1
|
Rummukainen P, Tarkkonen K, Al Majidi R, Puolakkainen T, Nieminen-Pihala V, Valensisi C, Saastamoinen L, Hawkins D, Heino TJ, Ivaska KK, Kiviranta R. The complex role of Rcor2: Regulates mesenchymal stromal cell differentiation in vitro but is dispensable in vivo. Bone 2024; 187:117180. [PMID: 38944098 DOI: 10.1016/j.bone.2024.117180] [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: 04/25/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Recent research has revealed several important pathways of epigenetic regulation leading to transcriptional changes in bone cells. Rest Corepressor 2 (Rcor2) is a coregulator of Lysine-specific histone demethylase 1 (Lsd1), a demethylase linked to osteoblast activity, hematopoietic stem cell differentiation and malignancy of different neoplasms. However, the role of Rcor2 in osteoblast differentiation has not yet been examined in detail. We have previously shown that Rcor2 is highly expressed in mesenchymal stromal cells (MSC) and particularly in the osteoblastic lineage. The role of Rcor2 in osteoblastic differentiation in vitro was further characterized and we demonstrate here that lentiviral silencing of Rcor2 in MC3T3-E1 cells led to a decrease in osteoblast differentiation. This was indicated by decreased alkaline phosphatase and von Kossa stainings as well as by decreased expression of several osteoblast-related marker genes. RNA-sequencing of the Rcor2-downregulated MC3T3-E1 cells showed decreased repression of Rcor2 target genes, as well as significant upregulation of majority of the differentially expressed genes. While the heterozygous, global loss of Rcor2 in vivo did not lead to a detectable bone phenotype, conditional deletion of Rcor2 in limb-bud mesenchymal cells led to a moderate decrease in cortical bone volume. These findings were not accentuated by challenging bone formation by ovariectomy or tibial fracture. Furthermore, a global deletion of Rcor2 led to decreased white adipose tissue in vivo and decreased the capacity of primary cells to differentiate into adipocytes in vitro. The conditional deletion of Rcor2 led to decreased adiposity in fracture callus. Taken together, these results suggest that epigenetic regulation of mesenchymal stromal cell differentiation is mediated by Rcor2, which could thus play an important role in defining the MSC fate.
Collapse
Affiliation(s)
- Petri Rummukainen
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland.
| | - Kati Tarkkonen
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - Rana Al Majidi
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - Tero Puolakkainen
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - Vappu Nieminen-Pihala
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - Cristina Valensisi
- Division of Medical Genetics, Department of Medicine, University of Washington, United States of America, Division of Medical Genetics Health Sciences Building, Rm K253 Box 357720, Seattle, WA 98195-7720
| | - Lauri Saastamoinen
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - David Hawkins
- Division of Medical Genetics, Department of Medicine, University of Washington, United States of America, Division of Medical Genetics Health Sciences Building, Rm K253 Box 357720, Seattle, WA 98195-7720
| | - Terhi J Heino
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - Kaisa K Ivaska
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland
| | - Riku Kiviranta
- Institute of Biomedicine, University of Turku, Turku, Faculty of Medicine, FI-20014, Finland; Department of Endocrinology, Turku University Hospital, PO Box 52 20521, Turku, Finland
| |
Collapse
|
2
|
Maksour S, Ng N, Hulme AJ, Miellet S, Engel M, Muñoz SS, Balez R, Rollo B, Finol-Urdaneta RK, Ooi L, Dottori M. REST and RCOR genes display distinct expression profiles in neurons and astrocytes using 2D and 3D human pluripotent stem cell models. Heliyon 2024; 10:e32680. [PMID: 38975076 PMCID: PMC11226837 DOI: 10.1016/j.heliyon.2024.e32680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
Repressor element-1 silencing transcription factor (REST) is a transcriptional repressor involved in neurodevelopment and neuroprotection. REST forms a complex with the REST corepressors, CoREST1, CoREST2, or CoREST3 (encoded by RCOR1, RCOR2, and RCOR3, respectively). Emerging evidence suggests that the CoREST family can target unique genes independently of REST, in various neural and glial cell types during different developmental stages. However, there is limited knowledge regarding the expression and function of the CoREST family in human neurodevelopment. To address this gap, we employed 2D and 3D human pluripotent stem cell (hPSC) models to investigate REST and RCOR gene expression levels. Our study revealed a significant increase in RCOR3 expression in glutamatergic cortical and GABAergic ventral forebrain neurons, as well as mature functional NGN2-induced neurons. Additionally, a simplified astrocyte transdifferentiation protocol resulted in a significant decrease in RCOR2 expression following differentiation. REST expression was notably reduced in mature neurons and cerebral organoids. In summary, our findings provide the first insights into the cell-type-specific expression patterns of RCOR genes in human neuronal and glial differentiation. Specifically, RCOR3 expression increases in neurons, while RCOR2 levels decrease in astrocytes. The dynamic expression patterns of REST and RCOR genes during hPSC neuronal and glial differentiation underscore the potential distinct roles played by REST and CoREST proteins in regulating the development of these cell types in humans.
Collapse
Affiliation(s)
- Simon Maksour
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Neville Ng
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Amy J. Hulme
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Sara Miellet
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Martin Engel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Sonia Sanz Muñoz
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Rachelle Balez
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Ben Rollo
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Rocio K. Finol-Urdaneta
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Mirella Dottori
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| |
Collapse
|
3
|
Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
Collapse
Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| |
Collapse
|
4
|
Shmal D, Mantero G, Floss T, Benfenati F, Maya-Vetencourt JF. Restoring vision in adult amblyopia by enhancing plasticity through deletion of the transcriptional repressor REST. iScience 2024; 27:109507. [PMID: 38591011 PMCID: PMC11000024 DOI: 10.1016/j.isci.2024.109507] [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: 09/27/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Visual cortical plasticity is high during early life, but gradually decreases with development. This is due to the Otx2-driven maturation of intracortical inhibition that parallels the condensation of extracellular matrix components into perineuronal nets mainly around parvalbumin-positive GABAergic neurons. Repressor Element 1 Silencing Transcription (REST) epigenetically controls the expression of a plethora of neuron-specific genes. We demonstrate that the conditional knockout of REST in the primary visual cortex of adult mice induces a shift of ocular dominance after short-term monocular deprivation and promotes the recovery of vision in long-term deprived animals after reverse suture. These phenomena paralleled a reduction of perineuronal net density and increased expression of REST target genes, but not of the homeoprotein Otx2 in the visual cortex contralateral to the deprived eye. This shows that REST regulates adult visual cortical plasticity and is a potential therapeutic target to restore vision in adult amblyopia by enhancing V1 plasticity.
Collapse
Affiliation(s)
- Dmytro Shmal
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Giulia Mantero
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Thomas Floss
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - José Fernando Maya-Vetencourt
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Biology, University of Pisa, Pisa, Italy
| |
Collapse
|
5
|
Han S, Fan H, Zhong G, Ni L, Shi W, Fang Y, Wang C, Wang L, Song L, Zhao J, Tang M, Yang B, Li L, Bai X, Zhang Q, Liang T, Xu Y, Feng XH, Ding C, Fang D, Zhao B. Nuclear KRT19 is a transcriptional corepressor promoting histone deacetylation and liver tumorigenesis. Hepatology 2024:01515467-990000000-00832. [PMID: 38557414 DOI: 10.1097/hep.0000000000000875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/10/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND AND AIMS Epigenetic reprogramming and escape from terminal differentiation are poorly understood enabling characteristics of liver cancer. Keratin 19 (KRT19), classically known to form the intermediate filament cytoskeleton, is a marker of stemness and worse prognosis in liver cancer. This study aimed to address the functional roles of KRT19 in liver tumorigenesis and to elucidate the underlying mechanisms. APPROACH AND RESULTS Using multiplexed genome editing of hepatocytes in vivo, we demonstrated that KRT19 promoted liver tumorigenesis in mice. Cell fractionation revealed a previously unrecognized nuclear fraction of KRT19. Tandem affinity purification identified histone deacetylase 1 and REST corepressor 1, components of the corepressor of RE-1 silencing transcription factor (CoREST) complex as KRT19-interacting proteins. KRT19 knockout markedly enhanced histone acetylation levels. Mechanistically, KRT19 promotes CoREST complex formation by enhancing histone deacetylase 1 and REST corepressor 1 interaction, thus increasing the deacetylase activity. ChIP-seq revealed hepatocyte-specific genes, such as hepatocyte nuclear factor 4 alpha ( HNF4A ), as direct targets of KRT19-CoREST. In addition, we identified forkhead box P4 as a direct activator of aberrant KRT19 expression in liver cancer. Furthermore, treatment of primary liver tumors and patient-derived xenografts in mice suggest that KRT19 expression has the potential to predict response to histone deacetylase 1 inhibitors especially in combination with lenvatinib. CONCLUSIONS Our data show that nuclear KRT19 acts as a transcriptional corepressor through promoting the deacetylase activity of the CoREST complex, resulting in dedifferentiation of liver cancer. These findings reveal a previously unrecognized function of KRT19 in directly shaping the epigenetic landscape in cancer.
Collapse
Affiliation(s)
- Shixun Han
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Haonan Fan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Guoxuan Zhong
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lei Ni
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenhao Shi
- Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yushan Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chenliang Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Li Wang
- Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Lang Song
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jianhui Zhao
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mei Tang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bing Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Li Li
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanhui Xu
- Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xin-Hua Feng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Chen Ding
- Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Dong Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bin Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| |
Collapse
|
6
|
Nagai M, Porter RS, Hughes E, Saunders TL, Iwase S. Asynchronous microexon splicing of LSD1 and PHF21A during neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586181. [PMID: 38562691 PMCID: PMC10983945 DOI: 10.1101/2024.03.21.586181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
LSD1 histone H3K4 demethylase and its binding partner PHF21A, a reader protein for unmethylated H3K4, both undergo neuron-specific microexon splicing. The LSD1 neuronal microexon weakens H3K4 demethylation activity and can alter the substrate specificity to H3K9 or H4K20. Meanwhile, the PHF21A neuronal microexon interferes with nucleosome binding. However, the temporal expression patterns of LSD1 and PHF21A splicing isoforms during brain development remain unknown. In this work, we report that neuronal PHF21A isoform expression precedes neuronal LSD1 isoform expression during human neuron differentiation and mouse brain development. The asynchronous splicing events resulted in stepwise deactivation of the LSD1-PHF21A complex in reversing H3K4 methylation. We further show that the enzymatically inactive LSD1-PHF21A complex interacts with neuron-specific binding partners, including MYT1-family transcription factors and post-transcriptional mRNA processing proteins such as VIRMA. The interaction with the neuron-specific components, however, did not require the PHF21A microexon, indicating that the neuronal proteomic milieu, rather than the microexon-encoded PHF21A segment, is responsible for neuron-specific complex formation. These results indicate that the PHF21A microexon is dispensable for neuron-specific protein-protein interactions, yet the enzymatically inactive LSD1-PHF21A complex might have unique gene-regulatory roles in neurons.
