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Nayak SS, Panigrahi M, Rajawat D, Ghildiyal K, Sharma A, Parida S, Bhushan B, Mishra BP, Dutt T. Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data. Mamm Genome 2023; 34:615-631. [PMID: 37843569 DOI: 10.1007/s00335-023-10021-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023]
Abstract
The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - B P Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
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Oliveira MDS, Cassiano LMG, Pioline J, de Carvalho KRA, Salim ACDM, Alves PA, Fernandes GDR, Machado ADMV, Coimbra RS. Organotypic hippocampal culture model reveals differential responses to highly similar Zika virus isolates. J Neuroinflammation 2023; 20:140. [PMID: 37301965 DOI: 10.1186/s12974-023-02826-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
INTRODUCTION Zika virus (ZIKV) caused an outbreak in Brazil, in 2015, being associated to microcephaly. ZIKV has a strong neurotropism leading to death of infected cells in different brain regions, including the hippocampus, a major site for neurogenesis. The neuronal populations of the brain are affected differently by ZIKV from Asian and African ancestral lineages. However, it remains to be investigated whether subtle variations in the ZIKV genome can impact hippocampus infection dynamics and host response. OBJECTIVE This study evaluated how two Brazilian ZIKV isolates, PE243 and SPH2015, that differ in two specific missense amino acid substitutions, one in the NS1 protein and the other in the NS4A protein, affect the hippocampal phenotype and transcriptome. METHODS Organotypic hippocampal cultures (OHC) from infant Wistar rats were infected with PE243 or SPH2015 and analyzed in time series using immunofluorescence, confocal microscopy, RNA-Seq and RT-qPCR. RESULTS Unique patterns of infection and changes in neuronal density in the OHC were observed for PE243 and SPH2015 between 8 and 48 h post infection (p.i.). Phenotypic analysis of microglia indicated that SPH2015 has a greater capacity for immune evasion. Transcriptome analysis of OHC at 16 h p.i. disclosed 32 and 113 differentially expressed genes (DEGs) in response to infection with PE243 and SPH2015, respectively. Functional enrichment analysis suggested that infection with SPH2015 activates mostly astrocytes rather than microglia. PE243 downregulated biological process of proliferation of brain cells and upregulated those associated with neuron death, while SPH2015 downregulated processes related to neuronal development. Both isolates downregulated cognitive and behavioral development processes. Ten genes were similarly regulated by both isolates. They are putative biomarkers of early hippocampus response to ZIKV infection. At 5, 7, and 10 days p.i., neuronal density of infected OHC remained below controls, and mature neurons of infected OHC showed an increase in the epigenetic mark H3K4me3, which is associated to a transcriptionally active state. This feature is more prominent in response to SPH2015. CONCLUSION Subtle genetic diversity of the ZIKV affects the dynamics of viral dissemination in the hippocampus and host response in the early stages of infection, which may lead to different long-term effects in neuronal population.
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Affiliation(s)
| | - Larissa Marcely Gomes Cassiano
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jeanne Pioline
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
- Aix-Marseille University, Marseille, France
| | | | - Anna Christina de Matos Salim
- Plataforma de Sequenciamento NGS (Next Generation Sequencing), Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Pedro Augusto Alves
- Imunologia de Doenças Virais, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | | | | | - Roney Santos Coimbra
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil.
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Defining Specific Cell States of MPTP-Induced Parkinson's Disease by Single-Nucleus RNA Sequencing. Int J Mol Sci 2022; 23:ijms231810774. [PMID: 36142685 PMCID: PMC9504791 DOI: 10.3390/ijms231810774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease with an impairment of movement execution that is related to age and genetic and environmental factors. 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin widely used to induce PD models, but the effect of MPTP on the cells and genes of PD has not been fully elucidated. By single-nucleus RNA sequencing, we uncovered the PD-specific cells and revealed the changes in their cellular states, including astrocytosis and endothelial cells' absence, as well as a cluster of medium spiny neuron cells unique to PD. Furthermore, trajectory analysis of astrocyte and endothelial cell populations predicted candidate target gene sets that might be associated with PD. Notably, the detailed regulatory roles of astrocyte-specific transcription factors Dbx2 and Sox13 in PD were revealed in our work. Finally, we characterized the cell-cell communications of PD-specific cells and found that the overall communication strength was enhanced in PD compared with a matched control, especially the signaling pathways of NRXN and NEGR. Our work provides an overview of the changes in cellular states of the MPTP-induced mouse brain.
