Single-Cell Genomics: Catalyst for Cell Fate Engineering.

Boxun Li,Gary C Hon

doi:10.3389/fbioe.2021.748942

Abstract

As we near a complete catalog of mammalian cell types, the capability to engineer specific cell types on demand would transform biomedical research and regenerative medicine. However, the current pace of discovering new cell types far outstrips our ability to engineer them. One attractive strategy for cellular engineering is direct reprogramming, where induction of specific transcription factor (TF) cocktails orchestrates cell state transitions. Here, we review the foundational studies of TF-mediated reprogramming in the context of a general framework for cell fate engineering, which consists of: discovering new reprogramming cocktails, assessing engineered cells, and revealing molecular mechanisms. Traditional bulk reprogramming methods established a strong foundation for TF-mediated reprogramming, but were limited by their small scale and difficulty resolving cellular heterogeneity. Recently, single-cell technologies have overcome these challenges to rapidly accelerate progress in cell fate engineering. In the next decade, we anticipate that these tools will enable unprecedented control of cell state.

Highlights

Progressive cell fate restriction is a central feature of organismal development famously illustrated by the “Waddington landscape” (Waddington, 1957)
To extend cell fate engineering more broadly across cell types, tissues, and organisms, here we propose a methodological framework consisting of three pillars, based on current progress and future prospects of the field: 1) generalizable approaches to discovering new reprogramming cocktails at scale, 2) reliable ways to assess the engineered cells, benchmarked to their endogenous counterparts, and 3) comprehensive molecular mechanisms underlying cell fate engineering (Figure 1)
Many studies rely on a single endogenous gene reporter that is engineered to be expressed in the target cell type (Takahashi and Yamanaka, 2006; Ieda et al, 2010; Vierbuchen et al, 2010; Song et al, 2012)

Summary

Introduction

Progressive cell fate restriction is a central feature of organismal development famously illustrated by the “Waddington landscape” (Waddington, 1957) This model views cell fate establishment as irreversible. John Gurdon observed in Xenopus that nuclear transplantation of terminally differentiated cells into enucleated oocytes resulted in the development of normal frogs (Gurdon, 1962; Gurdon, 1967). In Drosophila, over-expression of the eyeless gene ectopically, eye structures are strikingly induced on the wings, the legs and the antennae (Halder et al, 1995). These studies clearly demonstrated the plasticity of terminally differentiated cells, and the possibility of engineering cell fate by gene over-expression. Many studies have extended this approach to reprogram pancreatic β-cells, cardiomyocytes, neurons, hepatocytes, and epicardial cells, among others ((Feng et al, 2008; Zhou et al, 2008; Ieda et al, 2010; Vierbuchen et al, 2010; Huang et al, 2011; Sekiya and Suzuki, 2011; Ladewig et al, 2012; Song et al, 2012; Nam et al, 2013; Niu et al, 2013; Batta et al, 2014; Chanda et al, 2014; Du et al, 2014; Riddell et al, 2014; Lemper et al, 2015; Duan et al, 2019) and reviewed in Xu et al (2015), Wang et al (2021)

Methods

Conclusion