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Cao Y, Ai Y, Zhang X, Zhang J, Long X, Zhu Y, Wang L, Gu Q, Han H. Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep. Commun Biol 2023; 6:1077. [PMID: 37872364 PMCID: PMC10593826 DOI: 10.1038/s42003-023-05439-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
Hypertrophy and fiber transformation are two prominent features of postnatal skeletal muscle development. However, the role of epigenetic modifications is less understood. ATAC-seq, whole genome bisulfite sequencing, and RNA-seq were applied to investigate the epigenetic dynamics of muscle in Hu sheep at 3 days, 3 months, 6 months, and 12 months after birth. All 6865 differentially expressed genes were assigned into three distinct tendencies, highlighting the balanced protein synthesis, accumulated immune activities, and restrained cell division in postnatal development. We identified 3742 differentially accessible regions and 11799 differentially methylated regions that were associated with muscle-development-related pathways in certain stages, like D3-M6. Transcription factor network analysis, based on genomic loci with high chromatin accessibility and low methylation, showed that ARID5B, MYOG, and ENO1 were associated with muscle hypertrophy, while NR1D1, FADS1, ZFP36L2, and SLC25A1 were associated with muscle fiber transformation. Taken together, these results suggest that DNA methylation and chromatin accessibility contributed toward regulating the growth and fiber transformation of postnatal skeletal muscle in Hu sheep.
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Affiliation(s)
- Yutao Cao
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Ai
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaosheng Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, China
| | - Jinlong Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin, China
| | - Xianlei Long
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yaning Zhu
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Linli Wang
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingyi Gu
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Hongbing Han
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China.
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China.
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2
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Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl‐Wilson A, Benzie JAH, Houston RD, Wiener P. Genetic differentiation following recent domestication events: A study of farmed Nile tilapia ( Oreochromis niloticus) populations. Evol Appl 2023; 16:1220-1235. [PMID: 37360025 PMCID: PMC10286235 DOI: 10.1111/eva.13560] [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: 07/01/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark Genetics Norway ASBergenNorway
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark GeneticsMidlothianUK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Center of Environment Fisheries and Aquaculture ScienceWeymouthUK
| | | | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| | - John A. H. Benzie
- WorldFishBayan LepasPenangMalaysia
- School of Biological Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Benchmark GeneticsMidlothianUK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
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3
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Chu L, Terasaki M, Mattsson CL, Teinturier R, Charbord J, Dirice E, Liu KC, Miskelly MG, Zhou Q, Wierup N, Kulkarni RN, Andersson O. In vivo drug discovery for increasing incretin-expressing cells identifies DYRK inhibitors that reinforce the enteroendocrine system. Cell Chem Biol 2022; 29:1368-1380.e5. [PMID: 35998625 PMCID: PMC9557248 DOI: 10.1016/j.chembiol.2022.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/27/2022] [Accepted: 07/27/2022] [Indexed: 02/02/2023]
Abstract
Analogs of the incretin hormones Gip and Glp-1 are used to treat type 2 diabetes and obesity. Findings in experimental models suggest that manipulating several hormones simultaneously may be more effective. To identify small molecules that increase the number of incretin-expressing cells, we established a high-throughput in vivo chemical screen by using the gip promoter to drive the expression of luciferase in zebrafish. All hits increased the numbers of neurogenin 3-expressing enteroendocrine progenitors, Gip-expressing K-cells, and Glp-1-expressing L-cells. One of the hits, a dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) inhibitor, additionally decreased glucose levels in both larval and juvenile fish. Knock-down experiments indicated that nfatc4, a downstream mediator of DYRKs, regulates incretin+ cell number in zebrafish, and that Dyrk1b regulates Glp-1 expression in an enteroendocrine cell line. DYRK inhibition also increased the number of incretin-expressing cells in diabetic mice, suggesting a conserved reinforcement of the enteroendocrine system, with possible implications for diabetes.