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He R, Zhang X, Ding L. DBX2 promotes glioblastoma cell proliferation by regulating REST expression. Curr Pharm Biotechnol 2021; 23:1101-1108. [PMID: 34463226 DOI: 10.2174/1389201022666210830142827] [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: 03/06/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glioblastoma (GBM) is the most common but lethal brain cancer with poor prognosis. The developing brain homeobox 2 (DBX2) has been reported to play important roles in tumor growth. However, the mechanisms of DBX2 in GBM are still unknown. OBJECTIVE This study aims to investigate the function and mechanisms of DBX2 in GBM. METHODS The expressions of DBX2 and REST in GBM were measured by analyzing data from databases, and the results were checked by qPCR and/or western blot of GBM cell lines. Cell proliferation was determined by CCK8 assay, immunohistochemistry and colony formation assay. ChIP-qPCR was used to determine the binding sites of DBX2 on REST. RESULTS In this study, we found that the expression of DBX2 was upregulated in the GBM cell lines. The cell proliferation was damaged after blocking DBX2 expression in U87 and U251 GBM cell lines. The expression level of DBX2 had a positive relationship with that of REST. Our ChIP-qPCR results showed that DBX2 is directly bound to the promoter region of REST. Additionally, the increased GBM cell proliferation caused by DBX2 overexpression can be rescued by REST loss of function. CONCLUSION DBX2 could promote cell proliferation of GBM by binding to the promoter region of REST gene and increasing REST expression.
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Affiliation(s)
- Ruixing He
- Neurosurgery Department, the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Jiangsu. China
| | - Xiaotian Zhang
- Neurosurgery Department, Hongze Huai'an District People's Hospital, Jiangsu. China
| | - Lianshu Ding
- Neurosurgery Department, the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Jiangsu. China
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Wilmerding A, Bouteille L, Rinaldi L, Caruso N, Graba Y, Delfini MC. HOXB8 Counteracts MAPK/ERK Oncogenic Signaling in a Chicken Embryo Model of Neoplasia. Int J Mol Sci 2021; 22:8911. [PMID: 34445617 PMCID: PMC8396257 DOI: 10.3390/ijms22168911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/18/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
HOX transcription factors are members of an evolutionarily conserved family of proteins required for the establishment of the anteroposterior body axis during bilaterian development. Although they are often deregulated in cancers, the molecular mechanisms by which they act as oncogenes or tumor suppressor genes are only partially understood. Since the MAPK/ERK signaling pathway is deregulated in most cancers, we aimed at apprehending if and how the Hox proteins interact with ERK oncogenicity. Using an in vivo neoplasia model in the chicken embryo consisting in the overactivation of the ERK1/2 kinases in the trunk neural tube, we analyzed the consequences of the HOXB8 gain of function at the morphological and transcriptional levels. We found that HOXB8 acts as a tumor suppressor, counteracting ERK-induced neoplasia. The HOXB8 tumor suppressor function relies on a large reversion of the oncogenic transcriptome induced by ERK. In addition to showing that the HOXB8 protein controls the transcriptional responsiveness to ERK oncogenic signaling, our study identified new downstream targets of ERK oncogenic activation in an in vivo context that could provide clues for therapeutic strategies.
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Affiliation(s)
- Axelle Wilmerding
- Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France; (A.W.); (L.B.); (L.R.); (N.C.)
| | - Lauranne Bouteille
- Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France; (A.W.); (L.B.); (L.R.); (N.C.)
| | - Lucrezia Rinaldi
- Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France; (A.W.); (L.B.); (L.R.); (N.C.)
