1
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Minto MS, Sotelo-Fonseca JE, Ramesh V, West AE. Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation. BMC Biol 2024; 22:189. [PMID: 39218853 PMCID: PMC11367862 DOI: 10.1186/s12915-024-01989-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The Zic family of transcription factors (TFs) promote both proliferation and maturation of cerebellar granule neurons (CGNs), raising the question of how a single, constitutively expressed TF family can support distinct developmental processes. Here we use an integrative experimental and bioinformatic approach to discover the regulatory relationship between Zic TF binding and changing programs of gene transcription during postnatal CGN differentiation. RESULTS We first established a bioinformatic pipeline to integrate Zic ChIP-seq data from the developing mouse cerebellum with other genomic datasets from the same tissue. In newborn CGNs, Zic TF binding predominates at active enhancers that are co-bound by developmentally regulated TFs including Atoh1, whereas in mature CGNs, Zic TF binding consolidates toward promoters where it co-localizes with activity-regulated TFs. We then performed CUT&RUN-seq in differentiating CGNs to define both the time course of developmental shifts in Zic TF binding and their relationship to gene expression. Mapping Zic TF binding sites to genes using chromatin looping, we identified the set of Zic target genes that have altered expression in RNA-seq from Zic1 or Zic2 knockdown CGNs. CONCLUSIONS Our data show that Zic TFs are required for both induction and repression of distinct, developmentally regulated target genes through a mechanism that is largely independent of changes in Zic TF binding. We suggest that the differential collaboration of Zic TFs with other TF families underlies the shift in their biological functions across CGN development.
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Affiliation(s)
- Melyssa S Minto
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, 27710, USA
- Omics, Epidemiology and Analytics Program, RTI International, Research Triangle Park, NC, 27709, USA
| | | | - Vijyendra Ramesh
- Department of Neurobiology, Duke University, Durham, NC, 27710, USA
| | - Anne E West
- Department of Neurobiology, Duke University, Durham, NC, 27710, USA.
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2
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Zhang G, Fu Y, Yang L, Ye F, Zhang P, Zhang S, Ma L, Li J, Wu H, Han X, Wang J, Guo G. Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq. Dev Cell 2024; 59:793-811.e8. [PMID: 38330939 DOI: 10.1016/j.devcel.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Despite recent advances in single-cell genomics, the lack of maps for single-cell candidate cis-regulatory elements (cCREs) in non-mammal species has limited our exploration of conserved regulatory programs across vertebrates and invertebrates. Here, we developed a combinatorial-hybridization-based method for single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) named CH-ATAC-seq, enabling the construction of single-cell accessible chromatin landscapes for zebrafish, Drosophila, and earthworms (Eisenia andrei). By integrating scATAC censuses of humans, monkeys, and mice, we systematically identified 152 distinct main cell types and around 0.8 million cell-type-specific cCREs. Our analysis provided insights into the conservation of neural, muscle, and immune lineages across species, while epithelial cells exhibited a higher organ-origin heterogeneity. Additionally, a large-scale gene regulatory network (GRN) was constructed in four vertebrates by integrating scRNA-seq censuses. Overall, our study provides a valuable resource for comparative epigenomics, identifying the evolutionary conservation and divergence of gene regulation across different species.
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Affiliation(s)
- Guodong Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Shuang Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Hanyu Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China.
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China.
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou, China.
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3
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Li H, Cui J, Hu C, Li H, Luo X, Hao Y. Identification and Analysis of ZIC-Related Genes in Cerebellum of Autism Spectrum Disorders. Neuropsychiatr Dis Treat 2024; 20:325-339. [PMID: 38410689 PMCID: PMC10895985 DOI: 10.2147/ndt.s444138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
Objective Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with significant genetic heterogeneity. The ZIC gene family can regulate neurodevelopment, especially in the cerebellum, and has been implicated in ASD-like behaviors in mice. We performed bioinformatic analysis to identify the ZIC gene family in the ASD cerebellum. Methods We explored the roles of ZIC family genes in ASD by investigating (i) the association of ZIC genes with ASD risk genes from the Simons Foundation Autism Research Initiative (SFARI) database and ZIC genes in the brain regions of the Human Protein Atlas (HPA) database; (ii) co-expressed gene networks of genes positively and negatively correlated with ZIC1, ZIC2, and ZIC3, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and receiver operating characteristic (ROC) curve analysis of genes in these networks; and (iii) the relationship between ZIC1, ZIC2, ZIC3, and their related genes with cerebellar immune cells and stromal cells in ASD patients. Results (i) ZIC1, ZIC2, and ZIC3 were associated with neurodevelopmental disorders and risk genes related to ASD in the human cerebellum and (ii) ZIC1, ZIC2, and ZIC3 were highly expressed in the cerebellum, which may play a pathogenic role by affecting neuronal development and the cerebellar internal environment in patients with ASD, including immune cells, astrocytes, and endothelial cells. (iii) OLFM3, SLC27A4, GRB2, TMED1, NR2F1, and STRBP are closely related to ZIC1, ZIC2, and ZIC3 in ASD cerebellum and have good diagnostic accuracy. (iv) ASD mice in the maternal immune activation model demonstrated that Zic3 and Nr2f1 levels were decreased in the immune-activated cerebellum. Conclusion Our study supports the role of ZIC1, ZIC2, and ZIC3 in ASD pathogenesis and provides potential targets for early and accurate prediction of ASD.
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Affiliation(s)
- Heli Li
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jinru Cui
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Cong Hu
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Hao Li
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xiaoping Luo
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Yan Hao
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
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Masse O, Brumfield O, Ahmad E, Velasco-Annis C, Zhang J, Rollins CK, Connolly S, Barnewolt C, Shamshirsaz AA, Qaderi S, Javinani A, Warfield SK, Yang E, Gholipour A, Feldman HA, Grant PE, Mulliken JB, Pierotich L, Estroff J. Divergent growth of the transient brain compartments in fetuses with nonsyndromic isolated clefts involving the primary and secondary palate. Cereb Cortex 2024; 34:bhae024. [PMID: 38365268 PMCID: PMC10872676 DOI: 10.1093/cercor/bhae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 02/18/2024] Open
Abstract
Cleft lip/palate is a common orofacial malformation that often leads to speech/language difficulties as well as developmental delays in affected children, despite surgical repair. Our understanding of brain development in these children is limited. This study aimed to analyze prenatal brain development in fetuses with cleft lip/palate and controls. We examined in utero MRIs of 30 controls and 42 cleft lip/palate fetal cases and measured regional brain volumes. Cleft lip/palate was categorized into groups A (cleft lip or alveolus) and B (any combination of clefts involving the primary and secondary palates). Using a repeated-measures regression model with relative brain hemisphere volumes (%), and after adjusting for multiple comparisons, we did not identify significant differences in regional brain growth between group A and controls. Group B clefts had significantly slower weekly cerebellar growth compared with controls. We also observed divergent brain growth in transient brain structures (cortical plate, subplate, ganglionic eminence) within group B clefts, depending on severity (unilateral or bilateral) and defect location (hemisphere ipsilateral or contralateral to the defect). Further research is needed to explore the association between regional fetal brain growth and cleft lip/palate severity, with the potential to inform early neurodevelopmental biomarkers and personalized diagnostics.
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Affiliation(s)
- Olivia Masse
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Olivia Brumfield
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Esha Ahmad
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Clemente Velasco-Annis
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Jennings Zhang
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Caitlin K Rollins
- Department of Neurology Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Susan Connolly
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
- Maternal Fetal Care Center, Boston Children’s Hospital, Boston, MA 02115, United States
| | - Carol Barnewolt
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
- Maternal Fetal Care Center, Boston Children’s Hospital, Boston, MA 02115, United States
| | - Alireza A Shamshirsaz
- Maternal Fetal Care Center, Boston Children’s Hospital, Boston, MA 02115, United States
| | - Shohra Qaderi
- Maternal Fetal Care Center, Boston Children’s Hospital, Boston, MA 02115, United States
| | - Ali Javinani
- Maternal Fetal Care Center, Boston Children’s Hospital, Boston, MA 02115, United States
| | - Simon K Warfield
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Edward Yang
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Ali Gholipour
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Henry A Feldman
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Patricia E Grant
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - John B Mulliken
- Department of Plastic and Oral Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Lana Pierotich
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Judy Estroff
- Department of Radiology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, United States
- Maternal Fetal Care Center, Boston Children’s Hospital, Boston, MA 02115, United States
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5
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Minto M, Sotelo-Fonseca JE, Ramesh V, West AE. Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574185. [PMID: 38260638 PMCID: PMC10802290 DOI: 10.1101/2024.01.04.574185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background The Zic family of transcription factors (TFs) promote both proliferation and maturation of cerebellar granule neurons (CGNs), raising the question of how a single, constitutively expressed TF family can support distinct developmental processes. Here we use an integrative experimental and bioinformatic approach to discover the regulatory relationship between Zic TF binding and changing programs of gene transcription during CGN differentiation. Results We first established a bioinformatic pipeline to integrate Zic ChIP-seq data from the developing mouse cerebellum with other genomic datasets from the same tissue. In newborn CGNs, Zic TF binding predominates at active enhancers that are co-bound by developmentally-regulated TFs including Atoh1, whereas in mature CGNs, Zic TF binding consolidates toward promoters where it co-localizes with activity-regulated TFs. We then performed CUT&RUN-seq in differentiating CGNs to define both the time course of developmental shifts in Zic TF binding and their relationship to gene expression. Mapping Zic TF binding sites to genes using chromatin looping, we identified the set of Zic target genes that have altered expression in RNA-seq from Zic1 or Zic2 knockdown CGNs. Conclusion Our data show that Zic TFs are required for both induction and repression of distinct, developmentally regulated target genes through a mechanism that is largely independent of changes in Zic TF binding. We suggest that the differential collaboration of Zic TFs with other TF families underlies the shift in their biological functions across CGN development.
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Affiliation(s)
- Melyssa Minto
- Duke University, Program in Computational Biology and Bioinformatics, Durham, NC 27710
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC 27709
| | | | | | - Anne E. West
- Duke University, Department of Neurobiology, Durham, NC 27710
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6
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Micheli L, D'Andrea G, Creanza TM, Volpe D, Ancona N, Scardigli R, Tirone F. Transcriptome analysis reveals genes associated with stem cell activation by physical exercise in the dentate gyrus of aged p16Ink4a knockout mice. Front Cell Dev Biol 2023; 11:1270892. [PMID: 37928906 PMCID: PMC10621069 DOI: 10.3389/fcell.2023.1270892] [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: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Throughout adulthood neural stem cells divide in neurogenic niches-the dentate gyrus of the hippocampus and the subventricular zone-producing progenitor cells and new neurons. Stem cells self-renew, thus preserving their pool. Furthermore, the number of stem/progenitor cells in the neurogenic niches decreases with age. We have previously demonstrated that the cyclin-dependent kinase inhibitor p16Ink4a maintains, in aged mice, the pool of dentate gyrus stem cells by preventing their activation after a neurogenic stimulus such as exercise (running). We showed that, although p16Ink4a ablation by itself does not activate stem/progenitor cells, exercise strongly induced stem cell proliferation in p16Ink4a knockout dentate gyrus, but not in wild-type. As p16Ink4a regulates stem cell self-renewal during aging, we sought to profile the dentate gyrus transcriptome from p16Ink4a wild-type and knockout aged mice, either sedentary or running for 12 days. By pairwise comparisons of differentially expressed genes and by correlative analyses through the DESeq2 software, we identified genes regulated by p16Ink4a deletion, either without stimulus (running) added, or following running. The p16Ink4a knockout basic gene signature, i.e., in sedentary mice, involves upregulation of apoptotic, neuroinflammation- and synaptic activity-associated genes, suggesting a reactive cellular state. Conversely, another set of 106 genes we identified, whose differential expression specifically reflects the pattern of proliferative response of p16 knockout stem cells to running, are involved in processes that regulate stem cell activation, such as synaptic function, neurotransmitter metabolism, stem cell proliferation control, and reactive oxygen species level regulation. Moreover, we analyzed the regulation of these stem cell-specific genes after a second running stimulus. Surprisingly, the second running neither activated stem cell proliferation in the p16Ink4a knockout dentate gyrus nor changed the expression of these genes, confirming that they are correlated to the stem cell reactivity to stimulus, a process where they may play a role regulating stem cell activation.
