1
|
Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024; 20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Precision in the establishment and maintenance of cellular identities is crucial for the development of multicellular organisms and requires tight regulation of gene expression. While extensive research has focused on understanding cell type-specific gene activation, the complex mechanisms underlying the transcriptional repression of alternative fates are not fully understood. Here, we provide an overview of the repressive mechanisms involved in cell fate regulation. We discuss the molecular machinery responsible for suppressing alternative fates and highlight the crucial role of sequence-specific transcription factors (TFs) in this process. Depletion of these TFs can result in unwanted gene expression and increased cellular plasticity. We suggest that these TFs recruit cell type-specific repressive complexes to their cis-regulatory elements, enabling them to modulate chromatin accessibility in a context-dependent manner. This modulation effectively suppresses master regulators of alternative fate programs and their downstream targets. The modularity and dynamic behavior of these repressive complexes enables a limited number of repressors to canalize and maintain major and minor cell fate decisions at different stages of development.
Collapse
Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany.
| |
Collapse
|
2
|
Wang NB, Lende-Dorn BA, Adewumi HO, Beitz AM, Han P, O'Shea TM, Galloway KE. Proliferation history and transcription factor levels drive direct conversion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568736. [PMID: 38077004 PMCID: PMC10705288 DOI: 10.1101/2023.11.26.568736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The sparse and stochastic nature of reprogramming has obscured our understanding of how transcription factors drive cells to new identities. To overcome this limit, we developed a compact, portable reprogramming system that increases direct conversion of fibroblasts to motor neurons by two orders of magnitude. We show that subpopulations with different reprogramming potentials are distinguishable by proliferation history. By controlling for proliferation history and titrating each transcription factor, we find that conversion correlates with levels of the pioneer transcription factor Ngn2, whereas conversion shows a biphasic response to Lhx3. Increasing the proliferation rate of adult human fibroblasts generates morphologically mature, induced motor neurons at high rates. Using compact, optimized, polycistronic cassettes, we generate motor neurons that graft with the murine central nervous system, demonstrating the potential for in vivo therapies.
Collapse
Affiliation(s)
- Nathan B Wang
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Honour O Adewumi
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Adam M Beitz
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Patrick Han
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Timothy M O'Shea
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| |
Collapse
|
3
|
Zhao A, Pan Y, Cai S. Patient-Specific Cells for Modeling and Decoding Amyotrophic Lateral Sclerosis: Advances and Challenges. Stem Cell Rev Rep 2021; 16:482-502. [PMID: 31916190 DOI: 10.1007/s12015-019-09946-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Motor neuron loss or degeneration is the typical characteristic of amyotrophic lateral sclerosis (ALS), which often leads to weakness, paralysis, or even death. The underlying mechanisms of motor neuron degeneration and ALS progression remain elusive, and there is no effective treatment for ALS. The advances of stem cells and reprogramming techniques has made it possible to generate patient-specific motor neurons as cell models for studying disease mechanisms and drug discovery. This review comprehensively discusses recent approaches to generate motor neurons from stem cells and somatic cells and highlights the application of induced motor neurons to modeling ALS diseases, dissecting the pathogenesis, and screening new drugs. New perspectives are also discussed on generating patient-specific motor neuron subtypes that are affected by ALS or creating 3D spinal cord organoid models for better recapitulating and understanding ALS.
Collapse
Affiliation(s)
- Andong Zhao
- Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Yu Pan
- Department of Trauma and Orthopedics, The 2nd Affiliated Hospital of Shenzhen University, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, 518101, China.
| | - Sa Cai
- Health Science Center, Shenzhen University, Shenzhen, 518060, China.
| |
Collapse
|
4
|
Wang NB, Beitz AM, Galloway KE. Engineering cell fate: Applying synthetic biology to cellular reprogramming. ACTA ACUST UNITED AC 2020; 24:18-31. [PMID: 36330198 PMCID: PMC9629175 DOI: 10.1016/j.coisb.2020.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cellular reprogramming drives cells from one stable identity to a new cell fate. By generating a diversity of previously inaccessible cell types from diverse genetic backgrounds, cellular reprogramming is rapidly transforming how we study disease. However, low efficiency and limited maturity have limited the adoption of in vitro-derived cellular models. To overcome these limitations and improve mechanistic understanding of cellular reprogramming, a host of synthetic biology tools have been deployed. Recent synthetic biology approaches have advanced reprogramming by tackling three significant challenges to reprogramming: delivery of reprogramming factors, epigenetic roadblocks, and latent donor identity. In addition, emerging insight from the molecular systems biology of reprogramming reveal how systems-level drivers of reprogramming can be harnessed to further advance reprogramming technologies. Furthermore, recently developed synthetic biology tools offer new modes for engineering cell fate.