- Beth Israel Deaconess Medical Center, Department of Medicine and the Cancer Center, Division of Hematology, Harvard Initiative of RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Caruso
- Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France; (A.W.); (L.B.); (L.R.); (N.C.)
| | - Yacine Graba
- Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France; (A.W.); (L.B.); (L.R.); (N.C.)
| | - Marie-Claire Delfini
- Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France; (A.W.); (L.B.); (L.R.); (N.C.)
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Li K, Li Y, Wang J, Huo Y, Huang D, Li S, Liu J, Li X, Liu R, Chen X, Yao YG, Chen C, Xiao X, Li M, Luo XJ. A functional missense variant in ITIH3 affects protein expression and neurodevelopment and confers schizophrenia risk in the Han Chinese population. J Genet Genomics 2020; 47:233-248. [PMID: 32712163 DOI: 10.1016/j.jgg.2020.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022]
Abstract
The Psychiatric Genomics Consortium (PGC) has recently identified 10 potential functional coding variants for schizophrenia. However, how these coding variants confer schizophrenia risk remains largely unknown. Here, we investigate the associations between eight potential functional coding variants identified by PGC and schizophrenia in a large Han Chinese sample (n = 4022 cases and 9270 controls). Among the eight tested single nucelotide polymorphisms (SNPs), rs3617 (a missense variant, p.K315Q in the ITIH3 gene) showed genome-wide significant association with schizophrenia in the Han Chinese population (P = 8.36 × 10-16), with the same risk allele as in PGC. Interestingly, rs3617 is located in a genomic region that is highly evolutionarily conserved, and its schizophrenia risk allele (C allele) was associated with lower ITIH3 mRNA and protein expression. Intriguingly, mouse neural stem cells stably overexpressing ITIH3 with different alleles of rs3617 exhibited significant differences in proliferation, migration, and differentiation, suggesting the impact of rs3617 on neurodevelopment. Subsequent transcriptome analysis found that the differentially expressed genes in neural stem cells stably overexpressing different alleles of rs3617 were significantly enriched in schizophrenia-related pathways, including cell adhesion, synapse assembly, MAPK and PI3K-AKT pathways. Our study provides convergent lines of evidence suggesting that rs3617 in ITIH3 likely affects protein function and neurodevelopment and thereby confers risk of schizophrenia.
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Affiliation(s)
- Kaiqin Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yifan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Junyang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yongxia Huo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Di Huang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shiwu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiaogang Chen
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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Labonne JDJ, Driessen TM, Harris ME, Kong IK, Brakta S, Theisen J, Sangare M, Layman LC, Kim CH, Lim J, Kim HG. Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31. J Clin Med 2020; 9:jcm9010274. [PMID: 31963867 PMCID: PMC7019335 DOI: 10.3390/jcm9010274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023] Open
Abstract
We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning.
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Affiliation(s)
- Jonathan D. J. Labonne
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Terri M. Driessen
- Department of Genetics, Yale University, New Haven, CT 06510, USA; (T.M.D.); (J.L.)
| | - Marvin E. Harris
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Soumia Brakta
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - John Theisen
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Modibo Sangare
- Faculty of Medicine and Odontostomatology (FMOS), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali;
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA 30912, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Korea;
| | - Janghoo Lim
- Department of Genetics, Yale University, New Haven, CT 06510, USA; (T.M.D.); (J.L.)
- Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Stem Cell Center, Yale University, New Haven, CT 06510, USA
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
- Correspondence:
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Poiana G, Gioia R, Sineri S, Cardarelli S, Lupo G, Cacci E. Transcriptional regulation of adult neural stem/progenitor cells: tales from the subventricular zone. Neural Regen Res 2020; 15:1773-1783. [PMID: 32246617 PMCID: PMC7513981 DOI: 10.4103/1673-5374.280301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In rodents, well characterized neurogenic niches of the adult brain, such as the subventricular zone of the lateral ventricles and the subgranular zone of the hippocampus, support the maintenance of neural/stem progenitor cells (NSPCs) and the production of new neurons throughout the lifespan. The adult neurogenic process is dependent on the intrinsic gene expression signatures of NSPCs that make them competent for self-renewal and neuronal differentiation. At the same time, it is receptive to regulation by various extracellular signals that allow the modulation of neuronal production and integration into brain circuitries by various physiological stimuli. A drawback of this plasticity is the sensitivity of adult neurogenesis to alterations of the niche environment that can occur due to aging, injury or disease. At the core of the molecular mechanisms regulating neurogenesis, several transcription factors have been identified that maintain NSPC identity and mediate NSPC response to extrinsic cues. Here, we focus on REST, Egr1 and Dbx2 and their roles in adult neurogenesis, especially in the subventricular zone. We review recent work from our and other laboratories implicating these transcription factors in the control of NSPC proliferation and differentiation and in the response of NSPCs to extrinsic influences from the niche. We also discuss how their altered regulation may affect the neurogenic process in the aged and in the diseased brain. Finally, we highlight key open questions that need to be addressed to foster our understanding of the transcriptional mechanisms controlling adult neurogenesis.
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Affiliation(s)
- Giancarlo Poiana
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Roberta Gioia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Serena Sineri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Cardarelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
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Hu YT, Li BF, Zhang PJ, Wu D, Li YY, Li ZW, Shen L, Dong B, Gao J, Zhu X. Dbx2 exhibits a tumor-promoting function in hepatocellular carcinoma cell lines via regulating Shh-Gli1 signaling. World J Gastroenterol 2019; 25:923-940. [PMID: 30833799 PMCID: PMC6397724 DOI: 10.3748/wjg.v25.i8.923] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/25/2018] [Accepted: 12/28/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. HCC patients suffer from a high mortality-to-incidence ratio and low cure rate since we still have no specific and effective treatment. Although tremendous advances have been made in the investigation of HCC, the specific mechanisms of the progression of this disease are still only partially established. Hence, more research is needed to elucidate the underlying potential mechanisms to develop effective strategies for HCC.
AIM To determine the role of developing brain homeobox 2 (Dbx2) gene in promoting the development of HCC.
METHODS Dbx2 expression in clinical specimens and HCC cell lines was detected by Western blot (WB) and immunohistochemistry. Gain and loss of Dbx2 function assays were performed in vitro and in vivo. Cell viability assays were used to investigate cell growth, flow cytometry was employed to assess cell cycle and apoptosis, and trans-well assays were conducted to evaluate cell migration, invasion, and metastasis. The expression of key molecules in the sonic hedgehog (Shh) signaling was determined by WB.
RESULTS Compared to matched adjacent non-tumorous tissues, Dbx2 was overexpressed in 5 HCC cell lines and 76 surgically resected HCC tissues. Dbx2 overexpression was correlated with large tumor size. Both gain and loss of function assays indicated that Dbx2 promoted HCC cell proliferation by facilitating the transition from G1 to S phase, attenuating apoptosis and promoted HCC proliferation, migration, and invasion in vitro and in vivo. Mechanistically, Dbx2 modulated Shh signaling by enhancing FTCH1 and GLi1 expression in HCC cells that overexpressed Dbx2, which was reversed in HCC cells with Dbx2 knockdown.
CONCLUSION Our results indicate that Dbx2 is significantly upregulated in HCC tissues and plays significant roles in proliferation and metastasis of HCC cells by activating the Shh pathway.