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Affiliation(s)
- Lianhe Chu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Michishige Terasaki
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte L Mattsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Romain Teinturier
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jérémie Charbord
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ercument Dirice
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Ka-Cheuk Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Michael G Miskelly
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö 20502, Sweden
| | - Qiao Zhou
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Nils Wierup
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö 20502, Sweden
| | - Rohit N Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Boston, MA 02215, USA
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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4
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Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Ranking reprogramming factors for cell differentiation. Nat Methods 2022; 19:812-822. [PMID: 35710610 PMCID: PMC10460539 DOI: 10.1038/s41592-022-01522-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2022] [Indexed: 12/16/2022]
Abstract
Transcription factor over-expression is a proven method for reprogramming cells to a desired cell type for regenerative medicine and therapeutic discovery. However, a general method for the identification of reprogramming factors to create an arbitrary cell type is an open problem. Here we examine the success rate of methods and data for differentiation by testing the ability of nine computational methods (CellNet, GarNet, EBseq, AME, DREME, HOMER, KMAC, diffTF and DeepAccess) to discover and rank candidate factors for eight target cell types with known reprogramming solutions. We compare methods that use gene expression, biological networks and chromatin accessibility data, and comprehensively test parameter and preprocessing of input data to optimize performance. We find the best factor identification methods can identify an average of 50-60% of reprogramming factors within the top ten candidates, and methods that use chromatin accessibility perform the best. Among the chromatin accessibility methods, complex methods DeepAccess and diffTF have higher correlation with the ranked significance of transcription factor candidates within reprogramming protocols for differentiation. We provide evidence that AME and diffTF are optimal methods for transcription factor recovery that will allow for systematic prioritization of transcription factor candidates to aid in the design of new reprogramming protocols.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, MIT, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Tulsi Patel
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Closser
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - David Gifford
- Computational and Systems Biology, MIT, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
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5
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Wille CK, Sridharan R. DOT1L inhibition enhances pluripotency beyond acquisition of epithelial identity and without immediate suppression of the somatic transcriptome. Stem Cell Reports 2021; 17:384-396. [PMID: 34995500 PMCID: PMC8828533 DOI: 10.1016/j.stemcr.2021.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
Inhibiting the histone 3 lysine 79 (H3K79) methyltransferase, disruptor of telomeric silencing 1-like (DOT1L), increases the efficiency of reprogramming somatic cells to induced pluripotent stem cells (iPSCs). Here, we find that, despite the enrichment of H3K79 methylation on thousands of actively transcribed genes in somatic cells, DOT1L inhibition (DOT1Li) does not immediately cause the shutdown of the somatic transcriptional profile to enable transition to pluripotency. Contrary to the prevalent view, DOT1Li promotes iPSC generation beyond the mesenchymal to epithelial transition and even from already epithelial cell types. DOT1Li is most potent at the midpoint of reprogramming in part by repressing Nfix that persists at late stages of reprogramming. Importantly, regulation of single genes cannot substitute for DOT1Li, demonstrating that H3K79 methylation has pleiotropic effects in maintaining cell identity. DOT1L is a barrier of reprogramming, especially at the mid-point DOT1L inhibition increases pluripotency beyond MET DOT1L inhibition does not immediately suppress somatic expression Single factors cannot replace the pleiotropic effects of DOT1L inhibition
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Affiliation(s)
- Coral K Wille
- Wisconsin Institute for Discovery, University of Wisconsin, 330 North Orchard Street, Room 2118, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin, 330 North Orchard Street, Room 2118, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA.