Collapse
Affiliation(s)
- Masayoshi Nagai
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Robert S. Porter
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Elizabeth Hughes
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
7
|
Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons. Nat Commun 2024; 15:1781. [PMID: 38453932 PMCID: PMC10920760 DOI: 10.1038/s41467-024-45773-3] [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: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
Collapse
Affiliation(s)
- Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| | - Sergio Niñerola
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Ana M Martín-González
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Minji Kim
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Bioinformatics Unit, Hospital universitario Puerta de Hierro Majadahonda, 28220, Majadahonda, Spain
| | - Carina Racovac
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Jose V Sanchez-Mut
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Yijun Ruan
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| |
Collapse
|
8
|
Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024; 20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Precision in the establishment and maintenance of cellular identities is crucial for the development of multicellular organisms and requires tight regulation of gene expression. While extensive research has focused on understanding cell type-specific gene activation, the complex mechanisms underlying the transcriptional repression of alternative fates are not fully understood. Here, we provide an overview of the repressive mechanisms involved in cell fate regulation. We discuss the molecular machinery responsible for suppressing alternative fates and highlight the crucial role of sequence-specific transcription factors (TFs) in this process. Depletion of these TFs can result in unwanted gene expression and increased cellular plasticity. We suggest that these TFs recruit cell type-specific repressive complexes to their cis-regulatory elements, enabling them to modulate chromatin accessibility in a context-dependent manner. This modulation effectively suppresses master regulators of alternative fate programs and their downstream targets. The modularity and dynamic behavior of these repressive complexes enables a limited number of repressors to canalize and maintain major and minor cell fate decisions at different stages of development.
Collapse
Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany.
| |
Collapse
|
9
|
Wu M, Hanly A, Gibson F, Fisher R, Rogers S, Park K, Zuger A, Kuang K, Kalin JH, Nocco S, Cole M, Xiao A, Agus F, Labadorf A, Beck S, Collard M, Cole PA, Alani RM. The CoREST repressor complex mediates phenotype switching and therapy resistance in melanoma. J Clin Invest 2024; 134:e171063. [PMID: 38300709 PMCID: PMC10940100 DOI: 10.1172/jci171063] [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: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Virtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through nonmutational events. Although the epigenetic landscape is shown to be altered in therapy-resistant melanomas and other cancers, a specific targetable epigenetic mechanism has not been validated. Here, we evaluated the corepressor for element 1-silencing transcription factor (CoREST) epigenetic repressor complex and the recently developed bivalent inhibitor corin within the context of melanoma phenotype plasticity and therapeutic resistance. We found that CoREST was a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells led to phenotype reprogramming. Global assessment of transcript and chromatin changes conferred by corin revealed specific effects on histone marks connected to epithelial-mesenchymal transition-associated (EMT-associated) transcription factors and the dual-specificity phosphatases (DUSPs). Remarkably, treatment of BRAF inhibitor-resistant (BRAFi-R) melanomas with corin promoted resensitization to BRAFi therapy. DUSP1 was consistently downregulated in BRAFi-R melanomas, which was reversed by corin treatment and associated with inhibition of p38 MAPK activity and resensitization to BRAFi therapies. Moreover, this activity was recapitulated by the p38 MAPK inhibitor BIRB 796. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial for patients with BRAFi-resistant melanoma.
Collapse
Affiliation(s)
- Muzhou Wu
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Ailish Hanly
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Frederick Gibson
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Robert Fisher
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Samantha Rogers
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kihyun Park
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Angelina Zuger
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kevin Kuang
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jay H. Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Sarah Nocco
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Matthew Cole
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Amy Xiao
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Filisia Agus
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Samuel Beck
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Marianne Collard
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Philip A. Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Rhoda M. Alani
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Queiroz LY, Kageyama R, Cimarosti HI. SUMOylation effects on neural stem cells self-renewal, differentiation, and survival. Neurosci Res 2024; 199:1-11. [PMID: 37742800 DOI: 10.1016/j.neures.2023.09.006] [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: 06/23/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
SUMO (small ubiquitin-like modifier) conjugation or SUMOylation, a post-translational modification, is a crucial regulator of protein function and cellular processes. In the context of neural stem cells (NSCs), SUMOylation has emerged as a key player, affecting their proliferation, differentiation, and survival. By modifying transcription factors, such as SOX1, SOX2, SOX3, SOX6, Bmi1, and Nanog, SUMOylation can either enhance or impair their transcriptional activity, thus impacting on NSCs self-renewal. Moreover, SUMOylation regulates neurogenesis and neuronal differentiation by modulating key proteins, such as Foxp1, Mecp2, MEF2A, and SOX10. SUMOylation is also crucial for the survival and proliferation of NSCs in both developing and adult brains. By regulating the activity of transcription factors, coactivators, and corepressors, SUMOylation acts as a molecular switch, inducing cofactor recruitment and function during development. Importantly, dysregulation of NSCs SUMOylation has been implicated in various disorders, including embryonic defects, ischemic cerebrovascular disease, glioma, and the harmful effects of benzophenone-3 exposure. Here we review the main findings on SUMOylation-mediated regulation of NSCs self-renewal, differentiation and survival. Better understanding NSCs SUMOylation mechanisms and its functional consequences might provide new strategies to promote neuronal differentiation that could contribute for the development of novel therapies targeting neurodegenerative diseases.
Collapse
Affiliation(s)
- Letícia Yoshitome Queiroz
- Postgraduate Program in Pharmacology, Federal University of Santa Catarina (UFSC), Florianopolis, Brazil
| | - Ryoichiro Kageyama
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; RIKEN Center for Brain Science, Wako, Japan
| | - Helena I Cimarosti
- Postgraduate Program in Pharmacology, Federal University of Santa Catarina (UFSC), Florianopolis, Brazil; Postgraduate Program in Neuroscience, UFSC, Florianopolis, Brazil.
| |
Collapse
|
11
|
Nassar A, Kodi T, Satarker S, Gurram PC, Fayaz SM, Nampoothiri M. Astrocytic transcription factors REST, YY1, and putative microRNAs in Parkinson's disease and advanced therapeutic strategies. Gene 2024; 892:147898. [PMID: 37832803 DOI: 10.1016/j.gene.2023.147898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Transcription factors (TF) and microRNAs are regulatory factors in astrocytes and are linked to several Parkinson's disease (PD) progression causes, such as disruption of glutamine transporters in astrocytes and concomitant disrupted glutamine uptake and inflammation. REST, a crucial TF, has been documented as an epigenetic repressor that limits the expression of neuronal genes in non-neural cells. REST activity is significantly linked to its corepressors in astrocytes, specifically histone deacetylases (HDACs), CoREST, and MECP2. Another REST-regulating TF, YY1, has been studied in astrocytes, and its interaction with REST has been investigated. In this review, the molecular processes that support the astrocytic control of REST and YY1 in terms of the regulation of glutamate transporter EAAT2 were addressed in a more detailed and comprehensive manner. Both TFs' function in astrocytes and how astrocyte abnormalities cause PD is still a mystery. Moreover, microRNAs (short non-coding RNAs) are key regulators that have been correlated to the expression and regulation of numerous genes linked to PD. The identification of numerous miRs that are engaged in astrocyte dysfunction that triggers PD has been shown. The term "Gut-brain axis" refers to the two systems' mutual communication. Gut microbial dysbiosis, which mediates an imbalance of the gut-brain axis, might contribute to neurodegenerative illnesses through altered astrocytic regulation. New treatment approaches to modify the gut-brain axis and prevent astrocytic repercussions have also been investigated in this review.
Collapse
Affiliation(s)
- Ajmal Nassar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Triveni Kodi
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Prasada Chowdari Gurram
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - S M Fayaz
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| |
Collapse
|
12
|
DelRosso N, Bintu L. Using High-Throughput Measurements to Identify Principles of Transcriptional and Epigenetic Regulators. Methods Mol Biol 2024; 2842:79-101. [PMID: 39012591 DOI: 10.1007/978-1-0716-4051-7_4] [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] [Indexed: 07/17/2024]
Abstract
To achieve exquisite control over the epigenome, we need a better predictive understanding of how transcription factors, chromatin regulators, and their individual domain's function, both as modular parts and as full proteins. Transcriptional effector domains are one class of protein domains that regulate transcription and chromatin. These effector domains either repress or activate gene expression by interacting with chromatin-modifying enzymes, transcriptional cofactors, and/or general transcriptional machinery. Here, we discuss important design considerations for high-throughput investigations of effector domains, recent advances in discovering new domains in human cells and testing how domain function depends on amino acid sequence. For every effector domain, we would like to know the following: What role does the cell type, signaling state, and targeted context have on activation, silencing, and epigenetic memory? Large-scale measurements of transcriptional activities can help systematically answer these questions and identify general rules for how all these parameters affect effector domain activities. Last, we discuss what steps need to be taken to turn a newly discovered effector domain into a robust, precise epigenome editor. With more carefully considered high-throughput investigations, soon we will have better predictive control over the epigenome.