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Affiliation(s)
- Yan-Ting Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Bei-Fang Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Peng-Jun Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Interventional Therapy, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Di Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Interventional Therapy, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yan-Yan Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | | | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Bin Dong
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jing Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xu Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Interventional Therapy, Peking University Cancer Hospital and Institute, Beijing 100142, China
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10
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Ma P, Ren B, Yang X, Sun B, Liu X, Kong Q, Li C, Mao B. ZC4H2 stabilizes Smads to enhance BMP signalling, which is involved in neural development in Xenopus. Open Biol 2017; 7:rsob.170122. [PMID: 28814648 PMCID: PMC5577449 DOI: 10.1098/rsob.170122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/17/2017] [Indexed: 01/16/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) play vital roles in regulating stem cell maintenance, differentiation and embryonic development. Intracellularly, BMP signalling is mediated by Smad proteins, which are regulated post-transcriptionally through reversible phosphorylation and ubiquitination. ZC4H2 is a small nuclear protein associated with intellectual disability and neural development in humans. Here, we report that ZC4H2 is highly expressed in the developing neural system and is involved in neural patterning and BMP signalling in Xenopus Knockdown of ZC4H2 led to expansion of the expression of the pan neural plate marker Sox2 in Xenopus embryos. In mammalian cells, ZC4H2 promotes BMP signalling and is involved in BMP regulated myogenic and osteogenic differentiation of mouse myoblast cells. Mechanistically, ZC4H2 binds and stabilizes Smad1 and Smad5 proteins through reducing their association with the Smurf ubiquitin ligases and thus their ubiquitination. We also found that a group of ZC4H2 mutations, which have been isolated in patients with intellectual disorders, showed weaker Smad-stabilizing activity, suggesting that the ZC4H2-Smad interaction might contribute to proper neural development in humans.
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Affiliation(s)
- Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
| | - Biyu Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China.,Institute of Health Sciences, Anhui University, Hefei 230601, People's Republic of China
| | - Xiangcai Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650203, People's Republic of China
| | - Bin Sun
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650203, People's Republic of China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming 650223, People's Republic of China
| | - Xiaoliang Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650203, People's Republic of China
| | - Qinghua Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
| | - Chaocui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
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11
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Karaz S, Courgeon M, Lepetit H, Bruno E, Pannone R, Tarallo A, Thouzé F, Kerner P, Vervoort M, Causeret F, Pierani A, D'Onofrio G. Neuronal fate specification by the Dbx1 transcription factor is linked to the evolutionary acquisition of a novel functional domain. EvoDevo 2016; 7:18. [PMID: 27525057 PMCID: PMC4983035 DOI: 10.1186/s13227-016-0055-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background Dbx1 is a homeodomain transcription factor involved in neuronal fate specification belonging to a widely conserved family among bilaterians. In mammals, Dbx1 was proposed to act as a transcriptional repressor by interacting with the Groucho corepressors to allow the specification of neurons involved in essential biological functions such as locomotion or breathing. Results Sequence alignments of Dbx1 proteins from different species allowed us to identify two conserved domains related to the Groucho-dependent Engrailed repressor domain (RD), as well as a newly described domain composed of clusterized acidic residues at the C-terminus (Cter) which is present in tetrapods but also several invertebrates. Using a heterologous luciferase assay, we showed that the two putative repressor domains behave as such in a Groucho-dependent manner, whereas the Cter does not bear any intrinsic transcriptional activity. Consistently with in vitro data, we found that both RDs are involved in cell fate specification using in vivo electroporation experiments in the chick spinal cord. Surprisingly, we show that the Cter domain is required for Dbx1 function in vivo, acting as a modulator of its repressive activity and/or imparting specificity. Conclusion Our results strongly suggest that the presence of a Cter domain among tetrapods is essential for Dbx1 to regulate neuronal diversity and, in turn, nervous system complexity. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0055-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonia Karaz
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Maximilien Courgeon
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Hélène Lepetit
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Eugenia Bruno
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Raimondo Pannone
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Andrea Tarallo
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - France Thouzé
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Pierre Kerner
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Michel Vervoort
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Frédéric Causeret
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Alessandra Pierani
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Giuseppe D'Onofrio
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
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12
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Thélie A, Desiderio S, Hanotel J, Quigley I, Van Driessche B, Rodari A, Borromeo MD, Kricha S, Lahaye F, Croce J, Cerda-Moya G, Ordoño Fernandez J, Bolle B, Lewis KE, Sander M, Pierani A, Schubert M, Johnson JE, Kintner CR, Pieler T, Van Lint C, Henningfeld KA, Bellefroid EJ, Van Campenhout C. Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. Development 2016; 142:3416-28. [PMID: 26443638 DOI: 10.1242/dev.121871] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
V1 interneurons are inhibitory neurons that play an essential role in vertebrate locomotion. The molecular mechanisms underlying their genesis remain, however, largely undefined. Here, we show that the transcription factor Prdm12 is selectively expressed in p1 progenitors of the hindbrain and spinal cord in the frog embryo, and that a similar restricted expression profile is observed in the nerve cord of other vertebrates as well as of the cephalochordate amphioxus. Using frog, chick and mice, we analyzed the regulation of Prdm12 and found that its expression in the caudal neural tube is dependent on retinoic acid and Pax6, and that it is restricted to p1 progenitors, due to the repressive action of Dbx1 and Nkx6-1/2 expressed in the adjacent p0 and p2 domains. Functional studies in the frog, including genome-wide identification of its targets by RNA-seq and ChIP-Seq, reveal that vertebrate Prdm12 proteins act as a general determinant of V1 cell fate, at least in part, by directly repressing Dbx1 and Nkx6 genes. This probably occurs by recruiting the methyltransferase G9a, an activity that is not displayed by the amphioxus Prdm12 protein. Together, these findings indicate that Prdm12 promotes V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes, and suggest that this function might have only been acquired after the split of the vertebrate and cephalochordate lineages.