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6
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Xi H, Langerman J, Sabri S, Chien P, Young CS, Younesi S, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K, Pyle AD. A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. Cell Stem Cell 2020; 27:158-176.e10. [PMID: 32396864 PMCID: PMC7367475 DOI: 10.1016/j.stem.2020.04.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/12/2020] [Accepted: 04/23/2020] [Indexed: 12/17/2022]
Abstract
The developmental trajectory of human skeletal myogenesis and the transition between progenitor and stem cell states are unclear. We used single-cell RNA sequencing to profile human skeletal muscle tissues from embryonic, fetal, and postnatal stages. In silico, we identified myogenic as well as other cell types and constructed a "roadmap" of human skeletal muscle ontogeny across development. In a similar fashion, we also profiled the heterogeneous cell cultures generated from multiple human pluripotent stem cell (hPSC) myogenic differentiation protocols and mapped hPSC-derived myogenic progenitors to an embryonic-to-fetal transition period. We found differentially enriched biological processes and discovered co-regulated gene networks and transcription factors present at distinct myogenic stages. This work serves as a resource for advancing our knowledge of human myogenesis. It also provides a tool for a better understanding of hPSC-derived myogenic progenitors for translational applications in skeletal muscle-based regenerative medicine.
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Affiliation(s)
- Haibin Xi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Justin Langerman
- Deparment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shan Sabri
- Deparment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggie Chien
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Courtney S Young
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shahab Younesi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael Hicks
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karen Gonzalez
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wakana Fujiwara
- Department of Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julia Marzi
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany; The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Simone Liebscher
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Melissa Spencer
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ben Van Handel
- Department of Orthopaedic Surgery, Keck School of Medicine, Stem Cell Research and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Denis Evseenko
- Department of Orthopaedic Surgery, Keck School of Medicine, Stem Cell Research and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany; The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany; Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kathrin Plath
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Deparment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
| | - April D Pyle
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
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7
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Saclier M, Lapi M, Bonfanti C, Rossi G, Antonini S, Messina G. The Transcription Factor Nfix Requires RhoA-ROCK1 Dependent Phagocytosis to Mediate Macrophage Skewing during Skeletal Muscle Regeneration. Cells 2020; 9:E708. [PMID: 32183151 PMCID: PMC7140652 DOI: 10.3390/cells9030708] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 01/13/2023] Open
Abstract
Macrophages (MPs) are immune cells which are crucial for tissue repair. In skeletal muscle regeneration, pro-inflammatory cells first infiltrate to promote myogenic cell proliferation, then they switch into an anti-inflammatory phenotype to sustain myogenic cells differentiation and myofiber formation. This phenotypical switch is induced by dead cell phagocytosis. We previously demonstrated that the transcription factor Nfix, a member of the nuclear factor I (Nfi) family, plays a pivotal role during muscle development, regeneration and in the progression of muscular dystrophies. Here, we show that Nfix is mainly expressed by anti-inflammatory macrophages. Upon acute injury, mice deleted for Nfix in myeloid line displayed a significant defect in the process of muscle regeneration. Indeed, Nfix is involved in the macrophage phenotypical switch and macrophages lacking Nfix failed to adopt an anti-inflammatory phenotype and interact with myogenic cells. Moreover, we demonstrated that phagocytosis induced by the inhibition of the RhoA-ROCK1 pathway leads to Nfix expression and, consequently, to acquisition of the anti-inflammatory phenotype. Our study identified Nfix as a link between RhoA-ROCK1-dependent phagocytosis and the MP phenotypical switch, thus establishing a new role for Nfix in macrophage biology for the resolution of inflammation and tissue repair.
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Affiliation(s)
| | | | | | | | | | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy; (M.S.); (M.L.); (C.B.); (G.R.); (S.A.)