Collapse
|
13
|
Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer İ, Köseler A, Pellegrini M. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics 2023; 55:618-633. [PMID: 37781740 DOI: 10.1152/physiolgenomics.00063.2023] [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: 06/22/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023] Open
Abstract
Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unraveling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a noninvasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red blood cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs, and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.NEW & NOTEWORTHY We have developed a quantitative model to assess how the human methylome is associated with several factors and to identify the genomic loci significantly impacted by each trait. We reported novel health-related factors driving DNA methylation patterns and new site-specific regulations that further elucidate methylome dynamics. Our study contributes to a better understanding of the plasticity of the human methylome and unveils novel physiological traits with a potential role in future medical epigenomic investigations.
Collapse
Affiliation(s)
- Giulia Protti
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
| | - Tarik Gören
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Ramazan Sabirli
- Emergency Department, Bakircay University Faculty of Medicine Cigli Training and Research Hospital, Izmir, Turkey
| | - Serkan Civlan
- Department of Neurosurgery, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Özgür Kurt
- Department of Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - İbrahim Türkçüer
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Aylin Köseler
- Department of Biophysics, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
| |
Collapse
|
14
|
Zhou X, Wei J, Cheng H, Tian L, Zhu X, Zhang Y, Xu L, Wei G, Huo FQ, Liang L. CoREST1 in primary sensory neurons regulates neuropathic pain in male mice. Life Sci 2023; 332:122088. [PMID: 37730112 DOI: 10.1016/j.lfs.2023.122088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
AIMS Epigenetic regulation is implicated in the neurogenesis of neuropathic pain. The repressor element 1 (RE1) silencing transcription factor (REST) corepressor (CoREST) proteins function as corepressors in the REST complex and/or LSD1 epigenetic complex. In the current study, we aimed to find the expression profile of CoREST1 in the dorsal root ganglion (DRG) and investigate whether it plays a role in neuropathic pain. MAIN METHODS The evoked pain behaviors in mice were examined by the von Frey test and thermal test in a spinal nerve ligation (SNL)-induced neuropathic pain mice model. CoREST1 siRNA or virus was administered by DRG microinjection or intrathecal injection. The CoREST1 expression in DRGs was examined by immunofluorescence, quantitative PCR, Western blotting, and co-immunoprecipitation. KEY FINDINGS CoREST1 was non-selectively expressed in large, medium, and small DRG neurons, and it exclusively colocalized with LSD1. In neuropathic pain models, peripheral nerve injury induced the upregulation of CoREST1 and increased binding of CoREST1 with LSD1 in injured DRGs in male mice. Furthermore, CoREST1 siRNA prevented the development of SNL-induced pain hypersensitivity as well as led to the reduction of established pain hypersensitivity during the maintenance period in SNL mice. Conversely, the overexpression of CoREST1 in DRGs by in vivo transfection of virus-induced pain hypersensitivity in naive mice. SIGNIFICANCE Our study demonstrated that CoREST1, along with LSD1, was expressed in primary sensory neurons specifically in response to nerve injury, and promoted nociceptive pain hypersensitivity in mice. Thus, CoREST1 might serve as a potential target for treating neuropathic pain.
Collapse
Affiliation(s)
- Xiaoqiong Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Jianxiong Wei
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Hong Cheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Lixia Tian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Xuan Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Department of Anesthesiology, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Yidan Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China
| | - Linping Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Beijing, PR China
| | - Guihua Wei
- Institute of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, PR China
| | - Fu-Quan Huo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Beijing, PR China
| | - Lingli Liang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Beijing, PR China.
| |
Collapse
|
15
|
Porter RS, Nagai M, An S, Gavilan MC, Murata-Nakamura Y, Bonefas KM, Zhou B, Dionne O, Manuel JM, St-Germain J, Browning L, Laurent B, Cho US, Iwase S. A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563357. [PMID: 37904995 PMCID: PMC10614952 DOI: 10.1101/2023.10.20.563357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A -n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
Collapse
|
16
|
Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
Collapse
Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| |
Collapse
|
17
|
Nassar A, Satarker S, Gurram PC, Upadhya D, Fayaz SM, Nampoothiri M. Repressor Element-1 Binding Transcription Factor (REST) as a Possible Epigenetic Regulator of Neurodegeneration and MicroRNA-Based Therapeutic Strategies. Mol Neurobiol 2023; 60:5557-5577. [PMID: 37326903 PMCID: PMC10471693 DOI: 10.1007/s12035-023-03437-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
Neurodegenerative disorders (NDD) have grabbed significant scientific consideration due to their fast increase in prevalence worldwide. The specific pathophysiology of the disease and the amazing changes in the brain that take place as it advances are still the top issues of contemporary research. Transcription factors play a decisive role in integrating various signal transduction pathways to ensure homeostasis. Disruptions in the regulation of transcription can result in various pathologies, including NDD. Numerous microRNAs and epigenetic transcription factors have emerged as candidates for determining the precise etiology of NDD. Consequently, understanding by what means transcription factors are regulated and how the deregulation of transcription factors contributes to neurological dysfunction is important to the therapeutic targeting of pathways that they modulate. RE1-silencing transcription factor (REST) also named neuron-restrictive silencer factor (NRSF) has been studied in the pathophysiology of NDD. REST was realized to be a part of a neuroprotective element with the ability to be tuned and influenced by numerous microRNAs, such as microRNAs 124, 132, and 9 implicated in NDD. This article looks at the role of REST and the influence of various microRNAs in controlling REST function in the progression of Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD) disease. Furthermore, to therapeutically exploit the possibility of targeting various microRNAs, we bring forth an overview of drug-delivery systems to modulate the microRNAs regulating REST in NDD.
Collapse
Affiliation(s)
- Ajmal Nassar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Prasada Chowdari Gurram
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dinesh Upadhya
- Centre for Molecular Neurosciences, Kasturba Medical College Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - S M Fayaz
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
| |
Collapse
|
18
|
Lam XJ, Maniam S, Cheah PS, Ling KH. REST in the Road Map of Brain Development. Cell Mol Neurobiol 2023; 43:3417-3433. [PMID: 37517069 DOI: 10.1007/s10571-023-01394-w] [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: 04/05/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023]
Abstract
Repressor element-1 silencing transcription factor (REST) or also known as neuron-restrictive silencing factor (NRSF), is the key initiator of epigenetic neuronal gene-expression modification. Identification of a massive number of REST-targeted genes in the brain signifies its broad involvement in maintaining the functionality of the nervous system. Additionally, REST plays a crucial role in conferring neuroprotection to the neurons against various stressors or insults during injuries. At the cellular level, nuclear localisation of REST is a key determinant for the functional transcriptional regulation of REST towards its target genes. Emerging studies reveal the implication of REST nuclear mislocalisation or dysregulation in several neurological diseases. The expression of REST varies depending on different types of neurological disorders, which has created challenges in the discovery of REST-targeted interventions. Hence, this review presents a comprehensive summary on the physiological roles of REST throughout brain development and its implications in neurodegenerative and neurodevelopmental disorders, brain tumours and cerebrovascular diseases. This review offers valuable insights to the development of potential therapeutic approaches targeting REST to improve pathologies in the brain. The important roles of REST as a key player in the nervous system development, and its implications in several neurological diseases.
Collapse
Affiliation(s)
- Xin-Jieh Lam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Sandra Maniam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Pike-See Cheah
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Malaysian Research Institute on Ageing (MyAgeing), Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - King-Hwa Ling
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Malaysian Research Institute on Ageing (MyAgeing), Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| |
Collapse
|
19
|
Wu Z, Su J, Li FL, Chen T, Mayner J, Engler A, Ma S, Li Q, Guan KL. YAP silencing by RB1 mutation is essential for small-cell lung cancer metastasis. Nat Commun 2023; 14:5916. [PMID: 37739954 PMCID: PMC10516997 DOI: 10.1038/s41467-023-41585-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
Small cell lung cancer (SCLC) is highly lethal due to its prevalent metastasis. Most SCLCs have inactivating mutations in TP53 and RB1. We find that loss of YAP expression is key for SCLC cells to acquire rapid ameboid migration and high metastatic potential. YAP functions through its target genes CCN1/CCN2 to inhibit SCLC ameboid migration. RB1 mutation contributes to YAP transcriptional silencing via E2F7, which recruits the RCOR co-repressor complex to YAP promoter. We discover that benzamide family HDAC inhibitors stimulate YAP expression by inhibiting the RCOR-HDAC complex, thereby suppressing SCLC metastasis and improving survival in a mouse model. Our study unveils the molecular and cellular basis underlying SCLC's high metastatic potential, the previously unrecognized role of YAP in suppressing ameboid migration and tumor metastasis, and the mechanism of YAP transcription regulation involving E2F7, RCOR, and Sin3 HDAC. This study reveals a therapeutic potential of benzamides for SCLC treatment.
Collapse
Affiliation(s)
- Zhengming Wu
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Junhui Su
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Fu-Long Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Tao Chen
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Jaimie Mayner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adam Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shenghong Ma
- Wellcome Sanger Institute, Cambridge, CB10 1RQ, UK
| | - Qingquan Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China.
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
- School of Life Sciences, Westlake University, Hangzhou, 310030, China.
| |
Collapse
|
20
|
Jacobs J, Pagani M, Wenzl C, Stark A. Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila. Science 2023; 381:198-204. [PMID: 37440660 DOI: 10.1126/science.adf6149] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Gene expression is controlled by the precise activation and repression of transcription. Repression is mediated by specialized transcription factors (TFs) that recruit co-repressors (CoRs) to silence transcription, even in the presence of activating cues. However, whether CoRs can dominantly silence all enhancers or display distinct specificities is unclear. In this work, we report that most enhancers in Drosophila can be repressed by only a subset of CoRs, and enhancers classified by CoR sensitivity show distinct chromatin features, function, TF motifs, and binding. Distinct TF motifs render enhancers more resistant or sensitive to specific CoRs, as we demonstrate by motif mutagenesis and addition. These CoR-enhancer compatibilities constitute an additional layer of regulatory specificity that allows differential regulation at close genomic distances and is indicative of distinct mechanisms of transcriptional repression.
