1
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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2
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Fatma H, Siddique HR. Cancer cell plasticity, stem cell factors, and therapy resistance: how are they linked? Cancer Metastasis Rev 2024; 43:423-440. [PMID: 37796391 DOI: 10.1007/s10555-023-10144-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Cellular plasticity can occur naturally in an organism and is considered an adapting mechanism during the developmental stage. However, abnormal cellular plasticity is observed in different diseased conditions, including cancer. Cancer cell plasticity triggers the stimuli of epithelial-mesenchymal transition (EMT), abnormal epigenetic changes, expression of stem cell factors and implicated signaling pathways, etc., and helps in the maintenance of CSC phenotype. Conversely, CSC maintains the cancer cell plasticity, EMT, and epigenetic plasticity. EMT contributes to increased cell migration and greater diversity within tumors, while epigenetic changes, stem cell factors (OCT4, NANOG, and SOX2), and various signaling pathways allow cancer cells to maintain various phenotypes, giving rise to intra- and inter-tumoral heterogeneity. The intricate relationships between cancer cell plasticity and stem cell factors help the tumor cells adopt drug-tolerant states, evade senescence, and successfully acquire drug resistance with treatment dismissal. Inhibiting molecules/signaling pathways involved in promoting CSCs, cellular plasticity, EMT, and epigenetic plasticity might be helpful for successful cancer therapy management. This review discussed the role of cellular plasticity, EMT, and stem cell factors in tumor initiation, progression, reprogramming, and therapy resistance. Finally, we discussed how the intervention in this axis will help better manage cancers and improve patient survivability.
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Affiliation(s)
- Homa Fatma
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, UP, 202002, India
| | - Hifzur R Siddique
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, UP, 202002, India.
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3
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Wang L, Tan TK, Kim H, Kappei D, Tan SH, Look AT, Sanda T. ASCL1 characterizes adrenergic neuroblastoma via its pioneer function and cooperation with core regulatory circuit factors. Cell Rep 2023; 42:113541. [PMID: 38060444 DOI: 10.1016/j.celrep.2023.113541] [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: 05/19/2023] [Revised: 10/09/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Neuroblastoma originates from developing neural crest and can interconvert between the mesenchymal (MES) and adrenergic (ADRN) states, each of which are controlled by different sets of transcription factors forming the core regulatory circuit (CRC). However, the roles of CRC factors in induction and maintenance of specific state are poorly understood. Here, we demonstrate that overexpression of ASCL1, an ADRN CRC factor, in MES neuroblastoma cells opens closed chromatin at the promoters of key ADRN genes, accompanied by epigenetic activation and establishment of enhancer-promoter interactions, initiating the ADRN gene expression program. ASCL1 inhibits the transforming growth factor β-SMAD2/3 pathway but activates the bone morphogenetic protein SMAD1-ID3/4 pathway. ASCL1 and other CRC members potentiate each other's activity, increasing the expression of the original targets and inducing a new set of genes, thereby fully inducing the ADRN program. Our results demonstrate that ASCL1 serves as a pioneer factor and cooperates with CRC factors to characterize the ADRN gene expression program.
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Affiliation(s)
- Lu Wang
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Hyoju Kim
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02216, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.
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4
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Horisawa K, Suzuki A. The role of pioneer transcription factors in the induction of direct cellular reprogramming. Regen Ther 2023; 24:112-116. [PMID: 37397229 PMCID: PMC10314230 DOI: 10.1016/j.reth.2023.06.002] [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: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
Regenerative medicine is a highly advanced medical field that aims to restore tissues and organs lost due to diseases and injury using a person's own cells or those of others. Direct cellular reprogramming is a promising technology that can directly induce cell-fate conversion from terminally differentiated cells to other cell types and is expected to play a pivotal role in applications in regenerative medicine. The induction of direct cellular reprogramming requires one or more master transcription factors with the potential to reconstitute cell type-specific transcription factor networks. The set of master transcription factors may contain unique transcription factors called pioneer factors that can open compacted chromatin structures and drive the transcriptional activation of target genes. Therefore, pioneer factors may play a central role in direct cellular reprogramming. However, our understanding of the molecular mechanisms by which pioneer factors induce cell-fate conversion is still limited. This review briefly summarizes the outcomes of recent findings and discusses future perspectives, focusing on the role of pioneer factors in direct cellular reprogramming.
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5
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Felske T, Tocco C, Péron S, Harb K, Alfano C, Galante C, Berninger B, Studer M. Lmo4 synergizes with Fezf2 to promote direct in vivo reprogramming of upper layer cortical neurons and cortical glia towards deep-layer neuron identities. PLoS Biol 2023; 21:e3002237. [PMID: 37552690 PMCID: PMC10409279 DOI: 10.1371/journal.pbio.3002237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
In vivo direct neuronal reprogramming relies on the implementation of an exogenous transcriptional program allowing to achieve conversion of a particular neuronal or glial cell type towards a new identity. The transcription factor (TF) Fezf2 is known for its role in neuronal subtype specification of deep-layer (DL) subcortical projection neurons. High ectopic Fezf2 expression in mice can convert both upper-layer (UL) and striatal projection neurons into a corticofugal fate, even if at low efficiency. In this study, we show that Fezf2 synergizes with the nuclear co-adaptor Lmo4 to further enhance reprogramming of UL cortical pyramidal neurons into DL corticofugal neurons, at both embryonic and early postnatal stages. Reprogrammed neurons express DL molecular markers and project toward subcerebral targets, including thalamus, cerebral peduncle (CP), and spinal cord (SC). We also show that co-expression of Fezf2 with the reprogramming factors Neurog2 and Bcl2 in early postnatal mouse glia promotes glia-to-neuron conversion with partial hallmarks of DL neurons and with Lmo4 promoting further morphological complexity. These data support a novel role for Lmo4 in synergizing with Fezf2 during direct lineage conversion in vivo.
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Affiliation(s)
| | - Chiara Tocco
- Université Côte d’Azur, CNRS, Inserm, iBV, Nice, France
| | - Sophie Péron
- Research Group “Adult Neurogenesis and Cellular Reprogramming”, Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Kawssar Harb
- Université Côte d’Azur, CNRS, Inserm, iBV, Nice, France
| | | | - Chiara Galante
- Research Group “Adult Neurogenesis and Cellular Reprogramming”, Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany
| | - Benedikt Berninger
- Research Group “Adult Neurogenesis and Cellular Reprogramming”, Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
- Focus Program Translational Neuroscience, Johannes Gutenberg University, Mainz, Germany
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6
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Leclerc K, Remark LH, Ramsukh M, Josephson AM, Palma L, Parente PEL, Sambon M, Lee S, Lopez EM, Morgani SM, Leucht P. Hox genes are crucial regulators of periosteal stem cell identity. Development 2023; 150:dev201391. [PMID: 36912250 PMCID: PMC10112919 DOI: 10.1242/dev.201391] [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: 10/19/2022] [Accepted: 02/20/2023] [Indexed: 03/14/2023]
Abstract
Periosteal stem and progenitor cells (PSPCs) are major contributors to bone maintenance and repair. Deciphering the molecular mechanisms that regulate their function is crucial for the successful generation and application of future therapeutics. Here, we pinpoint Hox transcription factors as necessary and sufficient for periosteal stem cell function. Hox genes are transcriptionally enriched in periosteal stem cells and their overexpression in more committed progenitors drives reprogramming to a naïve, self-renewing stem cell-like state. Crucially, individual Hox family members are expressed in a location-specific manner and their stem cell-promoting activity is only observed when the Hox gene is matched to the anatomical origin of the PSPC, demonstrating a role for the embryonic Hox code in adult stem cells. Finally, we demonstrate that Hoxa10 overexpression partially restores the age-related decline in fracture repair. Together, our data highlight the importance of Hox genes as key regulators of PSPC identity in skeletal homeostasis and repair.
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Affiliation(s)
- Kevin Leclerc
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Lindsey H. Remark
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Malissa Ramsukh
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Anne Marie Josephson
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Laura Palma
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Paulo E. L. Parente
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Margaux Sambon
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Sooyeon Lee
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Institute of Comparative Molecular Endocrinology, Ulm University, Ulm 89081, Germany
| | - Emma Muiños Lopez
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Cell Therapy Area, Clínica Universidad de Navarra, Pamplona 31008, Spain
| | - Sophie M. Morgani
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Philipp Leucht
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
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7
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Future Pharmacotherapy for Sensorineural Hearing Loss by Protection and Regeneration of Auditory Hair Cells. Pharmaceutics 2023; 15:pharmaceutics15030777. [PMID: 36986638 PMCID: PMC10054686 DOI: 10.3390/pharmaceutics15030777] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Sensorineural hearing loss has been a global burden of diseases for decades. However, according to recent progress in experimental studies on hair cell regeneration and protection, clinical trials of pharmacotherapy for sensorineural hearing loss have rapidly progressed. In this review, we focus on recent clinical trials for hair cell protection and regeneration and outline mechanisms based on associated experimental studies. Outcomes of recent clinical trials provided valuable data regarding the safety and tolerability of intra-cochlear and intra-tympanic applications as drug delivery methods. Recent findings in molecular mechanisms of hair cell regeneration suggested the realization of regenerative medicine for sensorineural hearing loss in the near future.
