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Liu J, Castillo-Hair SM, Du LY, Wang Y, Carte AN, Colomer-Rosell M, Yin C, Seelig G, Schier AF. Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609971. [PMID: 39253514 PMCID: PMC11383055 DOI: 10.1101/2024.08.27.609971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
The interplay between transcription factors and chromatin accessibility regulates cell type diversification during vertebrate embryogenesis. To systematically decipher the gene regulatory logic guiding this process, we generated a single-cell multi-omics atlas of RNA expression and chromatin accessibility during early zebrafish embryogenesis. We developed a deep learning model to predict chromatin accessibility based on DNA sequence and found that a small number of transcription factors underlie cell-type-specific chromatin landscapes. While Nanog is well-established in promoting pluripotency, we discovered a new function in priming the enhancer accessibility of mesendodermal genes. In addition to the classical stepwise mode of differentiation, we describe instant differentiation, where pluripotent cells skip intermediate fate transitions and terminally differentiate. Reconstruction of gene regulatory interactions reveals that this process is driven by a shallow network in which maternally deposited regulators activate a small set of transcription factors that co-regulate hundreds of differentiation genes. Notably, misexpression of these transcription factors in pluripotent cells is sufficient to ectopically activate their targets. This study provides a rich resource for analyzing embryonic gene regulation and reveals the regulatory logic of instant differentiation.
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Affiliation(s)
- Jialin Liu
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
| | | | - Lucia Y Du
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
| | - Yiqun Wang
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UCSD, La Jolla, CA, 92037, USA
| | - Adam N Carte
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, 02115, USA
| | - Mariona Colomer-Rosell
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
| | - Christopher Yin
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Alexander F Schier
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
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2
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Jia T, Liu C, Guo P, Xu Y, Wang W, Liu X, Wang S, Zhang X, Guo H. FOXA1 regulates ribosomal RNA transcription in prostate cancer. Prostate 2024; 84:967-976. [PMID: 38632701 DOI: 10.1002/pros.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Ribosome biogenesis is excessively activated in tumor cells, yet it is little known whether oncogenic transcription factors (TFs) are involved in the ribosomal RNA (rRNA) transactivation. METHODS Nucleolar proteomics data and large-scale immunofluorescence were re-analyzed to jointly identify the proteins localized at nucleolus. RNA-Seq data of five prostate cancer (PCa) cohorts were combined and integrated with multi-dimensional data to define the upregulated nucleolar TFs in PCa tissues. Then, ChIP-Seq data of PCa cell lines and two PCa clinical cohorts were re-analyzed to reveal the TF binding patterns at ribosomal DNA (rDNA) repeats. The TF binding at rDNA was validated by ChIP-qPCR. The effect of the TF on rRNA transcription was determined by rDNA luciferase reporter, nascent RNA synthesis, and global protein translation assays. RESULTS In this study, we reveal the role of oncogenic TF FOXA1 in regulating rRNA transcription within nucleolar organization regions. By analyzing human TFs in prostate cancer clinical datasets and nucleolar proteomics data, we identified that FOXA1 is partially localized in the nucleolus and correlated with global protein translation. Our extensive FOXA1 ChIP-Seq analysis provides robust evidence of FOXA1 binding across rDNA repeats in prostate cancer cell lines, primary tumors, and castration-resistant variants. Notably, FOXA1 occupancy at rDNA repeats correlates with histone modifications associated with active transcription, namely H3K27ac and H3K4me3. Reducing FOXA1 expression results in decreased transactivation at rDNA, subsequently diminishing global protein synthesis. CONCLUSIONS Our results suggest FOXA1 regulates aberrant ribosome biogenesis downstream of oncogenic signaling in prostate cancer.
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Affiliation(s)
- Tianwei Jia
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Chenxu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Ping Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Yaning Xu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Wenzheng Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Song Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xianglin Zhang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
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3
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [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] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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4
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Stoeber S, Godin H, Xu C, Bai L. Pioneer factors: nature or nurture? Crit Rev Biochem Mol Biol 2024; 59:139-153. [PMID: 38778580 DOI: 10.1080/10409238.2024.2355885] [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: 03/03/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Chromatin is densely packed with nucleosomes, which limits the accessibility of many chromatin-associated proteins. Pioneer factors (PFs) are usually viewed as a special group of sequence-specific transcription factors (TFs) that can recognize nucleosome-embedded motifs, invade compact chromatin, and generate open chromatin regions. Through this process, PFs initiate a cascade of events that play key roles in gene regulation and cell differentiation. A current debate in the field is if PFs belong to a unique subset of TFs with intrinsic "pioneering activity", or if all TFs have the potential to function as PFs within certain cellular contexts. There are also different views regarding the key feature(s) that define pioneering activity. In this review, we present evidence from the literature related to these alternative views and discuss how to potentially reconcile them. It is possible that both intrinsic properties, like tight nucleosome binding and structural compatibility, and cellular conditions, like concentration and co-factor availability, are important for PF function.
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Affiliation(s)
- Shane Stoeber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Holly Godin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, USA
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5
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Yang Y, Li S, Luo L. Responses of organ precursors to correct and incorrect inductive signals. Trends Cell Biol 2024; 34:484-495. [PMID: 37739814 DOI: 10.1016/j.tcb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
During embryonic development, the inductive molecules produced by local origins normally arrive at their target tissues in a nondirectional, diffusion manner. The target organ precursor cells must correctly interpret these inductive signals to ensure proper specification/differentiation, which is dependent on two prerequisites: (i) obtaining cell-intrinsic competence; and (ii) receiving correct inductive signals while resisting incorrect ones. Gain of intrinsic competence could avoid a large number of misinductions because the incompetent cells are nonresponsive to inductive signals. However, in cases of different precursor cells with similar competence and located in close proximity, resistance to incorrect inductive signals is essential for accurate determination of cell fate. Here we outline the mechanisms of how organ precursors respond to correct and incorrect inductive signals.
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Affiliation(s)
- Yun Yang
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Shuang Li
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Lingfei Luo
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China; School of Life Sciences, Fudan University, Shanghai, China.
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6
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Jones T, Sigauke RF, Sanford L, Taatjes DJ, Allen MA, Dowell RD. A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585303. [PMID: 38559193 PMCID: PMC10980006 DOI: 10.1101/2024.03.15.585303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
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7
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Coda DM, Gräff J. From cellular to fear memory: An epigenetic toolbox to remember. Curr Opin Neurobiol 2024; 84:102829. [PMID: 38128422 DOI: 10.1016/j.conb.2023.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Throughout development, the neuronal epigenome is highly sensitive to external stimuli, yet capable of safeguarding cellular memory for a lifetime. In the adult brain, memories of fearful experiences are rapidly instantiated, yet can last for decades, but the mechanisms underlying such longevity remain unknown. Here, we showcase how fear memory formation and storage - traditionally thought to exclusively affect synapse-based events - elicit profound and enduring changes to the chromatin, proposing epigenetic regulation as a plausible molecular template for mnemonic processes. By comparing these to mechanisms occurring in development and differentiation, we notice that an epigenetic machinery similar to that preserving cellular memories might be employed by brain cells so as to form, store, and retrieve behavioral memories.
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Affiliation(s)
- Davide Martino Coda
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Federale Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Federale Lausanne (EPFL), 1015, Lausanne, Switzerland.
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8
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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9
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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10
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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11
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Robert S, Rada-Iglesias A. The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex disease. Bioessays 2023; 45:e2300038. [PMID: 37170707 DOI: 10.1002/bies.202300038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
The interactions between genetic and environmental risk factors contribute to the aetiology of complex human diseases. Genome-wide association studies (GWAS) have revealed that most of the genetic variants associated with complex diseases are located in the non-coding part of the genome, preferentially within enhancers. Enhancers are distal cis-regulatory elements composed of clusters of transcription factors binding sites that positively regulate the expression of their target genes. The generation of genome-wide maps for histone marks (e.g., H3K27ac), chromatin accessibility and transcription factor and coactivator (e.g., p300) binding profiles have enabled the identification of enhancers across many human cell types and tissues. Nonetheless, the functional and pathological consequences of the majority of disease-associated genetic variants located within enhancers seem to be rather minor under normal conditions, thus questioning their medical relevance. Here we propose that, due to the prevalence of enhancer redundancy, the pathological effects of many disease-associated non-coding genetic variants might be preferentially (or even only) manifested under environmental stress.
