# Dissecting and reconstructing the molecular roadmaps of cellular reprogramming to iPSCs in single-cell resolution

> **NIH NIH R00** · MASSACHUSETTS GENERAL HOSPITAL · 2022 · $241,418

## Abstract

Project Summary
Understanding the molecular programs that guide cell fate conversion will provide a foundation for the
development of tools to convert cell fate and eventually facilitate the generation of therapeutically relevant cell
types. Experimental approaches to understand such mechanisms have typically involved studying bulk
populations. These experiments are severely limited because they can only measure averaged effects.
Recently, large-scale profiling of single cells has opened new prospects for systematically dissecting the
processes underlying cell fate conversion. However, proper analysis of large-scale single cell data remains a
challenge. To combat this, we developed experimental and computational approaches to study scRNA-seq
data from 65,781 cells collected at 10 time points over 16 days during the reprogramming of fibroblasts to
iPSCs by Oct4, Sox2, Klf4, and cMyc. In my K99/R00 proposal, I hypothesize that dissecting complex
reprogramming processes in single-cell resolution will help us understand the mechanisms of reprogramming
for iPSCs, identify novel reprogramming factors that can enhance reprogramming efficiency and generate high-
quality iPSCs that can be used in clinical settings. I propose to 1) characterize the role of candidate
reprograming factors (K99); 2) validate the reprogramming trajectory predicted from single-cell RNA-
seq data by lineage tracing (K99); 3) investigate the reprogramming process through comparison of
different cocktails (K99/R00); 4) develop new methods to enhance cell fate conversion (R00). Together,
the proposed aims will have a broad impact on the journey to understand developmental processes and
provide rich resources for the scientific community. In the long term, these studies may reveal novel strategies
to generate therapeutically relevant cells. To succeed in these proposed aims, I will need additional training in
computational analysis and stem cell research, supported by my co-mentors Dr. Eric Lander (genetics and
genomics) and Dr. Rudolf Jaenisch (stem cells and genome engineering) as well as an Advisory Committee
including Dr. Aviv Regev (computational biology and single-cell techniques), Dr. Feng Zhang (genome
engineering). My career development plan integrates practical training in computational and experimental tools
as well as trainings in communication, management, mentorship, grant writing, etc. The Broad Institute is an
ideal environment, providing all of the facilities needed for the proposed research and a rich interdisciplinary
environment. With these additional skills gained through support by the NIH K99/R00 Pathway to
Independence Award, I will be qualified to execute these goals to make great strides at the interface of stem
cell research and single-cell techniques.

## Key facts

- **NIH application ID:** 10320077
- **Project number:** 5R00HD096049-04
- **Recipient organization:** MASSACHUSETTS GENERAL HOSPITAL
- **Principal Investigator:** Jian Shu
- **Activity code:** R00 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $241,418
- **Award type:** 5
- **Project period:** 2021-01-01 → 2023-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10320077

## Citation

> US National Institutes of Health, RePORTER application 10320077, Dissecting and reconstructing the molecular roadmaps of cellular reprogramming to iPSCs in single-cell resolution (5R00HD096049-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10320077. Licensed CC0.

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