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  1. Science & Research (Biologics)

Evaluation of Therapeutic Approaches Based on Genome Editing and Stem Cell Technologies


Zhaohui Ye

Zhaohui Ye, PhD

Office of Tissues and Advanced Therapies
Division of Cellular and Gene Therapies
Gene Transfer and Immunogenicity Branch



Zhaohui Ye received his PhD in immunology from Johns Hopkins University, where he studied stem cell biology and its applications to stem-cell biomedical research. Using reprogramming technology, he derived the first human induced pluripotent stem cell (iPSC) lines from patients with acquired blood diseases and established their disease modeling potential. Before joining FDA, he was an assistant professor of medicine at Johns Hopkins, where he studied differentiation and genetic engineering of human stem cells. He currently studies cell fate determination of human iPSCs, with an emphasis on hematopoietic and lymphoid differentiation. His laboratory also studies the efficacy and specificity of genetic engineering technologies.

General Overview

Human induced pluripotent stem cells (iPSCs) have great potential in cell replacement therapies due to their ability to give rise to all somatic cell types. iPSCs can also be directed to immune cell types for immunotherapies against cancers or autoimmune diseases. The unmet needs in developing iPSC-based therapies include methods to evaluate differentiation efficiency and to characterize cell populations during differentiation. Suboptimal differentiation, which results in unwanted cell types in the cellular products, not only undermines clinical efficacy of cellular therapy but also poses significant health risk to patients. In order to develop robust manufacturing of therapeutic stem cell products and to ensure patient safety, it is essential to Improve characterization of cell types during differentiation and achieve a better understanding of differentiation mechanisms.  
We investigate the biological processes required for blood and immune cell generation from iPSCs. Nearly all blood cells arise from hematopoietic stem cells (HSCs) that reside and self-renew in a bone marrow niche. The first HSCs arise during early embryonic development and later migrate to bone marrow.  We use human iPSC-based cell/tissue culture systems, genetic engineering technology, and animal transplantation models to recapitulate in the laboratory this early developmental. We also use this system to develop and optimize differentiation conditions required for immune cell generation from hematopoietic progenitors.

We also study the safe use of genetic engineering technologies that are increasing incorporated into regenerative medicine advanced therapy products. We are particularly interested in the specificity of modern genome editing technologies based on engineered endonucleases. These technologies enable modification of the human genome in live cells with unprecedented efficiency. However, genome editing can also result in unintended modifications in human genome. Understanding the specificity profiles of different genome editing tools is essential for improving the safety of products that incorporate these technologies. We use cell culture, high throughput sequencing, and animal models to study the impact of these endonucleases on human stem cell genome integrity, and the biological consequences of potential off-target genetic modifications. The resulting experimental data on efficiency and specificity of genome editing technologies will facilitate relevant regulatory policy development.

Scientific Overview

We use an in vitro, cell-based system to study biological processes that generate definitive hematopoietic stem and progenitor cells. Studies using animal models have provided strong evidence that such cells originate from endothelium in the aorta-gonad-mesonephros region during early embryonic development, providing a basis for recapitulating this process in vitro. However, there is a significant hurdle in translating animal results to humans due to a lack of human-based experimental models. The identity and functionality of the hematopoietic cells generated during iPSC differentiation are poorly understood.
In this study we use a human iPSC differentiation model to define in vitro-generated early hematopoietic progenitor cell populations. We aim to determine both their engraftment capacity in immunodeficient mice and their lymphoid differentiation potential. By targeted insertion of fluorescent reporters to the loci of genes essential for hematopoietic stem cell and lymphoid progenitor functions, we will create reporter iPSC lines that can facilitate real-time monitoring and flow-cytometry-mediated cell isolation of potential definitive hematopoietic progenitor populations generated. Our laboratory will evaluate each cell population for cell surface markers, gene expression patterns, differentiation potential, and engraftment capability. Through these phenotypic and functional analyses, we will establish methods for identifying the most suitable iPSC progeny for developing cell therapies and immunotherapies.

In addressing the safety of genome editing technologies, we aim to develop sensitive and unbiased methods for detecting genetic mutations after editing. In silico methods may not be sufficient to predict all the potential off-target modifications, particularly for newer technologies that do not yet have established safety profiles. We use a clonal, genome-wide sequencing strategy to detect genetic changes in iPSC clones that have undergone successful on-target genome editing. This strategy overcomes a limitation of whole genome sequencing in detection sensitivity, which is a significant advantage, since unintended modifications are often random and occur at low frequency. Our laboratory also uses cell-based functional assays and transcriptome analyses to examine the emerging genome editing tools and their effects on normal physiology.  In addition, the in vitro differentiation and genetic modification methods are used to establish iPSC-based methodologies for assessing biological consequences of genetic changes and their transformation potential.


  1. Stem Cell Res 2023 Jun;69:103113
    Generation of induced pluripotent stem cell lines from helper and cytotoxic T cells of healthy individuals.
    Kamaldinov T, Zhang L, Wang L, Ye Z
  2. Exp Biol Med 2021 Apr;246(7):861-75
    Convergence of human pluripotent stem cell, organoid, and genome editing technologies.
    Wang L, Ye Z, Jang YY
  3. Nat Commun 2019 Nov 25;10(1):5353
    Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing.
    McGrath E, Shin H, Zhang L, Phue JN, Wu WW, Shen RF, Jang YY, Revollo J, Ye Z
  4. Stem Cells Transl Med 2018 Jan;7(1):87-97
    A universal approach to correct various HBB gene mutations in human stem cells for gene therapy of beta-thalassemia and sickle cell disease.
    Cai L, Bai H, Mahairaki V, Gao Y, He C, Wen Y, Jin YC, Wang Y, Pan RL, Qasba A, Ye Z, Cheng L
  5. Stem Cell Res 2017 Oct;24:25-8
    Derivation of a disease-specific human induced pluripotent stem cell line from a biliary atresia patient.
    Tian L, Eldridge L, Chaudhari P, Zhang L, Anders RA, Schwarz KB, Ye Z, Jang YY


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