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Casoni F, Croci L, Marroni F, Demenego G, Marullo C, Cremona O, Codazzi F, Consalez GG. A spatial-temporal map of glutamatergic neurogenesis in the murine embryonic cerebellar nuclei uncovers a high degree of cellular heterogeneity. J Anat 2024; 245:560-571. [PMID: 38970393 PMCID: PMC11424815 DOI: 10.1111/joa.14107] [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: 12/18/2023] [Revised: 05/23/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
The nuclei are the main output structures of the cerebellum. Each and every cerebellar cortical computation reaches several areas of the brain by means of cerebellar nuclei processing and integration. Nevertheless, our knowledge of these structures is still limited compared to the cerebellar cortex. Here, we present a mouse genetic inducible fate-mapping study characterizing rhombic lip-derived glutamatergic neurons of the nuclei, the most conspicuous family of long-range cerebellar efferent neurons. Glutamatergic neurons mainly occupy dorsal and lateral territories of the lateral and interposed nuclei, as well as the entire medial nucleus. In mice, they are born starting from about embryonic day 9.5, with a peak between 10.5 and 12.5, and invade the nuclei with a lateral-to-medial progression. While some markers label a heterogeneous population of neurons sharing a common location (BRN2), others appear to be lineage specific (TBR1, LMX1a, and MEIS2). A comparative analysis of TBR1 and LMX1a distributions reveals an incomplete overlap in their expression domains, in keeping with the existence of separate efferent subpopulations. Finally, some tagged glutamatergic progenitors are not labeled by any of the markers used in this study, disclosing further complexity. Taken together, our results obtained in late embryonic nuclei shed light on the heterogeneity of the excitatory neuron pool, underlying the diversity in connectivity and functions of this largely unexplored cerebellar territory. Our findings contribute to laying the groundwork for a comprehensive functional analysis of nuclear neuron subpopulations.
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Affiliation(s)
- Filippo Casoni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Laura Croci
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Marroni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giulia Demenego
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Chiara Marullo
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ottavio Cremona
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Franca Codazzi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - G Giacomo Consalez
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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Saeliw T, Kanlayaprasit S, Thongkorn S, Songsritaya K, Sanannam B, Jindatip D, Hu VW, Sarachana T. Investigation of chimeric transcripts derived from LINE-1 and Alu retrotransposons in cerebellar tissues of individuals with autism spectrum disorder (ASD). Sci Rep 2024; 14:21889. [PMID: 39300110 DOI: 10.1038/s41598-024-72334-x] [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: 06/17/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024] Open
Abstract
LINE-1 and Alu retrotransposons are components of the human genome and have been implicated in many human diseases. These elements can influence human transcriptome plasticity in various mechanisms. Chimeric transcripts derived from LINE-1 and Alu can also impact the human transcriptome, such as exonization and post-transcriptional modification. However, its specific role in ASD neuropathology remains unclear, particularly in the cerebellum tissues. We performed RNA-sequencing of post-mortem cerebellum tissues from ASD and unaffected individuals for transposable elements profiling and chimeric transcript identification. The majority of free transcripts of transposable elements were not changed in the cerebellum tissues of ASD compared with unaffected individuals. Nevertheless, we observed that chimeric transcripts derived from LINE-1 and Alu were embedded in the transcripts of differentially expressed genes in the cerebellum of ASD, and these genes were related to developments and abnormalities of the cerebellum. In addition, the expression levels of these genes were correlated with the significantly decreased thickness of the molecular layer in the cerebellum of ASD. We also found that global methylation and expression of LINE-1 and Alu elements were not changed in ASD, but observed in the ASD sub-phenotypes. Our findings showed associations between transposable elements and cerebellar abnormalities in ASD, particularly in distinct phenotypic subgroups. Further investigations using appropriate models are warranted to elucidate the structural and functional implications of LINE-1 and Alu elements in ASD neuropathology.
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Affiliation(s)
- Thanit Saeliw
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Songphon Kanlayaprasit
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Surangrat Thongkorn
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Kwanjira Songsritaya
- The M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Bumpenporn Sanannam
- Division of Anatomy, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, 12120, Thailand
| | - Depicha Jindatip
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20052, USA
| | - Tewarit Sarachana
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Sacco JC, Starr E, Weaver A, Dietz R, Spocter MA. Resequencing of the TMF-1 (TATA Element Modulatory Factor) regulated protein (TRNP1) gene in domestic and wild canids. Canine Med Genet 2023; 10:10. [PMID: 37968761 PMCID: PMC10647097 DOI: 10.1186/s40575-023-00133-0] [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: 07/06/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Cortical folding is related to the functional organization of the brain. The TMF-1 regulated protein (TRNP1) regulates the expansion and folding of the mammalian cerebral cortex, a process that may have been accelerated by the domestication of dogs. The objectives of this study were to sequence the TRNP1 gene in dogs and related canid species, provide evidence of its expression in dog brain and compare the genetic variation within dogs and across the Canidae. The gene was located in silico to dog chromosome 2. The sequence was experimentally confirmed by amplifying and sequencing the TRNP1 exonic and promoter regions in 72 canids (36 purebred dogs, 20 Gy wolves and wolf-dog hybrids, 10 coyotes, 5 red foxes and 1 Gy fox). RESULTS A partial TRNP1 transcript was isolated from several regions in the dog brain. Thirty genetic polymorphisms were found in the Canis sp. with 17 common to both dogs and wolves, and only one unique to dogs. Seven polymorphisms were observed only in coyotes. An additional 9 variants were seen in red foxes. Dogs were the least genetically diverse. Several polymorphisms in the promoter and 3'untranslated region were predicted to alter TRNP1 function by interfering with the binding of transcriptional repressors and miRNAs expressed in neural precursors. A c.259_264 deletion variant that encodes a polyalanine expansion was polymorphic in all species studied except for dogs. A stretch of 15 nucleotides that is found in other mammalian sequences (corresponding to 5 amino acids located between Pro58 and Ala59 in the putative dog protein) was absent from the TRNP1 sequences of all 5 canid species sequenced. Both of these aforementioned coding sequence variations were predicted to affect the formation of alpha helices in the disordered region of the TRNP1 protein. CONCLUSIONS Potentially functionally important polymorphisms in the TRNP1 gene are found within and across various Canis species as well as the red fox, and unique differences in protein structure have evolved and been conserved in the Canidae compared to all other mammalian species.