Collapse
Affiliation(s)
- Jelle Jacobs
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Christoph Wenzl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| |
Collapse
|
21
|
Zheng R, Pan Y, Liu X, Liu F, Li A, Zheng D, Luo Y. Comprehensive analysis of REST corepressors ( RCORs) in pan-cancer. Front Cell Dev Biol 2023; 11:1162344. [PMID: 37342230 PMCID: PMC10277624 DOI: 10.3389/fcell.2023.1162344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
REST corepressors (RCORs) are the core component of the LSD1/CoREST/HDACs transcriptional repressor complex, which have been revealed differently expressed in various cancers, but the therapeutic and prognostic mechanisms in cancer are still poorly understood. In this study, we analyzed expression, prognostic value, molecular subtypes, genetic alteration, immunotherapy response and drug sensitivity of RCORs in pan-cancer. Clinical correlation, stemness index, immune infiltration and regulatory networks of RCORs in hepatocellular carcinoma (HCC) were detected through TCGA and GSCA database. In-vitro experiments were conducted to explore the role of RCOR1 in HCC cells. The expression of RCORs varied among different cancers, and have prognostic values in several cancers. Cancer subtypes were categorized according to the expression of RCORs with clinical information. RCORs were significantly correlated with immunotherapy response, MSI, drug sensitivity and genetic alteration in pan-cancer. In HCC, RCORs were considered as potential predictor of stemness and also had association with immune infiltration. The ceRNA-TF-kinase regulatory networks of RCORs were constructed. Besides, RCOR1 acts as an oncogene in HCC and promotes the proliferation of HCC cells by inhibiting cell cycle arrest and cell apoptosis. Taken together, our study revealed the potential molecular mechanisms of RCORs in pan-cancer, offering a benchmark for disease-related research.
Collapse
Affiliation(s)
- Rong Zheng
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Yingying Pan
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Xinhui Liu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Feiye Liu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Aimin Li
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Dayong Zheng
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| | - Yue Luo
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Cancer Center, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
- Department of Hepatology, TCM-Integrated Hospital of Southern Medical University, Guangzhou, China
| |
Collapse
|
22
|
Zhang S, Sun Y, Xiao Q, Niu M, Pan X, Zhu X. Lnc_000048 Promotes Histone H3K4 Methylation of MAP2K2 to Reduce Plaque Stability by Recruiting KDM1A in Carotid Atherosclerosis. Mol Neurobiol 2023; 60:2572-2586. [PMID: 36689133 PMCID: PMC10039837 DOI: 10.1007/s12035-023-03214-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023]
Abstract
Stabilizing and inhibiting plaque formation is a key challenge for preventing and treating ischemic stroke. KDM1A-mediated histone modifications, which involved in the development of training immunity, ultimately exacerbate the outcomes of inflammation. Although lncRNAs can recruit KDM1A to participate in histone methylation modification and regulate inflammation, cell proliferation, and other biological processes, little is known about the role of KDM1A-lncRNA interaction during atherosclerosis. The present study sought to delineate the effect of the interaction between lnc_000048 and KDM1A on plaque rupture in carotid atherosclerosis, as well as the potential mechanism. Our results revealed that lnc_000048 reduced the activity of histone demethylase and activated MAP2K2 expression by interacting with KDM1A. Furthermore, upregulated lnc_000048 indirectly regulated ERK phosphorylation by MAP2K2 and eventually activated the inflammatory response through the MAPK pathway, which was involved in atherosclerosis. Importantly, our study using ApoE-/- mice confirmed the regulatory role of lnc_000048 in promoting inflammation and collagen degradation in atherosclerotic plaques. These results suggest that targeting the lnc_000048 /KDM1A/MAP2K2/ERK axis may be a promising strategy for preventing atherosclerosis.
Collapse
Affiliation(s)
- Shuai Zhang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yu Sun
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qi Xiao
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mengying Niu
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xudong Pan
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Xiaoyan Zhu
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.
| |
Collapse
|
23
|
DelRosso N, Tycko J, Suzuki P, Andrews C, Aradhana, Mukund A, Liongson I, Ludwig C, Spees K, Fordyce P, Bassik MC, Bintu L. Large-scale mapping and mutagenesis of human transcriptional effector domains. Nature 2023; 616:365-372. [PMID: 37020022 PMCID: PMC10484233 DOI: 10.1038/s41586-023-05906-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.
Collapse
Affiliation(s)
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Peter Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Cecelia Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Adi Mukund
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ivan Liongson
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Connor Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Polly Fordyce
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| |
Collapse
|
24
|
The NRSF/REST transcription factor in hallmarks of cancer: From molecular mechanisms to clinical relevance. Biochimie 2023; 206:116-134. [PMID: 36283507 DOI: 10.1016/j.biochi.2022.10.012] [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: 08/27/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022]
Abstract
The RE-1 silencing transcription factor (REST), or neuron restrictive silencing factor (NRSF), was first identified as a repressor of neuronal genes in non-neuronal tissue. Interestingly, this transcription factor may act as a tumor suppressor or an oncogenic role in developing neuroendocrine and other tumors in patients. The hallmarks of cancer include six biological processes, including proliferative signaling, evasion of growth suppressors, resistance to cell death, replicative immortality, inducing angiogenesis, and activating invasion and metastasis. In addition to two emerging hallmarks, the reprogramming of energy metabolism and evasion of the immune response are all implicated in the development of human tumors. It is essential to know the role of these processes as they will affect the outcome of alternatives for cancer treatment. Various studies in this review demonstrate that NRSF/REST affects the different hallmarks of cancer that could position NRSF/REST as an essential target in the therapy and diagnosis of certain types of cancer.
Collapse
|
25
|
Molecular Mechanisms Involved in the Regulation of Neurodevelopment by miR-124. Mol Neurobiol 2023; 60:3569-3583. [PMID: 36840845 DOI: 10.1007/s12035-023-03271-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/04/2023] [Indexed: 02/26/2023]
Abstract
miR-124 is a miRNA predominantly expressed in the nervous system and accounts for more than a quarter of the total miRNAs in the brain. It regulates neurogenesis, neuronal differentiation, neuronal maturation, and synapse formation and is the most important miRNA in the brain. Furthermore, emerging evidence has suggested miR-124 may be associated with the pathogenesis of various neurodevelopmental and neuropsychiatric disorders. Here, we provide an overview of the role of miR-124 in neurodevelopment and the underling mechanisms, and finally, we prospect the significance of miR-124 research to the field of neuroscience.
Collapse
|
26
|
Histone deacetylase inhibitors as sanguine epitherapeutics against the deadliest lung cancer. Adv Cancer Res 2023; 158:163-198. [PMID: 36990532 DOI: 10.1016/bs.acr.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The back-breaking resistance mechanisms generated by lung cancer cells against epidermal growth factor receptor (EGFR), KRAS and Janus kinase 2 (JAK2) directed therapies strongly prioritizes the requirement of novel therapies which are perfectly tolerated, potentially cytotoxic and can reinstate the drug-sensitivity in lung cancer cells. Enzymatic proteins modifying the post-translational modifications of nucleosome-integrated histone substrates are appearing as current targets for defeating various malignancies. Histone deacetylases (HDACs) are hyperexpressed in diverse lung cancer types. Blocking the active pocket of these acetylation erasers through HDAC inhibitors (HDACi) has come out as an optimistic therapeutic recourse for annihilating lung cancer. This article in the beginning gives an overview about lung cancer statistics and predominant lung cancer types. Succeeding this, compendium about conventional therapies and their serious drawbacks has been provided. Then, connection of uncommon expression of classical HDACs in lung cancer onset and expansion has been detailed. Moreover, keeping the main theme in view this article deeply discusses HDACi in the context of aggressive lung cancer as single agents and spotlights various molecular targets suppressed or induced by these inhibitors for engendering cytotoxic effect. Most particularly, the raised pharmacological effects achieved on using these inhibitors in concerted form with other therapeutic molecules and the cancer-linked pathways altered by this procedure are described. The positive direction towards further heightening of efficacy and the pressing requirement of exhaustive clinical assessment has been proposed as a new focus point.
Collapse
|
27
|
Fan G, Chen S, Liang L, Zhang H, Yu R. Novel Small Molecule Positive Allosteric Modulator SPAM1 Triggers the Nuclear Translocation of PAC1-R to Exert Neuroprotective Effects through Neuron-Restrictive Silencer Factor. Int J Mol Sci 2022; 23:ijms232415996. [PMID: 36555637 PMCID: PMC9784932 DOI: 10.3390/ijms232415996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) exerts effective neuroprotective activity through its specific receptor, PAC1-R. We accidentally discovered that as a positive allosteric modulator (PAM) of PAC1-R, the small-molecule PAM (SPAM1) has a hydrazide-like structure, but different binding characteristics, from hydrazide for the N-terminal extracellular domain of PAC1-R (PAC1-R-EC1). SPAM1 had a significant neuroprotective effect against oxidative stress, both in a cell model treated with hydrogen peroxide (H2O2) and an aging mouse model induced by D-galactose (D-gal). SPAM1 was found to block the decrease in PACAP levels in brain tissues induced by D-gal and significantly induced the nuclear translocation of PAC1-R in PAC1R-CHO cells and mouse retinal ganglion cells. Nuclear PAC1-R was subjected to fragmentation and the nuclear 35 kDa, but not the 15 kDa fragments, of PAC1-R interacted with SP1 to upregulate the expression of Huntingtin (Htt), which then exerted a neuroprotective effect by attenuating the binding availability of the neuron-restrictive silencer factor (NRSF) to the neuron-restrictive silencer element (NRSE). This resulted in an upregulation of the expression of NRSF-related neuropeptides, including PACAP, the brain-derived neurotrophic factor (BDNF), tyrosine hydroxylase (TH), and synapsin-1 (SYN1). The novel mechanism reported in this study indicates that SPAM1 has potential use as a drug, as it exerts a neuroprotective effect by regulating NRSF.