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Affiliation(s)
- Laura Micheli
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
| | - Giorgio D'Andrea
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
| | - Teresa Maria Creanza
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Bari, Italy
| | - Daniel Volpe
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
| | - Nicola Ancona
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Bari, Italy
| | - Raffaella Scardigli
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
- European Brain Research Institute (EBRI), Rome, Italy
| | - Felice Tirone
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
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7
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Sun J, Hu L, Bok S, Yallowitz AR, Cung M, McCormick J, Zheng LJ, Debnath S, Niu Y, Tan AY, Lalani S, Morse KW, Shinn D, Pajak A, Hammad M, Suhardi VJ, Li Z, Li N, Wang L, Zou W, Mittal V, Bostrom MPG, Xu R, Iyer S, Greenblatt MB. A vertebral skeletal stem cell lineage driving metastasis. Nature 2023; 621:602-609. [PMID: 37704733 PMCID: PMC10829697 DOI: 10.1038/s41586-023-06519-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/04/2023] [Indexed: 09/15/2023]
Abstract
Vertebral bone is subject to a distinct set of disease processes from long bones, including a much higher rate of solid tumour metastases1-4. The basis for this distinct biology of vertebral bone has so far remained unknown. Here we identify a vertebral skeletal stem cell (vSSC) that co-expresses ZIC1 and PAX1 together with additional cell surface markers. vSSCs display formal evidence of stemness, including self-renewal, label retention and sitting at the apex of their differentiation hierarchy. vSSCs are physiologic mediators of vertebral bone formation, as genetic blockade of the ability of vSSCs to generate osteoblasts results in defects in the vertebral neural arch and body. Human counterparts of vSSCs can be identified in vertebral endplate specimens and display a conserved differentiation hierarchy and stemness features. Multiple lines of evidence indicate that vSSCs contribute to the high rates of vertebral metastatic tropism observed in breast cancer, owing in part to increased secretion of the novel metastatic trophic factor MFGE8. Together, our results indicate that vSSCs are distinct from other skeletal stem cells and mediate the unique physiology and pathology of vertebrae, including contributing to the high rate of vertebral metastasis.
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Affiliation(s)
- Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lingling Hu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Seoyeon Bok
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Ling J Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuzhe Niu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Sarfaraz Lalani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kyle W Morse
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Daniel Shinn
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Anthony Pajak
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Mohammed Hammad
- Research Division, Hospital for Special Surgery, New York, NY, USA
| | - Vincentius Jeremy Suhardi
- Research Division, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Zan Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Na Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, China
| | - Lijun Wang
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Weiguo Zou
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Mathias P G Bostrom
- Research Division, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, China
| | - Sravisht Iyer
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Research Division, Hospital for Special Surgery, New York, NY, USA.
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8
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Ramirez M, Robert R, Yeung J, Wu J, Abdalla-Wyse A, Goldowitz D. Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis. BMC Genomics 2023; 24:351. [PMID: 37365500 DOI: 10.1186/s12864-023-09368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The development of the brain requires precise coordination of molecular processes across many cell-types. Underpinning these events are gene expression programs which require intricate regulation by non-coding regulatory sequences known as enhancers. In the context of the developing brain, transcribed enhancers (TEs) regulate temporally-specific expression of genes critical for cell identity and differentiation. Transcription of non-coding RNAs at active enhancer sequences, known as enhancer RNAs (eRNAs), is tightly associated with enhancer activity and has been correlated with target gene expression. TEs have been characterized in a multitude of developing tissues, however their regulatory role has yet to be described in the context of embryonic and early postnatal brain development. In this study, eRNA transcription was analyzed to identify TEs active during cerebellar development, as a proxy for the developing brain. Cap Analysis of Gene Expression followed by sequencing (CAGE-seq) was conducted at 12 stages throughout embryonic and early postnatal cerebellar development. RESULTS Temporal analysis of eRNA transcription identified clusters of TEs that peak in activity during either embryonic or postnatal times, highlighting their importance for temporally specific developmental events. Functional analysis of putative target genes identified molecular mechanisms under TE regulation revealing that TEs regulate genes involved in biological processes specific to neurons. We validate enhancer activity using in situ hybridization of eRNA expression from TEs predicted to regulate Nfib, a gene critical for cerebellar granule cell differentiation. CONCLUSIONS The results of this analysis provide a valuable dataset for the identification of cerebellar enhancers and provide insight into the molecular mechanisms critical for brain development under TE regulation. This dataset is shared with the community through an online resource ( https://goldowitzlab.shinyapps.io/trans-enh-app/ ).
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada.
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada.
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9
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Ramesh V, Liu F, Minto MS, Chan U, West AE. Bidirectional regulation of postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics. eLife 2023; 12:e86273. [PMID: 37092728 PMCID: PMC10181825 DOI: 10.7554/elife.86273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 04/25/2023] Open
Abstract
The functional maturation of neurons is a prolonged process that extends past the mitotic exit and is mediated by the chromatin-dependent orchestration of gene transcription programs. We find that expression of this maturation gene program in mouse cerebellar granule neurons (CGNs) requires dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), demonstrating a function for this chromatin modification beyond its role in cell fate specification. The developmental loss of H3K27me3 at promoters of genes activated as CGNs mature is facilitated by the lysine demethylase and ASD-risk gene, Kdm6b. Interestingly, inhibition of the H3K27 methyltransferase EZH2 in newborn CGNs not only blocks the repression of progenitor genes but also impairs the induction of mature CGN genes, showing the importance of bidirectional H3K27me3 regulation across the genome. These data demonstrate that H3K27me3 turnover in developing postmitotic neurons regulates the temporal coordination of gene expression programs that underlie functional neuronal maturation.
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Affiliation(s)
- Vijyendra Ramesh
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
| | - Fang Liu
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Melyssa S Minto
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Urann Chan
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Anne E West
- Molecular Cancer Biology Program, Duke UniversityDurhamUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
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10
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Sun J, Hu L, Bok S, Yallowitz AR, Cung M, McCormick J, Zheng LJ, Debnath S, Niu Y, Tan AY, Lalani S, Morse KW, Shinn D, Pajak A, Li Z, Li N, Xu R, Iyer S, Greenblatt MB. Discovery of a Vertebral Skeletal Stem Cell Driving Spinal Metastases. RESEARCH SQUARE 2023:rs.3.rs-2106142. [PMID: 36747772 PMCID: PMC9901027 DOI: 10.21203/rs.3.rs-2106142/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Vertebral bone is subject to a distinct set of disease processes from those of long bones, notably including a much higher rate of solid tumor metastases that cannot be explained by passive blood flow distribution alone. The basis for this distinct biology of vertebral bone has remained elusive. Here we identify a vertebral skeletal stem cell (vSSC), co-expressing the transcription factors ZIC1 and PAX1 together with additional cell surface markers, whose expression profile and function are markedly distinct from those of long bone skeletal stem cells (lbSSCs). vSSCs display formal evidence of stemness, including self-renewal, label retention and sitting at the apex of their differentiation hierarchy. Lineage tracing of vSSCs confirms that they make a persistent contribution to multiple mature cell lineages in the native vertebrae. vSSCs are physiologic mediators of spine mineralization, as genetic blockade of the ability of vSSCs to generate osteoblasts results in defects in the vertebral neural arch and body. Human counterparts of vSSCs can be identified in vertebral endplate specimens and display a conserved differentiation hierarchy and stemness. Multiple lines of evidence indicate that vSSCs contribute to the high rates of vertebral metastatic tropism observed clinically in breast cancer. Specifically, when an organoid system is used to place both vSSCs and lbSSCs in an identical anatomic context, vSSC-lineage cells are more efficient than lbSSC-lineage cells at recruiting metastases, a phenotype that is due in part to increased secretion of the novel metastatic trophic factor MFGE8. Similarly, genetically targeting loss-of-function to the vSSC lineage results in reduced metastasis rates in the native vertebral environment. Taken together, vSSCs are distinct from other skeletal stem cells and mediate the unique physiology and pathology of vertebrae, including contributing to the high rate of metastatic seeding of the vertebrae.
