# Dissecting mechanisms of pioneer transcription factor-mediated lineage reprogramming

> **NIH NIH R01** · WASHINGTON UNIVERSITY · 2020 · $320,250

## Abstract

PROJECT SUMMARY/ABSTRACT
The reprogramming of abundant and accessible cells into therapeutically useful cell types holds great promise
for regenerative medicine. Cellular reprogramming can be achieved by ectopically expressing transcription
factors (TFs) that directly convert one differentiated cell type into another, bypassing embryonic states in an
attempt to boost the speed and efficiency of target cell production. A number of different cell types have been
generated by such “direct lineage reprogramming” methods, but their practical utility has been limited because,
in most protocols, only a small percentage of cells are successfully converted to the target cell type. Even then,
the resulting populations are often partially differentiated or incompletely specified. Most cell engineering
methods require the use of at least one pioneer factor, a unique class of TFs that are able to access their
binding sites in silent chromatin. Pioneer TFs have the capacity to impart lineage competence in a context-
specific manner, and play central roles in development, as reflected by their redeployment across disparate
developmental programs. Our long-term goal is to understand the mechanism of pioneer factor-mediated direct
lineage reprogramming. In this proposal we employ prototypical pioneer TFs, the FoxA family, to drive
conversion of fibroblasts to an endoderm progenitor-like (iEP) state, representing a paradigm for direct lineage
reprogramming. Based on our preliminary results and current evidence, we hypothesize that during direct
lineage reprogramming, pioneer TFs re-engage developmental GRNs, depending on the chromatin state of the
cells into which they are introduced. Our three independent yet related aims are directed at understanding:
(Aim 1) the nature of transcriptional changes during reprogramming from their origin and their relation to
developmental programs; (Aim 2) the direct targets of FoxA pioneer TFs and their cofactor, Hnf4a and their
activity to drive fate change; (Aim 3) the influence of chromatin context on target accessibility of pioneer TFs
and how this impacts efficiency of reprogramming and the potential of cells generated. Here we apply an
innovative single-cell lineage tracing methodology and genomic technology to record TF binding history in cells
undergoing reprogramming. Together, this will generate an unprecedented digital quantification of the
reprogramming process, and will reveal barriers to the successful conversion of cell identity. An improved
understanding of pioneer-mediated reprogramming mechanisms will facilitate enhanced conversion efficiency
and fidelity across an array of reprogramming strategies, and improve knowledge of the action of this important
class of transcriptional regulators.

## Key facts

- **NIH application ID:** 9999587
- **Project number:** 5R01GM126112-04
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Samantha Annette Morris
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $320,250
- **Award type:** 5
- **Project period:** 2017-09-15 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9999587

## Citation

> US National Institutes of Health, RePORTER application 9999587, Dissecting mechanisms of pioneer transcription factor-mediated lineage reprogramming (5R01GM126112-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9999587. Licensed CC0.

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