Collapse
Affiliation(s)
- Guangchun Fan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Shang Chen
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lili Liang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huahua Zhang
- Department of Medical Genetics, Guangdong Medical University, Dongguan 523808, China
| | - Rongjie Yu
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Correspondence: or ; Tel.: +86-133-9262-5921
| |
Collapse
|
28
|
Lee K, Whedon SD, Wang ZA, Cole PA. Distinct biochemical properties of the class I histone deacetylase complexes. Curr Opin Chem Biol 2022; 70:102179. [PMID: 35803024 PMCID: PMC10786639 DOI: 10.1016/j.cbpa.2022.102179] [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: 04/02/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/22/2022]
Abstract
Classical histone deacetylases (HDACs) are enzymes that can hydrolytically cleave acetyl-Lys in histones and other proteins and serve as established drug targets in some forms of cancer. Class I HDACs 1-3 typically exist in a range of multiprotein complexes inside cells and show distinct biological functions in modulating gene expression. In recent years, it has become possible to purify and analyze the structure and enzymatic properties of several of these HDAC complexes, including CoREST, MiDAC, NuRD, Sin3, SMRT, MIER, and RERE. Here, we summarize what is experimentally established and/or computationally predicted about the structure of these complexes to describe their particular catalytic activities and site-specificities with modified nucleosome substrates.
Collapse
Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
29
|
mTOR and HDAC2 are simultaneously activated during electrically induced kindling of seizures. Epilepsy Res 2022; 185:106991. [DOI: 10.1016/j.eplepsyres.2022.106991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022]
|
30
|
Gahan JM, Leclère L, Hernandez-Valladares M, Rentzsch F. A developmental role for the chromatin-regulating CoREST complex in the cnidarian Nematostella vectensis. BMC Biol 2022; 20:184. [PMID: 35999597 PMCID: PMC9400249 DOI: 10.1186/s12915-022-01385-1] [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: 01/04/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Chromatin-modifying proteins are key players in the regulation of development and cell differentiation in animals. Most chromatin modifiers, however, predate the evolution of animal multicellularity, and how they gained new functions and became integrated into the regulatory networks underlying development is unclear. One way this may occur is the evolution of new scaffolding proteins that integrate multiple chromatin regulators into larger complexes that facilitate coordinated deposition or removal of different chromatin modifications. We test this hypothesis by analyzing the evolution of the CoREST-Lsd1-HDAC complex. Results Using phylogenetic analyses, we show that a bona fide CoREST homolog is found only in choanoflagellates and animals. We then use the sea anemone Nematostella vectensis as a model for early branching metazoans and identify a conserved CoREST complex by immunoprecipitation and mass spectrometry of an endogenously tagged Lsd1 allele. In addition to CoREST, Lsd1 and HDAC1/2 this complex contains homologs of HMG20A/B and PHF21A, two subunits that have previously only been identified in mammalian CoREST complexes. NvCoREST expression overlaps fully with that of NvLsd1 throughout development, with higher levels in differentiated neural cells. NvCoREST mutants, generated using CRISPR-Cas9, fail to develop beyond the primary polyp stage, thereby revealing essential roles during development and for the differentiation of cnidocytes that phenocopy NvLsd1 mutants. We also show that this requirement is cell autonomous using a cell-type-specific rescue approach. Conclusions The identification of a Nematostella CoREST-Lsd1-HDAC1/2 complex, its similarity in composition with the vertebrate complex, and the near-identical expression patterns and mutant phenotypes of NvCoREST and NvLsd1 suggest that the complex was present before the last common cnidarian-bilaterian ancestor and thus represents an ancient component of the animal developmental toolkit.
Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01385-1.
Collapse
Affiliation(s)
- James M Gahan
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-Sur-Mer (LBDV), 06230, Villefranche-sur-Mer, France
| | - Maria Hernandez-Valladares
- Department of Physical Chemistry, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain.,Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020, Bergen, Norway
| | - Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway. .,Department for Biological Sciences, University of Bergen, Thormøhlensgate 53, 5006, Bergen, Norway.
| |
Collapse
|
31
|
Hess L, Moos V, Lauber AA, Reiter W, Schuster M, Hartl N, Lackner D, Boenke T, Koren A, Guzzardo PM, Gundacker B, Riegler A, Vician P, Miccolo C, Leiter S, Chandrasekharan MB, Vcelkova T, Tanzer A, Jun JQ, Bradner J, Brosch G, Hartl M, Bock C, Bürckstümmer T, Kubicek S, Chiocca S, Bhaskara S, Seiser C. A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation. PLoS Genet 2022; 18:e1010376. [PMID: 35994477 PMCID: PMC9436093 DOI: 10.1371/journal.pgen.1010376] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/01/2022] [Accepted: 08/06/2022] [Indexed: 02/07/2023] Open
Abstract
The class I histone deacetylases are essential regulators of cell fate decisions in health and disease. While pan- and class-specific HDAC inhibitors are available, these drugs do not allow a comprehensive understanding of individual HDAC function, or the therapeutic potential of isoform-specific targeting. To systematically compare the impact of individual catalytic functions of HDAC1, HDAC2 and HDAC3, we generated human HAP1 cell lines expressing catalytically inactive HDAC enzymes. Using this genetic toolbox we compare the effect of individual HDAC inhibition with the effects of class I specific inhibitors on cell viability, protein acetylation and gene expression. Individual inactivation of HDAC1 or HDAC2 has only mild effects on cell viability, while HDAC3 inactivation or loss results in DNA damage and apoptosis. Inactivation of HDAC1/HDAC2 led to increased acetylation of components of the COREST co-repressor complex, reduced deacetylase activity associated with this complex and derepression of neuronal genes. HDAC3 controls the acetylation of nuclear hormone receptor associated proteins and the expression of nuclear hormone receptor regulated genes. Acetylation of specific histone acetyltransferases and HDACs is sensitive to inactivation of HDAC1/HDAC2. Over a wide range of assays, we determined that in particular HDAC1 or HDAC2 catalytic inactivation mimics class I specific HDAC inhibitors. Importantly, we further demonstrate that catalytic inactivation of HDAC1 or HDAC2 sensitizes cells to specific cancer drugs. In summary, our systematic study revealed isoform-specific roles of HDAC1/2/3 catalytic functions. We suggest that targeted genetic inactivation of particular isoforms effectively mimics pharmacological HDAC inhibition allowing the identification of relevant HDACs as targets for therapeutic intervention.
Collapse
Affiliation(s)
- Lena Hess
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Verena Moos
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Arnel A. Lauber
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Natascha Hartl
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, Vienna, Austria
| | | | - Thorina Boenke
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Brigitte Gundacker
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Anna Riegler
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Petra Vician
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Claudia Miccolo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Susanna Leiter
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Mahesh B. Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Terezia Vcelkova
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Andrea Tanzer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Jun Qi Jun
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - James Bradner
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Gerald Brosch
- Institute of Molecular Biology, Innsbruck Medical University, Innsbruck, Austria
| | - Markus Hartl
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Susanna Chiocca
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Srividya Bhaskara
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
32
|
Chen YC, Li H, Martin-Caraballo M, Hsia SV. Establishing a Herpesvirus Quiescent Infection in Differentiated Human Dorsal Root Ganglion Neuronal Cell Line Mediated by Micro-RNA Overexpression. Pathogens 2022; 11:pathogens11070803. [PMID: 35890047 PMCID: PMC9317301 DOI: 10.3390/pathogens11070803] [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: 05/16/2022] [Revised: 06/28/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
HSV-1 is a neurotropic pathogen associated with severe encephalitis, excruciating orofacial sensation, and other chronic neuropathic complications. After the acute infection, the virus may establish a lifelong latency in the neurons of trigeminal ganglia (TG) and other sensory and autonomic ganglia, including the dorsal root ganglia (DRG), etc. The reactivation occurred periodically by a variety of physical or emotional stressors. We have been developing a human DRG neuronal cell-culture model HD10.6, which mimics the mature neurons for latency and reactivation with robust neuronal physiology. We found that miR124 overexpression without acyclovir (ACV) could maintain the virus in a quiescent infection, with the accumulation of latency-associate transcript (LAT). The immediate-early (IE) gene ICP0, on the other hand, was very low and the latent viruses could be reactivated by trichostatin A (TSA) treatment. Together, these observations suggested a putative role of microRNA in promoting HSV-1 latency in human neurons.
Collapse
Affiliation(s)
- Yu-Chih Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA; (Y.-C.C.); (M.M.-C.)
| | - Hedong Li
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Rm. CA4012, Augusta, GA 30912, USA;
| | - Miguel Martin-Caraballo
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA; (Y.-C.C.); (M.M.-C.)
| | - Shaochung Victor Hsia
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA; (Y.-C.C.); (M.M.-C.)
- Correspondence:
| |
Collapse
|
33
|
Park J, Lee K, Kim K, Yi SJ. The role of histone modifications: from neurodevelopment to neurodiseases. Signal Transduct Target Ther 2022; 7:217. [PMID: 35794091 PMCID: PMC9259618 DOI: 10.1038/s41392-022-01078-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/11/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulatory mechanisms, including DNA methylation, histone modification, chromatin remodeling, and microRNA expression, play critical roles in cell differentiation and organ development through spatial and temporal gene regulation. Neurogenesis is a sophisticated and complex process by which neural stem cells differentiate into specialized brain cell types at specific times and regions of the brain. A growing body of evidence suggests that epigenetic mechanisms, such as histone modifications, allow the fine-tuning and coordination of spatiotemporal gene expressions during neurogenesis. Aberrant histone modifications contribute to the development of neurodegenerative and neuropsychiatric diseases. Herein, recent progress in understanding histone modifications in regulating embryonic and adult neurogenesis is comprehensively reviewed. The histone modifications implicated in neurodegenerative and neuropsychiatric diseases are also covered, and future directions in this area are provided.
Collapse
Affiliation(s)
- Jisu Park
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyubin Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
| | - Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
| |
Collapse
|
34
|
Jafari H, Hussain S, Campbell MJ. Nuclear Receptor Coregulators in Hormone-Dependent Cancers. Cancers (Basel) 2022; 14:2402. [PMID: 35626007 PMCID: PMC9139824 DOI: 10.3390/cancers14102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
Abstract
Nuclear receptors (NRs) function collectively as a transcriptional signaling network that mediates gene regulatory actions to either maintain cellular homeostasis in response to hormonal, dietary and other environmental factors, or act as orphan receptors with no known ligand. NR complexes are large and interact with multiple protein partners, collectively termed coregulators. Coregulators are essential for regulating NR activity and can dictate whether a target gene is activated or repressed by a variety of mechanisms including the regulation of chromatin accessibility. Altered expression of coregulators contributes to a variety of hormone-dependent cancers including breast and prostate cancers. Therefore, understanding the mechanisms by which coregulators interact with and modulate the activity of NRs provides opportunities to develop better prognostic and diagnostic approaches, as well as novel therapeutic targets. This review aims to gather and summarize recent studies, techniques and bioinformatics methods used to identify distorted NR coregulator interactions that contribute as cancer drivers in hormone-dependent cancers.