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Affiliation(s)
- Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lingling Hu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Seoyeon Bok
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Ling J Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuzhe Niu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Sarfaraz Lalani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kyle W Morse
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Daniel Shinn
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Anthony Pajak
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Zan Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Na Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Sravisht Iyer
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Research Division, Hospital for Special Surgery, New York, NY, USA
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11
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Hopfner F, Tietz AK, Ruf VC, Ross OA, Koga S, Dickson D, Aguzzi A, Attems J, Beach T, Beller A, Cheshire WP, van Deerlin V, Desplats P, Deuschl G, Duyckaerts C, Ellinghaus D, Evsyukov V, Flanagan ME, Franke A, Frosch MP, Gearing M, Gelpi E, van Gerpen JA, Ghetti B, Glass JD, Grinberg LT, Halliday G, Helbig I, Höllerhage M, Huitinga I, Irwin DJ, Keene DC, Kovacs GG, Lee EB, Levin J, Martí MJ, Mackenzie I, McKeith I, Mclean C, Mollenhauer B, Neumann M, Newell KL, Pantelyat A, Pendziwiat M, Peters A, Porcel LM, Rabano A, Matěj R, Rajput A, Rajput A, Reimann R, Scott WK, Seeley W, Selvackadunco S, Simuni T, Stadelmann C, Svenningsson P, Thomas A, Trenkwalder C, Troakes C, Trojanowski JQ, Uitti RJ, White CL, Wszolek ZK, Xie T, Ximelis T, Justo Y, Müller U, Schellenberg GD, Herms J, Kuhlenbäumer G, Höglinger G. Common Variants Near ZIC1 and ZIC4 in Autopsy-Confirmed Multiple System Atrophy. Mov Disord 2022; 37:2110-2121. [PMID: 35997131 PMCID: PMC10052809 DOI: 10.1002/mds.29164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Multiple System Atrophy is a rare neurodegenerative disease with alpha-synuclein aggregation in glial cytoplasmic inclusions and either predominant olivopontocerebellar atrophy or striatonigral degeneration, leading to dysautonomia, parkinsonism, and cerebellar ataxia. One prior genome-wide association study in mainly clinically diagnosed patients with Multiple System Atrophy failed to identify genetic variants predisposing for the disease. OBJECTIVE Since the clinical diagnosis of Multiple System Atrophy yields a high rate of misdiagnosis when compared to the neuropathological gold standard, we studied only autopsy-confirmed cases. METHODS We studied common genetic variations in Multiple System Atrophy cases (N = 731) and controls (N = 2898). RESULTS The most strongly disease-associated markers were rs16859966 on chromosome 3, rs7013955 on chromosome 8, and rs116607983 on chromosome 4 with P-values below 5 × 10-6 , all of which were supported by at least one additional genotyped and several imputed single nucleotide polymorphisms. The genes closest to the chromosome 3 locus are ZIC1 and ZIC4 encoding the zinc finger proteins of cerebellum 1 and 4 (ZIC1 and ZIC4). INTERPRETATION Since mutations of ZIC1 and ZIC4 and paraneoplastic autoantibodies directed against ZIC4 are associated with severe cerebellar dysfunction, we conducted immunohistochemical analyses in brain tissue of the frontal cortex and the cerebellum from 24 Multiple System Atrophy patients. Strong immunohistochemical expression of ZIC4 was detected in a subset of neurons of the dentate nucleus in all healthy controls and in patients with striatonigral degeneration, whereas ZIC4-immunoreactive neurons were significantly reduced inpatients with olivopontocerebellar atrophy. These findings point to a potential ZIC4-mediated vulnerability of neurons in Multiple System Atrophy. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Anja K. Tietz
- Department of Neurology, Kiel University, Kiel, Germany
| | - Viktoria C. Ruf
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, Munich, Germany
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida, USA
| | - Shunsuke Koga
- 6Department of Neuroscience (Neuropathology), Mayo Clinic, Jacksonville, Florida, USA
| | - Dennis Dickson
- 6Department of Neuroscience (Neuropathology), Mayo Clinic, Jacksonville, Florida, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zürich, Zürich, Switzerland
| | - Johannes Attems
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | | | - Vivianna van Deerlin
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paula Desplats
- Department of Neurosciences, School of Medicine University of California San Diego, La Jolla, California, USA
- Department of Pathology, School of Medicine University of California San Diego, La Jolla, California, USA
| | | | - Charles Duyckaerts
- Institut du Cerveau, UMR 7225, Sorbonne Université, Paris Brain Institute-ICM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Inserm U1127 DMU Neurosciences, Paris, France
- Brainbank NeuroCEB Neuropathology Network: Plateforme de Ressources Biologiques, Hôpital de La Pitié-Salpêtrière, Bâtiment Roger Baillet, Paris Cedex, France
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Margaret Ellen Flanagan
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthew P. Frosch
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marla Gearing
- Departments of Pathology and Laboratory Medicine and Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ellen Gelpi
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
- Medical University of Vienna, Austrian Reference Center for Human Prion Diseases (OERPE), Vienna, Austria
| | | | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Lea T. Grinberg
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Global Health Institute, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
- Department of Pathology, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Glenda Halliday
- The University of Sydney, School of Medical Sciences, and Brain & Mind Centre, Sydney, New South Wales, Australia
| | - Ingo Helbig
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
- Brain Plasticity Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - David John Irwin
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dirk C. Keene
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Gabor G. Kovacs
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
- Department of Laboratory Medicine and Pathobiology and Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program and Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, Translational Neuropathology Research Laboratory Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Johannes Levin
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maria J. Martí
- Parkinson’s Disease and Movement Disorders Unit, Department of Neurology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institut de Neurociències, Maeztu Center, University of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Ian Mackenzie
- Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ian McKeith
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catriona Mclean
- Department of Anatomical Pathology, Alfred Health, Melbourne, Victoria, Australia
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurology, University Medical Center Goettingen, Gottingen, Germany
| | - Manuela Neumann
- Molecular Neuropathology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, Germany
- Department of Neuropathology, University Hospital of Tübingen, Tübingen, Germany
| | - Kathy L. Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alex Pantelyat
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Children’s Hospital, University Medical Center Schleswig-Holstein, University of Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Alberto Rabano
- Neuropathology Department, CIEN Foundation, Alzheimer’s Centre Queen Sofía Foundation, Madrid, Spain
| | - Radoslav Matěj
- Department of Pathology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, 3rd Faculty of Medicine, Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Alex Rajput
- Division of Neurology, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ali Rajput
- Saskatchewan Movement Disorders Program, Saskatchewan Health Authority/University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Regina Reimann
- Institute of Neuropathology, University Hospital Zürich, Zürich, Switzerland
| | - William K. Scott
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - William Seeley
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Global Health Institute, University of California, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, California, USA
| | - Sashika Selvackadunco
- Basic and Clinical Neuroscience Department, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Tanya Simuni
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christine Stadelmann
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Per Svenningsson
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurosurgery, University Medical Center Goettingen, Goettingen, Germany
| | - Claire Troakes
- Basic and Clinical Neuroscience Department, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ryan J. Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Charles L. White
- Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Tao Xie
- Department of Neurology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Teresa Ximelis
- Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Yebenes Justo
- Neurological Tissue Bank, Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
- Servicio de Neurología, Hospital Ramón y Cajal de Madrid, Madrid, Spain
| | | | - Ulrich Müller
- Institute of Human Genetics, JLU-Gießen, Giessen, Germany
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, Munich, Germany
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Günter Höglinger
- Department of Neurology Hannover Medical School, Hannover, Germany
- DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
- Zentrum für Systemische Neurowissenschaften, Hannover, Germany
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Luo TF, Wang YB, Wang DH, Zhan S, Deng SL. Lateral ventricle pleomorphic xanthoastrocytoma concurrent with Dandy-Walker complex: A case report. Medicine (Baltimore) 2022; 101:e30492. [PMID: 36086683 PMCID: PMC10980463 DOI: 10.1097/md.0000000000030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Dandy-Walker complex and pleomorphic xanthoastrocytomas are both rare disease entities that typically manifest early in life and are associated with congenital etiological factors. Dandy-Walker complex is a cerebellar malformation associated with a series of anatomical changes. The disease onset is usually at birth or during infancy. Late onset in adulthood is uncommon. Pleomorphic xanthoastrocytoma is a rare WHO grade II astrocytic tumor affecting mainly young adults. Concomitant occurrence of Dandy-Walker complex and pleomorphic xanthoastrocytoma has not been previously reported. PATIENT CONCERNS AND DIAGNOSIS A 30-year-old woman with a previous history of unconfirmed resected lateral ventricle meningioma presented with severe headache for 1 day. Imaging examination revealed a mass in the right lateral ventricle with heterogeneous signal patterns, changes in the posterior fossa corresponding to a Dandy-Walker variant, and mild hydrocephalus. INTERVENTIONS AND OUTCOMES Surgical complete resection of the mass was achieved. postoperative histopathological examination confirmed WHO grade II pleomorphic xanthoastrocytoma. Three years postsurgery, ventriculoperitoneal shunt was performed due to worsening of hydrocephalus. The patient has since remained symptom-free. CONCLUSION This is the first report of concomitant occurrence of Dandy-Walker complex and pleomorphic xanthoastrocytoma. The association of neurological congenital malformation with intracranial neoplasms may be multifactorial, with underlying role of genetic mutations or chromosome alterations.
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Affiliation(s)
- Tian-Fei Luo
- Department of Neurology, First Hospital of Jilin University, Chang Chun, China
| | - Yu-Bo Wang
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Chang Chun, China
| | - Dan-Hua Wang
- Department of Pathology, First Hospital of Jilin University, Chang Chun, China
| | - Shuang Zhan
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Chang Chun, China
| | - Shuang-Lin Deng
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Chang Chun, China
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13
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Moosavi A, Kanekar S. Congenital Malformations of Cerebellum. Clin Perinatol 2022; 49:603-621. [PMID: 36113925 DOI: 10.1016/j.clp.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Advances in pre and postnatal neuroimaging techniques, and molecular genetics have increased our understanding of the congenital malformation of the brain. Correct diagnosis of these malformations in regards to embryology, and molecular neurogenetics is of paramount importance to understand the inheritance pattern and risk of recurrence. Lesions detected on prenatal imaging require confirmation either with postnatal ultrasound and/or with MR imaging. With the advent of the faster (rapid) MRI techniques, which can be conducted without sedation, MRI is commonly used in the evaluation of congenital malformation of the brain. Based on neuroimaging pattern, the congenital malformations of the posterior fossa are classified into 4 main categories: (a) predominantly cerebellar, (b) cerebellar and brainstem, (c) predominantly brainstem, and (d) predominantly midbrain malformations.
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Affiliation(s)
- Ali Moosavi
- Radiology Research, Division of Neuroradiology, Penn State Health, Penn State College of Medicine, Mail Code H066 500 University Drive, Hershey, PA 17033, USA
| | - Sangam Kanekar
- Radiology Research, Division of Neuroradiology, Penn State Health, Penn State College of Medicine, Mail Code H066 500 University Drive, Hershey, PA 17033, USA.
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14
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Okano S, Makita Y, Kimura K, Fukuda I, Miyamoto A, Tanaka H. Wisconsin syndrome with brain volume laterality: a case report and review of the literature. J Med Case Rep 2022; 16:153. [PMID: 35428363 PMCID: PMC9013138 DOI: 10.1186/s13256-022-03332-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Wisconsin syndrome is a congenital anomaly caused by a 3q interstitial deletion. It is associated with characteristic facies and developmental delays. Only 33 cases with a deletion estimated to be in the associated region 3q25 have been reported. Case report We present the case of a 5-year-old Japanese girl with a 3q24q25.2 deletion. Her facial features corresponded to the Wisconsin syndrome phenotype, and she exhibited brain volume laterality, which has not been reported previously. Conclusion The clinical features of our case may contribute to narrowing down the list of candidate genes of Wisconsin syndrome.
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15
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Stanton E, Urata M, Chen JF, Chai Y. The clinical manifestations, molecular mechanisms and treatment of craniosynostosis. Dis Model Mech 2022; 15:dmm049390. [PMID: 35451466 PMCID: PMC9044212 DOI: 10.1242/dmm.049390] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Craniosynostosis is a major congenital craniofacial disorder characterized by the premature fusion of cranial suture(s). Patients with severe craniosynostosis often have impairments in hearing, vision, intracranial pressure and/or neurocognitive functions. Craniosynostosis can result from mutations, chromosomal abnormalities or adverse environmental effects, and can occur in isolation or in association with numerous syndromes. To date, surgical correction remains the primary treatment for craniosynostosis, but it is associated with complications and with the potential for re-synostosis. There is, therefore, a strong unmet need for new therapies. Here, we provide a comprehensive review of our current understanding of craniosynostosis, including typical craniosynostosis types, their clinical manifestations, cranial suture development, and genetic and environmental causes. Based on studies from animal models, we present a framework for understanding the pathogenesis of craniosynostosis, with an emphasis on the loss of postnatal suture mesenchymal stem cells as an emerging disease-driving mechanism. We evaluate emerging treatment options and highlight the potential of mesenchymal stem cell-based suture regeneration as a therapeutic approach for craniosynostosis.