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Affiliation(s)
- Sarah Robert
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de, Santander, Cantabria, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de, Santander, Cantabria, Spain
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12
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Fei L, Zhang K, Poddar N, Hautaniemi S, Sahu B. Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells. Dev Cell 2023; 58:1701-1715.e8. [PMID: 37751683 DOI: 10.1016/j.devcel.2023.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/13/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023]
Abstract
Cell fate can be reprogrammed by ectopic expression of lineage-specific transcription factors (TFs). However, the exact cell state transitions during transdifferentiation are still poorly understood. Here, we have generated pancreatic exocrine cells of ductal epithelial identity from human fibroblasts using a set of six TFs. We mapped the molecular determinants of lineage dynamics using a factor-indexing method based on single-nuclei multiome sequencing (FI-snMultiome-seq) that enables dissecting the role of each individual TF and pool of TFs in cell fate conversion. We show that transition from mesenchymal fibroblast identity to epithelial pancreatic exocrine fate involves two deterministic steps: an endodermal progenitor state defined by activation of HHEX with FOXA2 and SOX17 and a temporal GATA4 activation essential for the maintenance of pancreatic cell fate program. Collectively, our data suggest that transdifferentiation-although being considered a direct cell fate conversion method-occurs through transient progenitor states orchestrated by stepwise activation of distinct TFs.
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Affiliation(s)
- Liangru Fei
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland
| | - Kaiyang Zhang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland
| | - Nikita Poddar
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland; Medicum, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00014, Finland; Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Gaustadelléen 21, 0349 Oslo, Norway.
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13
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Kearns NA, Lobo M, Genga RMJ, Abramowitz RG, Parsi KM, Min J, Kernfeld EM, Huey JD, Kady J, Hennessy E, Brehm MA, Ziller MJ, Maehr R. Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm. Dev Cell 2023; 58:1801-1818.e15. [PMID: 37751684 PMCID: PMC10637111 DOI: 10.1016/j.devcel.2023.08.024] [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: 01/14/2023] [Revised: 05/15/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
Abstract
Approaches to study human pharyngeal foregut endoderm-a developmental intermediate that is linked to various human syndromes involving pharynx development and organogenesis of tissues such as thymus, parathyroid, and thyroid-have been hampered by scarcity of tissue access and cellular models. We present an efficient stepwise differentiation method to generate human pharyngeal foregut endoderm from pluripotent stem cells. We determine dose and temporal requirements of signaling pathway engagement for optimized differentiation and characterize the differentiation products on cellular and integrated molecular level. We present a computational classification tool, "CellMatch," and transcriptomic classification of differentiation products on an integrated mouse scRNA-seq developmental roadmap confirms cellular maturation. Integrated transcriptomic and chromatin analyses infer differentiation stage-specific gene regulatory networks. Our work provides the method and integrated multiomic resource for the investigation of disease-relevant loci and gene regulatory networks and their role in developmental defects affecting the pharyngeal endoderm and its derivatives.
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Affiliation(s)
- Nicola A Kearns
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Macrina Lobo
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ryan G Abramowitz
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Krishna M Parsi
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jiang Min
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Eric M Kernfeld
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jack D Huey
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jamie Kady
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erica Hennessy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A Brehm
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael J Ziller
- Department of Psychiatry, University of Münster, Münster, Germany
| | - René Maehr
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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14
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Mikaeili H, Habib AM, Yeung CWL, Santana-Varela S, Luiz AP, Panteleeva K, Zuberi S, Athanasiou-Fragkouli A, Houlden H, Wood JN, Okorokov AL, Cox JJ. Molecular basis of FAAH-OUT-associated human pain insensitivity. Brain 2023; 146:3851-3865. [PMID: 37222214 PMCID: PMC10473560 DOI: 10.1093/brain/awad098] [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: 11/03/2022] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 05/25/2023] Open
Abstract
Chronic pain affects millions of people worldwide and new treatments are needed urgently. One way to identify novel analgesic strategies is to understand the biological dysfunctions that lead to human inherited pain insensitivity disorders. Here we report how the recently discovered brain and dorsal root ganglia-expressed FAAH-OUT long non-coding RNA (lncRNA) gene, which was found from studying a pain-insensitive patient with reduced anxiety and fast wound healing, regulates the adjacent key endocannabinoid system gene FAAH, which encodes the anandamide-degrading fatty acid amide hydrolase enzyme. We demonstrate that the disruption in FAAH-OUT lncRNA transcription leads to DNMT1-dependent DNA methylation within the FAAH promoter. In addition, FAAH-OUT contains a conserved regulatory element, FAAH-AMP, that acts as an enhancer for FAAH expression. Furthermore, using transcriptomic analyses in patient-derived cells we have uncovered a network of genes that are dysregulated from disruption of the FAAH-FAAH-OUT axis, thus providing a coherent mechanistic basis to understand the human phenotype observed. Given that FAAH is a potential target for the treatment of pain, anxiety, depression and other neurological disorders, this new understanding of the regulatory role of the FAAH-OUT gene provides a platform for the development of future gene and small molecule therapies.
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Affiliation(s)
- Hajar Mikaeili
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Abdella M Habib
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Charlix Wai-Lok Yeung
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Sonia Santana-Varela
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Ana P Luiz
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Kseniia Panteleeva
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Sana Zuberi
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | | | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Andrei L Okorokov
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
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15
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Lotto J, Stephan TL, Hoodless PA. Fetal liver development and implications for liver disease pathogenesis. Nat Rev Gastroenterol Hepatol 2023; 20:561-581. [PMID: 37208503 DOI: 10.1038/s41575-023-00775-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/21/2023]
Abstract
The metabolic, digestive and homeostatic roles of the liver are dependent on proper crosstalk and organization of hepatic cell lineages. These hepatic cell lineages are derived from their respective progenitors early in organogenesis in a spatiotemporally controlled manner, contributing to the liver's specialized and diverse microarchitecture. Advances in genomics, lineage tracing and microscopy have led to seminal discoveries in the past decade that have elucidated liver cell lineage hierarchies. In particular, single-cell genomics has enabled researchers to explore diversity within the liver, especially early in development when the application of bulk genomics was previously constrained due to the organ's small scale, resulting in low cell numbers. These discoveries have substantially advanced our understanding of cell differentiation trajectories, cell fate decisions, cell lineage plasticity and the signalling microenvironment underlying the formation of the liver. In addition, they have provided insights into the pathogenesis of liver disease and cancer, in which developmental processes participate in disease emergence and regeneration. Future work will focus on the translation of this knowledge to optimize in vitro models of liver development and fine-tune regenerative medicine strategies to treat liver disease. In this Review, we discuss the emergence of hepatic parenchymal and non-parenchymal cells, advances that have been made in in vitro modelling of liver development and draw parallels between developmental and pathological processes.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
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16
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Lin KZ, Zhang NR. Quantifying common and distinct information in single-cell multimodal data with Tilted Canonical Correlation Analysis. Proc Natl Acad Sci U S A 2023; 120:e2303647120. [PMID: 37523521 PMCID: PMC10410705 DOI: 10.1073/pnas.2303647120] [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: 03/06/2023] [Accepted: 06/24/2023] [Indexed: 08/02/2023] Open
Abstract
Multimodal single-cell technologies profile multiple modalities for each cell simultaneously, enabling a more thorough characterization of cell populations. Existing dimension-reduction methods for multimodal data capture the "union of information," producing a lower-dimensional embedding that combines the information across modalities. While these tools are useful, we focus on a fundamentally different task of separating and quantifying the information among cells that is shared between the two modalities as well as unique to only one modality. Hence, we develop Tilted Canonical Correlation Analysis (Tilted-CCA), a method that decomposes a paired multimodal dataset into three lower-dimensional embeddings-one embedding captures the "intersection of information," representing the geometric relations among the cells that is common to both modalities, while the remaining two embeddings capture the "distinct information for a modality," representing the modality-specific geometric relations. We analyze single-cell multimodal datasets sequencing RNA along surface antibodies (i.e., CITE-seq) as well as RNA alongside chromatin accessibility (i.e., 10x) for blood cells and developing neurons via Tilted-CCA. These analyses show that Tilted-CCA enables meaningful visualization and quantification of the cross-modal information. Finally, Tilted-CCA's framework allows us to perform two specific downstream analyses. First, for single-cell datasets that simultaneously profile transcriptome and surface antibody markers, we show that Tilted-CCA helps design the target antibody panel to complement the transcriptome best. Second, for developmental single-cell datasets that simultaneously profile transcriptome and chromatin accessibility, we show that Tilted-CCA helps identify development-informative genes and distinguish between transient versus terminal cell types.