Collapse
Affiliation(s)
- Nathan B Wang
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA
| | - Adam M Beitz
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA, 02139, USA
| |
Collapse
|
5
|
Abstract
Organs-on-chips are broadly defined as microfabricated surfaces or devices designed to engineer cells into microscale tissues with native-like features and then extract physiologically relevant readouts at scale. Because they are generally compatible with patient-derived cells, these technologies can address many of the human relevance limitations of animal models. As a result, organs-on-chips have emerged as a promising new paradigm for patient-specific disease modeling and drug development. Because neuromuscular diseases span a broad range of rare conditions with diverse etiology and complex pathophysiology, they have been especially challenging to model in animals and thus are well suited for organ-on-chip approaches. In this Review, we first briefly summarize the challenges in neuromuscular disease modeling with animal models. Next, we describe a variety of existing organ-on-chip approaches for neuromuscular tissues, including a survey of cell sources for both muscle and nerve, and two- and three-dimensional neuromuscular tissue-engineering techniques. Although researchers have made tremendous advances in modeling neuromuscular diseases on a chip, the remaining challenges in cell sourcing, cell maturity, tissue assembly and readout capabilities limit their integration into the drug development pipeline today. However, as the field advances, models of healthy and diseased neuromuscular tissues on a chip, coupled with animal models, have vast potential as complementary tools for modeling multiple aspects of neuromuscular diseases and identifying new therapeutic strategies. Summary: Modeling neuromuscular diseases is challenging due to their complex etiology and pathophysiology. Here, we review the cell sources and tissue-engineering procedures that are being integrated as emerging neuromuscular disease models.
Collapse
Affiliation(s)
- Jeffrey W Santoso
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Megan L McCain
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA .,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
6
|
Menendez L, Trecek T, Gopalakrishnan S, Tao L, Markowitz AL, Yu HV, Wang X, Llamas J, Huang C, Lee J, Kalluri R, Ichida J, Segil N. Generation of inner ear hair cells by direct lineage conversion of primary somatic cells. eLife 2020; 9:e55249. [PMID: 32602462 PMCID: PMC7326493 DOI: 10.7554/elife.55249] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular dysfunction. Their paucity and inaccessibility has limited the search for otoprotective and regenerative strategies. Growing hair cells in vitro would provide a route to overcome this experimental bottleneck. We report a combination of four transcription factors (Six1, Atoh1, Pou4f3, and Gfi1) that can convert mouse embryonic fibroblasts, adult tail-tip fibroblasts and postnatal supporting cells into induced hair cell-like cells (iHCs). iHCs exhibit hair cell-like morphology, transcriptomic and epigenetic profiles, electrophysiological properties, mechanosensory channel expression, and vulnerability to ototoxin in a high-content phenotypic screening system. Thus, direct reprogramming provides a platform to identify causes and treatments for hair cell loss, and may help identify future gene therapy approaches for restoring hearing.