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Affiliation(s)
- Eloise Stanton
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mark Urata
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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16
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Wang L, Sun F, Wan ZY, Ye B, Wen Y, Liu H, Yang Z, Pang H, Meng Z, Fan B, Alfiko Y, Shen Y, Bai B, Lee MSQ, Piferrer F, Schartl M, Meyer A, Yue GH. Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish. Mol Biol Evol 2021; 38:3383-3396. [PMID: 33871625 PMCID: PMC8321530 DOI: 10.1093/molbev/msab110] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1/zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Baoqing Ye
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Yanfei Wen
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Huiming Liu
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zituo Yang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Hongyan Pang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, China
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Bin Bai
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - May Shu Qing Lee
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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17
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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: 82] [Impact Index Per Article: 27.3] [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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18
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Abu Hamdeh S, Ciuculete DM, Sarkisyan D, Bakalkin G, Ingelsson M, Schiöth HB, Marklund N. Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury. J Neurotrauma 2021; 38:1679-1688. [PMID: 33191850 DOI: 10.1089/neu.2020.7283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) is an established risk factor for neurodegenerative disorders and dementias. Epigenetic modifications, such as DNA methylation, may alter the expression of genes without altering the DNA sequence in response to environmental factors. We hypothesized that DNA methylation changes may occur in the injured human brain and be implicated in the neurodegenerative aftermath of TBI. The DNA methylation status of genes related to neurodegeneration; for example, amyloid beta precursor protein (APP), microtubule associated protein tau (MAPT), neurofilament heavy (NEFH), neurofilament medium (NEFM), and neurofilament light (NEFL), was analyzed in fresh, surgically resected human brain tissue from 17 severe TBI patients and compared with brain biopsy samples from 19 patients with idiopathic normal pressure hydrocephalus (iNPH). We also performed an epigenome-wide association study (EWAS) comparing TBI patients with iNPH controls. Thirty-eight CpG sites in the APP, MAPT, NEFH, and NEFL genes were differentially methylated by TBI. Among the top 20 differentially methylated CpG sites, 11 were in the APP gene. In addition, the EWAS evaluating 828,888 CpG sites revealed 308 differentially methylated CpG sites in genes related to cellular/anatomical structure development, cell differentiation, and anatomical morphogenesis. These preliminary findings provide the first evidence of an altered DNA methylome in the injured human brain, and may have implications for the neurodegenerative disorders associated with TBI.
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Affiliation(s)
- Sami Abu Hamdeh
- Department of Neuroscience, Section of Neurosurgery, Uppsala University, Uppsala, Sweden
| | - Diana-Maria Ciuculete
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Daniil Sarkisyan
- Department of Pharmaceutical Biosciences, and Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, and Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Niklas Marklund
- Department of Clinical Sciences Lund, Neurosurgery, Lund University, Skåne University Hospital, Lund, Sweden
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19
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Provenzano A, La Barbera A, Scagnet M, Pagliazzi A, Traficante G, Pantaleo M, Tiberi L, Vergani D, Kurtas NE, Guarducci S, Bargiacchi S, Forzano G, Artuso R, Palazzo V, Kura A, Giordano F, di Feo D, Mortilla M, De Filippi C, Mattei G, Garavelli L, Giusti B, Genitori L, Zuffardi O, Giglio S. Chiari 1 malformation and exome sequencing in 51 trios: the emerging role of rare missense variants in chromatin-remodeling genes. Hum Genet 2020; 140:625-647. [PMID: 33337535 PMCID: PMC7981314 DOI: 10.1007/s00439-020-02231-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023]
Abstract
Type 1 Chiari malformation (C1M) is characterized by cerebellar tonsillar herniation of 3–5 mm or more, the frequency of which is presumably much higher than one in 1000 births, as previously believed. Its etiology remains undefined, although a genetic basis is strongly supported by C1M presence in numerous genetic syndromes associated with different genes. Whole-exome sequencing (WES) in 51 between isolated and syndromic pediatric cases and their relatives was performed after confirmation of the defect by brain magnetic resonance image (MRI). Moreover, in all the cases showing an inherited candidate variant, brain MRI was performed in both parents and not only in the carrier one to investigate whether the defect segregated with the variant. More than half of the variants were Missense and belonged to the same chromatin-remodeling genes whose protein truncation variants are associated with severe neurodevelopmental syndromes. In the remaining cases, variants have been detected in genes with a role in cranial bone sutures, microcephaly, neural tube defects, and RASopathy. This study shows that the frequency of C1M is widely underestimated, in fact many of the variants, in particular those in the chromatin-remodeling genes, were inherited from a parent with C1M, either asymptomatic or with mild symptoms. In addition, C1M is a Mendelian trait, in most cases inherited as dominant. Finally, we demonstrate that modifications of the genes that regulate chromatin architecture can cause localized anatomical alterations, with symptoms of varying degrees.
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Affiliation(s)
- Aldesia Provenzano
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.
| | - Andrea La Barbera
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Mirko Scagnet
- Department of Neurosurgery, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Angelica Pagliazzi
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Marilena Pantaleo
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Lucia Tiberi
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Debora Vergani
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Nehir Edibe Kurtas
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Silvia Guarducci
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Giulia Forzano
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Rosangela Artuso
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Viviana Palazzo
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Ada Kura
- Department of Experimental and Clinical Medicine, Atherothrombotic Diseases Center, University of Florence, Careggi Hospital, Florence, Italy
| | - Flavio Giordano
- Department of Neurosurgery, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Daniele di Feo
- Department of Radiology, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Marzia Mortilla
- Department of Radiology, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Claudio De Filippi
- Department of Radiology, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Gianluca Mattei
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Department of Mother and Child, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, Atherothrombotic Diseases Center, University of Florence, Careggi Hospital, Florence, Italy
| | - Lorenzo Genitori
- Department of Neurosurgery, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Orsetta Zuffardi
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
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20
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Iskusnykh IY, Fattakhov N, Buddington RK, Chizhikov VV. Intrauterine growth restriction compromises cerebellar development by affecting radial migration of granule cells via the JamC/Pard3a molecular pathway. Exp Neurol 2020; 336:113537. [PMID: 33259808 DOI: 10.1016/j.expneurol.2020.113537] [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: 07/08/2020] [Revised: 10/30/2020] [Accepted: 11/22/2020] [Indexed: 12/30/2022]
Abstract
Intrauterine growth restriction (IUGR) affects ~10% of human pregnancies, results in infants born small for gestational age (SGA), and is associated with motor and cognitive deficits. Human studies suggest that some deficits in SGA patients originate in the cerebellum, a major motor-coordination and cognitive center, but the underlying mechanisms remain unknown. To identify the cerebellar developmental program affected by IUGR, we analyzed the pig as a translational animal model in which some fetuses spontaneously develop IUGR due to early-onset chronic placental insufficiency. Similar to humans, SGA pigs revealed small cerebella, which contained fewer mature granule cells (GCs) in the internal granule cell layer (IGL). Surprisingly, newborn SGA pigs had increased proliferation of GC precursors in the external granule cell layer (EGL), which was associated with an increased density of Purkinje cells, known to non-autonomously promote the proliferation of GCs. However, the GCs of SGA pigs did not properly initiate exit from the EGL to IGL, which was associated with a decreased density of guiding Bergmann glial fibers, reduced expression of pro-migratory genes Pard3a, JamC and Sema6a, and increased apoptosis. While proliferation spontaneously normalized during postnatal development, accumulation of pre-migratory GCs and apoptosis in the EGL were long-lasting consequences of IUGR. Using organotypic cerebellar slice cultures, we showed that normalizing expression of Pard3a and JamC, which operate in the same molecular pathway in GCs, was sufficient to rescue both migratory and, at a later time point, apoptotic defects of IUGR. Thus, a decreased exit of GCs from the EGL, due to disrupted Pard3a/JamC radial migration initiation pathway, is a major mechanism of IUGR-related cerebellar pathology.
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Affiliation(s)
- Igor Y Iskusnykh
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Nikolai Fattakhov
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Randal K Buddington
- Babies Taking Flight, Memphis, TN 38117, USA; School of Health Studies, University of Memphis, Memphis, TN 38152, USA; College of Nursing, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Victor V Chizhikov
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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21
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Ahmed JN, Diamand KEM, Bellchambers HM, Arkell RM. Systematized reporter assays reveal ZIC protein regulatory abilities are Subclass-specific and dependent upon transcription factor binding site context. Sci Rep 2020; 10:13130. [PMID: 32753700 PMCID: PMC7403390 DOI: 10.1038/s41598-020-69917-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
The ZIC proteins are a family of transcription regulators with a well-defined zinc finger DNA-binding domain and there is evidence that they elicit functional DNA binding at a ZIC DNA binding site. Little is known, however, regarding domains within ZIC proteins that confer trans-activation or -repression. To address this question, a new cell-based trans-activation assay system suitable for ZIC proteins in HEK293T cells was constructed. This identified two previously unannotated evolutionarily conserved regions of ZIC3 that are necessary for trans-activation. These domains are found in all Subclass A ZIC proteins, but not in the Subclass B proteins. Additionally, the Subclass B proteins fail to elicit functional binding at a multimerised ZIC DNA binding site. All ZIC proteins, however, exhibit functional binding when the ZIC DNA binding site is embedded in a multiple transcription factor locus derived from ZIC target genes in the mouse genome. This ability is due to several domains, some of which are found in all ZIC proteins, that exhibit context dependent trans-activation or -repression activity. This knowledge is valuable for assessing the likely pathogenicity of variant ZIC proteins associated with human disorders and for determining factors that influence functional transcription factor binding.
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Affiliation(s)
- Jehangir N Ahmed
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Koula E M Diamand
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Helen M Bellchambers
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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22
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Eura N, Matsui TK, Luginbühl J, Matsubayashi M, Nanaura H, Shiota T, Kinugawa K, Iguchi N, Kiriyama T, Zheng C, Kouno T, Lan YJ, Kongpracha P, Wiriyasermkul P, Sakaguchi YM, Nagata R, Komeda T, Morikawa N, Kitayoshi F, Jong M, Kobashigawa S, Nakanishi M, Hasegawa M, Saito Y, Shiromizu T, Nishimura Y, Kasai T, Takeda M, Kobayashi H, Inagaki Y, Tanaka Y, Makinodan M, Kishimoto T, Kuniyasu H, Nagamori S, Muotri AR, Shin JW, Sugie K, Mori E. Brainstem Organoids From Human Pluripotent Stem Cells. Front Neurosci 2020; 14:538. [PMID: 32670003 PMCID: PMC7332712 DOI: 10.3389/fnins.2020.00538] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/01/2020] [Indexed: 01/10/2023] Open
Abstract
The brainstem is a posterior region of the brain, composed of three parts, midbrain, pons, and medulla oblongata. It is critical in controlling heartbeat, blood pressure, and respiration, all of which are life-sustaining functions, and therefore, damages to or disorders of the brainstem can be lethal. Brain organoids derived from human pluripotent stem cells (hPSCs) recapitulate the course of human brain development and are expected to be useful for medical research on central nervous system disorders. However, existing organoid models are limited in the extent hPSCs recapitulate human brain development and hence are not able to fully elucidate the diseases affecting various components of the brain such as brainstem. Here, we developed a method to generate human brainstem organoids (hBSOs), containing midbrain/hindbrain progenitors, noradrenergic and cholinergic neurons, dopaminergic neurons, and neural crest lineage cells. Single-cell RNA sequence (scRNA-seq) analysis, together with evidence from proteomics and electrophysiology, revealed that the cellular population in these organoids was similar to that of the human brainstem, which raises the possibility of making use of hBSOs in investigating central nervous system disorders affecting brainstem and in efficient drug screenings.