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Affiliation(s)
- Kevin Z. Lin
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA19104
| | - Nancy R. Zhang
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA19104
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17
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Wang G, Wang Y, Lyu Y, He H, Liuyang S, Wang J, Sun S, Cheng L, Fu Y, Zhu J, Zhong X, Yang Z, Chen Q, Li C, Guan J, Deng H. Chemical-induced epigenome resetting for regeneration program activation in human cells. Cell Rep 2023; 42:112547. [PMID: 37224020 DOI: 10.1016/j.celrep.2023.112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/30/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Human somatic cells can be reprogrammed to pluripotent stem cells by small molecules through an intermediate stage with a regeneration signature, but how this regeneration state is induced remains largely unknown. Here, through integrated single-cell analysis of transcriptome, we demonstrate that the pathway of human chemical reprogramming with regeneration state is distinct from that of transcription-factor-mediated reprogramming. Time-course construction of chromatin landscapes unveils hierarchical histone modification remodeling underlying the regeneration program, which involved sequential enhancer recommissioning and mirrored the reversal process of regeneration potential lost in organisms as they mature. In addition, LEF1 is identified as a key upstream regulator for regeneration gene program activation. Furthermore, we reveal that regeneration program activation requires sequential enhancer silencing of somatic and proinflammatory programs. Altogether, chemical reprogramming resets the epigenome through reversal of the loss of natural regeneration, representing a distinct concept for cellular reprogramming and advancing the development of regenerative therapeutic strategies.
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Affiliation(s)
- Guan Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yanglu Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Academy for Advanced Interdisciplinary Studies, The Center for Biomed-X Research, Peking University, Beijing, China
| | - Yulin Lyu
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Huanjing He
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shijia Liuyang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jinlin Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shicheng Sun
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lin Cheng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yao Fu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jialiang Zhu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xinxing Zhong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zhihan Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qijing Chen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Jingyang Guan
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Hongkui Deng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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18
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Kerschner JL, Paranjapye A, Vaghela N, Wilson MD, Harris A. An ectopic enhancer restores CFTR expression through de novo chromatin looping. Gene Ther 2023; 30:478-486. [PMID: 36510002 PMCID: PMC11227122 DOI: 10.1038/s41434-022-00378-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/30/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Transcription of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is regulated by both ubiquitous and cell-type selective cis-regulatory elements (CREs). These CREs include extragenic and intronic enhancers that bind lineage-specific transcription factors, and architectural protein-marked structural elements. Deletion of the airway-selective -35 kb enhancer in 16HBE14o- lung epithelial cells was shown earlier to disrupt normal enhancer-promoter looping at the CFTR locus and nearly abolish its expression. Using a 16HBE14o- clone that lacks the endogenous -35 kb CRE, we explore the impact of relocating the functional core of this element to an ectopic site in intron 1. The -35 kb sequence establishes a de novo enhancer signature in chromatin at the insertion site, and augments CFTR expression, albeit not fully restoring WT levels. The relocated -35 kb enhancer also initiates de novo chromatin contacts with the CFTR promoter and other known CFTR CREs. These results are broadly relevant to therapeutic gene editing.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Michael D Wilson
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA.
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19
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Sullivan AE. Epigenetic Control of Cell Potency and Fate Determination during Mammalian Gastrulation. Genes (Basel) 2023; 14:1143. [PMID: 37372324 DOI: 10.3390/genes14061143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Pluripotent embryonic stem cells have a unique and characteristic epigenetic profile, which is critical for differentiation to all embryonic germ lineages. When stem cells exit the pluripotent state and commit to lineage-specific identities during the process of gastrulation in early embryogenesis, extensive epigenetic remodelling mediates both the switch in cellular programme and the loss of potential to adopt alternative lineage programmes. However, it remains to be understood how the stem cell epigenetic profile encodes pluripotency, or how dynamic epigenetic regulation helps to direct cell fate specification. Recent advances in stem cell culture techniques, cellular reprogramming, and single-cell technologies that can quantitatively profile epigenetic marks have led to significant insights into these questions, which are important for understanding both embryonic development and cell fate engineering. This review provides an overview of key concepts and highlights exciting new advances in the field.
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Affiliation(s)
- Adrienne E Sullivan
- Quantitative Stem Cell Biology Lab, Francis Crick Institute, London NW1 1AT, UK
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
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20
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Martin EW, Rodriguez y Baena A, Reggiardo RE, Worthington AK, Mattingly CS, Poscablo DM, Krietsch J, McManus MT, Carpenter S, Kim DH, Forsberg EC. Dynamics of Chromatin Accessibility During Hematopoietic Stem Cell Differentiation Into Progressively Lineage-Committed Progeny. Stem Cells 2023; 41:520-539. [PMID: 36945732 PMCID: PMC10183972 DOI: 10.1093/stmcls/sxad022] [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: 02/06/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023]
Abstract
Epigenetic mechanisms regulate the multilineage differentiation capacity of hematopoietic stem cells (HSCs) into a variety of blood and immune cells. Mapping the chromatin dynamics of functionally defined cell populations will shed mechanistic insight into 2 major, unanswered questions in stem cell biology: how does epigenetic identity contribute to a cell type's lineage potential, and how do cascades of chromatin remodeling dictate ensuing fate decisions? Our recent work revealed evidence of multilineage gene priming in HSCs, where open cis-regulatory elements (CREs) exclusively shared between HSCs and unipotent lineage cells were enriched for DNA binding motifs of known lineage-specific transcription factors. Oligopotent progenitor populations operating between the HSCs and unipotent cells play essential roles in effecting hematopoietic homeostasis. To test the hypothesis that selective HSC-primed lineage-specific CREs remain accessible throughout differentiation, we used ATAC-seq to map the temporal dynamics of chromatin remodeling during progenitor differentiation. We observed epigenetic-driven clustering of oligopotent and unipotent progenitors into distinct erythromyeloid and lymphoid branches, with multipotent HSCs and MPPs associating with the erythromyeloid lineage. We mapped the dynamics of lineage-primed CREs throughout hematopoiesis and identified both unique and shared CREs as potential lineage reinforcement mechanisms at fate branch points. Additionally, quantification of genome-wide peak count and size revealed overall greater chromatin accessibility in HSCs, allowing us to identify HSC-unique peaks as putative regulators of self-renewal and multilineage potential. Finally, CRISPRi-mediated targeting of ATACseq-identified putative CREs in HSCs allowed us to demonstrate the functional role of selective CREs in lineage-specific gene expression. These findings provide insight into the regulation of stem cell multipotency and lineage commitment throughout hematopoiesis and serve as a resource to test functional drivers of hematopoietic lineage fate.