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Affiliation(s)
- James C Sacco
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA.
| | - Emma Starr
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Alyssa Weaver
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Rachel Dietz
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Muhammad A Spocter
- Department of Anatomy, Des Moines University, 50266, Des Moines, IA, USA
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Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li Y, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 2023; 382:eadf5357. [PMID: 37824674 PMCID: PMC10572106 DOI: 10.1126/science.adf5357] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.
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Affiliation(s)
- Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Qiurui Zeng
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rosa G. Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jiaying Xu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas D. Johnson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia K. Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nora Emerson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jon Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jasper Lee
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yang Li
- Ludwig Institute for Cancer Research, La Jolla, CA 92037, USA
| | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; 171 77 Stockholm, Sweden
| | - Michelle Liem
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Caz O’Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | | | | | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Boaz P. Levi
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; 171 77 Stockholm, Sweden
| | - Ed Lein
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92037, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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5
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Lee SY, Park JL, Kim K, Bae JS, Kim JY, Kim SY, Jung CK. Identification of NIFTP-Specific mRNA Markers for Reliable Molecular Diagnosis of Thyroid Tumors. Endocr Pathol 2023; 34:311-322. [PMID: 37658903 PMCID: PMC10511606 DOI: 10.1007/s12022-023-09781-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/05/2023]
Abstract
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) is a low-risk thyroid tumor with a favorable prognosis. Nonetheless, differentiating NIFTP from other thyroid tumors remains challenging, necessitating reliable diagnostic markers. This study is aimed at discovering NIFTP-specific mRNA markers through RNA sequencing analysis of thyroid tumor tissues. We performed mRNA expression profiling for 74 fresh frozen thyroid tissue samples, including NIFTP and benign and malignant follicular-cell-derived tumors. NIFTP/malignant tumors showed 255 downregulated genes and 737 upregulated genes compared to benign tumors. Venn diagram analysis revealed 19 significantly upregulated and 7 downregulated mRNAs in NIFTP. Akaike information criterion analysis allowed us to select OCLN, ZNF423, LYG1, and AQP5 mRNA markers. We subsequently developed a predictive model based on logistic regression analysis using these four mRNAs, which we validated in independent samples (n = 90) using a qRT-PCR assay. This model demonstrated high accuracy in predicting NIFTP in discovery dataset (AUC (area under the receiver operating characteristic) = 0.960) and the validation dataset (AUC = 0.757). Our results suggest that OCLN, ZNF423, LYG1, and AQP5 mRNA markers might serve as reliable molecular markers for identifying NIFTP among other thyroid tumors, ultimately aiding in accurate diagnosis and management of NIFTP patients.
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Affiliation(s)
- So-Yeon Lee
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134 Korea
| | - Jong-Lyul Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
| | - Kwangsoon Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ja Seong Bae
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Yoon Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
| | - Chan Kwon Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- College of Medicine, Cancer Research Institute, The Catholic University of Korea, Seoul, Korea
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6
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Keleher MR, Shubhangi S, Brown A, Duensing AM, Lixandrão ME, Gavin KM, Smith HA, Kechris KJ, Yang IV, Dabelea D, Boyle KE. Adipocyte hypertrophy in mesenchymal stem cells from infants of mothers with obesity. Obesity (Silver Spring) 2023; 31:2090-2102. [PMID: 37475691 PMCID: PMC10372711 DOI: 10.1002/oby.23803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 07/22/2023]
Abstract
OBJECTIVE Fat content of adipocytes derived from infant umbilical cord mesenchymal stem cells (MSCs) predicts adiposity in children through 4 to 6 years of age. This study tested the hypothesis that MSCs from infants born to mothers with obesity (Ob-MSCs) exhibit adipocyte hypertrophy and perturbations in genes regulating adipogenesis compared with MSCs from infants of mothers with normal weight (NW-MSCs). METHODS Adipogenesis was induced in MSCs embedded in three-dimensional hydrogel structures, and cell size and number were measured by three-dimensional imaging. Proliferation and protein markers of proliferation and adipogenesis in undifferentiated and adipocyte differentiating cells were measured. RNA sequencing was performed to determine pathways linked to adipogenesis phenotype. RESULTS In undifferentiated MSCs, greater zinc finger protein (Zfp)423 protein content was observed in Ob- versus NW-MSCs. Adipocytes from Ob-MSCs were larger but fewer than adipocytes from NW-MSCs. RNA sequencing analysis showed that Zfp423 protein correlated with mRNA expression of genes enriched for cell cycle, MSC lineage specification, inflammation, and metabolism pathways. MSC proliferation was not different before differentiation but declined faster in Ob-MSCs upon adipogenic induction. CONCLUSIONS Ob-MSCs have an intrinsic propensity for adipocyte hypertrophy and reduced hyperplasia during adipogenesis in vitro, perhaps linked to greater Zfp423 content and changes in cell cycle pathway gene expression.