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8
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Fraser J, Essebier A, Brown AS, Davila RA, Harkins D, Zalucki O, Shapiro LP, Penzes P, Wainwright BJ, Scott MP, Gronostajski RM, Bodén M, Piper M, Harvey TJ. Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development. CEREBELLUM (LONDON, ENGLAND) 2020; 19:89-101. [PMID: 31838646 PMCID: PMC7815246 DOI: 10.1007/s12311-019-01089-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcriptional regulation plays a central role in controlling neural stem and progenitor cell proliferation and differentiation during neurogenesis. For instance, transcription factors from the nuclear factor I (NFI) family have been shown to co-ordinate neural stem and progenitor cell differentiation within multiple regions of the embryonic nervous system, including the neocortex, hippocampus, spinal cord and cerebellum. Knockout of individual Nfi genes culminates in similar phenotypes, suggestive of common target genes for these transcription factors. However, whether or not the NFI family regulates common suites of genes remains poorly defined. Here, we use granule neuron precursors (GNPs) of the postnatal murine cerebellum as a model system to analyse regulatory targets of three members of the NFI family: NFIA, NFIB and NFIX. By integrating transcriptomic profiling (RNA-seq) of Nfia- and Nfix-deficient GNPs with epigenomic profiling (ChIP-seq against NFIA, NFIB and NFIX, and DNase I hypersensitivity assays), we reveal that these transcription factors share a large set of potential transcriptional targets, suggestive of complementary roles for these NFI family members in promoting neural development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Lauren P Shapiro
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peter Penzes
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Matthew P Scott
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Mikael Bodén
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
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9
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Piper M, Gronostajski R, Messina G. Nuclear Factor One X in Development and Disease. Trends Cell Biol 2018; 29:20-30. [PMID: 30287093 DOI: 10.1016/j.tcb.2018.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
The past decade has seen incredible advances in the field of stem cell biology that have greatly improved our understanding of development and provided important insights into pathological processes. Transcription factors (TFs) play a central role in mediating stem cell proliferation, quiescence, and differentiation. One TF that contributes to these processes is Nuclear Factor One X (NFIX). Recently, NFIX activity has been shown to be essential in multiple organ systems and to have important translational impacts for human health. Here, we describe recent studies showing the contribution of NFIX to muscle development and muscular dystrophies, hematopoiesis, cancer, and neural stem cell biology, highlighting the importance of this knowledge in the development of therapeutic targets.
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Affiliation(s)
- Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Richard Gronostajski
- Department of Biochemistry, Genetics, Genomics & Bioinformatics Graduate Program, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.
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10
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Ferrari L, Bragato C, Brioschi L, Spreafico M, Esposito S, Pezzotta A, Pizzetti F, Moreno‐Fortuny A, Bellipanni G, Giordano A, Riva P, Frabetti F, Viani P, Cossu G, Mora M, Marozzi A, Pistocchi A. HDAC8 regulates canonical Wnt pathway to promote differentiation in skeletal muscles. J Cell Physiol 2018; 234:6067-6076. [DOI: 10.1002/jcp.27341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Cinzia Bragato
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta Milano Italy
- PhD Program in Neuroscience, University of Milano‐Bicocca Milano Italy
| | - Loredana Brioschi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Marco Spreafico
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Simona Esposito
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Alex Pezzotta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Fabrizio Pizzetti
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Artal Moreno‐Fortuny
- Division of Cell Matrix Biology and Regenerative Medicine Faculty of Biology, Medicine and Health, University of Manchester Manchester UK
- Developmental Genetics, Department of Biomedicine University of Basel Basel Switzerland
| | - Gianfranco Bellipanni
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University Philadelphia
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University Philadelphia
- Department of Medicine Surgery & Neuroscience, University of Siena Siena Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Flavia Frabetti
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Paola Viani
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine Faculty of Biology, Medicine and Health, University of Manchester Manchester UK
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta Milano Italy
| | - Anna Marozzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
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11
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Taglietti V, Angelini G, Mura G, Bonfanti C, Caruso E, Monteverde S, Le Carrou G, Tajbakhsh S, Relaix F, Messina G. RhoA and ERK signalling regulate the expression of the myogenic transcription factor Nfix. Development 2018; 145:dev.163956. [DOI: 10.1242/dev.163956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/18/2018] [Indexed: 12/27/2022]
Abstract
The transcription factor Nfix belongs to the nuclear factor one family and has an essential role in prenatal skeletal muscle development, where it is a master regulator of the transition from embryonic to foetal myogenesis. Recently, Nfix was shown to be involved in adult muscle regeneration and in muscular dystrophies. Here, we investigated the signalling that regulates Nfix expression, and show that JunB, a member of the AP-1 family, is an activator of Nfix, which then leads to foetal myogenesis. Moreover, we demonstrate that their expression is regulated through the RhoA/ROCK axis, which maintains embryonic myogenesis. Specifically, RhoA and ROCK repress ERK kinase activity, which promotes JunB and Nfix expression. Notably, the role of ERK in the activation of Nfix is conserved post-natally in satellite cells, which represent the canonical myogenic stem cells of adult muscle. As lack of Nfix in muscular dystrophies rescues the dystrophic phenotype, the identification of this pathway provides an opportunity to pharmacologically target Nfix in muscular dystrophies.