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8
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Hersbach BA, Fischer DS, Masserdotti G, Deeksha, Mojžišová K, Waltzhöni T, Rodriguez-Terrones D, Heinig M, Theis FJ, Götz M, Stricker SH. Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol Syst Biol 2022; 18:e11129. [PMID: 36106915 PMCID: PMC9476893 DOI: 10.15252/msb.202211129] [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: 05/19/2022] [Revised: 08/01/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single‐cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide‐seq. Collide‐seq revealed the lack of a common mechanism through which fibroblast‐specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system, in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide‐seq has shed light on several fundamental principles of fate conversion that may aid in improving current reprogramming paradigms.
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Affiliation(s)
- Bob A Hersbach
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany.,Graduate School of Systemic Neurosciences, Biocenter, Ludwig-Maximilians University, Munich, Germany
| | - David S Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Giacomo Masserdotti
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
| | - Deeksha
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
| | - Karolina Mojžišová
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany
| | - Thomas Waltzhöni
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Core Facility Genomics, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Diego Rodriguez-Terrones
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany.,German Excellence Cluster of Systems Neurology, Biomedical Center Munich, Munich, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany.,German Excellence Cluster of Systems Neurology, Biomedical Center Munich, Munich, Germany
| | - Stefan H Stricker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
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9
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Ren R, Fan Y, Peng Z, Wang S, Jiang Y, Fu L, Cao J, Zhao S, Wang H. Characterization and perturbation of CTCF-mediated chromatin interactions for enhancing myogenic transdifferentiation. Cell Rep 2022; 40:111206. [PMID: 35977522 DOI: 10.1016/j.celrep.2022.111206] [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: 04/23/2021] [Revised: 06/21/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022] Open
Abstract
Expression of key transcription factors can induce transdifferentiation in somatic cells; however, this conversion is usually incomplete due to undefined intrinsic barriers. Here, we employ MyoD-induced transdifferentiation of fibroblasts as a model to illustrate the chromatin structures that impede the cell-fate transition. Focusing on the three-dimensional (3D) chromatin interactions, we show that MyoD directly establishes chromatin loops to activate myogenic transcriptional program. Similarly, dynamic changes of CTCF-mediated chromatin interactions are favorable for fibroblast-to-myoblast conversion. However, a substantial portion of CTCF-mediated chromatin interactions remain stable, and the associated genes are steady in expression and enriched for fibroblast function that may restrict cell-identity transformation. Temporal CTCF depletion can interrupt the resistant chromatin loops to enhance myogenic transdifferentiation in mice, pig, and chicken fibroblasts. Therefore, during induced transdifferentiation, the transcription factor can directly reorganize the 3D chromatin interactions, and perturbation of CTCF-mediated genome topology may resolve the limitations of cell fate transitions.
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Affiliation(s)
- Ruimin Ren
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Yu Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhelun Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sheng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yunqi Jiang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liangliang Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianhua Cao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Heng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; College of Animal Science and Technology, Shandong Agricultural University, Taian, China.
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10
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Buzzi AL, Chen J, Thiery A, Delile J, Streit A. Sox8 remodels the cranial ectoderm to generate the ear. Proc Natl Acad Sci U S A 2022; 119:e2118938119. [PMID: 35867760 PMCID: PMC9282420 DOI: 10.1073/pnas.2118938119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
The vertebrate inner ear arises from a pool of progenitors with the potential to contribute to all the sense organs and cranial ganglia in the head. Here, we explore the molecular mechanisms that control ear specification from these precursors. Using a multiomics approach combined with loss-of-function experiments, we identify a core transcriptional circuit that imparts ear identity, along with a genome-wide characterization of noncoding elements that integrate this information. This analysis places the transcription factor Sox8 at the top of the ear determination network. Introducing Sox8 into the cranial ectoderm not only converts non-ear cells into ear progenitors but also activates the cellular programs for ear morphogenesis and neurogenesis. Thus, Sox8 has the unique ability to remodel transcriptional networks in the cranial ectoderm toward ear identity.
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Affiliation(s)
- Ailin Leticia Buzzi
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, United Kingdom
| | - Jingchen Chen
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, United Kingdom
| | - Alexandre Thiery
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, United Kingdom
| | - Julien Delile
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, United Kingdom
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11
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Aydin B, Sierk M, Moreno-Estelles M, Tejavibulya L, Kumar N, Flames N, Mahony S, Mazzoni EO. Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation. Front Neurosci 2022; 16:903881. [PMID: 35801179 PMCID: PMC9254625 DOI: 10.3389/fnins.2022.903881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Neuronal programming by forced expression of transcription factors (TFs) holds promise for clinical applications of regenerative medicine. However, the mechanisms by which TFs coordinate their activities on the genome and control distinct neuronal fates remain obscure. Using direct neuronal programming of embryonic stem cells, we dissected the contribution of a series of TFs to specific neuronal regulatory programs. We deconstructed the Ascl1-Lmx1b-Foxa2-Pet1 TF combination that has been shown to generate serotonergic neurons and found that stepwise addition of TFs to Ascl1 canalizes the neuronal fate into a diffuse monoaminergic fate. The addition of pioneer factor Foxa2 represses Phox2b to induce serotonergic fate, similar to in vivo regulatory networks. Foxa2 and Pet1 appear to act synergistically to upregulate serotonergic fate. Foxa2 and Pet1 co-bind to a small fraction of genomic regions but mostly bind to different regulatory sites. In contrast to the combinatorial binding activities of other programming TFs, Pet1 does not strictly follow the Foxa2 pioneer. These findings highlight the challenges in formulating generalizable rules for describing the behavior of TF combinations that program distinct neuronal subtypes.
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Affiliation(s)
- Begüm Aydin
- Department of Biology, New York University, New York City, NY, United States
| | - Michael Sierk
- Interdisciplinary Sciences Department, Saint Vincent College, Latrobe, PA, United States
| | - Mireia Moreno-Estelles
- Department of Biology, New York University, New York City, NY, United States
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IIBV-CSIC, Valencia, Spain
| | - Link Tejavibulya
- Department of Biology, New York University, New York City, NY, United States
| | - Nikathan Kumar
- Department of Biology, New York University, New York City, NY, United States
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IIBV-CSIC, Valencia, Spain
- *Correspondence: Nuria Flames,
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Shaun Mahony,
| | - Esteban O. Mazzoni
- Department of Biology, New York University, New York City, NY, United States
- Esteban O. Mazzoni,
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12
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Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression–methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
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Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.,Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway. .,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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13
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Direct neuronal reprogramming: Fast forward from new concepts toward therapeutic approaches. Neuron 2021; 110:366-393. [PMID: 34921778 DOI: 10.1016/j.neuron.2021.11.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/25/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
Differentiated cells have long been considered fixed in their identity. However, about 20 years ago, the first direct conversion of glial cells into neurons in vitro opened the field of "direct neuronal reprogramming." Since then, neuronal reprogramming has achieved the generation of fully functional, mature neurons with remarkable efficiency, even in diseased brain environments. Beyond their clinical implications, these discoveries provided basic insights into crucial mechanisms underlying conversion of specific cell types into neurons and maintenance of neuronal identity. Here we discuss such principles, including the importance of the starter cell for shaping the outcome of neuronal reprogramming. We further highlight technical concerns for in vivo reprogramming and propose a code of conduct to avoid artifacts and pitfalls. We end by pointing out next challenges for development of less invasive cell replacement therapies for humans.
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14
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Li B, Hon GC. Single-Cell Genomics: Catalyst for Cell Fate Engineering. Front Bioeng Biotechnol 2021; 9:748942. [PMID: 34733831 PMCID: PMC8558416 DOI: 10.3389/fbioe.2021.748942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
As we near a complete catalog of mammalian cell types, the capability to engineer specific cell types on demand would transform biomedical research and regenerative medicine. However, the current pace of discovering new cell types far outstrips our ability to engineer them. One attractive strategy for cellular engineering is direct reprogramming, where induction of specific transcription factor (TF) cocktails orchestrates cell state transitions. Here, we review the foundational studies of TF-mediated reprogramming in the context of a general framework for cell fate engineering, which consists of: discovering new reprogramming cocktails, assessing engineered cells, and revealing molecular mechanisms. Traditional bulk reprogramming methods established a strong foundation for TF-mediated reprogramming, but were limited by their small scale and difficulty resolving cellular heterogeneity. Recently, single-cell technologies have overcome these challenges to rapidly accelerate progress in cell fate engineering. In the next decade, we anticipate that these tools will enable unprecedented control of cell state.