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Affiliation(s)
- Madeline Rose Keleher
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
| | - Shreya Shubhangi
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Asya Brown
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Allison M. Duensing
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Manoel E. Lixandrão
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Kathleen M. Gavin
- Division of Geriatric Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
- Eastern Colorado VA Geriatric, Research, Education, and Clinical Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Harry A. Smith
- Department of Biostatistics & Informatics, Colorado School of Public Health, Aurora, CO USA
| | - Katerina J. Kechris
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
- Department of Biostatistics & Informatics, Colorado School of Public Health, Aurora, CO USA
| | - Ivana V. Yang
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO USA
| | - Dana Dabelea
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Kristen E. Boyle
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
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7
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Chang KJ, Wu HY, Yarmishyn AA, Li CY, Hsiao YJ, Chi YC, Lo TC, Dai HJ, Yang YC, Liu DH, Hwang DK, Chen SJ, Hsu CC, Kao CL. Genetics behind Cerebral Disease with Ocular Comorbidity: Finding Parallels between the Brain and Eye Molecular Pathology. Int J Mol Sci 2022; 23:9707. [PMID: 36077104 PMCID: PMC9456058 DOI: 10.3390/ijms23179707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cerebral visual impairments (CVIs) is an umbrella term that categorizes miscellaneous visual defects with parallel genetic brain disorders. While the manifestations of CVIs are diverse and ambiguous, molecular diagnostics stand out as a powerful approach for understanding pathomechanisms in CVIs. Nevertheless, the characterization of CVI disease cohorts has been fragmented and lacks integration. By revisiting the genome-wide and phenome-wide association studies (GWAS and PheWAS), we clustered a handful of renowned CVIs into five ontology groups, namely ciliopathies (Joubert syndrome, Bardet-Biedl syndrome, Alstrom syndrome), demyelination diseases (multiple sclerosis, Alexander disease, Pelizaeus-Merzbacher disease), transcriptional deregulation diseases (Mowat-Wilson disease, Pitt-Hopkins disease, Rett syndrome, Cockayne syndrome, X-linked alpha-thalassaemia mental retardation), compromised peroxisome disorders (Zellweger spectrum disorder, Refsum disease), and channelopathies (neuromyelitis optica spectrum disorder), and reviewed several mutation hotspots currently found to be associated with the CVIs. Moreover, we discussed the common manifestations in the brain and the eye, and collated animal study findings to discuss plausible gene editing strategies for future CVI correction.
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Affiliation(s)
- Kao-Jung Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Hsin-Yu Wu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | | | - Cheng-Yi Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yu-Jer Hsiao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chun Chi
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Tzu-Chen Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - He-Jhen Dai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chiang Yang
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ding-Hao Liu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - De-Kuang Hwang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Chien Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chung-Lan Kao
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Department of Physical Medicine and Rehabilitation, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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Hawkes R. Cerebellar Patterning Defects in Mutant Mice. Front Neurosci 2021; 15:787425. [PMID: 34955734 PMCID: PMC8692567 DOI: 10.3389/fnins.2021.787425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022] Open
Abstract
The cerebellar cortex is highly compartmentalized and serves as a remarkable model for pattern formation throughout the brain. In brief, the adult cerebellar cortex is subdivided into five anteroposterior units—transverse zones—and subsequently, each zone is divided into ∼20 parasagittal stripes. Zone-and-stripe pattern formation involves the interplay of two parallel developmental pathways—one for inhibitory neurons, the second for excitatory. In the inhibitory pathway, progenitor cells of the 4th ventricle generate the Purkinje cells and inhibitory interneurons. In the excitatory pathway, progenitor cells in the upper rhombic lip give rise to the external granular layer, and subsequently to the granular layer of the adult. Both the excitatory and inhibitory developmental pathways are spatially patterned and the interactions of the two generate the complex topography of the adult. This review briefly describes the cellular and molecular mechanisms that underly zone-and-stripe development with a particular focus on mutations known to interfere with normal cerebellar development and the light they cast on the mechanisms of pattern formation.
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Affiliation(s)
- Richard Hawkes
- Department of Cell Biology, Cumming School of Medicine, Anatomy and Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
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9
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Su C, Argenziano M, Lu S, Pippin JA, Pahl MC, Leonard ME, Cousminer DL, Johnson ME, Lasconi C, Wells AD, Chesi A, Grant SFA. 3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders. Prog Neurobiol 2021; 201:102000. [PMID: 33545232 PMCID: PMC8096691 DOI: 10.1016/j.pneurobio.2021.102000] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/07/2020] [Accepted: 01/23/2021] [Indexed: 12/27/2022]
Abstract
Neurodevelopmental disorders are thought to arise from interrupted development of the brain at an early age. Genome-wide association studies (GWAS) have identified hundreds of loci associated with susceptibility to neurodevelopmental disorders; however, which noncoding variants regulate which genes at these loci is often unclear. To implicate neuronal GWAS effector genes, we performed an integrated analysis of transcriptomics, epigenomics and chromatin conformation changes during the development from Induced pluripotent stem cell-derived neuronal progenitor cells (NPCs) into neurons using a combination of high-resolution promoter-focused Capture-C, ATAC-seq and RNA-seq. We observed that gene expression changes during the NPC-to-neuron transition were highly dependent on both promoter accessibility changes and long-range interactions which connect distal cis-regulatory elements (enhancer or silencers) to developmental-stage-specific genes. These genome-scale promoter-cis-regulatory-element atlases implicated 454 neurodevelopmental disorder-associated, putative causal variants mapping to 600 distal targets. These putative effector genes were significantly enriched for pathways involved in the regulation of neuronal development and chromatin organization, with 27 % expressed in a stage-specific manner. The intersection of open chromatin and chromatin conformation revealed development-stage-specific gene regulatory architectures during neuronal differentiation, providing a rich resource to aid characterization of the genetic and developmental basis of neurodevelopmental disorders.