Collapse
Affiliation(s)
- Hedieh Jafari
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Shahid Hussain
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Moray J. Campbell
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| |
Collapse
|
35
|
Swaminathan J, Maegawa S, Shaik S, Sharma A, Bravo-Alegria J, Guo L, Xu L, Harmanci A, Gopalakrishnan V. Cross-Talk Between Histone Methyltransferases and Demethylases Regulate REST Transcription During Neurogenesis. Front Oncol 2022; 12:855167. [PMID: 35600406 PMCID: PMC9120943 DOI: 10.3389/fonc.2022.855167] [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: 01/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The RE1 Silencing Transcription Factor (REST) is a major regulator of neurogenesis and brain development. Medulloblastoma (MB) is a pediatric brain cancer characterized by a blockade of neuronal specification. REST gene expression is aberrantly elevated in a subset of MBs that are driven by constitutive activation of sonic hedgehog (SHH) signaling in cerebellar granular progenitor cells (CGNPs), the cells of origin of this subgroup of tumors. To understand its transcriptional deregulation in MBs, we first studied control of Rest gene expression during neuronal differentiation of normal mouse CGNPs. Higher Rest expression was observed in proliferating CGNPs compared to differentiating neurons. Interestingly, two Rest isoforms were expressed in CGNPs, of which only one showed a significant reduction in expression during neurogenesis. In proliferating CGNPs, higher MLL4 and KDM7A activities opposed by the repressive polycomb repressive complex 2 (PRC2) and the G9A/G9A-like protein (GLP) complex function allowed Rest homeostasis. During differentiation, reduction in MLL4 enrichment on chromatin, in conjunction with an increase in PRC2/G9A/GLP/KDM7A activities promoted a decline in Rest expression. These findings suggest a lineage-context specific paradoxical role for KDM7A in the regulation of Rest expression in CGNPs. In human SHH-MBs (SHH-α and SHH-β) where elevated REST gene expression is associated with poor prognosis, up- or downregulation of KDM7A caused a significant worsening in patient survival. Our studies are the first to implicate KDM7A in REST regulation and in MB biology.
Collapse
Affiliation(s)
- Jyothishmathi Swaminathan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Ajay Sharma
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, United States
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Brain Tumor Center - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Center for Cancer Epigenetics - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- MD Anderson-UTHealth Science Center Graduate School of Biomedical Sciences, Houston, TX, United States
| |
Collapse
|
36
|
Unveiling RCOR1 as a rheostat at transcriptionally permissive chromatin. Nat Commun 2022; 13:1550. [PMID: 35322029 PMCID: PMC8943175 DOI: 10.1038/s41467-022-29261-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2022] [Indexed: 12/23/2022] Open
Abstract
RCOR1 is a known transcription repressor that recruits and positions LSD1 and HDAC1/2 on chromatin to erase histone methylation and acetylation. However, there is currently an incomplete understanding of RCOR1’s range of localization and function. Here, we probe RCOR1’s distribution on a genome-wide scale and unexpectedly find that RCOR1 is predominantly associated with transcriptionally active genes. Biochemical analysis reveals that RCOR1 associates with RNA Polymerase II (POL-II) during transcription and deacetylates its carboxy-terminal domain (CTD) at lysine 7. We provide evidence that this non-canonical RCOR1 activity is linked to dampening of POL-II productive elongation at actively transcribing genes. Thus, RCOR1 represses transcription in two ways—first, via a canonical mechanism by erasing transcriptionally permissive histone modifications through associating with HDACs and, second, via a non-canonical mechanism that deacetylates RNA POL-II’s CTD to inhibit productive elongation. We conclude that RCOR1 is a transcription rheostat. The classical neuronal-gene corepressor RCOR1/CoREST is paradoxically enriched in transcriptionally active chromatin. Here the authors show RCOR1 is recruited during promoter-proximal pausing and negatively regulates the nascent-transcript synthesis. They also show that an RCOR1-LSD1- HDAC1 complex removes lysine acetylation from RNA polymerase II to repress transcription.
Collapse
|
37
|
Roy B, Lee E, Li T, Rampersaud M. Role of miRNAs in Neurodegeneration: From Disease Cause to Tools of Biomarker Discovery and Therapeutics. Genes (Basel) 2022; 13:genes13030425. [PMID: 35327979 PMCID: PMC8951370 DOI: 10.3390/genes13030425] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
Neurodegenerative diseases originate from neuronal loss in the central nervous system (CNS). These debilitating diseases progress with age and have become common due to an increase in longevity. The National Institute of Environmental Health Science’s 2021 annual report suggests around 6.2 million Americans are living with Alzheimer’s disease, and there is a possibility that there will be 1.2 million Parkinson’s disease patients in the USA by 2030. There is no clear-cut universal mechanism for identifying neurodegenerative diseases, and therefore, they pose a challenge for neurobiology scientists. Genetic and environmental factors modulate these diseases leading to familial or sporadic forms. Prior studies have shown that miRNA levels are altered during the course of the disease, thereby suggesting that these noncoding RNAs may be the contributing factor in neurodegeneration. In this review, we highlight the role of miRNAs in the pathogenesis of neurodegenerative diseases. Through this review, we aim to achieve four main objectives: First, we highlight how dysregulation of miRNA biogenesis led to these diseases. Second, we highlight the computational or bioinformatics tools required to identify the putative molecular targets of miRNAs, leading to biological molecular pathways or mechanisms involved in these diseases. Third, we focus on the dysregulation of miRNAs and their target genes leading to several neurodegenerative diseases. In the final section, we highlight the use of miRNAs as potential diagnostic biomarkers in the early asymptomatic preclinical diagnosis of these age-dependent debilitating diseases. Additionally, we discuss the challenges and advances in the development of miRNA therapeutics for brain targeting. We list some of the innovative strategies employed to deliver miRNA into target cells and the relevance of these viral and non-viral carrier systems in RNA therapy for neurodegenerative diseases. In summary, this review highlights the relevance of studying brain-enriched miRNAs, the mechanisms underlying their regulation of target gene expression, their dysregulation leading to progressive neurodegeneration, and their potential for biomarker marker and therapeutic intervention. This review thereby highlights ways for the effective diagnosis and prevention of these neurodegenerative disorders in the near future.
Collapse
Affiliation(s)
- Bidisha Roy
- Life Science Centre, Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07012, USA
- Correspondence:
| | - Erica Lee
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Teresa Li
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Maria Rampersaud
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| |
Collapse
|
38
|
Cloud AS, Vargheese AM, Gunewardena S, Shimak RM, Ganeshkumar S, Kumaraswamy E, Jensen RA, Chennathukuzhi VM. Loss of REST in breast cancer promotes tumor progression through estrogen sensitization, MMP24 and CEMIP overexpression. BMC Cancer 2022; 22:180. [PMID: 35177031 PMCID: PMC8851790 DOI: 10.1186/s12885-022-09280-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Breast cancer is the most common malignancy in women, and is both pathologically and genetically heterogeneous, making early detection and treatment difficult. A subset of breast cancers express normal levels of REST (repressor element 1 silencing transcription factor) mRNA but lack functional REST protein. Loss of REST function is seen in ~ 20% of breast cancers and is associated with a more aggressive phenotype and poor prognosis. Despite the frequent loss of REST, little is known about the role of REST in the molecular pathogenesis of breast cancer. METHODS TCGA data was analyzed for the expression of REST target genes in breast cancer patient samples. We then utilized gene knockdown in MCF-7 cells in the presence or absence of steroid hormones estrogen and/ progesterone followed by RNA sequencing, as well as chromatin immunoprecipitation and PCR in an attempt to understand the tumor suppressor role of REST in breast cancer. RESULTS We show that REST directly regulates CEMIP (cell migration-inducing and hyaluronan-binding protein, KIAA1199) and MMP24 (matrix metallopeptidase 24), genes known to have roles in invasion and metastasis. REST knockdown in breast cancer cells leads to significant upregulation of CEMIP and MMP24. In addition, we found REST binds to RE-1 sites (repressor element-1) within the genes and influences their transcription. Furthermore, we found that the estrogen receptor (ESR1) signaling pathway is activated in the absence of REST, regardless of hormone treatment. CONCLUSIONS We demonstrate a critical role for the loss of REST in aggressive breast cancer pathogenesis and provide evidence for REST as an important diagnostic marker for personalized treatment plans.
Collapse
Affiliation(s)
- Ashley S. Cloud
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA
| | - Aditya M. Vargheese
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA ,grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.266515.30000 0001 2106 0692University of Kansas, Lawrence, KS USA
| | - Sumedha Gunewardena
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA
| | - Raeann M. Shimak
- grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS USA
| | - Sornakala Ganeshkumar
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA
| | - Easwari Kumaraswamy
- grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS USA
| | - Roy A. Jensen
- grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA ,grid.266515.30000 0001 2106 0692University of Kansas, Lawrence, KS USA ,grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS USA ,grid.412016.00000 0001 2177 6375Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS USA
| | - Vargheese M. Chennathukuzhi
- grid.412016.00000 0001 2177 6375Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS USA ,grid.468219.00000 0004 0408 2680The University of Kansas Cancer Center, Kansas City, KS USA
| |
Collapse
|
39
|
Abstract
Neuropathic pain is a challenging clinical problem and remains difficult to treat. Altered gene expression in peripheral sensory nerves and neurons due to nerve injury is well documented and contributes critically to the synaptic plasticity in the spinal cord and the initiation and maintenance of chronic pain. However, our understanding of the epigenetic mechanisms regulating the transcription of pro-nociceptive (e.g., NMDA receptors and α2δ-1) and antinociceptive (e.g., potassium channels and opioid and cannabinoid receptors) genes are still limited. In this review, we summarize recent studies determining the roles of histone modifications (including methylation, acetylation, and ubiquitination), DNA methylation, and noncoding RNAs in neuropathic pain development. We review the epigenetic writer, reader, and eraser proteins that participate in the transcriptional control of the expression of key ion channels and neurotransmitter receptors in the dorsal root ganglion after traumatic nerve injury, which is commonly used as a preclinical model of neuropathic pain. A better understanding of epigenetic reprogramming involved in the transition from acute to chronic pain could lead to the development of new treatments for neuropathic pain.