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Affiliation(s)
- Aurore Thélie
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Simon Desiderio
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Julie Hanotel
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Ian Quigley
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Anthony Rodari
- Laboratory of Molecular Virology, ULB, IBMM, Gosselies B-6041, Belgium
| | - Mark D Borromeo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sadia Kricha
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - François Lahaye
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Jenifer Croce
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Gustavo Cerda-Moya
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Jesús Ordoño Fernandez
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Barbara Bolle
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular and Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Alessandra Pierani
- Génétique et développement du cortex cerebral, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher R Kintner
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tomas Pieler
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Göttingen, 37077 Göttingen, Germany
| | - Carine Van Lint
- Laboratory of Molecular Virology, ULB, IBMM, Gosselies B-6041, Belgium
| | - Kristine A Henningfeld
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Göttingen, 37077 Göttingen, Germany
| | - Eric J Bellefroid
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Claude Van Campenhout
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
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13
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Carlsen EØ, Frengen E, Fannemel M, Misceo D. Haploinsufficiency of ANO6, NELL2 and DBX2 in a boy with intellectual disability and growth delay. Am J Med Genet A 2015; 167A:1890-6. [PMID: 25846056 DOI: 10.1002/ajmg.a.37079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/12/2015] [Indexed: 01/31/2023]
Abstract
We report on a 10-year-old-boy presenting with moderate intellectual disability (ID), impaired motor skills, hypotonia, growth delay, minor anomalies, misaligned teeth, pectus excavatum, small hands and feet, widely spaced nipples, and a 1.13 Mb de novo deletion on HSA12q12 (chr12:44,830,147-45,964,945 bp, hg19), deleting ANO6, NELL2, and DBX2 and the pseudogenes PLEKHA8P1 and RACGAP1P. We suggest DBX2 and NELL2 as disease-causing genes and their haploinsufficiency to be involved in the psychomotor delay in the patient. DBX2 encodes a homeobox protein, highly expressed during neuronal development and regulating differentiation of interneurons in brain and spinal cord. NELL2 is expressed in most of the central and peripheral nervous system, with highest expression in hippocampus and cerebellum, maximizing during neuronal differentiation. The deletion in our patient is the smallest in HSA12q12 reported to date, and it is included in the deletion carried by four previously reported patients. The clinical presentation of these patients points to the recurrence of the following manifestation, possibly delineating a 12q12 deletion syndrome phenotype: moderate to severe developmental/intellectual delay, hypotonia, postnatal growth retardation, skeletal and dental anomalies, minor facial anomalies including strabismus, down slanting palpebral fissures, and large/low-set ears.