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Affiliation(s)
- Chun Su
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Mariana Argenziano
- Heart Institute, University of South Florida, 560 Channelside Dr, Tampa FL 33602, United States
| | - Sumei Lu
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - James A Pippin
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Matthew C Pahl
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Michelle E Leonard
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Diana L Cousminer
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Matthew E Johnson
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Chiara Lasconi
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Andrew D Wells
- Department of Pathology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Alessandra Chesi
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States
| | - Struan F A Grant
- Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States; Division of Diabetes and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA, United States; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA, United States.
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10
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Stokman MF, Saunier S, Benmerah A. Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis. Front Cell Dev Biol 2021; 9:653138. [PMID: 34055783 PMCID: PMC8155538 DOI: 10.3389/fcell.2021.653138] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
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Affiliation(s)
- Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Sophie Saunier
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Alexandre Benmerah
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
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11
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Consalez GG, Goldowitz D, Casoni F, Hawkes R. Origins, Development, and Compartmentation of the Granule Cells of the Cerebellum. Front Neural Circuits 2021; 14:611841. [PMID: 33519389 PMCID: PMC7843939 DOI: 10.3389/fncir.2020.611841] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/17/2020] [Indexed: 12/21/2022] Open
Abstract
Granule cells (GCs) are the most numerous cell type in the cerebellum and indeed, in the brain: at least 99% of all cerebellar neurons are granule cells. In this review article, we first consider the formation of the upper rhombic lip, from which all granule cell precursors arise, and the way by which the upper rhombic lip generates the external granular layer, a secondary germinal epithelium that serves to amplify the upper rhombic lip precursors. Next, we review the mechanisms by which postmitotic granule cells are generated in the external granular layer and migrate radially to settle in the granular layer. In addition, we review the evidence that far from being a homogeneous population, granule cells come in multiple phenotypes with distinct topographical distributions and consider ways in which the heterogeneity of granule cells might arise during development.
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Affiliation(s)
- G Giacomo Consalez
- Division of Neuroscience, San Raffaele Scientific Institute, San Raffaele University, Milan, Italy
| | - Daniel Goldowitz
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Filippo Casoni
- Division of Neuroscience, San Raffaele Scientific Institute, San Raffaele University, Milan, Italy
| | - Richard Hawkes
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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12
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Casoni F, Croci L, Vincenti F, Podini P, Riba M, Massimino L, Cremona O, Consalez GG. ZFP423 regulates early patterning and multiciliogenesis in the hindbrain choroid plexus. Development 2020; 147:dev.190173. [PMID: 33046507 DOI: 10.1242/dev.190173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/05/2020] [Indexed: 12/28/2022]
Abstract
The choroid plexus (ChP) is a secretory tissue that produces cerebrospinal fluid (CSF) secreted into the ventricular system. It is a monolayer of secretory, multiciliated epithelial cells derived from neuroepithelial progenitors and overlying a stroma of mesenchymal cells of mesodermal origin. Zfp423, which encodes a Kruppel-type zinc-finger transcription factor essential for cerebellar development and mutated in rare cases of cerebellar vermis hypoplasia/Joubert syndrome and other ciliopathies, is expressed in the hindbrain roof plate, from which the IV ventricle ChP arises, and, later, in mesenchymal cells, which give rise to the stroma and leptomeninges. Mouse Zfp423 mutants display a marked reduction of the hindbrain ChP (hChP), which: (1) fails to express established markers of its secretory function and genes implicated in its development and maintenance (Lmx1a and Otx2); (2) shows a perturbed expression of signaling pathways previously unexplored in hChP patterning (Wnt3); and (3) displays a lack of multiciliated epithelial cells and a profound dysregulation of master genes of multiciliogenesis (Gmnc). Our results propose that Zfp423 is a master gene and one of the earliest known determinants of hChP development.