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Affiliation(s)
- Nobuyuki Eura
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Takeshi K. Matsui
- Department of Neurology, Nara Medical University, Kashihara, Japan
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Joachim Luginbühl
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama,Japan
| | - Masaya Matsubayashi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Hitoki Nanaura
- Department of Neurology, Nara Medical University, Kashihara, Japan
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Tomo Shiota
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Kaoru Kinugawa
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Naohiko Iguchi
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Takao Kiriyama
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Canbin Zheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Tsukasa Kouno
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama,Japan
| | - Yan Jun Lan
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama,Japan
| | - Pornparn Kongpracha
- Laboratory of Biomolecular Dynamics, Department of Collaborative Research, Nara Medical University, Kashihara, Japan
| | - Pattama Wiriyasermkul
- Laboratory of Biomolecular Dynamics, Department of Collaborative Research, Nara Medical University, Kashihara, Japan
| | | | - Riko Nagata
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Tomoya Komeda
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Naritaka Morikawa
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Fumika Kitayoshi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Miyong Jong
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Shinko Kobashigawa
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Mari Nakanishi
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
| | - Masatoshi Hasegawa
- Department of Radiation Oncology, Nara Medical University, Kashihara, Japan
| | - Yasuhiko Saito
- Department of Neurophysiology, Nara Medical University, Kashihara, Japan
| | - Takashi Shiromizu
- Department of Integrative Pharmacology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Takahiko Kasai
- Department of Laboratory Medicine and Pathology, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Japan
| | - Maiko Takeda
- Department of Laboratory Medicine and Pathology, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Japan
| | - Hiroshi Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
| | - Yusuke Inagaki
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Japan
| | - Yasuhito Tanaka
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Japan
| | - Manabu Makinodan
- Department of Psychiatry, Nara Medical University, Kashihara, Japan
| | | | - Hiroki Kuniyasu
- Department of Molecular Pathology, Nara Medical University, Kashihara, Japan
| | - Shushi Nagamori
- Laboratory of Biomolecular Dynamics, Department of Collaborative Research, Nara Medical University, Kashihara, Japan
| | - Alysson R. Muotri
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jay W. Shin
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama,Japan
| | - Kazuma Sugie
- Department of Neurology, Nara Medical University, Kashihara, Japan
| | - Eiichiro Mori
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Japan
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23
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Depicting the genetic architecture of pediatric cancers through an integrative gene network approach. Sci Rep 2020; 10:1224. [PMID: 31988326 PMCID: PMC6985191 DOI: 10.1038/s41598-020-58179-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
The genetic etiology of childhood cancers still remains largely unknown. It is therefore essential to develop novel strategies to unravel the spectrum of pediatric cancer genes. Statistical network modeling techniques have emerged as powerful methodologies for enabling the inference of gene-disease relationship and have been performed on adult but not pediatric cancers. We performed a deep multi-layer understanding of pan-cancer transcriptome data selected from the Treehouse Childhood Cancer Initiative through a co-expression network analysis. We identified six modules strongly associated with pediatric tumor histotypes that were functionally linked to developmental processes. Topological analyses highlighted that pediatric cancer predisposition genes and potential therapeutic targets were central regulators of cancer-histotype specific modules. A module was related to multiple pediatric malignancies with functions involved in DNA repair and cell cycle regulation. This canonical oncogenic module gathered most of the childhood cancer predisposition genes and clinically actionable genes. In pediatric acute leukemias, the driver genes were co-expressed in a module related to epigenetic and post-transcriptional processes, suggesting a critical role of these pathways in the progression of hematologic malignancies. This integrative pan-cancer study provides a thorough characterization of pediatric tumor-associated modules and paves the way for investigating novel candidate genes involved in childhood tumorigenesis.
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24
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Krüger A, Fabrizius A, Mikkelsen B, Siebert U, Folkow LP, Burmester T. Transcriptome analysis reveals a high aerobic capacity in the whale brain. Comp Biochem Physiol A Mol Integr Physiol 2019; 240:110593. [PMID: 31676411 DOI: 10.1016/j.cbpa.2019.110593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/30/2019] [Accepted: 10/22/2019] [Indexed: 01/04/2023]
Abstract
The brain of diving mammals is repeatedly exposed to low oxygen conditions (hypoxia) that would have caused severe damage to most terrestrial mammals. Some whales may dive for >2 h with their brain remaining active. Many of the physiological adaptations of whales to diving have been investigated, but little is known about the molecular mechanisms that enable their brain to survive sometimes prolonged periods of hypoxia. Here, we have used an RNA-Seq approach to compare the mRNA levels in the brains of whales with those of cattle, which serves as a terrestrial relative. We sequenced the transcriptomes of the brains from cattle (Bos taurus), killer whale (Orcinus orca), and long-finned pilot whale (Globicephala melas). Further, the brain transcriptomes of cattle, minke whale (Balaenoptera acutorostrata) and bowhead whale (Balaena mysticetus), which were available in the databases, were included. We found a high expression of genes related to oxidative phosphorylation and the respiratory electron chain in the whale brains. In the visual cortex of whales, transcripts related to the detoxification of reactive oxygen species were more highly expressed than in the visual cortex of cattle. These findings indicate a high oxidative capacity in the whale brain that might help to maintain aerobic metabolism in periods of reduced oxygen availability during dives.
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Affiliation(s)
- Alena Krüger
- Institute of Zoology, University of Hamburg, Germany.
| | | | | | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, D-25761 Büsum, Germany.
| | - Lars P Folkow
- University of Tromsø - The Arctic University of Norway, NO-9037 Tromsø, Norway.
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25
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Hemorrhagic Stroke in a Young Adult with Undiagnosed Asymptomatic Dandy-Walker Malformation. Case Rep Neurol Med 2019; 2019:1450703. [PMID: 31637069 PMCID: PMC6766112 DOI: 10.1155/2019/1450703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/10/2019] [Accepted: 08/09/2019] [Indexed: 11/18/2022] Open
Abstract
The Dandy–Walker Malformation was first described in 1914 by Dandy and Blackfan and is characterized by hypoplasia of the vermis, pseudocystic fourth ventricle, upward displacement of the tentorium, torcular and lateral sinuses, and anteroposterior enlargement of the posterior fossa. This syndrome commonly manifests as hydrocephalus in children, though rare adult cases have been reported. The literature reveals adult symptomatology including brainstem infarction, psychosis, and neuromuscular disease. Stroke is an exceptionally rare presentation of this malformation, with only one ischemic event reported in the literature. This case offers a rare opportunity for diagnosis in an adult presenting with a hemorrhagic stroke of the basal ganglia in an otherwise asymptomatic young adult male. To the best of our knowledge, this is the first reported case of a hemorrhagic stroke in an adult patient with Dandy–Walker Malformation.
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Abdusselamoglu MD, Eroglu E, Burkard TR, Knoblich JA. The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop. eLife 2019; 8:46566. [PMID: 31329099 PMCID: PMC6645715 DOI: 10.7554/elife.46566] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
Neural progenitors undergo temporal patterning to generate diverse neurons in a chronological order. This process is well-studied in the developing Drosophila brain and conserved in mammals. During larval stages, intermediate neural progenitors (INPs) serially express Dichaete (D), grainyhead (Grh) and eyeless (Ey/Pax6), but how the transitions are regulated is not precisely understood. Here, we developed a method to isolate transcriptomes of INPs in their distinct temporal states to identify a complete set of temporal patterning factors. Our analysis identifies odd-paired (opa), as a key regulator of temporal patterning. Temporal patterning is initiated when the SWI/SNF complex component Osa induces D and its repressor Opa at the same time but with distinct kinetics. Then, high Opa levels repress D to allow Grh transcription and progress to the next temporal state. We propose that Osa and its target genes opa and D form an incoherent feedforward loop (FFL) and a new mechanism allowing the successive expression of temporal identities. The brain consists of billions of neurons that come in a range of shapes and sizes, with different types of neurons specialized to perform different tasks. Despite their diversity, all of these neurons originate from a single population known as neural stem cells. As the brain develops, each neural stem cell divides to produce two daughter cells: one remains a stem cell, which can then divide again, and the other becomes a neuron. A longstanding question in developmental biology is how a limited pool of neural stem cells can generate so many different types of neurons. The answer seems to lie in a process known as temporal identity, whereby neural stem cells of different ages give rise to different types of neurons. This requires neural stem cells to keep track of their own age, but it is still unclear how they can do so. Abdusselamoglu et al. have now uncovered part of the underlying mechanism behind temporal identity by studying fruit flies, an insect in which the early stages of brain development are similar to the ones in mammals. A method was developed to sort fly neural stem cells into groups based on their age. Comparing these groups revealed that a protein called Opa make neural stem cells switch from being 'young' to being 'middle-aged'. Another protein, Osa activates Opa, which in turn represses a protein called Dichaete. As Dichaete is mainly active in young neural stem cells, the actions of Osa and Opa push neural stem cells into middle age. Fruit flies are therefore a valuable system with which to study the mechanisms that regulate neural stem cell aging. Revealing how the brain generates different types of neurons could help us study the way these cells organize themselves into complex circuits. This knowledge could then be harnessed to understand how these processes go wrong and disrupt development.
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Affiliation(s)
- Merve Deniz Abdusselamoglu
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Elif Eroglu
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas R Burkard
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Jürgen A Knoblich
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
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27
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Kuhlwilm M, Boeckx C. A catalog of single nucleotide changes distinguishing modern humans from archaic hominins. Sci Rep 2019; 9:8463. [PMID: 31186485 PMCID: PMC6560109 DOI: 10.1038/s41598-019-44877-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
Throughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - Cedric Boeckx
- ICREA, Barcelona, Spain.
- University of Barcelona, Barcelona, Spain.
- UB Institute of Complex Systems, Barcelona, Spain.
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28
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McNiven V, Ito YA, Hartley T, Kernohan K, Miller E, Armour CM. NID1 variant associated with occipital cephaloceles in a family expressing a spectrum of phenotypes. Am J Med Genet A 2019; 179:837-841. [PMID: 30773799 DOI: 10.1002/ajmg.a.61095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Autosomal dominant Dandy-Walker malformation and occipital cephalocele (ADDWOC) is a rare, congenital, and incompletely penetrant malformation that is considered to be part of the Dandy-Walker spectrum of disorders. Affected individuals often present with an occipital cephalocele with a bony skull defect, but typically have normal neurological development. Here, we report on a three-generation family in which individuals have variable phenotypes that are consistent with the ADDWOC spectrum: arachnoid cysts in the proband and his maternal grandfather, an occipital cephalocele in the proband and his brother, and a small bony defect in the proband's mother. Whole exome sequencing identified a rare heterozygous variant in NID1 (NM_002508.2:c.1162C>T, (p.Gln388Ter)) in the proband, his brother, and his mother. Sanger sequencing confirmed the presence of this variant in the maternal grandfather. The identical c.1162C>T variant was previously identified in variably affected members of a three-generation family with ADDWOC. This case report provides further evidence that variants in NID1 may be clinically relevant for the development of a phenotype that is consistent with ADDWOC, and extends the phenotype of NID1-associated ADDWOC to include arachnoid cysts. Given that the Dandy-Walker malformation itself is not a pre-requisite to this spectrum of phenotypes, we also suggest a novel term for the NID1-associated disorder in order to give emphasis to this phenotypic variability: "Autosomal Dominant Posterior Fossa Anomalies with Occipital Cephaloceles."
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Affiliation(s)
- Vanda McNiven
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yoko A Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Elka Miller
- Department of Medical Imaging, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Christine M Armour
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Unit, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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29
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Wizeman JW, Guo Q, Wilion EM, Li JYH. Specification of diverse cell types during early neurogenesis of the mouse cerebellum. eLife 2019; 8:e42388. [PMID: 30735127 PMCID: PMC6382353 DOI: 10.7554/elife.42388] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/07/2019] [Indexed: 12/22/2022] Open
Abstract
We applied single-cell RNA sequencing to profile genome-wide gene expression in about 9400 individual cerebellar cells from the mouse embryo at embryonic day 13.5. Reiterative clustering identified the major cerebellar cell types and subpopulations of different lineages. Through pseudotemporal ordering to reconstruct developmental trajectories, we identified novel transcriptional programs controlling cell fate specification of populations arising from the ventricular zone and the rhombic lip, two distinct germinal zones of the embryonic cerebellum. Together, our data revealed cell-specific markers for studying the cerebellum, gene-expression cascades underlying cell fate specification, and a number of previously unknown subpopulations that may play an integral role in the formation and function of the cerebellum. Our findings will facilitate new discovery by providing insights into the molecular and cell type diversity in the developing cerebellum.