Collapse
Affiliation(s)
- Louise Menendez
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Talon Trecek
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Suhasni Gopalakrishnan
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Litao Tao
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Alexander L Markowitz
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| | - Haoze V Yu
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Xizi Wang
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | | | - James Lee
- DRVision TechnologiesBellevueUnited States
| | - Radha Kalluri
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| | - Justin Ichida
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Neil Segil
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| |
Collapse
|
7
|
Fowler JL, Ang LT, Loh KM. A critical look: Challenges in differentiating human pluripotent stem cells into desired cell types and organoids. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 9:e368. [PMID: 31746148 DOI: 10.1002/wdev.368] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/17/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022]
Abstract
Too many choices can be problematic. This is certainly the case for human pluripotent stem cells (hPSCs): they harbor the potential to differentiate into hundreds of cell types; yet it is highly challenging to exclusively differentiate hPSCs into a single desired cell type. This review focuses on unresolved and fundamental questions regarding hPSC differentiation and critiquing the identity and purity of the resultant cell populations. These are timely issues in view of the fact that hPSC-derived cell populations have or are being transplanted into patients in over 30 ongoing clinical trials. While many in vitro differentiation protocols purport to "mimic development," the exact number and identity of intermediate steps that a pluripotent cell takes to differentiate into a given cell type in vivo remains largely unknown. Consequently, most differentiation efforts inevitably generate a heterogeneous cellular population, as revealed by single-cell RNA-sequencing and other analyses. The presence of unwanted cell types in differentiated hPSC populations does not portend well for transplantation therapies. This provides an impetus to precisely control differentiation to desired ends-for instance, by logically blocking the formation of unwanted cell types or by overexpressing lineage-specifying transcription factors-or by harnessing technologies to selectively purify desired cell types. Conversely, approaches to differentiate three-dimensional "organoids" from hPSCs intentionally generate heterogeneous cell populations. While this is intended to mimic the rich cellular diversity of developing tissues, whether all such organoids are spatially organized in a manner akin to native organs (and thus, whether they fully qualify as organoids) remains to be fully resolved. This article is categorized under: Adult Stem Cells > Tissue Renewal > Regeneration: Stem Cell Differentiation and Reversion Gene Expression > Transcriptional Hierarchies: Cellular Differentiation Early Embryonic Development: Gastrulation and Neurulation.
Collapse
Affiliation(s)
- Jonas L Fowler
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California.,Department of Developmental Biology, Bio-X, Cancer Institute, Cardiovascular Institute, ChEM-H, Diabetes Research Center, Maternal & Child Health Research Institute, Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California
| | - Lay Teng Ang
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California.,Department of Developmental Biology, Bio-X, Cancer Institute, Cardiovascular Institute, ChEM-H, Diabetes Research Center, Maternal & Child Health Research Institute, Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California
| |
Collapse
|
8
|
Flitsch LJ, Brüstle O. Evolving principles underlying neural lineage conversion and their relevance for biomedical translation. F1000Res 2019; 8. [PMID: 31559012 PMCID: PMC6743253 DOI: 10.12688/f1000research.18926.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Scientific and technological advances of the past decade have shed light on the mechanisms underlying cell fate acquisition, including its transcriptional and epigenetic regulation during embryonic development. This knowledge has enabled us to purposefully engineer cell fates
in vitro by manipulating expression levels of lineage-instructing transcription factors. Here, we review the state of the art in the cell programming field with a focus on the derivation of neural cells. We reflect on what we know about the mechanisms underlying fate changes in general and on the degree of epigenetic remodeling conveyed by the distinct reprogramming and direct conversion strategies available. Moreover, we discuss the implications of residual epigenetic memory for biomedical applications such as disease modeling and neuroregeneration. Finally, we cover recent developments approaching cell fate conversion in the living brain and define questions which need to be addressed before cell programming can become an integral part of translational medicine.
Collapse
Affiliation(s)
- Lea Jessica Flitsch
- Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany
| |
Collapse
|
9
|
Abstract
Cellular reprogramming experiments from somatic cell types have demonstrated the plasticity of terminally differentiated cell states. Recent efforts in understanding the mechanisms of cellular reprogramming have begun to elucidate the differentiation trajectories along the reprogramming processes. In this review, we focus mainly on direct reprogramming strategies by transcription factors and highlight the variables that contribute to cell fate conversion outcomes. We review key studies that shed light on the cellular and molecular mechanisms by investigating differentiation trajectories and alternative cell states as well as transcription factor regulatory activities during cell fate reprogramming. Finally, we highlight a few concepts that we believe require attention, particularly when measuring the success of cell reprogramming experiments.
Collapse
Affiliation(s)
- Begüm Aydin
- Department of Biology, New York University, New York, NY 10003, USA; .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY 10003, USA; .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| |
Collapse
|