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Affiliation(s)
- Filippo Casoni
- Università Vita-Salute San Raffaele, Milan, Italy .,Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Laura Croci
- Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | | | - Paola Podini
- Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Michela Riba
- Center for Omics Sciences, IRCCS, San Raffaele Hospital, Milan 20132, Italy
| | - Luca Massimino
- Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Ottavio Cremona
- Università Vita-Salute San Raffaele, Milan, Italy.,Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - G Giacomo Consalez
- Università Vita-Salute San Raffaele, Milan, Italy.,Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
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13
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Deshpande O, Lara RZ, Zhang OR, Concepcion D, Hamilton BA. ZNF423 patient variants, truncations, and in-frame deletions in mice define an allele-dependent range of midline brain abnormalities. PLoS Genet 2020; 16:e1009017. [PMID: 32925911 PMCID: PMC7515201 DOI: 10.1371/journal.pgen.1009017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/24/2020] [Accepted: 07/29/2020] [Indexed: 11/18/2022] Open
Abstract
Interpreting rare variants remains a challenge in personal genomics, especially for disorders with several causal genes and for genes that cause multiple disorders. ZNF423 encodes a transcriptional regulatory protein that intersects several developmental pathways. ZNF423 has been implicated in rare neurodevelopmental disorders, consistent with midline brain defects in Zfp423-mutant mice, but pathogenic potential of most patient variants remains uncertain. We engineered ~50 patient-derived and small deletion variants into the highly-conserved mouse ortholog and examined neuroanatomical measures for 791 littermate pairs. Three substitutions previously asserted pathogenic appeared benign, while a fourth was effectively null. Heterozygous premature termination codon (PTC) variants showed mild haploabnormality, consistent with loss-of-function intolerance inferred from human population data. In-frame deletions of specific zinc fingers showed mild to moderate abnormalities, as did low-expression variants. These results affirm the need for functional validation of rare variants in biological context and demonstrate cost-effective modeling of neuroanatomical abnormalities in mice.
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Affiliation(s)
- Ojas Deshpande
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, Gilman Drive, La Jolla, CA, United States of America
| | - Raquel Z. Lara
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, Gilman Drive, La Jolla, CA, United States of America
| | - Oliver R. Zhang
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, Gilman Drive, La Jolla, CA, United States of America
| | - Dorothy Concepcion
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, Gilman Drive, La Jolla, CA, United States of America
| | - Bruce A. Hamilton
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Medicine, Institute for Genomic Medicine, Rebecca and John Moores UCSD Cancer Center, University of California, San Diego School of Medicine, Gilman Drive, La Jolla, CA, United States of America
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14
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The Joubert Syndrome Gene arl13b is Critical for Early Cerebellar Development in Zebrafish. Neurosci Bull 2020; 36:1023-1034. [PMID: 32812127 PMCID: PMC7475164 DOI: 10.1007/s12264-020-00554-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/05/2020] [Indexed: 12/14/2022] Open
Abstract
Joubert syndrome is characterized by unique malformation of the cerebellar vermis. More than thirty Joubert syndrome genes have been identified, including ARL13B. However, its role in cerebellar development remains unexplored. We found that knockdown or knockout of arl13b impaired balance and locomotion in zebrafish larvae. Granule cells were selectively reduced in the corpus cerebelli, a structure homologous to the mammalian vermis. Purkinje cell progenitors were also selectively disturbed dorsomedially. The expression of atoh1 and ptf1, proneural genes of granule and Purkinje cells, respectively, were selectively down-regulated along the dorsal midline of the cerebellum. Moreover, wnt1, which is transiently expressed early in cerebellar development, was selectively reduced. Intriguingly, activating Wnt signaling partially rescued the granule cell defects in arl13b mutants. These findings suggested that Arl13b is necessary for the early development of cerebellar granule and Purkinje cells. The arl13b-deficient zebrafish can serve as a model organism for studying Joubert syndrome.
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15
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Fredrickx E, Colombo E, Canevazzi P, La Marca R, Pellegatta M, Dina G, Podini P, Nave KA, Quattrini A, Taveggia C. Ablation of neuronal ADAM17 impairs oligodendrocyte differentiation and myelination. Glia 2019; 68:1148-1164. [PMID: 31851405 DOI: 10.1002/glia.23765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 11/09/2022]
Abstract
Myelin, one of the most important adaptations of vertebrates, is essential to ensure efficient propagation of the electric impulse in the nervous system and to maintain neuronal integrity. In the central nervous system (CNS), the development of oligodendrocytes and the process of myelination are regulated by the coordinated action of several positive and negative cell-extrinsic factors. We and others previously showed that secretases regulate the activity of proteins essential for myelination. We now report that the neuronal α-secretase ADAM17 controls oligodendrocyte differentiation and myelin formation in the CNS. Ablation of Adam17 in neurons impairs in vivo and in vitro oligodendrocyte differentiation, delays myelin formation throughout development and results in hypomyelination. Furthermore, we show that this developmental defect is, in part, the result of altered Notch/Jagged 1 signaling. Surprisingly, in vivo conditional loss of Adam17 in immature oligodendrocytes has no effect on myelin formation. Collectively, our data indicate that the neuronal α-secretase ADAM17 is required for proper CNS myelination. Further, our studies confirm that secretases are important post-translational regulators of myelination although the mechanisms controlling CNS and peripheral nervous system (PNS) myelination are distinct.
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Affiliation(s)
- Evelien Fredrickx
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Colombo
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Canevazzi
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rosa La Marca
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marta Pellegatta
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgia Dina
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Klaus A Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Angelo Quattrini
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carla Taveggia
- INSPE, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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16
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Paul JL, Dashtipour K, Chen Z, Wang C. DNA methylome study of human cerebellar tissues identified genes and pathways possibly involved in essential tremor. PRECISION CLINICAL MEDICINE 2019; 2:221-234. [PMID: 31886034 PMCID: PMC6927097 DOI: 10.1093/pcmedi/pbz028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/30/2019] [Accepted: 12/01/2019] [Indexed: 01/13/2023] Open
Abstract
Background Essential tremor (ET) is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis. It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of ET. DNA methylome interrogation of cerebellar tissue may help shine some light on the understanding of the mechanism of the development of ET. Our study used postmortem human cerebellum tissue samples collected from 12 ET patients and 11 matched non-ET controls for DNA methylome study to identify differentially methylated genes in ET. Results Using Nugen’s Ovation reduced representation bisulfite sequencing (RRBS), we identified 753 genes encompassing 938 CpG sites with significant differences in DNA methylation between the ET and the control group. Identified genes were further analyzed with Ingenuity Pathway Analysis (IPA) by which we identified certain significant pathways, upstream regulators, diseases and functions, and networks associated with ET. Conclusions Our study provides evidence that there are significant differences in DNA methylation patterns between the ET and control samples, suggesting that the methylation alteration of certain genes in the cerebellum may be associated with ET pathogenesis. The identified genes allude to the GABAergic hypothesis which supports the notation that ET is a neurodegenerative disease, particularly involving the cerebellum.