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Affiliation(s)
- John W Wizeman
- Department of Genetics and Genome Sciences, School of MedicineUniversity of ConnecticutFarmingtonUnited States
| | - Qiuxia Guo
- Department of Genetics and Genome Sciences, School of MedicineUniversity of ConnecticutFarmingtonUnited States
| | | | - James YH Li
- Department of Genetics and Genome Sciences, School of MedicineUniversity of ConnecticutFarmingtonUnited States
- Institute for Systems GenomicsUniversity of ConnecticutFarmingtonUnited States
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30
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Haldipur P, Millen KJ. What cerebellar malformations tell us about cerebellar development. Neurosci Lett 2019; 688:14-25. [PMID: 29802918 PMCID: PMC6240394 DOI: 10.1016/j.neulet.2018.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 02/06/2023]
Abstract
Structural birth defects of the cerebellum, or cerebellar malformations, in humans, have long been recognized. However, until recently there has been little progress in elucidating their developmental pathogenesis. Innovations in brain imaging and human genetic technologies over the last 2 decades have led to better classifications of these disorders and identification of several causative genes. In contrast, cerebellar malformations in model organisms, particularly mice, have been the focus of intense study for more than 70 years. As a result, many of the molecular, genetic and cellular programs that drive formation of the cerebellum have been delineated in mice. In this review, we overview the basic epochs and key molecular regulators of the developmental programs that build the structure of the mouse cerebellum. This mouse-centric approach has been a useful to interpret the developmental pathogenesis of human cerebellar malformations. However, it is becoming apparent that we actually know very little regarding the specifics of human cerebellar development beyond what is inferred from mice. A better understanding of human cerebellar development will not only facilitate improved diagnosis of human cerebellar malformations, but also lead to the development of treatment paradigms for these important neurodevelopmental disorders.
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Affiliation(s)
- Parthiv Haldipur
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, United States
| | - Kathleen J Millen
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, United States; University of Washington, Department of Pediatrics, Division of Genetics, Seattle, WA, United States.
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31
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Shalata A, Lauhasurayotin S, Leibovitz Z, Li H, Hebert D, Dhanraj S, Hadid Y, Mahroum M, Bajar J, Egenburg S, Arad A, Shohat M, Haddad S, Bakry H, Moshiri H, Scherer SW, Tzur S, Dror Y. Biallelic mutations in EXOC3L2 cause a novel syndrome that affects the brain, kidney and blood. J Med Genet 2018; 56:340-346. [PMID: 30327448 DOI: 10.1136/jmedgenet-2018-105421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/18/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND Dandy-Walker malformation features agenesis/hypoplasia of the cerebellar vermis, cystic dilatation of the fourth ventricle and enlargement of posterior fossa. Although Dandy-Walker malformation is relatively common and several genes were linked to the syndrome, the genetic cause in the majority of cases is unknown. OBJECTIVE To identify the mutated gene responsible for Dandy-Walker malformation, kidney disease and bone marrow failure in four patients from two unrelated families. METHODS Medical assessment, sonographic, MRI and pathological studies were used to define phenotype. Chromosomal microarray analysis and whole-exome sequence were performed to unravel the genotype. RESULTS We report four subjects from two unrelated families with homozygous mutations in the Exocyst Complex Component 3-Like-2 gene (EXOC3L2).EXOC3L2 functions in trafficking of post-Golgi vesicles to the plasma membrane. In the first family a missense mutation in a highly conserved amino acid, p.Leu41Gln, was found in three fetuses; all had severe forms of Dandy-Walker malformation that was detectable by prenatal ultrasonography and confirmed by autopsy. In the second family, the affected child carried a nonsense mutation, p.Arg72*, and no detected protein. He had peritrigonal and cerebellar white matter abnormalities with enlargement of the ventricular trigones, developmental delay, pituitary hypoplasia, severe renal dysplasia and bone marrow failure. CONCLUSION We propose that biallelic EXOC3L2 mutations lead to a novel syndrome that affects hindbrain development, kidney and possibly the bone marrow.
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Affiliation(s)
- Adel Shalata
- Pediatrics and Medical Genetics and The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa, Israel
| | - Supanun Lauhasurayotin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/ Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Israel
| | - Zvi Leibovitz
- Obstetrics-Gynecology Ultrasound Unit, Bnai-Zion Medical Center and Rappaport Faculty of Medicine, The Technion, Haifa, Israel
| | - Hongbing Li
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/ Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Israel
| | - Diane Hebert
- Division of Nephrology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Santhosh Dhanraj
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/ Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Israel
| | - Yarin Hadid
- Pediatrics and Medical Genetics and The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa, Israel
| | - Mohammed Mahroum
- Pediatrics and Medical Genetics and The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa, Israel
| | - Jacob Bajar
- Department of Pathology, Bnai Zion Medical Center, Haifa, Israel
| | - Sandro Egenburg
- Department of Pathology, Bnai Zion Medical Center, Haifa, Israel
| | - Ayala Arad
- Department of Pathology, Bnai Zion Medical Center, Haifa, Israel
| | - Mordechai Shohat
- Sheba Cancer Research Center, Sackler School of Medicine, Tel Aviva University, Maccabi Genetic Institute, Tel Aviv, Israel
| | - Sami Haddad
- Ultrasound unit, Obstetrics-Gynecology Department, Baruch Padeh Peoria Hospital, Tiberias, Israel
| | - Hassan Bakry
- Obstetrics-Gynecology Ultrasound Unit, Bnai-Zion Medical Center and Rappaport Faculty of Medicine, The Technion, Haifa, Israel
| | - Houtan Moshiri
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shay Tzur
- Laboratory of Molecular Medicine, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
- Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel
| | - Yigal Dror
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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32
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Yang CA, Chou IC, Cho DY, Lin CY, Huang HY, Ho YC, Liu TY, Li YH, Chang JG. Whole exome sequencing in Dandy-Walker variant with intellectual disability reveals an activating CIP2A mutation as novel genetic cause. Neurogenetics 2018; 19:157-163. [DOI: 10.1007/s10048-018-0548-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/11/2018] [Indexed: 11/30/2022]
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ZIC1 Function in Normal Cerebellar Development and Human Developmental Pathology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:249-268. [PMID: 29442326 DOI: 10.1007/978-981-10-7311-3_13] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Zic genes are strongly expressed in the cerebellum. This feature leads to their initial identification and their name "zic," as the abbreviation of "zinc finger protein of the cerebellum." Zic gene function in cerebellar development has been investigated mainly in mice. However, association of heterozygous loss of ZIC1 and ZIC4 with Dandy-Walker malformation, a structural birth defect of the human cerebellum, highlights the clinical relevance of these studies. Two proposed mechanisms for Zic-mediated cerebellar developmental control have been documented: regulation of neuronal progenitor proliferation-differentiation and the patterning of the cerebellar primordium. Clinical studies have also revealed that ZIC1 gain of function mutations contribute to coronal craniosynostosis, a rare skull malformation. The molecular pathways contributing to these phenotypes are not fully explored; however, embryonic interactions with sonic hedgehog signaling, retinoic acid signaling, and TGFβ signaling have been described during mouse cerebellar development. Further, Zic1/2 target a multitude of genes associated with cerebellar granule cell maturation during postnatal mouse cerebellar development.
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34
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Diamand KEM, Barratt KS, Arkell RM. Overview of Rodent Zic Genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:179-207. [PMID: 29442323 DOI: 10.1007/978-981-10-7311-3_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The five murine Zic genes encode multifunctional transcriptional regulator proteins important for a large number of processes during embryonic development. The genes and proteins are highly conserved with respect to the orthologous human genes, an attribute evidently mirrored by functional conservation, since the murine and human genes mutate to give the same phenotypes. Each ZIC protein contains a zinc finger domain that participates in both protein-DNA and protein-protein interactions. The ZIC proteins are capable of interacting with the key transcriptional mediators of the SHH, WNT and NODAL signalling pathways as well as with components of the transcriptional machinery and chromatin-modifying complexes. It is possible that this diverse range of protein partners underlies characteristics uncovered by mutagenesis and phenotyping of the murine Zic genes. These features include redundant and unique roles for ZIC proteins, regulatory interdependencies amongst family members and pleiotropic Zic gene function. Future investigations into the complex nature of the Zic gene family activity should be facilitated by recent advances in genome engineering and functional genomics.
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Affiliation(s)
- Koula E M Diamand
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kristen S Barratt
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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35
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Bellchambers HM, Ware SM. ZIC3 in Heterotaxy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:301-327. [PMID: 29442328 DOI: 10.1007/978-981-10-7311-3_15] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mutation of ZIC3 causes X-linked heterotaxy, a syndrome in which the laterality of internal organs is disrupted. Analysis of model organisms and gene expression during early development suggests ZIC3-related heterotaxy occurs due to defects at the earliest stage of left-right axis formation. Although there are data to support abnormalities of the node and cilia as underlying causes, it is unclear at the molecular level why loss of ZIC3 function causes such these defects. ZIC3 has putative roles in a number of developmental signalling pathways that have distinct roles in establishing the left-right axis. This complicates the understanding of the mechanistic basis of Zic3 in early development and left-right patterning. Here we summarise our current understanding of ZIC3 function and describe the potential role ZIC3 plays in important signalling pathways and their links to heterotaxy.
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Affiliation(s)
- Helen M Bellchambers
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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36
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Wijayatunge R, Liu F, Shpargel KB, Wayne NJ, Chan U, Boua JV, Magnuson T, West AE. The histone demethylase Kdm6b regulates a mature gene expression program in differentiating cerebellar granule neurons. Mol Cell Neurosci 2017; 87:4-17. [PMID: 29254825 DOI: 10.1016/j.mcn.2017.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/21/2017] [Accepted: 11/06/2017] [Indexed: 02/09/2023] Open
Abstract
The histone H3 lysine 27 (H3K27) demethylase Kdm6b (Jmjd3) can promote cellular differentiation, however its physiological functions in neurons remain to be fully determined. We studied the expression and function of Kdm6b in differentiating granule neurons of the developing postnatal mouse cerebellum. At postnatal day 7, Kdm6b is expressed throughout the layers of the developing cerebellar cortex, but its expression is upregulated in newborn cerebellar granule neurons (CGNs). Atoh1-Cre mediated conditional knockout of Kdm6b in CGN precursors either alone or in combination with Kdm6a did not disturb the gross morphological development of the cerebellum. Furthermore, RNAi-mediated knockdown of Kdm6b in cultured CGN precursors did not alter the induced expression of early neuronal marker genes upon cell cycle exit. By contrast, knockdown of Kdm6b significantly impaired the induction of a mature neuronal gene expression program, which includes gene products required for functional synapse maturation. Loss of Kdm6b also impaired the ability of Brain-Derived Neurotrophic Factor (BDNF) to induce expression of Grin2c and Tiam1 in maturing CGNs. Taken together, these data reveal a previously unknown role for Kdm6b in the postmitotic stages of CGN maturation and suggest that Kdm6b may work, at least in part, by a transcriptional mechanism that promotes gene sensitivity to regulation by BDNF.
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Affiliation(s)
- Ranjula Wijayatunge
- Dept. of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Fang Liu
- Dept. of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Karl B Shpargel
- Dept. of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Nicole J Wayne
- Dept. of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Urann Chan
- Dept. of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Jane-Valeriane Boua
- Dept. of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Terry Magnuson
- Dept. of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Anne E West
- Dept. of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States.