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Affiliation(s)
- Boxun Li
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States
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15
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Zhou S, Cisse B. Regulation of Microglia for the Treatment of Glioma. World Neurosurg 2021; 154:222-227. [PMID: 34583499 DOI: 10.1016/j.wneu.2021.06.107] [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: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
Microglia are the resident macrophages of the central nervous system (CNS). They are derived from the erythromyeloid progenitors in the embryonic yolk sac, and they are maintained postnatally by limited self-renewal and longevity. As the most abundant immune cells in the CNS, they play critical roles in homeostasis and various CNS pathologies, including tumor, stroke, and neurodegenerative disease. For instance, in gliomas, up to more than 30% of cells in the tumor microenvironment can be microglia and tumor-associated macrophages. These cells are typically coopted by tumor cells to create a pro-tumorigenic microenvironment. The transcriptional regulation of the development and function of microglia in health and disease is not well understood. Transcription factors are master regulators of cell fates and functions and activate target genes that execute a genetic program typically initiated by external stimuli. Several transcription factors, not necessarily specific to microglia, have been shown to play roles in the development, function, and activation state of microglia. In this review, we summarize our current understanding of the roles of transcription factors in the functions of microglia in normal CNS homeostasis and in gliomas. A thorough understanding of the transcription factors and their target genes that mediate and regulate the functions of microglia in gliomas may help identify new targets for immune therapies. These stroma-directed therapies may be combined with tumor cell-directed therapies for more effective treatment of these diseases.
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Affiliation(s)
- Sichang Zhou
- Department of Neurosurgery, NewYork-Presbyterian/Weill Cornell Medicine, New York, New York, USA
| | - Babacar Cisse
- Department of Neurosurgery, NewYork-Presbyterian/Weill Cornell Medicine, New York, New York, USA.
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16
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Canals I, Quist E, Ahlenius H. Transcription Factor-Based Strategies to Generate Neural Cell Types from Human Pluripotent Stem Cells. Cell Reprogram 2021; 23:206-220. [PMID: 34388027 DOI: 10.1089/cell.2021.0045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the last years, the use of pluripotent stem cells in studies of human biology has grown exponentially. These cells represent an infinite source for differentiation into several human cell types facilitating the investigation on biological processes, functionality of cells, or diseases mechanisms in relevant human models. In the neurobiology field, pluripotent stem cells have been extensively used to generate the main neuronal and glial cells of the brain. Traditionally, protocols following developmental cues have been applied to pluripotent stem cells to drive differentiation toward different cell lineages; however, these protocols give rise to populations with mixed identities. Interestingly, new protocols applying overexpression of lineage-specific transcription factors (TFs) have emerged and facilitated the generation of highly pure populations of specific subtypes of neurons and glial cells in an easy, reproducible, and rapid manner. In this study, we review protocols based on this strategy to generate excitatory, inhibitory, dopaminergic, and motor neurons as well as astrocytes, oligodendrocytes, and microglia. In addition, we will discuss the main applications for cells generated with these protocols, including disease modeling, drug screening, and mechanistic studies. Finally, we will discuss the advantages and disadvantages of TF-based protocols and present our view of the future in this field.
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Affiliation(s)
- Isaac Canals
- Stem Cells, Aging and Neurodegeneration Group, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Neurology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund, Sweden
| | - Ella Quist
- Stem Cells, Aging and Neurodegeneration Group, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Neurology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund, Sweden
| | - Henrik Ahlenius
- Stem Cells, Aging and Neurodegeneration Group, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Neurology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund, Sweden
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17
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Enhancer decommissioning imposes an epigenetic barrier to sensory hair cell regeneration. Dev Cell 2021; 56:2471-2485.e5. [PMID: 34331868 DOI: 10.1016/j.devcel.2021.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023]
Abstract
Adult mammalian tissues such as heart, brain, retina, and the sensory structures of the inner ear do not effectively regenerate, although a latent capacity for regeneration exists at embryonic and perinatal times. We explored the epigenetic basis for this latent regenerative potential in the mouse inner ear and its rapid loss during maturation. In perinatal supporting cells, whose fate is maintained by Notch-mediated lateral inhibition, the hair cell enhancer network is epigenetically primed (H3K4me1) but silenced (active H3K27 de-acetylation and trimethylation). Blocking Notch signaling during the perinatal period of plasticity rapidly eliminates epigenetic silencing and allows supporting cells to transdifferentiate into hair cells. Importantly, H3K4me1 priming of the hair cell enhancers in supporting cells is removed during the first post-natal week, coinciding with the loss of transdifferentiation potential. We hypothesize that enhancer decommissioning during cochlear maturation contributes to the failure of hair cell regeneration in the mature organ of Corti.
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18
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Isaacson A, Spagnoli FM. Pancreatic cell fate specification: insights into developmental mechanisms and their application for lineage reprogramming. Curr Opin Genet Dev 2021; 70:32-39. [PMID: 34062490 DOI: 10.1016/j.gde.2021.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 12/15/2022]
Abstract
Diabetes is a group of metabolic disorders, which results from insufficient functional pancreatic β-cell mass either due to the autoimmune destruction of insulin producing β-cells, or their death or de-differentiation as compensation for insulin resistance. The ability to reprogram cell types within close developmental proximity to β-cells offers a strategy to replenish β-cell mass and a future possible treatment of diabetes. Here, we review recent advances in the fields of pancreas development and lineage reprogramming. We also probe the possibility of using reprogrammed cells as an approach by which to further understand developmental mechanisms, in particular roadblocks to changing cell identity. Finally, we highlight fundamental challenges that need to be overcome to advance lineage reprogramming for generating pancreatic cells.
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Affiliation(s)
- Abigail Isaacson
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK
| | - Francesca M Spagnoli
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK.
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19
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Larson ED, Marsh AJ, Harrison MM. Pioneering the developmental frontier. Mol Cell 2021; 81:1640-1650. [PMID: 33689750 PMCID: PMC8052302 DOI: 10.1016/j.molcel.2021.02.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022]
Abstract
Coordinated changes in gene expression allow a single fertilized oocyte to develop into a complex multi-cellular organism. These changes in expression are controlled by transcription factors that gain access to discrete cis-regulatory elements in the genome, allowing them to activate gene expression. Although nucleosomes present barriers to transcription factor occupancy, pioneer transcription factors have unique properties that allow them to bind DNA in the context of nucleosomes, define cis-regulatory elements, and facilitate the subsequent binding of additional factors that determine gene expression. In this capacity, pioneer factors act at the top of gene-regulatory networks to control developmental transitions. Developmental context also influences pioneer factor binding and activity. Here we discuss the interplay between pioneer factors and development, their role in driving developmental transitions, and the influence of the cellular environment on pioneer factor binding and activity.
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Affiliation(s)
- Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Audrey J Marsh
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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20
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Iyer AA, Groves AK. Transcription Factor Reprogramming in the Inner Ear: Turning on Cell Fate Switches to Regenerate Sensory Hair Cells. Front Cell Neurosci 2021; 15:660748. [PMID: 33854418 PMCID: PMC8039129 DOI: 10.3389/fncel.2021.660748] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
Non-mammalian vertebrates can restore their auditory and vestibular hair cells naturally by triggering the regeneration of adjacent supporting cells. The transcription factor ATOH1 is a key regulator of hair cell development and regeneration in the inner ear. Following the death of hair cells, supporting cells upregulate ATOH1 and give rise to new hair cells. However, in the mature mammalian cochlea, such natural regeneration of hair cells is largely absent. Transcription factor reprogramming has been used in many tissues to convert one cell type into another, with the long-term hope of achieving tissue regeneration. Reprogramming transcription factors work by altering the transcriptomic and epigenetic landscapes in a target cell, resulting in a fate change to the desired cell type. Several studies have shown that ATOH1 is capable of reprogramming cochlear non-sensory tissue into cells resembling hair cells in young animals. However, the reprogramming ability of ATOH1 is lost with age, implying that the potency of individual hair cell-specific transcription factors may be reduced or lost over time by mechanisms that are still not clear. To circumvent this, combinations of key hair cell transcription factors have been used to promote hair cell regeneration in older animals. In this review, we summarize recent findings that have identified and studied these reprogramming factor combinations for hair cell regeneration. Finally, we discuss the important questions that emerge from these findings, particularly the feasibility of therapeutic strategies using reprogramming factors to restore human hearing in the future.