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Affiliation(s)
- Valentina Taglietti
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Giuseppe Angelini
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Giada Mura
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Chiara Bonfanti
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Enrico Caruso
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Stefania Monteverde
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Gilles Le Carrou
- Stem Cells & Development, Dept. of Developmental & Stem Cell Biology, Institut Pasteur, Paris, 75015 France
| | - Shahragim Tajbakhsh
- Stem Cells & Development, Dept. of Developmental & Stem Cell Biology, Institut Pasteur, Paris, 75015 France
- CNRS UMR 3738, Institut Pasteur, Paris, 75015 France
| | - Frédéric Relaix
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
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12
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Taglietti V, Maroli G, Cermenati S, Monteverde S, Ferrante A, Rossi G, Cossu G, Beltrame M, Messina G. Nfix Induces a Switch in Sox6 Transcriptional Activity to Regulate MyHC-I Expression in Fetal Muscle. Cell Rep 2017; 17:2354-2366. [PMID: 27880909 PMCID: PMC5149531 DOI: 10.1016/j.celrep.2016.10.082] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/08/2016] [Accepted: 10/24/2016] [Indexed: 02/01/2023] Open
Abstract
Sox6 belongs to the Sox gene family and plays a pivotal role in fiber type differentiation, suppressing transcription of slow-fiber-specific genes during fetal development. Here, we show that Sox6 plays opposite roles in MyHC-I regulation, acting as a positive and negative regulator of MyHC-I expression during embryonic and fetal myogenesis, respectively. During embryonic myogenesis, Sox6 positively regulates MyHC-I via transcriptional activation of Mef2C, whereas during fetal myogenesis, Sox6 requires and cooperates with the transcription factor Nfix in repressing MyHC-I expression. Mechanistically, Nfix is necessary for Sox6 binding to the MyHC-I promoter and thus for Sox6 repressive function, revealing a key role for Nfix in driving Sox6 activity. This feature is evolutionarily conserved, since the orthologs Nfixa and Sox6 contribute to repression of the slow-twitch phenotype in zebrafish embryos. These data demonstrate functional cooperation between Sox6 and Nfix in regulating MyHC-I expression during prenatal muscle development. Sox6 has opposite roles in MyHC-I regulation during embryonic and fetal myogenesis In embryonic muscle, Sox6 enhances MyHC-I expression via regulation of Mef2C In fetal muscle, Nfix is required for Sox6-mediated repression of MyHC-I The Sox6 and Nfixa orthologs cooperate in repressing smyhc1 in zebrafish
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Affiliation(s)
| | - Giovanni Maroli
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Solei Cermenati
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | | | - Andrea Ferrante
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Giuliana Rossi
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Giulio Cossu
- Department of Biosciences, University of Milan, Milan 20133, Italy; Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Oxford Road, M13 9PL Manchester, UK
| | - Monica Beltrame
- Department of Biosciences, University of Milan, Milan 20133, Italy
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13
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Cell-type-specific expression of NFIX in the developing and adult cerebellum. Brain Struct Funct 2016; 222:2251-2270. [PMID: 27878595 DOI: 10.1007/s00429-016-1340-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022]
Abstract
Transcription factors from the nuclear factor one (NFI) family have been shown to play a central role in regulating neural progenitor cell differentiation within the embryonic and post-natal brain. NFIA and NFIB, for instance, promote the differentiation and functional maturation of granule neurons within the cerebellum. Mice lacking Nfix exhibit delays in the development of neuronal and glial lineages within the cerebellum, but the cell-type-specific expression of this transcription factor remains undefined. Here, we examined the expression of NFIX, together with various cell-type-specific markers, within the developing and adult cerebellum using both chromogenic immunohistochemistry and co-immunofluorescence labelling and confocal microscopy. In embryos, NFIX was expressed by progenitor cells within the rhombic lip and ventricular zone. After birth, progenitor cells within the external granule layer, as well as migrating and mature granule neurons, expressed NFIX. Within the adult cerebellum, NFIX displayed a broad expression profile, and was evident within granule cells, Bergmann glia, and interneurons, but not within Purkinje neurons. Furthermore, transcriptomic profiling of cerebellar granule neuron progenitor cells showed that multiple splice variants of Nfix are expressed within this germinal zone of the post-natal brain. Collectively, these data suggest that NFIX plays a role in regulating progenitor cell biology within the embryonic and post-natal cerebellum, as well as an ongoing role within multiple neuronal and glial populations within the adult cerebellum.