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37
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Whittaker DE, Kasah S, Donovan APA, Ellegood J, Riegman KLH, Volk HA, McGonnell I, Lerch JP, Basson MA. Distinct cerebellar foliation anomalies in a CHD7 haploinsufficient mouse model of CHARGE syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175. [PMID: 29168327 PMCID: PMC5765394 DOI: 10.1002/ajmg.c.31595] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/22/2017] [Accepted: 09/24/2017] [Indexed: 11/13/2022]
Abstract
Mutations in the gene encoding the ATP dependent chromatin‐remodeling factor, CHD7 are the major cause of CHARGE (Coloboma, Heart defects, Atresia of the choanae, Retarded growth and development, Genital‐urinary anomalies, and Ear defects) syndrome. Neurodevelopmental defects and a range of neurological signs have been identified in individuals with CHARGE syndrome, including developmental delay, lack of coordination, intellectual disability, and autistic traits. We previously identified cerebellar vermis hypoplasia and abnormal cerebellar foliation in individuals with CHARGE syndrome. Here, we report mild cerebellar hypoplasia and distinct cerebellar foliation anomalies in a Chd7 haploinsufficient mouse model. We describe specific alterations in the precise spatio‐temporal sequence of fissure formation during perinatal cerebellar development responsible for these foliation anomalies. The altered cerebellar foliation pattern in Chd7 haploinsufficient mice show some similarities to those reported in mice with altered Engrailed, Fgf8 or Zic1 gene expression and we propose that mutations or polymorphisms in these genes may modify the cerebellar phenotype in CHARGE syndrome. Our findings in a mouse model of CHARGE syndrome indicate that a careful analysis of cerebellar foliation may be warranted in patients with CHARGE syndrome, particularly in patients with cerebellar hypoplasia and developmental delay.
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Affiliation(s)
- Danielle E Whittaker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom.,Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - Sahrunizam Kasah
- Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
| | - Alex P A Donovan
- Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
| | - Jacob Ellegood
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kimberley L H Riegman
- Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
| | - Holger A Volk
- Department of Clinical Science and Services, Royal Veterinary College, London, United Kingdom
| | - Imelda McGonnell
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, United Kingdom
| | - Jason P Lerch
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
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38
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Stambolliu E, Ioakeim-Ioannidou M, Kontokostas K, Dakoutrou M, Kousoulis AA. The Most Common Comorbidities in Dandy-Walker Syndrome Patients: A Systematic Review of Case Reports. J Child Neurol 2017. [PMID: 28635420 DOI: 10.1177/0883073817712589] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Dandy-Walker syndrome (DWS) is a rare neurologic multi-entity malformation. This review aimed at reporting its main nonneurologic comorbidities. METHODS Following PRISMA guidelines, search in Medline was conducted (2000-2014, keyword: dandy-walker). Age, sex, country, DWS type, consanguinity or siblings with DWS, and recorded coexistent conditions (by ICD10 category) were extracted for 187 patients (46.5% male, 43% from Asia) from 168 case reports. RESULTS Diagnosis was most often set in <1 year old (40.6%) or >12 years old (27.8%). One-third of cases had a chromosomal abnormality or syndrome (n = 8 PHACE), 27% had a cardiovascular condition (n = 7 Patent Ductus Arteriosus), 24% had a disease of eye and ear (n = 9 cataract); most common malignancy was nephroblastoma (n = 8, all Asian). Almost one-fifth had a mental illness diagnosis; only 6.4% had mild or severe intellectual disability. CONCLUSION The spread of comorbidities calls for early diagnosis and multidisciplinary research and practice, especially as many cases remain clinically asymptomatic for years.
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Affiliation(s)
- Emelina Stambolliu
- 1 Society of Junior Doctors, Athens, Greece.,2 Department of Internal Medicine, General Hospital of Kalavryta, Kalavryta, Greece
| | | | | | - Maria Dakoutrou
- 1 Society of Junior Doctors, Athens, Greece.,5 First Department of Paediatrics, "Aghia Sophia" Children's Hospital, University of Athens, Greece
| | - Antonis A Kousoulis
- 1 Society of Junior Doctors, Athens, Greece.,6 Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Moodley AW, Nel S, Oosthuizen E, Lundgren C. Anaesthetic management for ventriculoperitoneal shunt insertion in an infant with Dandy–Walker Syndrome. SOUTHERN AFRICAN JOURNAL OF ANAESTHESIA AND ANALGESIA 2017. [DOI: 10.1080/22201181.2017.1283741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Alastair Wayne Moodley
- Department of Anaesthesia, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Steven Nel
- Department of Anaesthesia, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eduard Oosthuizen
- Department of Anaesthesia, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christina Lundgren
- Department of Anaesthesia, Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Haldipur P, Dang D, Aldinger KA, Janson OK, Guimiot F, Adle-Biasette H, Dobyns WB, Siebert JR, Russo R, Millen KJ. Phenotypic outcomes in Mouse and Human Foxc1 dependent Dandy-Walker cerebellar malformation suggest shared mechanisms. eLife 2017; 6:20898. [PMID: 28092268 PMCID: PMC5271606 DOI: 10.7554/elife.20898] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/15/2017] [Indexed: 12/13/2022] Open
Abstract
FOXC1 loss contributes to Dandy-Walker malformation (DWM), a common human cerebellar malformation. Previously, we found that complete Foxc1 loss leads to aberrations in proliferation, neuronal differentiation and migration in the embryonic mouse cerebellum (Haldipur et al., 2014). We now demonstrate that hypomorphic Foxc1 mutant mice have granule and Purkinje cell abnormalities causing subsequent disruptions in postnatal cerebellar foliation and lamination. Particularly striking is the presence of a partially formed posterior lobule which echoes the posterior vermis DW 'tail sign' observed in human imaging studies. Lineage tracing experiments in Foxc1 mutant mouse cerebella indicate that aberrant migration of granule cell progenitors destined to form the posterior-most lobule causes this unique phenotype. Analyses of rare human del chr 6p25 fetal cerebella demonstrate extensive phenotypic overlap with our Foxc1 mutant mouse models, validating our DWM models and demonstrating that many key mechanisms controlling cerebellar development are likely conserved between mouse and human. DOI:http://dx.doi.org/10.7554/eLife.20898.001
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Affiliation(s)
- Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, United States
| | - Derek Dang
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, United States
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, United States
| | - Olivia K Janson
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, United States
| | | | | | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, Genetics Division, University of Washington, Seattle, United States
| | - Joseph R Siebert
- Department of Laboratories, Seattle Children's Hospital, Seattle, United States.,Department of Pathology, University of Washington, Seattle, United States
| | - Rosa Russo
- Department of Pathology, Molecular Genetics Laboratory, University Medical Hospital, Salerno, Italy
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, Genetics Division, University of Washington, Seattle, United States
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D'Souza M, Sulakhe D, Wang S, Xie B, Hashemifar S, Taylor A, Dubchak I, Conrad Gilliam T, Maltsev N. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks. Methods Mol Biol 2017; 1613:85-99. [PMID: 28849559 DOI: 10.1007/978-1-4939-7027-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.
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Affiliation(s)
- Mark D'Souza
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA.
- Argonne National Laboratory, Building 221, Room: A142, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
| | - Sheng Wang
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, 60637, USA
| | - Bing Xie
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Somaye Hashemifar
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, 60637, USA
| | - Andrew Taylor
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
| | - Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T Conrad Gilliam
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
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Sankar S, Yellajoshyula D, Zhang B, Teets B, Rockweiler N, Kroll KL. Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1. Sci Rep 2016; 6:37412. [PMID: 27881878 PMCID: PMC5121602 DOI: 10.1038/srep37412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/28/2016] [Indexed: 12/30/2022] Open
Abstract
Neural cell fate acquisition is mediated by transcription factors expressed in nascent neuroectoderm, including Geminin and members of the Zic transcription factor family. However, regulatory networks through which this occurs are not well defined. Here, we identified Geminin-associated chromatin locations in embryonic stem cells and Geminin- and Zic1-associated locations during neural fate acquisition at a genome-wide level. We determined how Geminin deficiency affected histone acetylation at gene promoters during this process. We integrated these data to demonstrate that Geminin associates with and promotes histone acetylation at neurodevelopmental genes, while Geminin and Zic1 bind a shared gene subset. Geminin- and Zic1-associated genes exhibit embryonic nervous system-enriched expression and encode other regulators of neural development. Both Geminin and Zic1-associated peaks are enriched for Zic1 consensus binding motifs, while Zic1-bound peaks are also enriched for Sox3 motifs, suggesting co-regulatory potential. Accordingly, we found that Geminin and Zic1 could cooperatively activate the expression of several shared targets encoding transcription factors that control neurogenesis, neural plate patterning, and neuronal differentiation. We used these data to construct gene regulatory networks underlying neural fate acquisition. Establishment of this molecular program in nascent neuroectoderm directly links early neural cell fate acquisition with regulatory control of later neurodevelopment.
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Affiliation(s)
- Savita Sankar
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Dhananjay Yellajoshyula
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Bryan Teets
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Nicole Rockweiler
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
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Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. Neurogenetics 2015; 17:1-9. [PMID: 26382291 PMCID: PMC4701781 DOI: 10.1007/s10048-015-0458-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/02/2015] [Indexed: 11/25/2022]
Abstract
Regulatory elements are more evolutionarily conserved and provide a larger mutational target than coding regions of the human genome, suggesting that mutations in non-coding regions contribute significantly to development and disease. Using a computational approach to predict gene regulatory enhancers, we found that many known and predicted embryonic enhancers cluster in genomic loci harboring development-associated genes. One of the densest clusters of predicted enhancers in the human genome is near the genes GMDS and FOXC1. GMDS encodes a short-chain mannose dehydrogenase enzyme involved in the regulation of hindbrain neural migration, and FOXC1 encodes a developmental transcription factor required for brain, heart, and eye development. We experimentally validate four novel enhancers in this locus and demonstrate that these enhancers show consistent activity during embryonic development in domains that overlap with the expression of FOXC1 and GMDS. These four enhancers contain binding motifs for several transcription factors, including the ZIC family of transcription factors. Removal of the ZIC binding sites significantly alters enhancer activity in three of these enhancers, reducing expression in the eye, hindbrain, and limb, suggesting a mechanism whereby ZIC family members may transcriptionally regulate FOXC1 and/or GMDS expression. Our findings uncover novel enhancer regions that may control transcription in a topological domain important for embryonic development.
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45
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Spontaneous malformations of the cerebellar vermis: Prevalence, inheritance, and relationship to lobule/fissure organization in the C57BL/6 lineage. Neuroscience 2015; 310:242-51. [PMID: 26383253 DOI: 10.1016/j.neuroscience.2015.09.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/09/2015] [Indexed: 11/22/2022]
Abstract
The complex neuronal circuitry of the cerebellum is embedded within its lamina, folia, and lobules, which together play an important role in sensory and motor function. Studies in mouse models have demonstrated that both cerebellar lamination and lobule/fissure development are under genetic control. The cerebellar vermis of C57BL/6 mice exhibits spontaneous malformations of neuronal migration of posterior lobules (VIII-IX; molecular layer heterotopia); however, the extent to which other inbred mice also exhibit these malformations is unknown. Using seven different inbred mouse strains and two first filial generation (F1) hybrids, we show that only the C57BL/6 strain exhibits heterotopia. Furthermore, we observed heterotopia in consomic and recombinant inbred strains. These data indicate that heterotopia formation is a weakly penetrant trait requiring homozygosity of one or more C57BL/6 alleles outside of chromosome 1 and the sex chromosomes. Additional morphological analyses showed no relationship between heterotopia formation and other features of lobule/fissure organization. These data are relevant toward understanding normal cerebellar development and disorders affecting cerebellar foliation and lamination.