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Affiliation(s)
- Jennifer L Paul
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Khashayar Dashtipour
- Division of Movement Disorders, Department of Neurology, Loma Linda University Medical Center, Loma Linda, CA 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.,Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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17
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Zheng JT, Zhang N, Yu YH, Gong PT, Li XH, Wu N, Wang C, Wang XC, Li X, Li JH, Zhang XC. Identification of a TRBD zinc finger-interacting protein in Giardia duodenalis and its regulation of telomerase. Parasit Vectors 2019; 12:568. [PMID: 31783771 PMCID: PMC6884763 DOI: 10.1186/s13071-019-3821-0] [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: 07/16/2019] [Accepted: 11/21/2019] [Indexed: 11/10/2022] Open
Abstract
Background Giardia duodenalis causes giardiasis, with diarrhea as the primary symptom. The trophozoite proliferation of this zoonotic parasite is mainly affected by telomerase, although the mechanism of telomerase regulation has not been thoroughly analyzed. Methods This study was performed to identify the telomerase RNA-binding domain (TRBD)-interacting protein in G. duodenalis and its regulation of telomerase. Interaction between TRBD and interacting proteins was verified via pulldown assays and co-immunoprecipitation (co-IP) techniques, and the subcellular localization of the protein interactions was determined in vivo via split SNAP-tag labeling. The hammerhead ribozyme was designed to deplete the mRNA of TRBD-interacting proteins. Results Using TRBD as bait, we identified zinc-finger domain (ZFD)-containing proteins and verified it via pulldown and co-IP experiments. Protein-protein interaction occurred in the nuclei of 293T cells and both nuclei of G. duodenalis. The hammerhead ribozyme depleted ZFD mRNA levels, which reduced the reproduction rate of G. duodenalis, telomerase activity and telomere length. Conclusions Our findings suggest that ZFD may regulate telomere function in G. duodenalis nuclei.
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Affiliation(s)
- Jing-Tong Zheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.,Department of Pathogenobiology, College of Basic Medicine, Jilin University, Changchun, 130021, Jilin, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.,State and Local Joint Engineering Laboratory for Animal Models of Human Diseases, Academy of Translational Medicine, First Hospital, Jilin University, Changchun, 130021, China
| | - Yan-Hui Yu
- Clinical Laboratory of Second Hospital, Jilin University, Changchun, 130021, China
| | - Peng-Tao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xian-He Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Na Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Can Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xiao-Cen Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jian-Hua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
| | - Xi-Chen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
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18
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Forese MG, Pellegatta M, Canevazzi P, Gullotta GS, Podini P, Rivellini C, Previtali SC, Bacigaluppi M, Quattrini A, Taveggia C. Prostaglandin D2 synthase modulates macrophage activity and accumulation in injured peripheral nerves. Glia 2019; 68:95-110. [DOI: 10.1002/glia.23705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Maria Grazia Forese
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Marta Pellegatta
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Paolo Canevazzi
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Giorgia S. Gullotta
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Paola Podini
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Cristina Rivellini
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Stefano C. Previtali
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Marco Bacigaluppi
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Angelo Quattrini
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
| | - Carla Taveggia
- Division of Neuroscience, INSPEIRCCS San Raffaele Scientific Institute Milan Italy
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19
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Shang Y, Li Y, Zhang Y, Wang J. ZNF436 promotes tumor cell proliferation through transcriptional activation of BCL10 in glioma. Biochem Biophys Res Commun 2019; 515:572-578. [PMID: 31178130 DOI: 10.1016/j.bbrc.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 01/20/2023]
Abstract
Transcriptional factors (TFs) are key regulators in orchestrating gene transcription during cancer development. However, their roles in glioma remain elusive. Here, we analyzed the differential expression of TFs and identified ZNF436 is upregulated in glioblastoma and Lower Grade Glioma patients. High expression of ZNF436 is positively associated with poor overall survival and regulated by CREB1 in glioma cells. Knockdown of ZNF436 significantly abolished glioma cells proliferation in vitro. RNA sequencing revealed that ZNF436 regulates cell cycle and controlling BCL10 expression. Overexpression of BCL10 promoted glioma cells growth and rescued the malignant behavior in ZNF436-knockdown cells. High levels of BCL10 also result in a worse prognosis in glioma patients. Taken together, our findings identify the CREB1/ZNF436/BCL10 axis represents a novel, potential therapeutic target for glioma interventions.
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Affiliation(s)
- Yinwu Shang
- Department of Neurosurgery, Gansu Provincial People's Hospital, Lanzhou City, 730000, Gansu Province, China
| | - Yuchen Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yinian Zhang
- Department of Neurosurgery and Laboratory of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Jianjun Wang
- Department of Pediatric Medicine, Gansu Provincial People's Hospital, Lanzhou City, 730000, Gansu Province, China.