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14
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Rossi G, Antonini S, Bonfanti C, Monteverde S, Vezzali C, Tajbakhsh S, Cossu G, Messina G. Nfix Regulates Temporal Progression of Muscle Regeneration through Modulation of Myostatin Expression. Cell Rep 2016; 14:2238-2249. [PMID: 26923583 PMCID: PMC4793149 DOI: 10.1016/j.celrep.2016.02.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 12/02/2015] [Accepted: 01/28/2016] [Indexed: 10/25/2022] Open
Abstract
Nfix belongs to a family of four highly conserved proteins that act as transcriptional activators and/or repressors of cellular and viral genes. We previously showed a pivotal role for Nfix in regulating the transcriptional switch from embryonic to fetal myogenesis. Here, we show that Nfix directly represses the Myostatin promoter, thus controlling the proper timing of satellite cell differentiation and muscle regeneration. Nfix-null mice display delayed regeneration after injury, and this deficit is reversed upon in vivo Myostatin silencing. Conditional deletion of Nfix in satellite cells results in a similar delay in regeneration, confirming the functional requirement for Nfix in satellite cells. Moreover, mice lacking Nfix show reduced myofiber cross sectional area and a predominant slow twitching phenotype. These data define a role for Nfix in postnatal skeletal muscle and unveil a mechanism for Myostatin regulation, thus providing insights into the modulation of its complex signaling pathway.
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Affiliation(s)
- Giuliana Rossi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Stefania Antonini
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Chiara Bonfanti
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Stefania Monteverde
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Chiara Vezzali
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr. Roux, 75015 Paris, France
| | - Giulio Cossu
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; Institute of Inflammation and Repair, University of Manchester, Oxford Road, M13 9PL Manchester, UK
| | - Graziella Messina
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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15
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Bragato C, Gaudenzi G, Blasevich F, Pavesi G, Maggi L, Giunta M, Cotelli F, Mora M. Zebrafish as a Model to Investigate Dynamin 2-Related Diseases. Sci Rep 2016; 6:20466. [PMID: 26842864 PMCID: PMC4740890 DOI: 10.1038/srep20466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
Mutations in the dynamin-2 gene (DNM2) cause autosomal dominant centronuclear myopathy (CNM) and dominant intermediate Charcot-Marie-Tooth (CMT) neuropathy type B (CMTDIB). As the relation between these DNM2-related diseases is poorly understood, we used zebrafish to investigate the effects of two different DNM2 mutations. First we identified a new alternatively spliced zebrafish dynamin-2a mRNA (dnm2a-v2) with greater similarity to human DNM2 than the deposited sequence. Then we knocked-down the zebrafish dnm2a, producing defects in muscle morphology. Finally, we expressed two mutated DNM2 mRNA by injecting zebrafish embryos with human mRNAs carrying the R522H mutation, causing CNM, or the G537C mutation, causing CMT. Defects arose especially in secondary motor neuron formation, with incorrect branching in embryos injected with CNM-mutated mRNA, and total absence of branching in those injected with CMT-mutated mRNA. Muscle morphology in embryos injected with CMT-mutated mRNA appeared less regularly organized than in those injected with CNM-mutated mRNA. Our results showing, a continuum between CNM and CMTDIB phenotypes in zebrafish, similarly to the human conditions, confirm this animal model to be a powerful tool to investigate mutations of DNM2 in vivo.