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Affiliation(s)
- Eric W Martin
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alessandra Rodriguez y Baena
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Roman E Reggiardo
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Atesh K Worthington
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Connor S Mattingly
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Donna M Poscablo
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jana Krietsch
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, Diabetes Center, W.M. Keck Center for Noncoding RNAs, University of California San Francisco, San Francisco, CA, USA
| | - Susan Carpenter
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Kim
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
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21
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Wong YF, Kumar Y, Proks M, Herrera JAR, Rothová MM, Monteiro RS, Pozzi S, Jennings RE, Hanley NA, Bickmore WA, Brickman JM. Expansion of ventral foregut is linked to changes in the enhancer landscape for organ-specific differentiation. Nat Cell Biol 2023; 25:481-492. [PMID: 36690849 PMCID: PMC10014581 DOI: 10.1038/s41556-022-01075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Cell proliferation is fundamental for almost all stages of development and differentiation that require an increase in cell number. Although cell cycle phase has been associated with differentiation, the actual process of proliferation has not been considered as having a specific role. Here we exploit human embryonic stem cell-derived endodermal progenitors that we find are an in vitro model for the ventral foregut. These cells exhibit expansion-dependent increases in differentiation efficiency to pancreatic progenitors that are linked to organ-specific enhancer priming at the level of chromatin accessibility and the decommissioning of lineage-inappropriate enhancers. Our findings suggest that cell proliferation in embryonic development is about more than tissue expansion; it is required to ensure equilibration of gene regulatory networks allowing cells to become primed for future differentiation. Expansion of lineage-specific intermediates may therefore be an important step in achieving high-fidelity in vitro differentiation.
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Affiliation(s)
- Yan Fung Wong
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Yatendra Kumar
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Jose Alejandro Romero Herrera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Michaela Mrugala Rothová
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rita S Monteiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rachel E Jennings
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil A Hanley
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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22
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Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023; 14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We observed that transcription of key differentiation markers occurs before cell division, while chromatin accessibility analyses revealed the early inhibition of alternative cell fates. We found that Activator protein-1 members controlled by p38/MAPK signalling are necessary for inducing endoderm while blocking cell fate shifting toward mesoderm, and that enhancers are rapidly established and decommissioned between different cell divisions. Our study has practical biomedical utility for producing hPSC-derived patient-specific cell types since p38/MAPK induction increased the differentiation efficiency of insulin-producing pancreatic beta-cells.
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Affiliation(s)
- Pedro Madrigal
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Kim Jee Goh
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Rodrigo Grandy
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Anna Osnato
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK.
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23
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Delás MJ, Kalaitzis CM, Fawzi T, Demuth M, Zhang I, Stuart HT, Costantini E, Ivanovitch K, Tanaka EM, Briscoe J. Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies. Dev Cell 2023; 58:3-17.e8. [PMID: 36516856 PMCID: PMC7614300 DOI: 10.1016/j.devcel.2022.11.016] [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: 08/21/2022] [Revised: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
In many developing tissues, the patterns of gene expression that assign cell fate are organized by graded secreted signals. Cis-regulatory elements (CREs) interpret these signals to control gene expression, but how this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen sonic hedgehog (Shh) patterns neural progenitors. We identify two distinct ways in which CREs translate graded Shh into differential gene expression in mouse neural progenitors. In most progenitors, a common set of CREs control gene activity by integrating cell-type-specific inputs. By contrast, the most ventral progenitors use a unique set of CREs, established by the pioneer factor FOXA2. This parallels the role of FOXA2 in endoderm, where FOXA2 binds some of the same sites. Together, the data identify distinct cis-regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2 across tissues.
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Affiliation(s)
| | | | - Tamara Fawzi
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Isabel Zhang
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hannah T Stuart
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Elena Costantini
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | | | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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24
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Warren I, Moeller MM, Guiggey D, Chiang A, Maloy M, Ogoke O, Groth T, Mon T, Meamardoost S, Liu X, Thompson S, Szeglowski A, Thompson R, Chen P, Paulmurugan R, Yarmush ML, Kidambi S, Parashurama N. FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells. FASEB J 2023; 37:e22652. [PMID: 36515690 DOI: 10.1096/fj.202101506rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022]
Abstract
FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA factors dictate human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in controlling hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA mediated knockdown of FOXA1/2 in HepG2 cells significantly downregulated albumin (p < .05) and GRN TF gene expression (HNF4α, HEX, HNF1ß, TBX3) (p < .05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid [GSC], FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < .05), all consistent with partial/transient reprograming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility of phenotype. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, with concomitant accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiation in vitro. During human pluripotent stem cells (hPSC)-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate that FOXA1/2 controls hepatic and developmental GRN, and their knockdown leads to reprogramming of both differentiation and metabolism, with applications in studies of cancer, differentiation, and organogenesis.
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Affiliation(s)
- Iyan Warren
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Michael M Moeller
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Daniel Guiggey
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Alexander Chiang
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Mitchell Maloy
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Theodore Groth
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Tala Mon
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Xiaojun Liu
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Sarah Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Antoni Szeglowski
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ryan Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Peter Chen
- Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ramasamy Paulmurugan
- Department of Radiology, Canary Center for Early Cancer Detection and the Molecular Imaging Program at Stanford, Stanford University, Palo Alto, California, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, New York, USA
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25
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Benaglio P, Zhu H, Okino ML, Yan J, Elgamal R, Nariai N, Beebe E, Korgaonkar K, Qiu Y, Donovan MK, Chiou J, Wang G, Newsome J, Kaur J, Miller M, Preissl S, Corban S, Aylward A, Taipale J, Ren B, Frazer KA, Sander M, Gaulton KJ. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines. CELL GENOMICS 2022; 2:100214. [PMID: 36778047 PMCID: PMC9903835 DOI: 10.1016/j.xgen.2022.100214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/17/2022] [Accepted: 10/15/2022] [Indexed: 11/13/2022]
Abstract
We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate cis-regulatory elements (cCREs) in beta cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells, we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation, and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with SOCS1, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta cells during inflammation that modulate T1D risk.
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Affiliation(s)
- Paola Benaglio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Han Zhu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jian Yan
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Ruth Elgamal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Naoki Nariai
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elisha Beebe
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Katha Korgaonkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Joshua Chiou
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Gaowei Wang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jacklyn Newsome
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jaspreet Kaur
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Sierra Corban
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Aylward
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Kelly A. Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Maike Sander
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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26
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Wu F, Liufu Z, Liu Y, Guo L, Wu J, Cao S, Qin Y, Guo N, Fu Y, Liu H, Li Q, Shu X, Pei D, Hutchins AP, Chen J, He J. Species-specific rewiring of definitive endoderm developmental gene activation via endogenous retroviruses through TET1-mediated demethylation. Cell Rep 2022; 41:111791. [PMID: 36516776 DOI: 10.1016/j.celrep.2022.111791] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/03/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are the major sources of lineage-specific genomic innovation and comprise nearly half of the human genome, but most of their functions remain unclear. Here, we identify that a series of endogenous retroviruses (ERVs), a TE subclass, regulate the transcriptome at the definitive endoderm stage with in vitro differentiation model from human embryonic stem cell. Notably, these ERVs perform as enhancers containing binding sites for critical transcription factors for endoderm lineage specification. Genome-wide methylation analysis shows most of these ERVs are derepressed by TET1-mediated DNA demethylation. LTR6B, a representative definitive endoderm activating ERV, contains binding sites for FOXA2 and GATA4 and governs the primate-specific expression of its neighboring developmental genes such as ERBB4 in definitive endoderm. Together, our study proposes evidence that recently evolved ERVs represent potent de novo developmental regulatory elements, which, in turn, fine-tune species-specific transcriptomes during endoderm and embryonic development.
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Affiliation(s)
- Fang Wu
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongqi Liufu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510799, China
| | - Yujian Liu
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lin Guo
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jian Wu
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shangtao Cao
- Guangzhou Laboratory, Bio-island, Guangzhou 510320, China
| | - Yue Qin
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Ning Guo
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yunyun Fu
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Qiuhong Li
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaodong Shu
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Duanqing Pei
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, Westlake University, Hangzhou, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiekai Chen
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Jiangping He
- Guangzhou Laboratory, Bio-island, Guangzhou 510320, China.