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46
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Twigg SRF, Forecki J, Goos JAC, Richardson ICA, Hoogeboom AJM, van den Ouweland AMW, Swagemakers SMA, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA, van der Spek PJ, Mathijssen IMJ, Pauws E, Merzdorf CS, Wilkie AOM. Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability. Am J Hum Genet 2015; 97:378-88. [PMID: 26340333 PMCID: PMC4564895 DOI: 10.1016/j.ajhg.2015.07.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/14/2015] [Indexed: 12/03/2022] Open
Abstract
Human ZIC1 (zinc finger protein of cerebellum 1), one of five homologs of the Drosophila pair-rule gene odd-paired, encodes a transcription factor previously implicated in vertebrate brain development. Heterozygous deletions of ZIC1 and its nearby paralog ZIC4 on chromosome 3q25.1 are associated with Dandy-Walker malformation of the cerebellum, and loss of the orthologous Zic1 gene in the mouse causes cerebellar hypoplasia and vertebral defects. We describe individuals from five families with heterozygous mutations located in the final (third) exon of ZIC1 (encoding four nonsense and one missense change) who have a distinct phenotype in which severe craniosynostosis, specifically involving the coronal sutures, and variable learning disability are the most characteristic features. The location of the nonsense mutations predicts escape of mutant ZIC1 transcripts from nonsense-mediated decay, which was confirmed in a cell line from an affected individual. Both nonsense and missense mutations are associated with altered and/or enhanced expression of a target gene, engrailed-2, in a Xenopus embryo assay. Analysis of mouse embryos revealed a localized domain of Zic1 expression at embryonic days 11.5-12.5 in a region overlapping the supraorbital regulatory center, which patterns the coronal suture. We conclude that the human mutations uncover a previously unsuspected role for Zic1 in early cranial suture development, potentially by regulating engrailed 1, which was previously shown to be critical for positioning of the murine coronal suture. The diagnosis of a ZIC1 mutation has significant implications for prognosis and we recommend genetic testing when common causes of coronal synostosis have been excluded.
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Affiliation(s)
- Stephen R F Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Jennifer Forecki
- Department of Cell Biology and Neuroscience, 513 Leon Johnson Hall, Montana State University, Bozeman, MT 59717, USA
| | - Jacqueline A C Goos
- Department of Plastic Surgery, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Ivy C A Richardson
- Developmental Biology and Cancer Programme, UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - A Jeannette M Hoogeboom
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Ans M W van den Ouweland
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Sigrid M A Swagemakers
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Maarten H Lequin
- Department of Pediatric Radiology, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Daniel Van Antwerp
- Department of Cell Biology and Neuroscience, 513 Leon Johnson Hall, Montana State University, Bozeman, MT 59717, USA
| | - Simon J McGowan
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Isabelle Westbury
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Kerry A Miller
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Peter J van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Irene M J Mathijssen
- Department of Plastic Surgery, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Erwin Pauws
- Developmental Biology and Cancer Programme, UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Christa S Merzdorf
- Department of Cell Biology and Neuroscience, 513 Leon Johnson Hall, Montana State University, Bozeman, MT 59717, USA
| | - Andrew O M Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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Reeder MR, Botto LD, Keppler-Noreuil KM, Carey JC, Byrne JLB, Feldkamp ML. Risk factors for Dandy-Walker malformation: A population-based assessment. Am J Med Genet A 2015; 167A:2009-16. [DOI: 10.1002/ajmg.a.37124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Matthew R. Reeder
- Division of Medical Genetics, Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
| | - Lorenzo D. Botto
- Division of Medical Genetics, Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
| | - Kim M. Keppler-Noreuil
- National Human Genome Research Institute; National Institutes of Health; Bethesda Maryland
| | - John C. Carey
- Division of Medical Genetics, Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
| | - Janice L. B. Byrne
- Division of Medical Genetics, Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology; University of Utah School of Medicine; Salt Lake City Utah
| | - Marcia L. Feldkamp
- Division of Medical Genetics, Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
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Bernardino F, Rentmeister K, Schmidt MJ, Bruehschwein A, Matiasek K, Matiasek LA, Lauda A, Schoon HA, Fischer A. Inferior cerebellar hypoplasia resembling a Dandy-Walker-like malformation in purebred Eurasier dogs with familial non-progressive ataxia: a retrospective and prospective clinical cohort study. PLoS One 2015; 10:e0117670. [PMID: 25668516 PMCID: PMC4323131 DOI: 10.1371/journal.pone.0117670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 12/10/2014] [Indexed: 12/16/2022] Open
Abstract
Cerebellar malformations can be inherited or caused by insults during cerebellar development. To date, only sporadic cases of cerebellar malformations have been reported in dogs, and the genetic background has remained obscure. Therefore, this study`s objective was to describe the clinical characteristics, imaging features and pedigree data of a familial cerebellar hypoplasia in purebred Eurasier dogs. A uniform cerebellar malformation characterized by consistent absence of the caudal portions of the cerebellar vermis and, to a lesser degree, the caudal portions of the cerebellar hemispheres in association with large retrocerebellar fluid accumulations was recognized in 14 closely related Eurasier dogs. Hydrocephalus was an additional feature in some dogs. All dogs displayed non-progressive ataxia, which had already been noted when the dogs were 5 – 6 weeks old. The severity of the ataxia varied between dogs, from mild truncal sway, subtle dysmetric gait, dysequilibrium and pelvic limb ataxia to severe cerebellar ataxia in puppies and episodic falling or rolling. Follow-up examinations in adult dogs showed improvement of the cerebellar ataxia and a still absent menace response. Epileptic seizures occurred in some dogs. The association of partial vermis agenesis with an enlarged fourth ventricle and an enlarged caudal (posterior) fossa resembled a Dandy-Walker-like malformation in some dogs. Pedigree analyses were consistent with autosomal recessive inheritance.
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Affiliation(s)
- Filipa Bernardino
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, Ludwig Maximilian University, Munich, Germany
| | | | - Martin J. Schmidt
- Department of Veterinary Clinical Science, Small Animal Clinic, Justus-Liebig-University, Giessen, Germany
| | - Andreas Bruehschwein
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Surgery and Reproduction, Ludwig Maximilian University, Munich, Germany
| | - Kaspar Matiasek
- Centre for Clinical Veterinary Medicine, Section of Clinical and Comparative Neuropathology, Ludwig Maximilian University, Munich, Germany
| | - Lara A. Matiasek
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, Ludwig Maximilian University, Munich, Germany
| | - Alexander Lauda
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, Ludwig Maximilian University, Munich, Germany
| | - Heinz A. Schoon
- Institute of Pathology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Andrea Fischer
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, Ludwig Maximilian University, Munich, Germany
- * E-mail:
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Cunningham D, DeBarber AE, Bir N, Binkley L, Merkens LS, Steiner RD, Herman GE. Analysis of hedgehog signaling in cerebellar granule cell precursors in a conditional Nsdhl allele demonstrates an essential role for cholesterol in postnatal CNS development. Hum Mol Genet 2015; 24:2808-25. [PMID: 25652406 DOI: 10.1093/hmg/ddv042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/02/2015] [Indexed: 12/21/2022] Open
Abstract
NSDHL is a 3β-hydroxysterol dehydrogenase that is involved in the removal of two C-4 methyl groups in one of the later steps of cholesterol biosynthesis. Mutations in the gene encoding the enzyme are responsible for the X-linked, male lethal mouse mutations bare patches and striated, as well as most cases of human CHILD syndrome. Rare, hypomorphic NSDHL mutations are also associated with X-linked intellectual disability in males with CK syndrome. Since hemizygous male mice with Nsdhl mutations die by midgestation, we generated a conditional targeted Nsdhl mutation (Nsdhl(tm1.1Hrm)) to investigate the essential role of cholesterol in the early postnatal CNS. Ablation of Nsdhl in radial glia using GFAP-cre resulted in live-born, normal appearing affected male pups. However, the pups develop overt ataxia by postnatal day 8-10 and die shortly thereafter. Histological abnormalities include progressive loss of cortical and hippocampal neurons, as well as deficits in the proliferation and migration of cerebellar granule precursors and subsequent massive apoptosis of the cerebellar cortex. We replicated the granule cell precursor proliferation defect in vitro and demonstrate that it results from defective signaling by SHH. Furthermore, this defect is almost completely rescued by supplementation of the culture media with exogenous cholesterol, while methylsterol accumulation above the enzymatic block appears to be associated with increased cell death. These data support the absolute requirement for cholesterol synthesis in situ once the blood-brain-barrier forms and cholesterol transport to the fetus is abolished. They further emphasize the complex ramifications of cholesterogenic enzyme deficiency on cellular metabolism.
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Affiliation(s)
- David Cunningham
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | | | - Natalie Bir
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Laura Binkley
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | | | - Robert D Steiner
- Department of Pediatrics, Department of Molecular and Medical Genetics and Institute on Development and Disability, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, OR, USA and Marshfield Clinic Research Foundation and the Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Marshfield and Madison, WI, USA
| | - Gail E Herman
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH, USA,
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Marzban H, Del Bigio MR, Alizadeh J, Ghavami S, Zachariah RM, Rastegar M. Cellular commitment in the developing cerebellum. Front Cell Neurosci 2015; 8:450. [PMID: 25628535 PMCID: PMC4290586 DOI: 10.3389/fncel.2014.00450] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/12/2014] [Indexed: 12/11/2022] Open
Abstract
The mammalian cerebellum is located in the posterior cranial fossa and is critical for motor coordination and non-motor functions including cognitive and emotional processes. The anatomical structure of cerebellum is distinct with a three-layered cortex. During development, neurogenesis and fate decisions of cerebellar primordium cells are orchestrated through tightly controlled molecular events involving multiple genetic pathways. In this review, we will highlight the anatomical structure of human and mouse cerebellum, the cellular composition of developing cerebellum, and the underlying gene expression programs involved in cell fate commitments in the cerebellum. A critical evaluation of the cell death literature suggests that apoptosis occurs in ~5% of cerebellar cells, most shortly after mitosis. Apoptosis and cellular autophagy likely play significant roles in cerebellar development, we provide a comprehensive discussion of their role in cerebellar development and organization. We also address the possible function of unfolded protein response in regulation of cerebellar neurogenesis. We discuss recent advancements in understanding the epigenetic signature of cerebellar compartments and possible connections between DNA methylation, microRNAs and cerebellar neurodegeneration. Finally, we discuss genetic diseases associated with cerebellar dysfunction and their role in the aging cerebellum.
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Affiliation(s)
- Hassan Marzban
- Department of Human Anatomy and Cell Science, University of Manitoba Winnipeg, MB, Canada
| | - Marc R Del Bigio
- Department of Human Anatomy and Cell Science, University of Manitoba Winnipeg, MB, Canada ; Department of Pathology, University of Manitoba Winnipeg, MB, Canada
| | - Javad Alizadeh
- Department of Human Anatomy and Cell Science, University of Manitoba Winnipeg, MB, Canada
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, University of Manitoba Winnipeg, MB, Canada
| | - Robby M Zachariah
- Department of Biochemistry and Medical Genetics, University of Manitoba Winnipeg, MB, Canada ; Regenerative Medicine Program, University of Manitoba Winnipeg, MB, Canada
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, University of Manitoba Winnipeg, MB, Canada ; Regenerative Medicine Program, University of Manitoba Winnipeg, MB, Canada
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