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Affiliation(s)
- Cinzia Bragato
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Germano Gaudenzi
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Flavia Blasevich
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Lorenzo Maggi
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Michele Giunta
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Franco Cotelli
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
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16
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Zhang X, Zhou Y, Pan C, Lei C, Dang R, Chen H, Lan X. Novel alternative splice variants of NFIX and their diverse mRNA expression patterns in dairy goat. Gene 2015; 569:250-8. [DOI: 10.1016/j.gene.2015.05.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/18/2015] [Accepted: 05/26/2015] [Indexed: 10/23/2022]
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17
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Villaruz LC, Huang G, Romkes M, Kirkwood JM, Buch SC, Nukui T, Flaherty KT, Lee SJ, Wilson MA, Nathanson KL, Benos PV, Tawbi HA. MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603. Clin Epigenetics 2015; 7:58. [PMID: 26052356 PMCID: PMC4457092 DOI: 10.1186/s13148-015-0092-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/27/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Carboplatin/paclitaxel (CP), with or without sorafenib, result in objective response rates of 18-20 % in unselected chemotherapy-naïve patients. Molecular predictors of survival and response to CP-based chemotherapy in metastatic melanoma (MM) are critical to improving the therapeutic index. Intergroup trial E2603 randomized MM patients to CP with or without sorafenib. Expression data were collected from pre-treatment formalin-fixed paraffin-embedded (FFPE) tumor tissues from 115 of 823 patients enrolled on E2603. The selected patients were balanced across treatment arms, BRAF status, and clinical outcome. We generated data using Nanostring array (microRNA (miRNA) expression) and DNA-mediated annealing, selection, extension and ligation (DASL)/Illumina microarrays (HT12 v4) (mRNA expression) with protocols optimized for FFPE samples. Integrative computational analysis was performed using a novel Tree-guided Recursive Cluster Selection (T-ReCS) [1] algorithm to select the most informative features/genes, followed by TargetScan miRNA target prediction (Human v6.2) and mirConnX [2] for network inference. RESULTS T-ReCS identified PLXNB1 as negatively associated with progression-free survival (PFS) and miR-659-3p as the primary miRNA associated positively with PFS. miR-659-3p was differentially expressed based on PFS but not based on treatment arm, BRAF or NRAS status. Dichotomized by median PFS (less vs greater than 4 months), miR-659-3p expression was significantly different. High miR-659-3p expression distinguished patients with responsive disease (complete or partial response) from patients with stable disease. miR-659-3p predicted gene targets include NFIX, which is a transcription factor known to interact with c-Jun and AP-1 in the context of developmental processes and disease. CONCLUSIONS This novel integrative analysis implicates miR-659-3p as a candidate predictive biomarker for MM patients treated with platinum-based chemotherapy and may serve to improve patient selection.