Collapse
Affiliation(s)
- Krishna Ghosh
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Hui-Lin Pan
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| |
Collapse
|
40
|
Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
Collapse
Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
41
|
Barnes CE, English DM, Broderick M, Collins MO, Cowley SM. Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation. Mol Omics 2022; 18:31-44. [PMID: 34709266 PMCID: PMC8763317 DOI: 10.1039/d1mo00236h] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Lysine specific demethylase 1 (LSD1) regulates gene expression as part of the CoREST complex, along with co-repressor of REST (CoREST) and histone deacetylase 1 (HDAC1). CoREST is recruited to specific genomic loci by core components and numerous transient interactions with chromatin-associated factors and transcription factors. We hypothesise that many of these weaker and transient associations may be difficult to identify using traditional co-immunoprecipitation methods. We have therefore employed proximity-dependent biotin-identification (BioID) with four different members of the CoREST complex, in three different cell types, to identify a comprehensive network of LSD1/CoREST associated proteins. In HEK293T cells, we identified 302 CoREST-associated proteins. Among this group were 16 of 18 known CoREST components and numerous novel associations, including readers (CHD3, 4, 6, 7 and 8), writers (KMT2B and KMT2D) and erasers (KDM2B) of histone methylation. However, components of other HDAC1 containing complexes (e.g. Sin3) were largely absent. To examine the dynamic nature of the CoREST interactome in a primary cell type, we replaced endogenous LSD1 with BirA*-LSD1 in embryonic stem (ES) cells and performed BioID in pluripotent, early- and late-differentiating environments. We identified 156 LSD1-associated proteins of which 67 were constitutively associated across all three time-points (43%), including novel associations with the MMB and ChAHP complexes, implying that the majority of interactors are both dynamic and cell type dependent. In total, we have performed 16 independent BioID experiments for LSD1 in three different cell types, producing a definitive network of LSD1-assoicated proteins that should provide a major resource for the field.
Collapse
Affiliation(s)
- Claire E Barnes
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - David M English
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - Megan Broderick
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
- Faculty of Science Mass Spectrometry Centre, University of Sheffield, Brook Hill Road, Sheffield, S3 7HF, UK
| | - Shaun M Cowley
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| |
Collapse
|
42
|
Yu Z, Chen F, Liu H, Fan J, Ding X, Zhu X, Cui S, Yi H, Zhou X, Hu Y, Liu W. Silencing CoREST inhibits the viability and migration of fibroblast‑like synoviocytes in TNF‑α‑induced rheumatoid arthritis. Exp Ther Med 2021; 23:148. [PMID: 35069829 PMCID: PMC8756401 DOI: 10.3892/etm.2021.11071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 10/08/2021] [Indexed: 11/05/2022] Open
Abstract
Fibroblast-like synoviocytes (FLSs) have functions in the pathogenesis of rheumatoid arthritis (RA) through the onset of synovitis, the growth of pannus and the destruction of cartilage and bone. The significant increase in the proliferation, migration and invasion of FLSs induces the onset and advancement of RA. To date, the exact function of corepressor element-1 silencing transcription factor (CoREST) in RA remains unclear, but its expression has been determined in RA synovial tissues. In this study, the effects of CoREST were investigated in a TNF-α-induced FLS activation model. Following the silencing of CoREST expression with small interfering (si)RNA, the viability and migration of FLSs were evaluated. Furthermore, the possible molecular mechanisms were explored by detecting the expression of key factors, including matrix metalloproteinases (MMPs), lysine-specific histone demethylase 1 (LSD1) and associated cytokines, via reverse transcription-quantitative PCR and western blotting. CoREST expression increased not only in the RA synovial tissues, but also in the TNF-α-induced FLS activation model. Following the silencing of CoREST in the FLSs treated with TNF-α, cell viability was inhibited, and the migratory capacity of FLSs was suppressed, which was accompanied by the reduced expression of MMP-3 and MMP-9. The expression of LSD1 was also downregulated. There was a notable decrease in the synthesis of interferon-γ and interleukin (IL)-17, while IL-10 expression was increased. The knockdown of CoREST inhibited the viability and migration of FLSs stimulated with TNF-α. Thus, the suppression of CoREST may have crucial roles in the occurrence and development of RA.
Collapse
Affiliation(s)
- Ziliang Yu
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Feihu Chen
- Department of Orthopaedics, Xuyi People's Hospital, Xuyi, Jiangsu 211700, P.R. China
| | - Hao Liu
- School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Jianbo Fan
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xiaomin Ding
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xinhui Zhu
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Shengyu Cui
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hong Yi
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xiaogang Zhou
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yalong Hu
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Wei Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| |
Collapse
|
43
|
Greenan E, Gallagher S, Khalil R, Murphy CC, Ní Gabhann-Dromgoole J. Advancing Our Understanding of Corneal Herpes Simplex Virus-1 Immune Evasion Mechanisms and Future Therapeutics. Viruses 2021; 13:v13091856. [PMID: 34578437 PMCID: PMC8473450 DOI: 10.3390/v13091856] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/24/2022] Open
Abstract
Herpes stromal keratitis (HSK) is a disease that commonly affects the cornea and external eye and is caused by Herpes Simplex Virus type 1 (HSV-1). This virus infects approximately 66% of people worldwide; however, only a small portion of these people will develop symptoms in their lifetime. There is no cure or vaccine available for HSV-1; however, there are treatments available that aim to control the inflammation caused by the virus and prevent its recurrence. While these treatments are beneficial to those suffering with HSK, there is a need for more effective treatments to minimise the need for topical steroids, which can have harmful effects, and to prevent bouts of disease reactivation, which can lead to progressive corneal scarring and visual impairment. This review details the current understanding of HSV-1 infection and discusses potential novel treatment options including microRNAs, TLRs, mAbs, and aptamers.
Collapse
Affiliation(s)
- Emily Greenan
- Department of Ophthalmology, Royal College of Surgeons in Ireland, D02 XK51 Dublin, Ireland; (E.G.); (C.C.M.)
- School of Pharmacy and Biomolecular Sciences (PBS), RSCI Research Institute, Royal College of Surgeons in Ireland, D02 XK51 Dublin, Ireland;
| | - Sophie Gallagher
- School of Biological and Health Sciences, Technological University (TU) Dublin, Kevin Street, D02 XK51 Dublin, Ireland;
| | - Rana Khalil
- School of Pharmacy and Biomolecular Sciences (PBS), RSCI Research Institute, Royal College of Surgeons in Ireland, D02 XK51 Dublin, Ireland;
| | - Conor C. Murphy
- Department of Ophthalmology, Royal College of Surgeons in Ireland, D02 XK51 Dublin, Ireland; (E.G.); (C.C.M.)
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, D02 XK51 Dublin, Ireland
| | - Joan Ní Gabhann-Dromgoole
- Department of Ophthalmology, Royal College of Surgeons in Ireland, D02 XK51 Dublin, Ireland; (E.G.); (C.C.M.)
- School of Pharmacy and Biomolecular Sciences (PBS), RSCI Research Institute, Royal College of Surgeons in Ireland, D02 XK51 Dublin, Ireland;
- Correspondence:
| |
Collapse
|
44
|
Butler-Ryan R, Wood IC. The functions of repressor element 1-silencing transcription factor in models of epileptogenesis and post-ischemia. Metab Brain Dis 2021; 36:1135-1150. [PMID: 33813634 PMCID: PMC8272694 DOI: 10.1007/s11011-021-00719-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022]
Abstract
Epilepsy is a debilitating neurological disorder characterised by recurrent seizures for which 30% of patients are refractory to current treatments. The genetic and molecular aetiologies behind epilepsy are under investigation with the goal of developing new epilepsy medications. The transcriptional repressor REST (Repressor Element 1-Silencing Transcription factor) is a focus of interest as it is consistently upregulated in epilepsy patients and following brain insult in animal models of epilepsy and ischemia. This review analyses data from different epilepsy models and discusses the contribution of REST to epileptogenesis. We propose that in healthy brains REST acts in a protective manner to homeostatically downregulate increases in excitability, to protect against seizure through downregulation of BDNF (Brain-Derived Neurotrophic Factor) and its receptor, TrkB (Tropomyosin receptor kinase B). However, in epilepsy patients and post-seizure, REST may increase to a larger degree, which allows downregulation of the glutamate receptor subunit GluR2. This leads to AMPA glutamate receptors lacking GluR2 subunits, which have increased permeability to Ca2+, causing excitotoxicity, cell death and seizure. This concept highlights therapeutic potential of REST modulation through gene therapy in epilepsy patients.
Collapse
Affiliation(s)
- Ruth Butler-Ryan
- School of Biomedical Sciences, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT UK
| | - Ian C. Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT UK
| |
Collapse
|
45
|
Kamgar-Dayhoff P, Brelidze TI. Multifaceted effect of chlorpromazine in cancer: implications for cancer treatment. Oncotarget 2021; 12:1406-1426. [PMID: 34262651 PMCID: PMC8274723 DOI: 10.18632/oncotarget.28010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Since its discovery in 1951, chlorpromazine (CPZ) has been one of the most widely used antipsychotic medications for treating schizophrenia and other psychiatric disorders. In addition to its antipsychotic effect, many studies in the last several decades have found that CPZ has a potent antitumorigenic effect. These studies have shown that CPZ affects a number of molecular oncogenic targets through multiple pathways, including the regulation of cell cycle, cancer growth and metastasis, chemo-resistance and stemness of cancer cells. Here we review studies on molecular mechanisms of CPZ’s action on key proteins involved in cancer, including p53, YAP, Ras protein, ion channels, and MAPKs. We discuss common and overlapping signaling pathways of CPZ’s action, its cancer-type specificity, antitumorigenic effects of CPZ reported in animal models and population studies on the rate of cancer in psychiatric patients. We also discuss the potential benefits and limitations of repurposing CPZ for cancer treatment.