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Affiliation(s)
- Ellen Ø Carlsen
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Madeleine Fannemel
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
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14
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Holland LZ, Carvalho JE, Escriva H, Laudet V, Schubert M, Shimeld SM, Yu JK. Evolution of bilaterian central nervous systems: a single origin? EvoDevo 2013; 4:27. [PMID: 24098981 PMCID: PMC3856589 DOI: 10.1186/2041-9139-4-27] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/14/2013] [Indexed: 12/21/2022] Open
Abstract
The question of whether the ancestral bilaterian had a central nervous system (CNS) or a diffuse ectodermal nervous system has been hotly debated. Considerable evidence supports the theory that a CNS evolved just once. However, an alternative view proposes that the chordate CNS evolved from the ectodermal nerve net of a hemichordate-like ancestral deuterostome, implying independent evolution of the CNS in chordates and protostomes. To specify morphological divisions along the anterior/posterior axis, this ancestor used gene networks homologous to those patterning three organizing centers in the vertebrate brain: the anterior neural ridge, the zona limitans intrathalamica and the isthmic organizer, and subsequent evolution of the vertebrate brain involved elaboration of these ancestral signaling centers; however, all or part of these signaling centers were lost from the CNS of invertebrate chordates. The present review analyzes the evidence for and against these theories. The bulk of the evidence indicates that a CNS evolved just once - in the ancestral bilaterian. Importantly, in both protostomes and deuterostomes, the CNS represents a portion of a generally neurogenic ectoderm that is internalized and receives and integrates inputs from sensory cells in the remainder of the ectoderm. The expression patterns of genes involved in medio/lateral (dorso/ventral) patterning of the CNS are similar in protostomes and chordates; however, these genes are not similarly expressed in the ectoderm outside the CNS. Thus, their expression is a better criterion for CNS homologs than the expression of anterior/posterior patterning genes, many of which (for example, Hox genes) are similarly expressed both in the CNS and in the remainder of the ectoderm in many bilaterians. The evidence leaves hemichordates in an ambiguous position - either CNS centralization was lost to some extent at the base of the hemichordates, or even earlier, at the base of the hemichordates + echinoderms, or one of the two hemichordate nerve cords is homologous to the CNS of protostomes and chordates. In any event, the presence of part of the genetic machinery for the anterior neural ridge, the zona limitans intrathalamica and the isthmic organizer in invertebrate chordates together with similar morphology indicates that these organizers were present, at least in part, at the base of the chordates and were probably elaborated upon in the vertebrate lineage.
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Affiliation(s)
- Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202, USA
| | - João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009 – CNRS/UPMC), Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, B.P. 28, 06230 Villefranche-sur-Mer, France
| | - Hector Escriva
- CNRS, UMR 7232, BIOM, Université Pierre et Marie Curie Paris 06, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Vincent Laudet
- Institut de Génomique Fonctionnelle de Lyon (CNRS UMR5242, UCBL, ENS, INRA 1288), Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009 – CNRS/UPMC), Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, B.P. 28, 06230 Villefranche-sur-Mer, France
| | - Sebastian M Shimeld
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
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15
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Cox-Limpens KEM, Vles JSH, Schlechter J, Zimmermann LJI, Strackx E, Gavilanes AWD. Fetal brain genomic reprogramming following asphyctic preconditioning. BMC Neurosci 2013; 14:61. [PMID: 23800330 PMCID: PMC3724485 DOI: 10.1186/1471-2202-14-61] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 06/20/2013] [Indexed: 12/25/2022] Open
Abstract
Background Fetal asphyctic (FA) preconditioning is effective in attenuating brain damage incurred by a subsequent perinatal asphyctic insult. Unraveling mechanisms of this endogenous neuroprotection, activated by FA preconditioning, is an important step towards new clinical strategies for asphyctic neonates. Genomic reprogramming is thought to be, at least in part, responsible for the protective effect of preconditioning. Therefore we investigated whole genome differential gene expression in the preconditioned rat brain. FA preconditioning was induced on embryonic day 17 by reversibly clamping uterine circulation. Male control and FA offspring were sacrificed 96 h after FA preconditioning. Whole genome transcription was investigated with Affymetrix Gene1.0ST chip. Results Data were analyzed with the Bioconductor Limma package, which showed 53 down-regulated and 35 up-regulated transcripts in the FA-group. We validated these findings with RT-qPCR for adh1, edn1, leptin, rdh2, and smad6. Moreover, we investigated differences in gene expression across different brain regions. In addition, we performed Gene Set Enrichment Analysis (GSEA) which revealed 19 significantly down-regulated gene sets, mainly involved in neurotransmission and ion transport. 10 Gene sets were significantly up-regulated, these are mainly involved in nucleosomal structure and transcription, including genes such as mecp2. Conclusions Here we identify for the first time differential gene expression after asphyctic preconditioning in fetal brain tissue, with the majority of differentially expressed transcripts being down-regulated. The observed down-regulation of cellular processes such as neurotransmission and ion transport could represent a restriction in energy turnover which could prevent energy failure and subsequent neuronal damage in an asphyctic event. Up-regulated transcripts seem to exert their function mainly within the cell nucleus, and subsequent Gene Set Enrichment Analysis suggests that epigenetic mechanisms play an important role in preconditioning induced neuroprotection.