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Affiliation(s)
- Amrita A. Iyer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
| | - Andrew K. Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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21
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Han JK, Shin Y, Sohn MH, Choi SB, Shin D, You Y, Shin JY, Seo JS, Kim HS. Direct conversion of adult human fibroblasts into functional endothelial cells using defined factors. Biomaterials 2021; 272:120781. [PMID: 33848809 DOI: 10.1016/j.biomaterials.2021.120781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 12/02/2020] [Accepted: 03/20/2021] [Indexed: 02/06/2023]
Abstract
We aimed to directly convert adult human dermal fibroblasts (aHDFs) into functional endothelial cells (ECs). Lentiviral vectors encoding endothelial transcription factors (TFs) were constructed. We examined whether five TFs (FOXO1, ER71, KLF2, TAL1, and LMO2) used for the generation of mouse induced ECs (iECs) could convert the aHDFs into human iECs. Twenty-eight days after transduction with lentiviral constructs, 32.1 ± 5.1% cells expressed vascular endothelial (VE)-cadherin. Factor screening revealed that only three factors (3F: ER71, KLF2, and TAL1) were necessary to induce VE-cadherin (+) cells (49.4 ± 3.5%). However, whole transcriptome sequencing showed that VE-cadherin (+) cells were not completely reprogrammed. Mature iECs double-positive for VE-cadherin/Pecam1 (DP cells) with a cobblestone appearance were obtained at a frequency of only 5.1 ± 0.6%. Using whole transcriptome analysis, the potential factors that could block the conversion were screened. Among candidates TWIST1-knockdown enhanced efficiency of conversion. Rosiglitazone, an inhibitor of epithelial-mesenchymal transition (EMT), also improved the conversion efficiency. Moreover, a 2nd second-stage conversion process, in which VE-cadherin (+) cells were incubated for additional two weeks, further enhanced the efficiency. The final protocol for 6 weeks yielded a conversion rate of 19.6 ± 3.0% iECs, defined by DP cells depicting the nature of mature ECs in various analyses. Further analyses revealed that the genetic and epigenetic profiles of iECs resembled those of functional ECs. Collectively, aHDFs can be converted into functional ECs through the transduction of ER71, KLF2, and TAL1, combined with two EMT inhibitors (siTWIST1 and rosiglitazone), followed by 2nd stage conversion.
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Affiliation(s)
- Jung-Kyu Han
- Division of Cardiology, Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Youngchul Shin
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital, Seoul, South Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Min-Hwan Sohn
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea; Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, South Korea; Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea; Macrogen Inc., Seoul, South Korea
| | - Saet-Byeol Choi
- Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Dasom Shin
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital, Seoul, South Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Youngrang You
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital, Seoul, South Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Jong-Yeon Shin
- Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, South Korea; Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea; Macrogen Inc., Seoul, South Korea
| | - Jeong-Sun Seo
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea; Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, South Korea; Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea; Macrogen Inc., Seoul, South Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- Division of Cardiology, Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea.
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22
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FOLFOX Therapy Induces Feedback Upregulation of CD44v6 through YB-1 to Maintain Stemness in Colon Initiating Cells. Int J Mol Sci 2021; 22:ijms22020753. [PMID: 33451103 PMCID: PMC7828641 DOI: 10.3390/ijms22020753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer initiating cells (CICs) drive tumor formation and drug-resistance, but how they develop drug-resistance characteristics is not well understood. In this study, we demonstrate that chemotherapeutic agent FOLFOX, commonly used for drug-resistant/metastatic colorectal cancer (CRC) treatment, induces overexpression of CD44v6, MDR1, and oncogenic transcription/translation factor Y-box-binding protein-1 (YB-1). Our study revealed that CD44v6, a receptor for hyaluronan, increased the YB-1 expression through PGE2/EP1-mTOR pathway. Deleting CD44v6, and YB-1 by the CRISPR/Cas9 system attenuates the in vitro and in vivo tumor growth of CICs from FOLFOX resistant cells. The results of DNA:CD44v6 immunoprecipitated complexes by ChIP (chromatin-immunoprecipitation) assay showed that CD44v6 maintained the stemness traits by promoting several antiapoptotic and stemness genes, including cyclin-D1,BCL2,FZD1,GINS-1, and MMP9. Further, computer-based analysis of the clones obtained from the DNA:CD44v6 complex revealed the presence of various consensus binding sites for core stemness-associated transcription factors “CTOS” (c-Myc, TWIST1, OCT4, and SOX2). Simultaneous expressions of CD44v6 and CTOS in CD44v6 knockout CICs reverted differentiated CD44v6-knockout CICs into CICs. Finally, this study for the first time describes a positive feedback loop that couples YB-1 induction and CD44 alternative splicing to sustain the MDR1 and CD44v6 expressions, and CD44v6 is required for the reversion of differentiated tumor cells into CICs.
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23
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Matei IV, Meivar-Levy I, Lixandru D, Dima S, Florea IR, Ilie VM, Albulescu R, Popescu I, Ferber S. The effect of liver donors' age, gender and metabolic state on pancreatic lineage activation. Regen Med 2021; 16:19-31. [PMID: 33527839 DOI: 10.2217/rme-2020-0092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Autologous cells replacement therapy by liver to pancreas transdifferentiation (TD) allows diabetic patients to be also the donors of their own therapeutic tissue. Aim: To analyze whether the efficiency of the process is affected by liver donors' heterogeneity with regard to age, gender and the metabolic state. Materials & methods: TD of liver cells derived from nondiabetic and diabetic donors at different ages was characterized at molecular and cellular levels, in vitro. Results: Neither liver cells proliferation nor the propagated cells TD efficiency directly correlate with the age (3-60 years), gender or the metabolic state of the donors. Conclusion: Human liver cells derived from a wide array of ages and metabolic states can be used for autologous cells therapies for diabetics.
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Affiliation(s)
- Ioan V Matei
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
| | - Irit Meivar-Levy
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- The Sheba Regenerative Medicine, Stem Cell & Tissue Engineering Center, Sheba Medical Center, Tel-Hashomer, 5262100, Israel
- Orgenesis Ltd, Ness Ziona, 7414002, Israel
| | - Daniela Lixandru
- Fundeni Clinical Institute, Bucharest, 022328, Romania
- University of Medicine & Pharmacy 'Carol Davila', Bucharest, 050474, Romania
| | - Simona Dima
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- Fundeni Clinical Institute, Bucharest, 022328, Romania
| | - Ioana R Florea
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- Fundeni Clinical Institute, Bucharest, 022328, Romania
- University of Bucharest, Faculty of Biology, Bucharest, 050663, Romania
| | - Veronica M Ilie
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- Fundeni Clinical Institute, Bucharest, 022328, Romania
- University of Bucharest, Faculty of Biology, Bucharest, 050663, Romania
| | - Radu Albulescu
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- National Institute for Chemical Pharmaceutical R&D, Bucharest,031299, Romania
- Victor Babes National Institute of Pathology, Bucharest, 050096, Romania
| | - Irinel Popescu
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- Fundeni Clinical Institute, Bucharest, 022328, Romania
| | - Sarah Ferber
- Dia-Cure, Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University Bucharest, 040441, Romania
- The Sheba Regenerative Medicine, Stem Cell & Tissue Engineering Center, Sheba Medical Center, Tel-Hashomer, 5262100, Israel
- Orgenesis Ltd, Ness Ziona, 7414002, Israel
- ,Department of Human Genetics, Tel Aviv University, Sackler School of Medicine, Tel Aviv, 6997801, Israel
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24
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Abstract
Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors subsequently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activating or repressive regulatory sequence. Thus, pioneer factors endow the competence for fate changes in embryonic development, are essential for cellular reprogramming, and rewire gene networks in cancer cells. Recent studies with reconstituted nucleosomes in vitro and chromatin binding in vivo reveal that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in different ways. This review focuses on our current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to our ability to control cell fates at will.
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Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA;
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25
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Kumar A, Mali P. Mapping regulators of cell fate determination: Approaches and challenges. APL Bioeng 2020; 4:031501. [PMID: 32637855 PMCID: PMC7332300 DOI: 10.1063/5.0004611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Given the limited regenerative capacities of most organs, strategies are needed to efficiently generate large numbers of parenchymal cells capable of integration into the diseased organ. Although it was initially thought that terminally differentiated cells lacked the ability to transdifferentiate, it has since been shown that cellular reprogramming of stromal cells to parenchymal cells through direct lineage conversion holds great potential for the replacement of post-mitotic parenchymal cells lost to disease. To this end, an assortment of genetic, chemical, and mechanical cues have been identified to reprogram cells to different lineages both in vitro and in vivo. However, some key challenges persist that limit broader applications of reprogramming technologies. These include: (1) low reprogramming efficiencies; (2) incomplete functional maturation of derived cells; and (3) difficulty in determining the typically multi-factor combinatorial recipes required for successful transdifferentiation. To improve efficiency by comprehensively identifying factors that regulate cell fate, large scale genetic and chemical screening methods have thus been utilized. Here, we provide an overview of the underlying concept of cell reprogramming as well as the rationale, considerations, and limitations of high throughput screening methods. We next follow with a summary of unique hits that have been identified by high throughput screens to induce reprogramming to various parenchymal lineages. Finally, we discuss future directions of applying this technology toward human disease biology via disease modeling, drug screening, and regenerative medicine.