Collapse
Affiliation(s)
- Pareesa Kamgar-Dayhoff
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D.C., USA
| | - Tinatin I Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D.C., USA
| |
Collapse
|
46
|
Pereira V, Lamoine S, Cuménal M, Lolignier S, Aissouni Y, Pizzoccaro A, Prival L, Balayssac D, Eschalier A, Bourinet E, Busserolles J. Epigenetics Involvement in Oxaliplatin-Induced Potassium Channel Transcriptional Downregulation and Hypersensitivity. Mol Neurobiol 2021; 58:3575-3587. [PMID: 33772465 DOI: 10.1007/s12035-021-02361-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/15/2021] [Indexed: 01/10/2023]
Abstract
Peripheral neuropathy is the most frequent dose-limiting adverse effect of oxaliplatin. Acute pain symptoms that are induced or exacerbated by cold occur in almost all patients immediately following the first infusions. Evidence has shown that oxaliplatin causes ion channel expression modulations in dorsal root ganglia neurons, which are thought to contribute to peripheral hypersensitivity. Most dysregulated genes encode ion channels involved in cold and mechanical perception, noteworthy members of a sub-group of potassium channels of the K2P family, TREK and TRAAK. Downregulation of these K2P channels has been identified as an important tuner of acute oxaliplatin-induced hypersensitivity. We investigated the molecular mechanisms underlying this peripheral dysregulation in a murine model of neuropathic pain triggered by a single oxaliplatin administration. We found that oxaliplatin-mediated TREK-TRAAK downregulation, as well as downregulation of other K+ channels of the K2P and Kv families, involves a transcription factor known as the neuron-restrictive silencer factor (NRSF) and its epigenetic co-repressors histone deacetylases (HDACs). NRSF knockdown was able to prevent most of these K+ channel mRNA downregulation in mice dorsal root ganglion neurons as well as oxaliplatin-induced acute cold and mechanical hypersensitivity. Interestingly, pharmacological inhibition of class I HDAC reproduces the antinociceptive effects of NRSF knockdown and leads to an increased K+ channel expression in oxaliplatin-treated mice.
Collapse
Affiliation(s)
- Vanessa Pereira
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Sylvain Lamoine
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Mélissa Cuménal
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Stéphane Lolignier
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Youssef Aissouni
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Anne Pizzoccaro
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS UMR-5203, INSERM U1091, F-34094, Montpellier, France
| | - Laetitia Prival
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - David Balayssac
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Alain Eschalier
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Emmanuel Bourinet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS UMR-5203, INSERM U1091, F-34094, Montpellier, France
| | - Jérôme Busserolles
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France.
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France.
| |
Collapse
|
47
|
The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus. J Neurosci 2021; 41:6582-6595. [PMID: 34210779 DOI: 10.1523/jneurosci.2059-20.2021] [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] [Received: 08/05/2020] [Revised: 05/12/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Early studies in mouse neurodevelopment led to the discovery of the RE1 Silencing Transcription Factor (REST) and its role as a master repressor of neuronal gene expression. Recently, REST was reported to also repress neuronal genes in the human adult brain. These genes were found to be involved in pro-apoptotic pathways; and their repression, associated with increased REST levels during aging, were found to be neuroprotective and conserved across species. However, direct genome-wide REST binding profiles for REST in adult brain have not been identified for any species. Here, we apply this approach to mouse and human hippocampus. We find an expansion of REST binding sites in the human hippocampus that are lacking in both mouse hippocampus and other human non-neuronal cell types. The unique human REST binding sites are associated with genes involved in innate immunity processes and inflammation signaling which, on the basis of histology and recent public transcriptomic analyses, suggest that these new target genes are repressed in glia. We propose that the increases in REST expression in mid-adulthood presage the beginning of brain aging, and that human REST function has evolved to protect the longevity and function of both neurons and glia in human brain.SIGNIFICANCE STATEMENT The RE1 Silencing Transcription Factor (REST) repressor has served historically as a model for gene regulation during mouse neurogenesis. Recent studies of REST have also suggested a conserved role for REST repressor function across lower species during aging. However, direct genome-wide studies for REST have been lacking for human brain. Here, we perform the first genome-wide analysis of REST binding in both human and mouse hippocampus. The majority of REST-occupied genes in human hippocampus are distinct from those in mouse. Further, the REST-associated genes unique to human hippocampus represent a new set related to innate immunity and inflammation, where their gene dysregulation has been implicated in aging-related neuropathology, such as Alzheimer's disease.
Collapse
|
48
|
Suster I, Feng Y. Multifaceted Regulation of MicroRNA Biogenesis: Essential Roles and Functional Integration in Neuronal and Glial Development. Int J Mol Sci 2021; 22:ijms22136765. [PMID: 34201807 PMCID: PMC8269442 DOI: 10.3390/ijms22136765] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that function as endogenous gene silencers. Soon after the discovery of miRNAs, a subset of brain-enriched and brain-specific miRNAs were identified and significant advancements were made in delineating miRNA function in brain development. However, understanding the molecular mechanisms that regulate miRNA biogenesis in normal and diseased brains has become a prevailing challenge. Besides transcriptional regulation of miRNA host genes, miRNA processing intermediates are subjected to multifaceted regulation by canonical miRNA processing enzymes, RNA binding proteins (RBPs) and epitranscriptomic modifications. Further still, miRNA activity can be regulated by the sponging activity of other non-coding RNA classes, namely circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs). Differential abundance of these factors in neuronal and glial lineages partly underlies the spatiotemporal expression and function of lineage-specific miRNAs. Here, we review the continuously evolving understanding of the regulation of neuronal and glial miRNA biogenesis at the transcriptional and posttranscriptional levels and the cooperativity of miRNA species in targeting key mRNAs to drive lineage-specific development. In addition, we review dysregulation of neuronal and glial miRNAs and the detrimental impacts which contribute to developmental brain disorders.
Collapse
Affiliation(s)
| | - Yue Feng
- Correspondence: ; Tel.: +1-404-727-0351
| |
Collapse
|
49
|
Sauer M, Was N, Ziegenhals T, Wang X, Hafner M, Becker M, Fischer U. The miR-26 family regulates neural differentiation-associated microRNAs and mRNAs by directly targeting REST. J Cell Sci 2021; 134:jcs257535. [PMID: 34151974 DOI: 10.1242/jcs.257535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/11/2021] [Indexed: 01/13/2023] Open
Abstract
Repressor element 1-silencing transcription factor (REST) plays a crucial role in the differentiation of neural progenitor cells (NPCs). C-terminal domain small phosphatases (CTDSPs) are REST effector proteins that reduce RNA polymerase II activity on genes required for neurogenesis. miR-26b regulates neurogenesis in zebrafish by targeting ctdsp2 mRNA, but the molecular events triggered by this microRNA (miR) remain unknown. Here, we show in a murine embryonic stem cell differentiation paradigm that inactivation of miR-26 family members disrupts the formation of neurons and astroglia and arrests neurogenesis at the neural progenitor level. Furthermore, we show that miR-26 directly targets Rest, thereby inducing the expression of a large set of REST complex-repressed neuronal genes, including miRs required for induction of the neuronal gene expression program. Our data identify the miR-26 family as the trigger of a self-amplifying system required for neural differentiation that acts upstream of REST-controlled miRs.
Collapse
Affiliation(s)
- Mark Sauer
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Nina Was
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Thomas Ziegenhals
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, D-97074 Würzburg, Germany
| | - Xiantao Wang
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Markus Hafner
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Matthias Becker
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, D-97074 Würzburg, Germany
| |
Collapse
|
50
|
Pogoda A, Chmielewska N, Maciejak P, Szyndler J. Transcriptional Dysregulation in Huntington's Disease: The Role in Pathogenesis and Potency for Pharmacological Targeting. Curr Med Chem 2021; 28:2783-2806. [PMID: 32628586 DOI: 10.2174/0929867327666200705225821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/15/2020] [Accepted: 06/19/2020] [Indexed: 11/22/2022]
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by a mutation in the gene that encodes a critical cell regulatory protein, huntingtin (Htt). The expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats causes improper folding of functional proteins and is an initial trigger of pathological changes in the brain. Recent research has indicated that the functional dysregulation of many transcription factors underlies the neurodegenerative processes that accompany HD. These disturbances are caused not only by the loss of wild-type Htt (WT Htt) function but also by the occurrence of abnormalities that result from the action of mutant Htt (mHtt). In this review, we aim to describe the role of transcription factors that are currently thought to be strongly associated with HD pathogenesis, namely, RE1-silencing transcription factor, also known as neuron-restrictive silencer factor (REST/NRSF), forkhead box proteins (FOXPs), peroxisome proliferator-activated receptor gamma coactivator-1a (PGC1α), heat shock transcription factor 1 (HSF1), and nuclear factor κ light-chain-enhancer of activated B cells (NF- κB). We also take into account the role of these factors in the phenotype of HD as well as potential pharmacological interventions targeting the analyzed proteins. Furthermore, we considered whether molecular manipulation resulting in changes in transcription factor function may have clinical potency for treating HD.
Collapse
Affiliation(s)
- Aleksandra Pogoda
- Faculty of Medicine, Medical University of Warsaw, Zwirki i Wigury Street 61, 02-097 Warsaw, Poland
| | - Natalia Chmielewska
- Department of Neurochemistry, Institute of Psychiatry and Neurology, Sobieskiego Street 9, 02-957 Warsaw, Poland
| | - Piotr Maciejak
- Department of Neurochemistry, Institute of Psychiatry and Neurology, Sobieskiego Street 9, 02-957 Warsaw, Poland
| | - Janusz Szyndler
- Department of Experimental and Clinical Pharmacology, Centre for Preclinical Research and Technology CePT, Medical University of Warsaw, Banacha Street 1B, 02-097 Warsaw, Poland
| |
Collapse
|