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20
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Addison WN, Hall KC, Kokabu S, Matsubara T, Fu MM, Gori F, Baron R. Zfp423 Regulates Skeletal Muscle Regeneration and Proliferation. Mol Cell Biol 2019; 39:e00447-18. [PMID: 30692273 PMCID: PMC6447414 DOI: 10.1128/mcb.00447-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/07/2018] [Accepted: 01/23/2019] [Indexed: 12/27/2022] Open
Abstract
Satellite cells (SCs) are skeletal muscle stem cells that proliferate in response to injury and provide myogenic precursors for growth and repair. Zfp423 is a transcriptional cofactor expressed in multiple immature cell populations, such as neuronal precursors, mesenchymal stem cells, and preadipocytes, where it regulates lineage allocation, proliferation, and differentiation. Here, we show that Zfp423 regulates myogenic progression during muscle regeneration. Zfp423 is undetectable in quiescent SCs but becomes expressed during SC activation. After expansion, Zfp423 is gradually downregulated as committed SCs terminally differentiate. Mice with satellite-cell-specific Zfp423 deletion exhibit severely impaired muscle regeneration following injury, with aberrant SC expansion, defective cell cycle exit, and failure to transition efficiently from the proliferative stage toward commitment. Consistent with a cell-autonomous role of Zfp423, shRNA-mediated knockdown of Zfp423 in myoblasts inhibits differentiation. Surprisingly, forced expression of Zfp423 in myoblasts induces differentiation into adipocytes and arrests myogenesis. Affinity purification of Zfp423 in myoblasts identified Satb2 as a nuclear partner of Zfp423 that cooperatively enhances Zfp423 transcriptional activity, which in turn affects myoblast differentiation. In conclusion, by controlling SC expansion and proliferation, Zfp423 is essential for muscle regeneration. Tight regulation of Zfp423 expression is essential for normal progression of muscle progenitors from proliferation to differentiation.
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MESH Headings
- Adipocytes/cytology
- Animals
- Cell Differentiation/physiology
- Cell Proliferation/physiology
- Cells, Cultured
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Mesenchymal Stem Cells/cytology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Muscle Development/physiology
- Muscle Fibers, Skeletal/metabolism
- Muscle, Skeletal/cytology
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/physiology
- Regeneration/physiology
- Satellite Cells, Skeletal Muscle/cytology
- Satellite Cells, Skeletal Muscle/metabolism
- Satellite Cells, Skeletal Muscle/physiology
- Signal Transduction
- Stem Cells/cytology
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Wound Healing
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Affiliation(s)
- William N Addison
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Katherine C Hall
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Shoichiro Kokabu
- Division of Molecular Signaling and Biochemistry, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - Takuma Matsubara
- Division of Molecular Signaling and Biochemistry, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - Martin M Fu
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Francesca Gori
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Roland Baron
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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21
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4-Hydroxytamoxifen enhances sensitivity of estrogen receptor α-positive breast cancer to docetaxel in an estrogen and ZNF423 SNP-dependent fashion. Breast Cancer Res Treat 2019; 175:567-578. [DOI: 10.1007/s10549-019-05194-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/05/2019] [Indexed: 01/12/2023]
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22
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Chen C, Meng Q, Xia Y, Ding C, Wang L, Dai R, Cheng L, Gunaratne P, Gibbs RA, Min S, Coarfa C, Reid JG, Zhang C, Jiao C, Jiang Y, Giase G, Thomas A, Fitzgerald D, Brunetti T, Shieh A, Xia C, Wang Y, Wang Y, Badner JA, Gershon ES, White KP, Liu C. The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders. Sci Transl Med 2018; 10:eaat8178. [PMID: 30545964 PMCID: PMC6494100 DOI: 10.1126/scitranslmed.aat8178] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022]
Abstract
Schizophrenia and bipolar disorder are complex psychiatric diseases with risks contributed by multiple genes. Dysregulation of gene expression has been implicated in these disorders, but little is known about such dysregulation in the human brain. We analyzed three transcriptome datasets from 394 postmortem brain tissue samples from patients with schizophrenia or bipolar disorder or from healthy control individuals without a known history of psychiatric disease. We built genome-wide coexpression networks that included microRNAs (miRNAs). We identified a coexpression network module that was differentially expressed in the brain tissue from patients compared to healthy control individuals. This module contained genes that were principally involved in glial and neural cell genesis and glial cell differentiation, and included schizophrenia risk genes carrying rare variants. This module included five miRNAs and 545 mRNAs, with six transcription factors serving as hub genes in this module. We found that the most connected transcription factor gene POU3F2, also identified on a genome-wide association study for bipolar disorder, could regulate the miRNA hsa-miR-320e and other putative target mRNAs. These regulatory relationships were replicated using PsychENCODE/BrainGVEX datasets and validated by knockdown and overexpression experiments in SH-SY5Y cells and human neural progenitor cells in vitro. Thus, we identified a brain gene expression module that was enriched for rare coding variants in genes associated with schizophrenia and that contained the putative bipolar disorder risk gene POU3F2 The transcription factor POU3F2 may be a key regulator of gene expression in this disease-associated gene coexpression module.