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27
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Leavens KF, Alvarez-Dominguez JR, Vo LT, Russ HA, Parent AV. Stem cell-based multi-tissue platforms to model human autoimmune diabetes. Mol Metab 2022; 66:101610. [PMID: 36209784 PMCID: PMC9587366 DOI: 10.1016/j.molmet.2022.101610] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic insulin-producing β cells are specifically destroyed by the immune system. Understanding the initiation and progression of human T1D has been hampered by the lack of appropriate models that can reproduce the complexity and heterogeneity of the disease. The development of platforms combining multiple human pluripotent stem cell (hPSC) derived tissues to model distinct aspects of T1D has the potential to provide critical novel insights into the etiology and pathogenesis of the human disease. SCOPE OF REVIEW In this review, we summarize the state of hPSC differentiation approaches to generate cell types and tissues relevant to T1D, with a particular focus on pancreatic islet cells, T cells, and thymic epithelium. We present current applications as well as limitations of using these hPSC-derived cells for disease modeling and discuss efforts to optimize platforms combining multiple cell types to model human T1D. Finally, we outline remaining challenges and emphasize future improvements needed to accelerate progress in this emerging field of research. MAJOR CONCLUSIONS Recent advances in reprogramming approaches to create patient-specific induced pluripotent stem cell lines (iPSCs), genome engineering technologies to efficiently modify DNA of hPSCs, and protocols to direct their differentiation into mature cell types have empowered the use of stem cell derivatives to accurately model human disease. While challenges remain before complex interactions occurring in human T1D can be modeled with these derivatives, experiments combining hPSC-derived β cells and immune cells are already providing exciting insight into how these cells interact in the context of T1D, supporting the viability of this approach.
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Affiliation(s)
- Karla F Leavens
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania and Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Juan R Alvarez-Dominguez
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Linda T Vo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Holger A Russ
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Audrey V Parent
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
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28
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Ideno H, Imaizumi K, Shimada H, Sanosaka T, Nemoto A, Kohyama J, Okano H. Human PSCs determine the competency of cerebral organoid differentiation via FGF signaling and epigenetic mechanisms. iScience 2022; 25:105140. [PMID: 36185382 PMCID: PMC9523398 DOI: 10.1016/j.isci.2022.105140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/06/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Hirosato Ideno
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kent Imaizumi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Corresponding author
| | - Hiroko Shimada
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akisa Nemoto
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Corresponding author
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29
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Tomaz RA, Zacharis ED, Bachinger F, Wurmser A, Yamamoto D, Petrus-Reurer S, Morell CM, Dziedzicka D, Wesley BT, Geti I, Segeritz CP, de Brito MC, Chhatriwala M, Ortmann D, Saeb-Parsy K, Vallier L. Generation of functional hepatocytes by forward programming with nuclear receptors. eLife 2022; 11:71591. [PMID: 35959725 PMCID: PMC9374437 DOI: 10.7554/elife.71591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Production of large quantities of hepatocytes remains a major challenge for a number of clinical applications in the biomedical field. Directed differentiation of human pluripotent stem cells (hPSCs) into hepatocyte-like cells (HLCs) provides an advantageous solution and a number of protocols have been developed for this purpose. However, these methods usually follow different steps of liver development in vitro, which is time consuming and requires complex culture conditions. In addition, HLCs lack the full repertoire of functionalities characterising primary hepatocytes. Here, we explore the interest of forward programming to generate hepatocytes from hPSCs and to bypass these limitations. This approach relies on the overexpression of three hepatocyte nuclear factors (HNF1A, HNF6, and FOXA3) in combination with different nuclear receptors expressed in the adult liver using the OPTi-OX platform. Forward programming allows for the rapid production of hepatocytes (FoP-Heps) with functional characteristics using a simplified process. We also uncovered that the overexpression of nuclear receptors such as RORc can enhance specific functionalities of FoP-Heps thereby validating its role in lipid/glucose metabolism. Together, our results show that forward programming could offer a versatile alternative to direct differentiation for generating hepatocytes in vitro.
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Affiliation(s)
- Rute A Tomaz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Ekaterini D Zacharis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Fabian Bachinger
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Annabelle Wurmser
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Daniel Yamamoto
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Sandra Petrus-Reurer
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Carola M Morell
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Dominika Dziedzicka
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Brandon T Wesley
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Imbisaat Geti
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Charis-Patricia Segeritz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Miguel C de Brito
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Mariya Chhatriwala
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Daniel Ortmann
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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30
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Lee IS, Takebe T. Narrative engineering of the liver. Curr Opin Genet Dev 2022; 75:101925. [PMID: 35700688 PMCID: PMC10118678 DOI: 10.1016/j.gde.2022.101925] [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: 03/13/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022]
Abstract
Liver organoids are primary or pluripotent stem cell-derived three-dimensional structures that recapitulate regenerative or ontogenetic processes in vitro towards biomedical applications including disease modelling and diagnostics, drug safety and efficacy prediction, and therapeutic use. The cellular composition and structural organization of liver organoids may vary depending on the goal at hand, and the key challenge in general is to direct their development in a rational and controlled fashion for gaining targeted maturity, reproducibility, and scalability. Such endeavor begins with a detailed understanding of the biological processes in space and time behind hepatogenesis, followed by precise translation of these narrative processes through a bioengineering approach. Here, we discuss advancements in liver organoid technology through the lens of 'narrative engineering' in an attempt to synergize evolving understanding around molecular and cellular landscape governing hepatogenesis with engineering-inspired approaches for organoidgenesis.
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Affiliation(s)
- Inkyu S Lee
- Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Communication Design Center, Advanced Medical Research Center, Yokohama City University Graduate School of Medicine, Japan.
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31
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Li J, Wu X, Ke J, Lee M, Lan Q, Li J, Yu J, Huang Y, Sun DQ, Xie R. TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation. Nat Commun 2022; 13:3907. [PMID: 35798741 PMCID: PMC9263144 DOI: 10.1038/s41467-022-31611-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/17/2022] [Indexed: 12/02/2022] Open
Abstract
Existing knowledge of the role of epigenetic modifiers in pancreas development has exponentially increased. However, the function of TET dioxygenases in pancreatic endocrine specification remains obscure. We set out to tackle this issue using a human embryonic stem cell (hESC) differentiation system, in which TET1/TET2/TET3 triple knockout cells display severe defects in pancreatic β-cell specification. The integrative whole-genome analysis identifies unique cell-type-specific hypermethylated regions (hyper-DMRs) displaying reduced chromatin activity and remarkable enrichment of FOXA2, a pioneer transcription factor essential for pancreatic endoderm specification. Intriguingly, TET depletion leads to significant changes in FOXA2 binding at the pancreatic progenitor stage, in which gene loci with decreased FOXA2 binding feature low levels of active chromatin modifications and enriches for bHLH motifs. Transduction of full-length TET1 but not the TET1-catalytic-domain in TET-deficient cells effectively rescues β-cell differentiation accompanied by restoring PAX4 hypomethylation. Taking these findings together with the defective generation of functional β-cells upon TET1-inactivation, our study unveils an essential role of TET1-dependent demethylation in establishing β-cell identity. Moreover, we discover a physical interaction between TET1 and FOXA2 in endodermal lineage intermediates, which provides a mechanistic clue regarding the complex crosstalk between TET dioxygenases and pioneer transcription factors in epigenetic regulation during pancreas specification. Here the authors show that TET1 is required for the generation of functional insulin-producing cells, FOXA2 physically interacts with TET1 and contributes to specific recruitment of TET1 to mediate chromatin opening at the regulatory elements of pancreatic lineage determinants.
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Affiliation(s)
- Jianfang Li
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.,Innovation Center for Advanced Interdisciplinary Medicine, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510530, China.,Guangzhou Laboratory, Guangzhou, 510005, China
| | - Xinwei Wu
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.,Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jie Ke
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Minjung Lee
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Qingping Lan
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - De-Qiang Sun
- Innovation Center for Advanced Interdisciplinary Medicine, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510530, China. .,Cardiology Department, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
| | - Ruiyu Xie
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China. .,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, 999078, China.
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32
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Yang X, Raum JC, Kim J, Yu R, Yang J, Rice G, Li C, Won KJ, Stanescu DE, Stoffers DA. A PDX1 cistrome and single-cell transcriptome resource of the developing pancreas. Development 2022; 149:dev200432. [PMID: 35708349 PMCID: PMC9340549 DOI: 10.1242/dev.200432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/31/2022] [Indexed: 09/09/2023]
Abstract
Pancreatic and duodenal homeobox 1 (PDX1) is crucial for pancreas organogenesis, yet the dynamic changes in PDX1 binding in human or mouse developing pancreas have not been examined. To address this knowledge gap, we performed PDX1 ChIP-seq and single-cell RNA-seq using fetal human pancreata. We integrated our datasets with published datasets and revealed the dynamics of PDX1 binding and potential cell lineage-specific PDX1-bound genes in the pancreas from fetal to adult stages. We identified a core set of developmentally conserved PDX1-bound genes that reveal the broad multifaceted role of PDX1 in pancreas development. Despite the well-known dramatic changes in PDX1 function and expression, we found that PDX1-bound genes are largely conserved from embryonic to adult stages. This points towards a dual role of PDX1 in regulating the expression of its targets at different ages, dependent on other functionally congruent or directly interacting partners. We also showed that PDX1 binding is largely conserved in mouse pancreas. Together, our study reveals PDX1 targets in the developing pancreas in vivo and provides an essential resource for future studies on pancreas development.
