recording activities in cell lineages (5R01GM139894-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10528482. Licensed CC0.

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