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16
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Xenopus Nkx6.1 and Nkx6.2 are required for mid-hindbrain boundary development. Dev Genes Evol 2013; 223:253-9. [PMID: 23423436 DOI: 10.1007/s00427-013-0437-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 02/05/2013] [Indexed: 01/25/2023]
Abstract
The mid-hindbrain boundary (MHB) organizer is among the best studied local organizers that patterns the midbrain and cerebellum in vertebrates and is established by a regulatory network of several transcription factors and signals, including Wnt signaling. In the present study, we found that Xenopus Nkx6.1 and Nkx6.2, two transcription factors of the Nkx homeobox family, are required for MHB formation. In Xenopus embryos, nkx6.1 and nkx6.2 are expressed in the MHB, and knockdown of either nkx6.1 or nkx6.2 by specific morpholinos disrupts the MHB expression of en2 as well as wnt1, a key regulator for vertebrate MHB formation. In the nkx6.1/nkx6.2 morphants, co-injection of wnt1 or dngsk3β mRNA, which activates Wnt signaling, rescues the expression of en2. Nkx6.1 and Nkx6.2 activate canonical Wnt signaling in reporter assays in both cultured mammalian cells and Xenopus embryos. An Nkx6.2 deletion construct, which inhibits the ability of wild type Nkx6.2 to activate Wnt signaling, also reduces the MHB expression of en2 in Xenopus embryos. These results suggest that Nkx6.1 and Nkx6.2 are involved in MHB formation in Xenopus embryos, likely by modulating wnt1 expression.
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17
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Moore KL, Moronne MM, Mehlhorn RJ. Electron spin resonance study of peroxidase activity and kinetics. Arch Biochem Biophys 1992; 299:47-56. [PMID: 1332617 DOI: 10.1016/0003-9861(92)90242-o] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An electron spin resonance (ESR) assay has been developed for peroxidase activity. The assay measures the formation of the paramagnetic nitroxide Tempol from the oxidation of its hydroxylamine derivative (TOLH) by short-lived radicals produced by peroxidase cycle intermediates, Compounds I and II. Using phenol as a peroxidase electron donor, the ESR approach is suitable for measurements of peroxidase activity ( > or = 0.003 U/ml) and micromolar quantities of H2O2 in sample sizes as small as 2 microliters. In addition, the ESR method can be used to continuously monitor activity in cell suspensions and other media that are susceptible to optical artifacts. The high membrane permeability of TOLH also makes it possible to estimate peroxidase activity in membrane-enclosed compartments, provided that TOLH oxidation rates can be stimulated with exogenous peroxidase reductants, e.g., phenol. Analysis of TOLH oxidation rates under conditions of low electron donor concentrations and high concentrations of H2O2 also shows clear indications of substrate-dependent inhibition and increased catalytic activity. Computer simulations indicate that the results obtained are consistent with the peroxidase reaction scheme proposed by Kohler et al. (1988, Arch. Biochem. Biophys. 264, 438-449) modified to correct for a nitroxide dependent stimulation of peroxidase catalytic activity.
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Affiliation(s)
- K L Moore
- Division of Energy and Environment, Lawrence Berkeley Laboratory, California 94720
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