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Affiliation(s)
- Chao Chen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qingtuan Meng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yan Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chaodong Ding
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Le Wang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Child Health Institute of New Jersey, Department of Neuroscience, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Rujia Dai
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Lijun Cheng
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Preethi Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shishi Min
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Cristian Coarfa
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Chunling Zhang
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chuan Jiao
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Yi Jiang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Gina Giase
- School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Amber Thomas
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Tonya Brunetti
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Annie Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Cuihua Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yongjun Wang
- The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yunpeng Wang
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- LifeSpan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway
| | - Judith A Badner
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, USA
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Tempus Labs Inc., Chicago, IL, USA
| | - Chunyu Liu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Psychology, Shaanxi Normal University, Xi'an, China
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23
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Schilling K. Moving into shape: cell migration during the development and histogenesis of the cerebellum. Histochem Cell Biol 2018; 150:13-36. [DOI: 10.1007/s00418-018-1677-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
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24
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Massimino L, Flores-Garcia L, Di Stefano B, Colasante G, Icoresi-Mazzeo C, Zaghi M, Hamilton BA, Sessa A. TBR2 antagonizes retinoic acid dependent neuronal differentiation by repressing Zfp423 during corticogenesis. Dev Biol 2018; 434:231-248. [PMID: 29305158 PMCID: PMC7032051 DOI: 10.1016/j.ydbio.2017.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/26/2017] [Accepted: 12/28/2017] [Indexed: 01/14/2023]
Abstract
During cerebral cortex development, neural progenitors are required to elaborate a variety of cell differentiation signals to which they are continuously exposed. RA acid is a potent inducer of neuronal differentiation as it was found to influence cortical development. We report herein that TBR2, a transcription factor specific to Intermediate (Basal) Neural Progenitors (INPs), represses activation of the RA responsive element and expression of RA target genes in cell lines. This repressive action on RA signaling was functionally confirmed by the decrease of RA-mediated neuronal differentiation in neural stem cells stably overexpressing TBR2. In vivo mapping of RA activity in the developing cortex indicated that RA activity is detected in radial glial cells and subsequently downregulated in INPs, revealing a fine cell-type specific regulation of its signaling. Thus, TBR2 might be a molecular player in opposing RA signaling in INPs. Interestingly, this negative regulation is achieved at least in part by directly repressing the critical nuclear RA co-factor ZFP423. Indeed, we found ZFP423 to be expressed in the developing cortex and promote RA-dependent neuronal differentiation. These data indicate that TBR2 contributes to suppressing RA signaling in INPs, thereby enabling them to re-enter the cell cycle and delay neuronal differentiation.
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Affiliation(s)
- Luca Massimino
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Lisbeth Flores-Garcia
- Departments of Cellular&Molecular Medicine and Medicine, Moores Cancer Center, and Institute for Genomic Medicine, University of California, 9500 Gilman Drive, La Jolla, San Diego, CA 92093-0644, USA
| | - Bruno Di Stefano
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gaia Colasante
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Cecilia Icoresi-Mazzeo
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Bruce A Hamilton
- Departments of Cellular&Molecular Medicine and Medicine, Moores Cancer Center, and Institute for Genomic Medicine, University of California, 9500 Gilman Drive, La Jolla, San Diego, CA 92093-0644, USA
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.
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25
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Bond HM, Scicchitano S, Chiarella E, Amodio N, Lucchino V, Aloisio A, Montalcini Y, Mesuraca M, Morrone G. ZNF423: A New Player in Estrogen Receptor-Positive Breast Cancer. Front Endocrinol (Lausanne) 2018; 9:255. [PMID: 29867779 PMCID: PMC5968090 DOI: 10.3389/fendo.2018.00255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/03/2018] [Indexed: 01/13/2023] Open
Abstract
Preventive therapy can target hormone-responsive breast cancer (BC) by treatment with selective estrogen receptor modulators (SERMs) and reduce the incidence of BC. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) with relevant predictive values, SNPs in the ZNF423 gene were associated with decreased risk of BC during SERM therapy, and SNPs in the Cathepsin O gene with an increased risk. ZNF423, which was not previously associated with BC is a multifunctional transcription factor known to have a role in development, neurogenesis, and adipogenesis and is implicated in other types of cancer. ZNF423 is transcriptionally controlled by the homolog ZNF521, early B cell factor transcription factor, epigenetic silencing of the promoter by CpG island hyper-methylation, and also by ZNF423 itself in an auto-regulatory loop. In BC cells, ZNF423 expression is found to be induced by estrogen, dependent on the binding of the estrogen receptor and calmodulin-like 3 to SNPs in ZNP423 intronic sites in proximity to consensus estrogen response elements. ZNF423 has also been shown to play a mechanistic role by trans-activating the tumor suppressor BRCA1 and thus modulating the DNA damage response. Even though recent extensive trial studies did not classify these SNPs with the highest predictive values, for inclusion in polygenic SNP analysis, the mechanism unveiled in these studies has introduced ZNF423 as a factor important in the control of the estrogen response. Here, we aim at providing an overview of ZNF423 expression and functional role in human malignancies, with a specific focus on its implication in hormone-responsive BC.
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Affiliation(s)
- Heather M. Bond
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Heather M. Bond, ; Maria Mesuraca, ; Giovanni Morrone,
| | - Stefania Scicchitano
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Emanuela Chiarella
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Nicola Amodio
- Laboratory of Medical Oncology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Valeria Lucchino
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Annamaria Aloisio
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Ylenia Montalcini
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Maria Mesuraca
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Heather M. Bond, ; Maria Mesuraca, ; Giovanni Morrone,
| | - Giovanni Morrone
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Heather M. Bond, ; Maria Mesuraca, ; Giovanni Morrone,
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