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Affiliation(s)
- Xiaodun Yang
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey C. Raum
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978, Republic of Korea
| | - Reynold Yu
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juxiang Yang
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gabriella Rice
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Changhong Li
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
| | - Diana E. Stanescu
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris A. Stoffers
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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33
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Karimova MV, Gvazava IG, Vorotelyak EA. Overcoming the Limitations of Stem Cell-Derived Beta Cells. Biomolecules 2022; 12:biom12060810. [PMID: 35740935 PMCID: PMC9221417 DOI: 10.3390/biom12060810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/13/2022] Open
Abstract
Great advances in type 1 diabetes (T1D) and type 2 diabetes (T2D) treatment have been made to this day. However, modern diabetes therapy based on insulin injections and cadaveric islets transplantation has many disadvantages. That is why researchers are developing new methods to regenerate the pancreatic hormone-producing cells in vitro. The most promising approach is the generation of stem cell-derived beta cells that could provide an unlimited source of insulin-secreting cells. Recent studies provide methods to produce beta-like cell clusters that display glucose-stimulated insulin secretion—one of the key characteristics of the beta cell. However, in comparison with native beta cells, stem cell-derived beta cells do not undergo full functional maturation. In this paper we review the development and current state of various protocols, consider advantages, and propose ways to improve them. We examine molecular pathways, epigenetic modifications, intracellular components, and the microenvironment as a possible leverage to promote beta cell functional maturation. A possibility to create islet organoids from stem cell-derived components, as well as their encapsulation and further transplantation, is also examined. We try to combine modern research on beta cells and their crosstalk to create a holistic overview of developing insulin-secreting systems.
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Affiliation(s)
- Mariana V. Karimova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 119334 Moscow, Russia; (M.V.K.); (I.G.G.)
| | - Inessa G. Gvazava
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 119334 Moscow, Russia; (M.V.K.); (I.G.G.)
| | - Ekaterina A. Vorotelyak
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 119334 Moscow, Russia; (M.V.K.); (I.G.G.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence:
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34
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Smith RJ, Zhang H, Hu SS, Yung T, Francis R, Lee L, Onaitis MW, Dirks PB, Zang C, Kim TH. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions. Nat Commun 2022; 13:2965. [PMID: 35618699 PMCID: PMC9135761 DOI: 10.1038/s41467-022-30624-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/06/2022] [Indexed: 01/07/2023] Open
Abstract
Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-cell chromatin profiling of the primitive gut tube to reveal organ-specific chromatin patterns that reflect the anatomical patterns of distinct organs. We generate a comprehensive map of epigenomic changes throughout gut development, demonstrating that dynamic chromatin accessibility patterns associate with lineage-specific transcription factor binding events to regulate organ-specific gene expression. Additionally, we show that loss of Sox2 and Cdx2, foregut and hindgut lineage-specific transcription factors, respectively, leads to fate shifts in epigenomic patterns, linking transcription factor binding, chromatin accessibility, and lineage fate decisions in gut development. Notably, abnormal expression of Sox2 in the pancreas and intestine impairs lineage fate decisions in both development and adult homeostasis. Together, our findings define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and adult homeostasis.
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Affiliation(s)
- Ryan J Smith
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Hongpan Zhang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Theodora Yung
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Roshane Francis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Lilian Lee
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Mark W Onaitis
- Division of Cardiovascular and Thoracic Surgery, University of California San Diego Medical Center, San Diego, CA, USA
| | - Peter B Dirks
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| | - Tae-Hee Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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35
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Yin S, Mazumdar MN, Paranjapye A, Harris A. Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene. Genomics 2022; 114:110350. [PMID: 35346781 PMCID: PMC9509493 DOI: 10.1016/j.ygeno.2022.110350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 01/14/2023]
Abstract
Robust protocols to examine 3D chromatin structure have greatly advanced knowledge of gene regulatory mechanisms. Here we focus on the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which provides a paradigm for validating models of gene regulation built upon genome-wide analysis. We examine the mechanisms by which multiple cis-regulatory elements (CREs) at the CFTR gene coordinate its expression in intestinal epithelial cells. Using CRISPR/Cas9 to remove CREs, individually and in tandem, followed by assays of gene expression and higher-order chromatin structure (4C-seq), we reveal the cross-talk and dependency of two cell-specific intronic enhancers. The results suggest a mechanism whereby the locus responds when CREs are lost, which may involve activating transcription factors such as FOXA2. Also, by removing the 5' topologically-associating domain (TAD) boundary, we illustrate its impact on CFTR gene expression and architecture. These data suggest a multi-layered regulatory hierarchy that is highly sensitive to perturbations.
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36
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Liu D, Yang KY, Chan VW, Ye W, Chong CC, Wang CC, Wang H, Zhou B, Cheng KK, Lui KO. YY1 Regulates Glucose Homeostasis Through Controlling Insulin Transcription in Pancreatic β-Cells. Diabetes 2022; 71:961-977. [PMID: 35113157 PMCID: PMC9044128 DOI: 10.2337/db21-0695] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022]
Abstract
To date, identification of nonislet-specific transcriptional factors in the regulation of insulin gene expression has been little studied. Here, we report that the expression level of the transcription factor YY1 is increased dramatically in both human and mouse pancreatic β-cells after birth. Nevertheless, the physiological role of YY1 during β-cell development and its regulatory mechanism in β-cell function remain largely unknown. After β-cell ablation of Yy1, we observed rapid onset of hyperglycemia, impaired glucose tolerance, and reduced β-cell mass in neonatal and adult mice. These mice also had hypoinsulinemia with normal insulin sensitivity compared with their wild-type littermates, manifesting as a type 1 diabetic phenotype. Mechanistically, genome-wide RNA sequencing has defined dysregulated insulin signaling and defective glucose responsiveness in β-cells devoid of YY1. Integrative analyses coupled with chromatin immunoprecipitation assays targeting YY1, and histone modifications, including H3K4me1, H3K27ac, and H3K27me3, have further identified Ins1 and Ins2 as direct gene targets of YY1. Luciferase reporter assays and loss- and gain-of-function experiments also demonstrated that YY1 binds to the enhancer regions in exon 2 of Ins1 and Ins2, activating insulin transcription and, therefore, proinsulin and insulin production in pancreatic β-cells. YY1 also directly interacts with RNA polymerase II, potentially stabilizing the enhancer-promoter interaction in the multiprotein-DNA complex during transcription initiation. Taken together, our findings suggest a role for YY1 as a transcriptional activator of insulin gene expression, assisting β-cell maturation and function after birth. These analyses may advance our understanding of β-cell biology and provide clinically relevant insights targeting the pathophysiological origins of diabetes.
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Affiliation(s)
- Di Liu
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin Y. Yang
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Vicken W. Chan
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenchu Ye
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Charing C.N. Chong
- Department of Surgery, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Li Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Li Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Department of Orthopaedics and Traumatology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Kenneth K.Y. Cheng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Kathy O. Lui
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Li Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Corresponding author: Kathy O. Lui,
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37
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Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells 2022; 11:cells11091404. [PMID: 35563711 PMCID: PMC9105757 DOI: 10.3390/cells11091404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.