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Affiliation(s)
- Aditya Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
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26
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Egawa N, Suzuki H, Takahashi R, Hayakawa K, Li W, Lo EH, Arai K, Inoue H. From in vitro to in vivo reprogramming for neural transdifferentiation: An approach for CNS tissue remodeling using stem cell technology. J Cereb Blood Flow Metab 2020; 40:1739-1751. [PMID: 32423328 PMCID: PMC7446571 DOI: 10.1177/0271678x20910324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in stem cell technology have provided three approaches to address the demanding issue of the treatment of intractable neurological disease. One of the approaches is the screening of compounds attenuating pathological phenotypes in stem-cell based models. A second approach consists of exogenous-targeted cell supplementation to the lesion with stem cell-derived differentiated cells. A third approach involves in vivo direct programming to transdifferentiate endogenous somatic cells and to boost CNS tissue remodeling. In this review, we outline research advances in stem cell technology of direct reprogramming in vitro and in vivo and discuss the future challenge of tissue remodeling by neural transdifferentiation.
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Affiliation(s)
- Naohiro Egawa
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Hidefumi Suzuki
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazuhide Hayakawa
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenlu Li
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eng H Lo
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ken Arai
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Haruhisa Inoue
- iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
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27
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Horisawa K, Udono M, Ueno K, Ohkawa Y, Nagasaki M, Sekiya S, Suzuki A. The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors. Mol Cell 2020; 79:660-676.e8. [PMID: 32755593 DOI: 10.1016/j.molcel.2020.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Specific combinations of two transcription factors (Hnf4α plus Foxa1, Foxa2, or Foxa3) can induce direct conversion of mouse fibroblasts into hepatocyte-like cells. However, the molecular mechanisms underlying hepatic reprogramming are largely unknown. Here, we show that the Foxa protein family members and Hnf4α sequentially and cooperatively bind to chromatin to activate liver-specific gene expression. Although all Foxa proteins bind to and open regions of closed chromatin as pioneer factors, Foxa3 has the unique potential of transferring from the distal to proximal regions of the transcription start site of target genes, binding RNA polymerase II, and co-traversing target genes. These distinctive characteristics of Foxa3 are essential for inducing the hepatic fate in fibroblasts. Similar functional coupling of transcription factors to RNA polymerase II may occur in other contexts whereby transcriptional activation can induce cell differentiation.
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Affiliation(s)
- Kenichi Horisawa
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Miyako Udono
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Masao Nagasaki
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan; Human Biosciences Unit for the Top Global Course, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto 606-8507, Japan
| | - Sayaka Sekiya
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
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28
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Hand2 Selectively Reorganizes Chromatin Accessibility to Induce Pacemaker-like Transcriptional Reprogramming. Cell Rep 2020; 27:2354-2369.e7. [PMID: 31116981 PMCID: PMC6657359 DOI: 10.1016/j.celrep.2019.04.077] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/25/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
Gata4, Hand2, Mef2c, and Tbx5 (GHMT) can reprogram transduced fibroblasts into induced pacemaker-like myocytes (iPMs), but the underlying mechanisms remain obscure. Here, we explore the role of Hand2 in iPM formation by using a combination of transcriptome, genome, and biochemical as-says. We found many shared transcriptional signatures between iPMs and the endogenous sinoatrial node (SAN), yet key regulatory networks remain missing. We demonstrate that Hand2 augments chromatin accessibility at loci involved in sarcomere organization, electrical coupling, and membrane depolarization. Focusing on an established cardiac Hand2 cistrome, we observe selective reorganization of chromatin accessibility to promote pacemaker-specific gene expression. Moreover, we identify a Hand2 cardiac subtype diversity (CSD) domain through biochemical analysis of the N terminus. By integrating our RNA-seq and ATAC-seq datasets, we highlight desmosome organization as a hallmark feature of iPM formation. Collectively, our results illuminate Hand2-dependent mechanisms that may guide future efforts to rationally improve iPM formation. Gata4, Hand2, Mef2c, and Tbx5 can reprogram fibroblasts into cardiomyocyte-like cells, including induced pacemakers (iPMs). Fernandez-Perez et al. show that Hand2 coordinates this process by influencing chromatin accessibility and gene expression in fibroblasts undergoing iPM lineage conversion. These insights could eventually inform the production of superior replacement cells.
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29
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Ruzittu S, Willnow D, Spagnoli FM. Direct Lineage Reprogramming: Harnessing Cell Plasticity between Liver and Pancreas. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035626. [PMID: 31767653 DOI: 10.1101/cshperspect.a035626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Direct lineage reprogramming of abundant and accessible cells into therapeutically useful cell types holds tremendous potential in regenerative medicine. To date, a number of different cell types have been generated by lineage reprogramming methods, including cells from the neural, cardiac, hepatic, and pancreatic lineages. The success of this strategy relies on developmental biology and the knowledge of cell-fate-defining transcriptional networks. Hepatocytes represent a prime target for β cell conversion for numerous reasons, including close developmental origin, accessibility, and regenerative potential. We present here an overview of pancreatic and hepatic development, with a particular focus on the mechanisms underlying the divergence between the two cell lineages. Additionally, we discuss to what extent this lineage relationship can be exploited in efforts to reprogram one cell type into the other and whether such an approach may provide a suitable strategy for regenerative therapies of diabetes.
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Affiliation(s)
- Silvia Ruzittu
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom.,Max Delbrück Center for Molecular Medicine (MDC), D-13125 Berlin, Germany
| | - David Willnow
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Francesca M Spagnoli
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
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30
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HORISAWA K, SUZUKI A. Direct cell-fate conversion of somatic cells: Toward regenerative medicine and industries. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:131-158. [PMID: 32281550 PMCID: PMC7247973 DOI: 10.2183/pjab.96.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cells of multicellular organisms have diverse characteristics despite having the same genetic identity. The distinctive phenotype of each cell is determined by molecular mechanisms such as epigenetic changes that occur throughout the lifetime of an individual. Recently, technologies that enable modification of the fate of somatic cells have been developed, and the number of studies using these technologies has increased drastically in the last decade. Various cell types, including neuronal cells, cardiomyocytes, and hepatocytes, have been generated using these technologies. Although most direct reprogramming methods employ forced transduction of a defined sets of transcription factors to reprogram cells in a manner similar to induced pluripotent cell technology, many other strategies, such as methods utilizing chemical compounds and microRNAs to change the fate of somatic cells, have also been developed. In this review, we summarize transcription factor-based reprogramming and various other reprogramming methods. Additionally, we describe the various industrial applications of direct reprogramming technologies.
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Affiliation(s)
- Kenichi HORISAWA
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Atsushi SUZUKI
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
- Correspondence should be addressed: A. Suzuki, Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan (e-mail: )
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31
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Traxler L, Edenhofer F, Mertens J. Next-generation disease modeling with direct conversion: a new path to old neurons. FEBS Lett 2019; 593:3316-3337. [PMID: 31715002 PMCID: PMC6907729 DOI: 10.1002/1873-3468.13678] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/20/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
Within just over a decade, human reprogramming-based disease modeling has developed from a rather outlandish idea into an essential part of disease research. While iPSCs are a valuable tool for modeling developmental and monogenetic disorders, their rejuvenated identity poses limitations for modeling age-associated diseases. Direct cell-type conversion of fibroblasts into induced neurons (iNs) circumvents rejuvenation and preserves hallmarks of cellular aging. iNs are thus advantageous for modeling diseases that possess strong age-related and epigenetic contributions and can complement iPSC-based strategies for disease modeling. In this review, we provide an overview of the state of the art of direct iN conversion and describe the key epigenetic, transcriptomic, and metabolic changes that occur in converting fibroblasts. Furthermore, we summarize new insights into this fascinating process, particularly focusing on the rapidly changing criteria used to define and characterize in vitro-born human neurons. Finally, we discuss the unique features that distinguish iNs from other reprogramming-based neuronal cell models and how iNs are relevant to disease modeling.
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Affiliation(s)
- Larissa Traxler
- Department of GenomicsStem Cell Biology & Regenerative MedicineInstitute of Molecular Biology & CMBILeopold‐Franzens‐University InnsbruckInnsbruckAustria
- Laboratory of GeneticsThe Salk Institute for Biological StudiesLa JollaCAUSA
| | - Frank Edenhofer
- Department of GenomicsStem Cell Biology & Regenerative MedicineInstitute of Molecular Biology & CMBILeopold‐Franzens‐University InnsbruckInnsbruckAustria
| | - Jerome Mertens
- Department of GenomicsStem Cell Biology & Regenerative MedicineInstitute of Molecular Biology & CMBILeopold‐Franzens‐University InnsbruckInnsbruckAustria
- Laboratory of GeneticsThe Salk Institute for Biological StudiesLa JollaCAUSA
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32
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Vignoles R, Lentini C, d'Orange M, Heinrich C. Direct Lineage Reprogramming for Brain Repair: Breakthroughs and Challenges. Trends Mol Med 2019; 25:897-914. [PMID: 31371156 DOI: 10.1016/j.molmed.2019.06.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/17/2019] [Accepted: 06/20/2019] [Indexed: 01/10/2023]
Abstract
Injury to the human central nervous system (CNS) is devastating because our adult mammalian brain lacks intrinsic regenerative capacity to replace lost neurons and induce functional recovery. An emerging approach towards brain repair is to instruct fate conversion of brain-resident non-neuronal cells into induced neurons (iNs) by direct lineage reprogramming. Considerable progress has been made in converting various source cell types of mouse and human origin into clinically relevant iNs. Recent achievements using transcriptomics and epigenetics have shed light on the molecular mechanisms underpinning neuronal reprogramming, while the potential capability of iNs in promoting functional recovery in pathological contexts has started to be evaluated. Although future challenges need to be overcome before clinical translation, lineage reprogramming holds promise for effective cell-replacement therapy in regenerative medicine.