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Affiliation(s)
- Liza C Villaruz
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
| | - Grace Huang
- University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Marjorie Romkes
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
| | - John M Kirkwood
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
| | - Shama C Buch
- University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Tomoko Nukui
- University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Keith T Flaherty
- University of Pennsylvania, Philadelphia, PA USA.,Massachusetts General Hospital, Boston, MA USA
| | | | - Melissa A Wilson
- University of Pennsylvania, Philadelphia, PA USA.,New York University, New York, NY USA
| | | | | | - Hussein A Tawbi
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
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18
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Caprara GA, Perni S, Morabito C, Mariggiò MA, Guarnieri S. Specific association of growth-associated protein 43 with calcium release units in skeletal muscles of lower vertebrates. Eur J Histochem 2014; 58:2453. [PMID: 25578978 PMCID: PMC4289850 DOI: 10.4081/ejh.2014.2453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/06/2014] [Accepted: 11/06/2014] [Indexed: 11/22/2022] Open
Abstract
Growth-associated protein 43 (GAP43), is a strictly conserved protein among vertebrates implicated in neuronal development and neurite branching. Since GAP43 structure contains a calmodulin-binding domain, this protein is able to bind calmodulin and gather it nearby membrane network, thus regulating cytosolic calcium and consequently calcium-dependent intracellular events. Even if for many years GAP43 has been considered a neuronal-specific protein, evidence from different laboratories described its presence in myoblasts, myotubes and adult skeletal muscle fibers. Data from our laboratory showed that GAP43 is localized between calcium release units (CRUs) and mitochondria in mammalian skeletal muscle suggesting that, also in skeletal muscle, this protein can be a key player in calcium/calmodulin homeostasis. However, the previous studies could not clearly distinguish between a mitochondrion- or a triad-related positioning of GAP43. To solve this question, the expression and localization of GAP43 was studied in skeletal muscle of Xenopus and Zebrafish known to have triads located at the level of the Z-lines and mitochondria not closely associated with them. Western blotting and immunostaining experiments revealed the expression of GAP43 also in skeletal muscle of lower vertebrates (like amphibians and fishes), and that the protein is localized closely to the triad junction. Once more, these results and GAP43 structural features, support an involvement of the protein in the dynamic intracellular Ca2+ homeostasis, a common conserved role among the different species.
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Harris L, Genovesi LA, Gronostajski RM, Wainwright BJ, Piper M. Nuclear factor one transcription factors: Divergent functions in developmental versus adult stem cell populations. Dev Dyn 2014; 244:227-38. [PMID: 25156673 DOI: 10.1002/dvdy.24182] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor one (NFI) transcription factors are a group of site-specific DNA-binding proteins that are emerging as critical regulators of stem cell biology. During development NFIs promote the production of differentiated progeny at the expense of stem cell fate, with Nfi null mice exhibiting defects such as severely delayed brain and lung maturation, skeletomuscular defects and renal abnormalities, phenotypes that are often consistent with patients with congenital Nfi mutations. Intriguingly, recent research suggests that in adult tissues NFI factors play a qualitatively different role than during development, with NFIs serving to promote the survival and maintenance of slow-cycling adult stem cell populations rather than their differentiation. Here we review the role of NFI factors in development, largely focusing on their role as promoters of stem cell differentiation, and attempt to reconcile this with the emerging role of NFIs in adult stem cell niches.
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Affiliation(s)
- Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
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20
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Rossi G, Messina G. Comparative myogenesis in teleosts and mammals. Cell Mol Life Sci 2014; 71:3081-99. [PMID: 24664432 PMCID: PMC4111864 DOI: 10.1007/s00018-014-1604-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/17/2014] [Accepted: 03/06/2014] [Indexed: 01/02/2023]
Abstract
Skeletal myogenesis has been and is currently under extensive study in both mammals and teleosts, with the latter providing a good model for skeletal myogenesis because of their flexible and conserved genome. Parallel investigations of muscle studies using both these models have strongly accelerated the advances in the field. However, when transferring the knowledge from one model to the other, it is important to take into account both their similarities and differences. The main difficulties in comparing mammals and teleosts arise from their different temporal development. Conserved aspects can be seen for muscle developmental origin and segmentation, and for the presence of multiple myogenic waves. Among the divergences, many fish have an indeterminate growth capacity throughout their entire life span, which is absent in mammals, thus implying different post-natal growth mechanisms. This review covers the current state of the art on myogenesis, with a focus on the most conserved and divergent aspects between mammals and teleosts.
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Affiliation(s)
- Giuliana Rossi
- Department of Biosciences, University of Milan, 20133, Milan, Italy
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