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Affiliation(s)
- Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
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38
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Yan J, Huangfu D. Epigenome rewiring in human pluripotent stem cells. Trends Cell Biol 2022; 32:259-271. [PMID: 34955367 PMCID: PMC8840982 DOI: 10.1016/j.tcb.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/10/2023]
Abstract
The epigenome plays a crucial role in modulating the activity of regulatory elements, thereby orchestrating diverse transcriptional programs during embryonic development. Human (h)PSC stepwise differentiation provides an excellent platform for capturing dynamic epigenomic events during lineage transition in human development. Here we discuss how recent technological advances, from epigenomic mapping to targeted perturbation, are providing a more comprehensive appreciation of remodeling of the chromatin landscape during human development with implications for aberrant rewiring in disease. We predict that the continuous innovation of hPSC differentiation methods, epigenome mapping, and CRISPR (clustered regularly interspaced short palindromic repeats) perturbation technologies will allow researchers to build toward not only a comprehensive understanding of the epigenomic mechanisms governing development, but also a highly flexible way to model diseases with opportunities for translation.
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Affiliation(s)
- Jielin Yan
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Danwei Huangfu
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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39
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Fang H, Luo Z, Lin C. Epigenetic reorganization during early embryonic lineage specification. Genes Genomics 2022; 44:379-387. [PMID: 35133623 DOI: 10.1007/s13258-021-01213-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dynamic chromatin reorganization occurs during two waves of cell lineage specification process, blastocyst formation and gastrulation, to generate distinct cell types. Epigenetic defects have been associated with severe developmental defects and diseases. How epigenetic remodeling coordinates the two lineage specification waves is becoming uncovered, benefiting from the development and application of new technologies including low-input or single-cell epigenome analysis approached in the past few years. OBJECTIVE In this review, we aim to highlight the most recent findings on epigenetic remodeling in cell lineage specification during blastocyst formation and gastrulation. METHODS First, we introduce how DNA methylation dynamically changes in blastocyst formation and gastrulation and its function in transcriptional regulation lineage-specific genes. Then, we discuss widespread remodeling of histone modification at promoters and enhancers in orchestrating the trajectory of cell lineage specification. Finally, we review dynamics of chromatin accessibility and 3D structure regulating developmental gene expression and associating with specific transcription factor binding events at stage specific manner. We also highlight the key questions that remain to be answered to fully understand chromatin regulation and reorganization in lineage specification. CONCLUSION Here, we summarize the recent advances and discoveries on epigenetic reorganization and its roles in blastocyst formation and gastrulation, and how it cooperates with the lineage specification, painting from global sequencing data from mouse in vivo tissues.
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Affiliation(s)
- Haitong Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
| | - Zhuojuan Luo
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Chengqi Lin
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China. .,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
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40
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Metabolic and epigenetic regulation of endoderm differentiation. Trends Cell Biol 2022; 32:151-164. [PMID: 34607773 PMCID: PMC8760149 DOI: 10.1016/j.tcb.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/31/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023]
Abstract
The endoderm, one of the three primary germ layers, gives rise to lung, liver, stomach, intestine, colon, pancreas, bladder, and thyroid. These endoderm-originated organs are subject to many life-threatening diseases. However, primary cells/tissues from endodermal organs are often difficult to grow in vitro. Human pluripotent stem cells (hPSCs), therefore, hold great promise for generating endodermal cells and their derivatives for the development of new therapeutics against these human diseases. Although a wealth of research has provided crucial information on the mechanisms underlying endoderm differentiation from hPSCs, increasing evidence has shown that metabolism, in connection with epigenetics, actively regulates endoderm differentiation in addition to the conventional endoderm inducing signals. Here we review recent advances in metabolic and epigenetic regulation of endoderm differentiation.
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41
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Gjaltema RAF, Schwämmle T, Kautz P, Robson M, Schöpflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Mol Cell 2022; 82:190-208.e17. [PMID: 34932975 DOI: 10.1016/j.molcel.2021.11.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Pauline Kautz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael Robson
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, Edinburgh, UK
| | - Robert Schöpflin
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lennart Brandenburg
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Carolina Vechiatto
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vera Schmiedel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center München, 85764 Neuherberg, Germany
| | - Stefan Mundlos
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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Dissecting the Complexity of Early Heart Progenitor Cells. J Cardiovasc Dev Dis 2021; 9:jcdd9010005. [PMID: 35050215 PMCID: PMC8779398 DOI: 10.3390/jcdd9010005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
Early heart development depends on the coordinated participation of heterogeneous cell sources. As pioneer work from Adriana C. Gittenberger-de Groot demonstrated, characterizing these distinct cell sources helps us to understand congenital heart defects. Despite decades of research on the segregation of lineages that form the primitive heart tube, we are far from understanding its full complexity. Currently, single-cell approaches are providing an unprecedented level of detail on cellular heterogeneity, offering new opportunities to decipher its functional role. In this review, we will focus on three key aspects of early heart morphogenesis: First, the segregation of myocardial and endocardial lineages, which yields an early lineage diversification in cardiac development; second, the signaling cues driving differentiation in these progenitor cells; and third, the transcriptional heterogeneity of cardiomyocyte progenitors of the primitive heart tube. Finally, we discuss how single-cell transcriptomics and epigenomics, together with live imaging and functional analyses, will likely transform the way we delve into the complexity of cardiac development and its links with congenital defects.
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43
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Stutt N, Song M, Wilson MD, Scott IC. Cardiac specification during gastrulation - The Yellow Brick Road leading to Tinman. Semin Cell Dev Biol 2021; 127:46-58. [PMID: 34865988 DOI: 10.1016/j.semcdb.2021.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]
Abstract
The question of how the heart develops, and the genetic networks governing this process have become intense areas of research over the past several decades. This research is propelled by classical developmental studies and potential clinical applications to understand and treat congenital conditions in which cardiac development is disrupted. Discovery of the tinman gene in Drosophila, and examination of its vertebrate homolog Nkx2.5, along with other core cardiac transcription factors has revealed how cardiac progenitor differentiation and maturation drives heart development. Careful observation of cardiac morphogenesis along with lineage tracing approaches indicated that cardiac progenitors can be divided into two broad classes of cells, namely the first and second heart fields, that contribute to the heart in two distinct waves of differentiation. Ample evidence suggests that the fate of individual cardiac progenitors is restricted to distinct cardiac structures quite early in development, well before the expression of canonical cardiac progenitor markers like Nkx2.5. Here we review the initial specification of cardiac progenitors, discuss evidence for the early patterning of cardiac progenitors during gastrulation, and consider how early gene expression programs and epigenetic patterns can direct their development. A complete understanding of when and how the developmental potential of cardiac progenitors is determined, and their potential plasticity, is of great interest developmentally and also has important implications for both the study of congenital heart disease and therapeutic approaches based on cardiac stem cell programming.
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Affiliation(s)
- Nathan Stutt
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Mengyi Song
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Michael D Wilson
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Ian C Scott
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.
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44
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Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nat Commun 2021; 12:6636. [PMID: 34789735 PMCID: PMC8599738 DOI: 10.1038/s41467-021-26950-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.
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Affiliation(s)
- Ryan J. Geusz
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Biomedical Graduate Studies Program, University of California San Diego, La Jolla, San Diego, CA 92037 USA
| | - Allen Wang
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Dieter K. Lam
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Nicholas K. Vinckier
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Konstantinos-Dionysios Alysandratos
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - David A. Roberts
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA
| | - Jinzhao Wang
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Samy Kefalopoulou
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Araceli Ramirez
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA 92093 USA
| | - Yunjiang Qiu
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA
| | - Joshua Chiou
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Biomedical Graduate Studies Program, University of California San Diego, La Jolla, San Diego, CA 92037 USA
| | - Kyle J. Gaulton
- grid.266100.30000 0001 2107 4242Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA 92093 USA
| | - Bing Ren
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA 92093 USA ,grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, San Diego, CA 92093-0653 USA
| | - Darrell N. Kotton
- grid.239424.a0000 0001 2183 6745Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - Maike Sander
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA, 92093, USA. .,Department of Cellular & Molecular Medicine, University of California, La Jolla, San Diego, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, San Diego, CA, 92093, USA.