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Affiliation(s)
- Rory Vignoles
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500 Bron, France
| | - Célia Lentini
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500 Bron, France
| | - Marie d'Orange
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500 Bron, France
| | - Christophe Heinrich
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500 Bron, France.
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33
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Sato T, Higashioka K, Sakurai H, Yamamoto T, Goshima N, Ueno M, Sotozono C. Core Transcription Factors Promote Induction of PAX3-Positive Skeletal Muscle Stem Cells. Stem Cell Reports 2019; 13:352-365. [PMID: 31353225 PMCID: PMC6700474 DOI: 10.1016/j.stemcr.2019.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 06/14/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
The use of adult skeletal muscle stem cells (MuSCs) for cell therapy has been attempted for decades, but still encounters considerable difficulties. MuSCs derived from human induced pluripotent stem cells (hiPSCs) are promising candidates for stem cell therapy to treat Duchenne muscular dystrophy (DMD). Here we report that four transcription factors, HEYL, KLF4, MYOD, and PAX3, selected by comprehensive screening of different MuSC populations, enhance the derivation of PAX3-positive myogenic progenitors from fibroblasts and hiPSCs, using medium that promotes the formation of presomitic mesoderm. These induced PAX3-positive cells contribute efficiently to the repair of DMD-damaged myofibers and also reconstitute the MuSC population. These studies demonstrate how a combination of core transcription factors can fine-tune the derivation of MuSCs capable of contributing to the repair of adult skeletal muscle. Persistent single MyoD can induce myogenic cells, not muscle stem cells The combination of Heyl, Klf4, Pax3, and transient MyoD can induce muscle stem cells Induced PAX3+ cells revealed incorporation into regenerating myofibers of DMD mice
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Affiliation(s)
- Takahiko Sato
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Department of Anatomy, Fujita Health University, Toyoake, Aichi, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda, Tokyo, Japan.
| | - Koki Higashioka
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Hidetoshi Sakurai
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda, Tokyo, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Morio Ueno
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
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34
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Flint Brodsly N, Bitman-Lotan E, Boico O, Shafat A, Monastirioti M, Gessler M, Delidakis C, Rincon-Arano H, Orian A. The transcription factor Hey and nuclear lamins specify and maintain cell identity. eLife 2019; 8:44745. [PMID: 31310235 PMCID: PMC6634966 DOI: 10.7554/elife.44745] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
The inability of differentiated cells to maintain their identity is a hallmark of age-related diseases. We found that the transcription factor Hey supervises the identity of differentiated enterocytes (ECs) in the adult Drosophila midgut. Lineage tracing established that Hey-deficient ECs are unable to maintain their unique nuclear organization and identity. To supervise cell identity, Hey determines the expression of nuclear lamins, switching from a stem-cell lamin configuration to a differentiated lamin configuration. Moreover, continued Hey expression is required to conserve large-scale nuclear organization. During aging, Hey levels decline, and EC identity and gut homeostasis are impaired, including pathological reprograming and compromised gut integrity. These phenotypes are highly similar to those observed upon acute targeting of Hey or perturbation of lamin expression in ECs in young adults. Indeed, aging phenotypes were suppressed by continued expression of Hey in ECs, suggesting that a Hey-lamin network safeguards nuclear organization and differentiated cell identity.
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Affiliation(s)
- Naama Flint Brodsly
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Olga Boico
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adi Shafat
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria Monastirioti
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Manfred Gessler
- Biocenter of Developmental Biochemistry, University of Würzburg, Würzburg, Germany
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Hector Rincon-Arano
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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35
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Gao R, Liang X, Cheedipudi S, Cordero J, Jiang X, Zhang Q, Caputo L, Günther S, Kuenne C, Ren Y, Bhattacharya S, Yuan X, Barreto G, Chen Y, Braun T, Evans SM, Sun Y, Dobreva G. Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate. Cell Res 2019; 29:486-501. [PMID: 31024170 PMCID: PMC6796926 DOI: 10.1038/s41422-019-0168-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/01/2019] [Indexed: 01/25/2023] Open
Abstract
Generation of widely differing and specialized cell types from a single totipotent zygote involves large-scale transcriptional changes and chromatin reorganization. Pioneer transcription factors play key roles in programming the epigenome and facilitating recruitment of additional regulatory factors during successive cell lineage specification and differentiation steps. Here we show that Isl1 acts as a pioneer factor driving cardiomyocyte lineage commitment by shaping the chromatin landscape of cardiac progenitor cells. Using an Isl1 hypomorphic mouse line which shows congenital heart defects, genome-wide profiling of Isl1 binding together with RNA- and ATAC-sequencing of cardiac progenitor cells and their derivatives, we uncover a regulatory network downstream of Isl1 that orchestrates cardiogenesis. Mechanistically, we show that Isl1 binds to compacted chromatin and works in concert with the Brg1-Baf60c-based SWI/SNF complex to promote permissive cardiac lineage-specific alterations in the chromatin landscape not only of genes with critical functions in cardiac progenitor cells, but also of cardiomyocyte structural genes that are highly expressed when Isl1 itself is no longer present. Thus, the Isl1/Brg1-Baf60c complex plays a crucial role in orchestrating proper cardiogenesis and in establishing epigenetic memory of cardiomyocyte fate commitment.
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Affiliation(s)
- Rui Gao
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xingqun Liang
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | | | - Julio Cordero
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xue Jiang
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Qingquan Zhang
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Luca Caputo
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Yonggang Ren
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Xuejun Yuan
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Guillermo Barreto
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Yihan Chen
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sylvia M Evans
- Department of Medicine, Skaggs School of Pharmacy, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Yunfu Sun
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Gergana Dobreva
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Medical Faculty, University of Frankfurt, 60590, Frankfurt am Main, Germany.
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36
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Zhao Y. Chemically induced cell fate reprogramming and the acquisition of plasticity in somatic cells. Curr Opin Chem Biol 2019; 51:146-153. [PMID: 31153758 DOI: 10.1016/j.cbpa.2019.04.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/08/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
The nature of somatic cell fate has always been considered relatively unchangeable. Only in rare cases, in response to highly specific environmental cues, do differentiated mammalian somatic cells transform into other cell types. However, the fact that cell fate reprogramming can be accomplished by utilizing chemical cocktails, in the absence of any genetic alterations, suggests that the fate determination of somatic cells is much more malleable than previously believed. The use of chemical cocktails to directly alter cell fate sheds light on an important, yet less explored approach to regenerative medicine: the use of chemicals to restore functions to injured, aging or diseased tissues. Here, we review and discuss the recent developments, inspirations, and challenges encountered when modulating cell fate reprogramming with chemicals, and investigate how chemical biology impacts the future of cell fate reprogramming and regenerative medicine.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China.
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37
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Direct conversion of pig fibroblasts to chondrocyte-like cells by c-Myc. Cell Death Discov 2019; 5:55. [PMID: 30675392 PMCID: PMC6338791 DOI: 10.1038/s41420-018-0136-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 01/14/2023] Open
Abstract
Unexpectedly, we found that c-Myc-expressing porcine embryonic fibroblasts (PEFs) subcutaneously implanted into nude mice formed cartilage-like tissues in vivo, while previous studies revealed the direct conversion of mouse and human somatic cells into chondrocytes by the combined use of several defined factors, including c-Myc, which prompted us to explore whether PEFs can be reprogrammed to become pig induced chondrocyte-like cells (piCLCs) via ectopic expression of c-Myc alone. In this study, c-Myc-expressing PEFs, designated piCLCs, which exhibited a significantly enhanced proliferation ability in vitro, displayed a chondrogenic phenotypes in vitro, as shown by the cell morphology, toluidine blue staining, alcian blue staining and chondrocyte marker gene expression. Additionally, piCLCs with a polygonal chondrocyte-like morphology were readily and efficiently converted from PEFs by enforced c-Myc expression within 10 days, while piCLCs maintained the chondrocytic phenotype and normal karyotype during long-term subculture. piCLC-derived single clones with a chondrogenic phenotype in vitro exhibited homogeneity in cell morphology and staining intensity compared with mixed piCLCs. Although the mixtures of cartilaginous tissues and tumorous tissues accounted for ~12% (6/51) of all xenografts (51), piCLCs generated stable, homogenous, hyaline cartilage-like tissues without tumour formation at 45 out of the 51 injected sites when subcutaneously injected into nude mice. The hyaline cartilage-like tissues remained for at least 16 weeks. Taken together, these findings demonstrate for the first time the direct induction of chondrocyte-like cells from PEFs with only c-Myc.
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38
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Kostyuchenko RP, Kozin VV, Filippova NA, Sorokina EV. FoxA expression pattern in two polychaete species, Alitta virens and Platynereis dumerilii: Examination of the conserved key regulator of the gut development from cleavage through larval life, postlarval growth, and regeneration. Dev Dyn 2019; 248:728-743. [PMID: 30566266 DOI: 10.1002/dvdy.7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/23/2018] [Accepted: 11/29/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND foxA orthologs are involved in various processes from embryo patterning to regulation of metabolism. Since foxA conserved role in the development of the gut of errant annelids has never been thoroughly studied, we used a candidate gene approach to unravel the molecular profile of the alimentary canal in two closely related nereid worms with a trochophore-type lecithotrophic larva. RESULTS The character of foxA expression in the two polychaetes was similar but not identical. The genes were successively activated first in blastoporal cells, then in the stomodeum, the midgut, and hindgut primordia, and in the cells of central and peripheral nervous system. Before the start of active feeding of nectochaetes, we observed a short phase of foxA expression in the entire digestive tract. After amputation of posterior segments, foxA expression was established de novo in the new terminal part of the intestine, and then in the developing hindgut and the anus. CONCLUSIONS We discovered an early marker of endoderm formation previously unknown in errant annelids. Its expression dynamics provided valuable insights into the gut development. Comparative analysis of foxA activity suggests its primary role in gastrulation morphogenesis independently of its type and in midgut and foregut specification. Developmental Dynamics 248:728-743, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Roman P Kostyuchenko
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Vitaly V Kozin
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Nadezhda A Filippova
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Ekaterina V Sorokina
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
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Venkatesh I, Mehra V, Wang Z, Califf B, Blackmore MG. Developmental Chromatin Restriction of Pro-Growth Gene Networks Acts as an Epigenetic Barrier to Axon Regeneration in Cortical Neurons. Dev Neurobiol 2018; 78:960-977. [PMID: 29786967 PMCID: PMC6204296 DOI: 10.1002/dneu.22605] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/01/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022]
Abstract
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility. When applied to the developing cortex, this pipeline detected overall closure of chromatin in sub-networks of genes associated with axon growth. We next analyzed mature CNS neurons that were supplied with various pro-regenerative transcription factors. Unlike prior results with SOX11 and KLF7, here we found that neither JUN nor an activated form of STAT3 promoted substantial corticospinal tract regeneration. Correspondingly, chromatin accessibility in JUN or STAT3 target genes was substantially lower than in predicted targets of SOX11 and KLF7. Finally, we used the pipeline to predict pioneer factors that could potentially relieve chromatin constraints at growth-associated loci. Overall this integrated analysis substantiates the hypothesis that dynamic chromatin accessibility contributes to the developmental decline in axon growth ability and influences the efficacy of pro-regenerative interventions in the adult, while also pointing toward selected pioneer factors as high-priority candidates for future combinatorial experiments. © 2018 Wiley Periodicals, Inc. Develop Neurobiol 00: 000-000, 2018.
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Affiliation(s)
| | - Vatsal Mehra
- Department of Biomedical Sciences, Marquette University, 53201
| | - Zimei Wang
- Department of Biomedical Sciences, Marquette University, 53201
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Reid A, Tursun B. Transdifferentiation: do transition states lie on the path of development? CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 11:18-23. [PMID: 30386832 PMCID: PMC6202785 DOI: 10.1016/j.coisb.2018.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The direct conversion of one differentiated cell fate into another identity is a process known as Transdifferentiation. During Transdifferentiation, cells pass through intermediate states that are not well understood. Given the potential application of transdifferentiation in regenerative medicine and disease modeling, a better understanding of intermediate states is crucial to avoid uncontrolled conversion or proliferation, which pose a risk for patients. Researchers have begun to analyze the transcriptomes of donor, converting and target cells of Transdifferentiation with single cell resolution to compare transitional states to those found along the path of development. Here, we review examples of Transdifferentiation in a range of model systems and organisms. We propose that cells pass either through a mixed, unspecific intermediate or progenitor-like state during Transdifferentiation, which, to varying degrees, resemble states seen during development.
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Affiliation(s)
- Anna Reid
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
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41
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Uli N, Michelen-Gomez E, Ramos EI, Druley TE. Age-specific changes in genome-wide methylation enrich for Foxa2 and estrogen receptor alpha binding sites. PLoS One 2018; 13:e0203147. [PMID: 30256791 PMCID: PMC6157835 DOI: 10.1371/journal.pone.0203147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/15/2018] [Indexed: 12/26/2022] Open
Abstract
The role of DNA methylation patterns in complex phenotypes remains unclear. To explore this question, we adapted our methods for rare variant analysis to characterize genome-wide murine DNA hybridization array to investigate methylation at CpG islands, shores, and regulatory elements. We have applied this platform to compare age and tissue- specific methylation differences in the brain and spleen of young and aged mice. As expected from prior studies, there are clear global differences in organ-specific, but not age-specific, methylation due mostly to changes at repetitive elements. Surprisingly, out of 200,000 loci there were only 946 differentially methylated cytosines (DMCs) between young and old samples (529 hypermethylated, 417 hypomethylated in aged mice) compared to thousands of tissue-specific DMCs. Hypermethylated loci were clustered around the promoter region of Sfi1, exon 2 of Slc11a2, Drg1, Esr1 and Foxa2 transcription factor binding sites. In particular, there were 75 hypermethylated Foxa2 binding sites across a 2.7 Mb region of chromosome 11. Hypomethylated loci were clustered around Mid1, Isoc2b and genome-wide loci with binding sites for Foxa2 and Esr1, which are known to play important roles in development and aging. These data suggest discreet tissue-independent methylation changes associated with aging processes such as cell division (Sfi1, Mid1), energy production (Drg1, Isoc2b) and cell death (Foxa2, Esr1).
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Affiliation(s)
- Nishanth Uli
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Eduardo Michelen-Gomez
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Enrique I. Ramos
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Todd E. Druley
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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42
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Bragança J. SMAD2/3, versatile molecular tools for cellular engineering. Stem Cell Investig 2018; 5:24. [PMID: 30148157 DOI: 10.21037/sci.2018.07.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/17/2018] [Indexed: 01/01/2023]
Affiliation(s)
- José Bragança
- Department of Biomedical Sciences and Medicine, University of Algarve, 8005-139 Faro, Portugal.,Centre for Biomedical Research-CBMR, University of Algarve, Campus of Gambelas, 8005-139 Faro, Portugal.,ABC - Algarve Biomedical Centre, 8005-139 Faro, Portugal
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43
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High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor. PLoS Genet 2018; 14:e1007552. [PMID: 30063705 PMCID: PMC6086484 DOI: 10.1371/journal.pgen.1007552] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/10/2018] [Accepted: 07/10/2018] [Indexed: 12/24/2022] Open
Abstract
In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion. The ongoing ATOH1 gene therapy clinical trial offers promise for hearing restoration in humans. However, in animal models, Atoh1-mediated sensory regeneration is inefficient and incomplete. Here we performed high-resolution gene expression profiling of single cochlear cells at multiple time points in a mouse model whereby we discovered a continuous regeneration process that leads to the formation of immature sensory cells. We identified 51 key reprogramming transcription factors that may increase the efficiency and completion of the regeneration process and confirmed that Isl1 in transgenic mice promotes Atoh1-mediated sensory regeneration as a co-reprogramming factor. Our studies identify molecular mechanisms and novel co-reprogramming factors for sensory restoration in humans with irreversible hearing loss.
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44
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Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nat Neurosci 2018; 21:932-940. [PMID: 29915193 PMCID: PMC6319609 DOI: 10.1038/s41593-018-0168-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
Abstract
Ectopic expression of defined transcription factors can force direct cell fate conversion from one lineage to another in the absence of cell division. Several transcription factor cocktails have enabled successful reprogramming of various somatic cell types into induced neurons (iNs) of distinct neurotransmitter phenotype. However, the nature of the intermediate states that drive the reprogramming trajectory towards distinct iN types is largely unknown. Here we show that successful direct reprogramming of adult human brain pericytes into functional iNs by Ascl1 and Sox2 (AS) encompasses transient activation of a neural stem cell-like gene expression program that precedes bifurcation into distinct neuronal lineages. Intriguingly, during this transient state key signaling components relevant for neural induction and neural stem cell maintenance are regulated and functionally contribute to iN reprogramming and maturation. Thus, AS-mediated reprogramming into a broad spectrum of iN types involves the unfolding of a developmental program via neural stem cell-like intermediates.