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45
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Heller S, Li Z, Lin Q, Geusz R, Breunig M, Hohwieler M, Zhang X, Nair GG, Seufferlein T, Hebrok M, Sander M, Julier C, Kleger A, Costa IG. Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation. Commun Biol 2021; 4:1298. [PMID: 34789845 PMCID: PMC8599846 DOI: 10.1038/s42003-021-02818-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/24/2021] [Indexed: 02/07/2023] Open
Abstract
Cell type specification during pancreatic development is tightly controlled by a transcriptional and epigenetic network. The precise role of most transcription factors, however, has been only described in mice. To convey such concepts to human pancreatic development, alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells can be employed. Here, we analyzed stage-specific RNA-, ChIP-, and ATAC-sequencing data to dissect transcriptional and regulatory mechanisms during pancreatic development. Transcriptome and open chromatin maps of pancreatic differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreatic transcription factors and indicate ONECUT1 as a crucial fate regulator in pancreas progenitors. Moreover, our data suggest that ONECUT1 is also involved in preparing pancreatic progenitors for later endocrine specification. The dissection of the transcriptional and regulatory circuitry revealed an important role for ONECUT1 within such network and will serve as resource to study human development and disease.
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Affiliation(s)
- Sandra Heller
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Zhijian Li
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, RWTH Aachen University Medical School, Aachen, Germany
| | - Qiong Lin
- grid.420044.60000 0004 0374 4101Bayer AG, Research & Development, Pharmaceuticals, Bioinformatics, Berlin, Germany
| | - Ryan Geusz
- grid.266100.30000 0001 2107 4242Pediatric Diabetes Research Center (PDRC) at the University of California, San Diego, USA
| | - Markus Breunig
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Meike Hohwieler
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Xi Zhang
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Gopika G. Nair
- grid.266102.10000 0001 2297 6811Diabetes Center at the University of California, San Francisco, USA
| | - Thomas Seufferlein
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Matthias Hebrok
- grid.266102.10000 0001 2297 6811Diabetes Center at the University of California, San Francisco, USA
| | - Maike Sander
- grid.266100.30000 0001 2107 4242Pediatric Diabetes Research Center (PDRC) at the University of California, San Diego, USA
| | - Cécile Julier
- grid.4444.00000 0001 2112 9282Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR-8104, Paris, France
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany.
| | - Ivan G. Costa
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, RWTH Aachen University Medical School, Aachen, Germany
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46
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Abstract
Neurodevelopmental disorders (NDDs) affect about 1% of the population and can be caused by mutations in genes that affect the epigenetic code. There is limited functional understanding of most of these epigenetic modifiers, and we suggest that associated NDDs are caused, in part, by deficits in epigenetic priming, a prepatterning step that alters the genome in preparation to make cells competent to signaling cues. We provide evidence from high-resolution epigenetic and transcriptomic mapping studies to demonstrate how a failure to adequately prime the genome for neural induction could lead to impairment of terminally differentiated cells. This idea provides a framework for NDD pathogenesis and treatment.
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47
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Mutations and variants of ONECUT1 in diabetes. Nat Med 2021; 27:1928-1940. [PMID: 34663987 DOI: 10.1038/s41591-021-01502-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/13/2021] [Indexed: 12/12/2022]
Abstract
Genes involved in distinct diabetes types suggest shared disease mechanisms. Here we show that One Cut Homeobox 1 (ONECUT1) mutations cause monogenic recessive syndromic diabetes in two unrelated patients, characterized by intrauterine growth retardation, pancreas hypoplasia and gallbladder agenesis/hypoplasia, and early-onset diabetes in heterozygous relatives. Heterozygous carriers of rare coding variants of ONECUT1 define a distinctive subgroup of diabetic patients with early-onset, nonautoimmune diabetes, who respond well to diabetes treatment. In addition, common regulatory ONECUT1 variants are associated with multifactorial type 2 diabetes. Directed differentiation of human pluripotent stem cells revealed that loss of ONECUT1 impairs pancreatic progenitor formation and a subsequent endocrine program. Loss of ONECUT1 altered transcription factor binding and enhancer activity and NKX2.2/NKX6.1 expression in pancreatic progenitor cells. Collectively, we demonstrate that ONECUT1 controls a transcriptional and epigenetic machinery regulating endocrine development, involved in a spectrum of diabetes, encompassing monogenic (recessive and dominant) as well as multifactorial inheritance. Our findings highlight the broad contribution of ONECUT1 in diabetes pathogenesis, marking an important step toward precision diabetes medicine.
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48
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Rankin SA, Steimle JD, Yang XH, Rydeen AB, Agarwal K, Chaturvedi P, Ikegami K, Herriges MJ, Moskowitz IP, Zorn AM. Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development. eLife 2021; 10:69288. [PMID: 34643182 PMCID: PMC8555986 DOI: 10.7554/elife.69288] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
The gene regulatory networks that coordinate the development of the cardiac and pulmonary systems are essential for terrestrial life but poorly understood. The T-box transcription factor Tbx5 is critical for both pulmonary specification and heart development, but how these activities are mechanistically integrated remains unclear. Here using Xenopus and mouse embryos, we establish molecular links between Tbx5 and retinoic acid (RA) signaling in the mesoderm and between RA signaling and sonic hedgehog expression in the endoderm to unveil a conserved RA-Hedgehog-Wnt signaling cascade coordinating cardiopulmonary (CP) development. We demonstrate that Tbx5 directly maintains expression of aldh1a2, the RA-synthesizing enzyme, in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer. Tbx5 promotes posterior second heart field identity in a positive feedback loop with RA, antagonizing a Fgf8-Cyp regulatory module to restrict FGF activity to the anterior. We find that Tbx5/Aldh1a2-dependent RA signaling directly activates shh transcription in the adjacent foregut endoderm through a conserved MACS1 enhancer. Hedgehog signaling coordinates with Tbx5 in the mesoderm to activate expression of wnt2/2b, which induces pulmonary fate in the foregut endoderm. These results provide mechanistic insight into the interrelationship between heart and lung development informing CP evolution and birth defects.
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Affiliation(s)
- Scott A Rankin
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Jeffrey D Steimle
- Department of Pediatrics, University of Chicago, Chicago, United States.,Department of Pathology, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| | - Xinan H Yang
- Department of Pediatrics, University of Chicago, Chicago, United States.,Department of Pathology, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| | - Ariel B Rydeen
- Department of Pediatrics, University of Chicago, Chicago, United States.,Department of Pathology, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| | - Kunal Agarwal
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Praneet Chaturvedi
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Kohta Ikegami
- Department of Pediatrics, University of Chicago, Chicago, United States
| | | | - Ivan P Moskowitz
- Department of Pediatrics, University of Chicago, Chicago, United States.,Department of Pathology, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| | - Aaron M Zorn
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States.,University of Cincinnati, College of Medicine, Department of Pediatrics, Chicago, United States
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49
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Maurya SS. Role of Enhancers in Development and Diseases. EPIGENOMES 2021; 5:epigenomes5040021. [PMID: 34968246 PMCID: PMC8715447 DOI: 10.3390/epigenomes5040021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Enhancers are cis-regulatory elements containing short DNA sequences that serve as binding sites for pioneer/regulatory transcription factors, thus orchestrating the regulation of genes critical for lineage determination. The activity of enhancer elements is believed to be determined by transcription factor binding, thus determining the cell state identity during development. Precise spatio-temporal control of the transcriptome during lineage specification requires the coordinated binding of lineage-specific transcription factors to enhancers. Thus, enhancers are the primary determinants of cell identity. Numerous studies have explored the role and mechanism of enhancers during development and disease, and various basic questions related to the functions and mechanisms of enhancers have not yet been fully answered. In this review, we discuss the recently published literature regarding the roles of enhancers, which are critical for various biological processes governing development. Furthermore, we also highlight that altered enhancer landscapes provide an essential context to understand the etiologies and mechanisms behind numerous complex human diseases, providing new avenues for effective enhancer-based therapeutic interventions.
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Affiliation(s)
- Shailendra S Maurya
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Department of Developmental Biology, School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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50
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Enhancer-associated H3K4 methylation safeguards in vitro germline competence. Nat Commun 2021; 12:5771. [PMID: 34599190 PMCID: PMC8486853 DOI: 10.1038/s41467-021-26065-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/16/2021] [Indexed: 01/27/2023] Open
Abstract
Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1-deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.
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