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45
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Ninkovic J, Götz M. Understanding direct neuronal reprogramming-from pioneer factors to 3D chromatin. Curr Opin Genet Dev 2018; 52:65-69. [PMID: 29909355 DOI: 10.1016/j.gde.2018.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/19/2018] [Accepted: 05/29/2018] [Indexed: 01/10/2023]
Abstract
Cell replacement therapies aim at reestablishment of neuronal circuits after brain injury, stroke or neurodegeneration. Recently, direct reprogramming of resident glial cells into the affected neuronal subtypes has become a feasible and promising option for central nervous system regeneration. Direct reprogramming relies on the implementation of a new transcriptional program defining the desired neuronal identity in fully differentiated glial cells implying the more or less complete down-regulation of the program for the former identity of the glial cell. Despite the enormous progress achieved in this regard with highly efficient in vivo reprogramming after injury, a number of hurdles still need to be resolved. One way to further improve direct neuronal reprogramming is to understand the molecular hurdles which we discuss with the focus on chromatin states of the starting versus the reprogrammed cells.
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Affiliation(s)
- Jovica Ninkovic
- Institute of Stem Cell Research, Helmholtz Center Munich, Germany; Physiological Genomics, Biomedical Center, University of Munich, Germany; Department for Cell Biology and Anatomy, Biomedical Center, University of Munich, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, Germany; Physiological Genomics, Biomedical Center, University of Munich, Germany; Munich Cluster for Systems Neurology SYNERGY, LMU, Munich, Germany.
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46
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Guerrero-Ramirez GI, Valdez-Cordoba CM, Islas-Cisneros JF, Trevino V. Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). Mol Med Rep 2018; 18:1225-1237. [PMID: 29845286 PMCID: PMC6072137 DOI: 10.3892/mmr.2018.9092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/27/2018] [Indexed: 12/27/2022] Open
Abstract
There is a need for specific cell types in regenerative medicine and biological research. Frequently, specific cell types may not be easily obtained or the quantity obtained is insufficient for study. Therefore, reprogramming by the direct conversion (transdifferentiation) or re‑induction of induced pluripotent stem cells has been used to obtain cells expressing similar profiles to those of the desired types. Therefore, a specific cocktail of transcription factors (TFs) is required for induction. Nevertheless, identifying the correct combination of TFs is difficult. Although certain computational approaches have been proposed for this task, their methods are complex, and corresponding implementations are difficult to use and generalize for specific source or target cell types. In the present review four computational approaches that have been proposed to obtain likely TFs were compared and discussed. A simplified view of the computational complexity of these methods is provided that consists of three basic ideas: i) The definition of target and non‑target cell types; ii) the estimation of candidate TFs; and iii) filtering candidates. This simplified view was validated by analyzing a well‑documented cardiomyocyte differentiation. Subsequently, these reviewed methods were compared when applied to an unknown differentiation of corneal endothelial cells. The generated results may provide important insights for laboratory assays. Data and computer scripts that may assist with direct conversions in other cell types are also provided.
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Affiliation(s)
| | | | | | - Victor Trevino
- Tecnológico de Monterrey, Escuela de Medicina, Monterrey, Nuevo León 64710, México
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47
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Abstract
Tissue-specific transcription factors primarily act to define the phenotype of the cell. The power of a single transcription factor to alter cell fate is often minimal, as seen in gain-of-function analyses, but when multiple transcription factors cooperate synergistically it potentiates their ability to induce changes in cell fate. By contrast, transcription factor function is often dispensable in the maintenance of cell phenotype, as is evident in loss-of-function assays. Why does this phenomenon, commonly known as redundancy, occur? Here, I discuss the role that transcription factor networks play in collaboratively regulating stem cell fate and differentiation by providing multiple explanations for their functional redundancy.
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Affiliation(s)
- Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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48
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Casey BH, Kollipara RK, Pozo K, Johnson JE. Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors. Genome Res 2018; 28:484-496. [PMID: 29500235 PMCID: PMC5880239 DOI: 10.1101/gr.224360.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 02/28/2018] [Indexed: 12/27/2022]
Abstract
During development, transcription factors select distinct gene programs, providing the necessary regulatory complexity for temporal and tissue-specific gene expression. How related factors retain specificity, especially when they recognize the same DNA motifs, is not understood. We address this paradox using basic helix-loop-helix (bHLH) transcription factors ASCL1, ASCL2, and MYOD1, crucial mediators of lineage specification. In vivo, these factors recognize the same DNA motifs, yet bind largely different genomic sites and regulate distinct transcriptional programs. This suggests that their ability to identify regulatory targets is defined either by the cellular environment of the partially defined lineages in which they are endogenously expressed, or by intrinsic properties of the factors themselves. To distinguish between these mechanisms, we directly compared the chromatin binding properties of this subset of bHLH factors when ectopically expressed in embryonic stem cells, presenting them with a common chromatin landscape and cellular components. We find that these factors retain distinct binding sites; thus, specificity of binding is an intrinsic property not requiring a restricted landscape or lineage-specific cofactors. Although the ASCL factors and MYOD1 have some distinct DNA motif preference, it is not sufficient to explain the extent of the differential binding. All three factors can bind inaccessible chromatin and induce changes in chromatin accessibility and H3K27ac. A reiterated pattern of DNA binding motifs is uniquely enriched in inaccessible chromatin at sites bound by these bHLH factors. These combined properties define a subclass of lineage-specific bHLH factors and provide context for their central roles in development and disease.
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Affiliation(s)
- Bradford H Casey
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Karine Pozo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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49
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The Biology of SUMO-Targeted Ubiquitin Ligases in Drosophila Development, Immunity, and Cancer. J Dev Biol 2018; 6:jdb6010002. [PMID: 29615551 PMCID: PMC5875560 DOI: 10.3390/jdb6010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin and SUMO (small ubiquitin-like modifier) pathways modify proteins that in turn regulate diverse cellular processes, embryonic development, and adult tissue physiology. These pathways were originally discovered biochemically in vitro, leading to a long-standing challenge of elucidating both the molecular cross-talk between these pathways and their biological importance. Recent discoveries in Drosophila established that ubiquitin and SUMO pathways are interconnected via evolutionally conserved SUMO-targeted ubiquitin ligase (STUbL) proteins. STUbL are RING ubiquitin ligases that recognize SUMOylated substrates and catalyze their ubiquitination, and include Degringolade (Dgrn) in Drosophila and RNF4 and RNF111 in humans. STUbL are essential for early development of both the fly and mouse embryos. In the fly embryo, Dgrn regulates early cell cycle progression, sex determination, zygotic gene transcription, segmentation, and neurogenesis, among other processes. In the fly adult, Dgrn is required for systemic immune response to pathogens and intestinal stem cell regeneration upon infection. These functions of Dgrn are highly conserved in humans, where RNF4-dependent ubiquitination potentiates key oncoproteins, thereby accelerating tumorigenesis. Here, we review the lessons learned to date in Drosophila and highlight their relevance to cancer biology.
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50
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Asada R, Umeda M, Adachi A, Senmatsu S, Abe T, Iwasaki H, Ohta K, Hoffman CS, Hirota K. Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors. Nucleic Acids Res 2017; 45:9361-9371. [PMID: 28934464 PMCID: PMC5766161 DOI: 10.1093/nar/gkx555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/14/2017] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) determine the transcription activity of target genes and play a central role in controlling the transcription in response to various environmental stresses. Three dimensional genome structures such as local loops play a fundamental role in the regulation of transcription, although the link between such structures and the regulation of TF binding to cis-regulatory elements remains to be elucidated. Here, we show that during transcriptional activation of the fission yeast fbp1 gene, binding of Rst2 (a critical C2H2 zinc-finger TF) is mediated by a local loop structure. During fbp1 activation, Rst2 is first recruited to upstream-activating sequence 1 (UAS1), then it subsequently binds to UAS2 (a critical cis-regulatory site located approximately 600 base pairs downstream of UAS1) through a loop structure that brings UAS1 and UAS2 into spatially close proximity. Tup11/12 (the Tup-family corepressors) suppress direct binding of Rst2 to UAS2, but this suppression is counteracted by the recruitment of Rst2 at UAS1 and following delivery to UAS2 through a loop structure. These data demonstrate a previously unappreciated mechanism for the recruitment and expansion of TF-DNA interactions within a promoter mediated by local three-dimensional genome structures and for timely TF-binding via counteractive regulation by the Tup-family corepressors.
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Affiliation(s)
- Ryuta Asada
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Miki Umeda
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Akira Adachi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Satoshi Senmatsu
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Iwasaki
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology M6-11, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan.,Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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