1
|
Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife 2024; 13:e80803. [PMID: 38323609 PMCID: PMC10849676 DOI: 10.7554/elife.80803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/28/2024] [Indexed: 02/08/2024] Open
Abstract
BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.
Collapse
Affiliation(s)
- Paul Knabl
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of ViennaViennaAustria
| | - Alexandra Schauer
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | | | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
- University of KonstanzKonstanzGermany
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| |
Collapse
|
2
|
Parker CG, Gruenhagen GW, Hegarty BE, Histed AR, Streelman JT, Rhodes JS, Johnson ZV. Adult sex change leads to extensive forebrain reorganization in clownfish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577753. [PMID: 38352560 PMCID: PMC10862741 DOI: 10.1101/2024.01.29.577753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Sexual differentiation of the brain occurs in all major vertebrate lineages but is not well understood at a molecular and cellular level. Unlike most vertebrates, sex-changing fishes have the remarkable ability to change reproductive sex during adulthood in response to social stimuli, offering a unique opportunity to understand mechanisms by which the nervous system can initiate and coordinate sexual differentiation. This study explores sexual differentiation of the forebrain using single nucleus RNA-sequencing in the anemonefish Amphiprion ocellaris, producing the first cellular atlas of a sex-changing brain. We uncover extensive sex differences in cell type-specific gene expression, relative proportions of cells, baseline neuronal excitation, and predicted inter-neuronal communication. Additionally, we identify the cholecystokinin, galanin, and estrogen systems as central molecular axes of sexual differentiation. Supported by these findings, we propose a model of neurosexual differentiation in the conserved vertebrate social decision-making network spanning multiple subtypes of neurons and glia, including neuronal subpopulations within the preoptic area that are positioned to regulate gonadal differentiation. This work deepens our understanding of sexual differentiation in the vertebrate brain and defines a rich suite of molecular and cellular pathways that differentiate during adult sex change in anemonefish.
Collapse
Affiliation(s)
- Coltan G. Parker
- Neuroscience Program, University of Illinois, Urbana-Champaign, Illinois, USA
| | - George W. Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Brianna E. Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Abigail R. Histed
- Neuroscience Program, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Jeffrey T. Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Justin S. Rhodes
- Neuroscience Program, University of Illinois, Urbana-Champaign, Illinois, USA
- Department of Psychology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Zachary V. Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| |
Collapse
|
3
|
Frith MC, Ni S. DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development. Mol Biol Evol 2023; 40:msad275. [PMID: 38085182 PMCID: PMC10735318 DOI: 10.1093/molbev/msad275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
DNA that controls gene expression (e.g. enhancers, promoters) has seemed almost never to be conserved between distantly related animals, like vertebrates and arthropods. This is mysterious, because development of such animals is partly organized by homologous genes with similar complex expression patterns, termed "deep homology." Here, we report 25 regulatory DNA segments conserved across bilaterian animals, of which 7 are also conserved in cnidaria (coral and sea anemone). They control developmental genes (e.g. Nr2f, Ptch, Rfx1/3, Sall, Smad6, Sp5, Tbx2/3), including six homeobox genes: Gsx, Hmx, Meis, Msx, Six1/2, and Zfhx3/4. The segments contain perfectly or near-perfectly conserved CCAAT boxes, E-boxes, and other sequences recognized by regulatory proteins. More such DNA conservation will surely be found soon, as more genomes are published and sequence comparison is optimized. This reveals a control system for animal development conserved since the Precambrian.
Collapse
Affiliation(s)
- Martin C Frith
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Computational Bio Big Data Open Innovation Laboratory, AIST, Tokyo, Japan
| | - Shengliang Ni
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| |
Collapse
|
4
|
Faria JAD, Moraes DR, Kulikowski LD, Batista RL, Gomes NL, Nishi MY, Zanardo E, Nonaka CKV, de Freitas Souza BS, Mendonca BB, Domenice S. Cytogenomic Investigation of Syndromic Brazilian Patients with Differences of Sexual Development. Diagnostics (Basel) 2023; 13:2235. [PMID: 37443631 DOI: 10.3390/diagnostics13132235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Cytogenomic methods have gained space in the clinical investigation of patients with disorders/differences in sexual development (DSD). Here we evaluated the role of the SNP array in achieving a molecular diagnosis in Brazilian patients with syndromic DSD of unknown etiology. METHODS Twenty-two patients with DSD and syndromic features were included in the study and underwent SNP-array analysis. RESULTS In two patients, the diagnosis of 46,XX SRY + DSD was established. Additionally, two deletions were revealed (3q29 and Xp22.33), justifying the syndromic phenotype in these patients. Two pathogenic CNVs, a 10q25.3-q26.2 and a 13q33.1 deletion encompassing the FGFR2 and the EFNB2 gene, were associated with genital atypia and syndromic characteristics in two patients with 46,XY DSD. In a third 46,XY DSD patient, we identified a duplication in the 14q11.2-q12 region of 6.5 Mb associated with a deletion in the 21p11.2-q21.3 region of 12.7 Mb. In a 46,XY DSD patient with delayed neuropsychomotor development and congenital cataracts, a 12 Kb deletion on chromosome 10 was found, partially clarifying the syndromic phenotype, but not the genital atypia. CONCLUSIONS The SNP array is a useful tool for DSD patients, identifying the molecular etiology in 40% (2/5) of patients with 46,XX DSD and 17.6% (3/17) of patients with 46,XY DSD.
Collapse
Affiliation(s)
- José Antonio Diniz Faria
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador 40110-909, Brazil
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Daniela R Moraes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Leslie Domenici Kulikowski
- Laboratório de Citogenômica e Patologia Molecular LIM/03, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Rafael Loch Batista
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Nathalia Lisboa Gomes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Mirian Yumie Nishi
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Evelin Zanardo
- Laboratório de Citogenômica e Patologia Molecular LIM/03, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Carolina Kymie Vasques Nonaka
- Centro de Biotecnologia e Terapia Celular, Hospital São Rafael, Salvador 41253-190, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Salvador 41253-190, Brazil
| | - Bruno Solano de Freitas Souza
- Centro de Biotecnologia e Terapia Celular, Hospital São Rafael, Salvador 41253-190, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Salvador 41253-190, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador 40296-710, Brazil
| | - Berenice Bilharinho Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| |
Collapse
|
5
|
Sun L, Ping L, Gao R, Zhang B, Chen X. lmo4a Contributes to Zebrafish Inner Ear and Vestibular Development via Regulation of the Bmp Pathway. Genes (Basel) 2023; 14:1371. [PMID: 37510276 PMCID: PMC10378989 DOI: 10.3390/genes14071371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND In vertebrates, the development of the inner ear is a delicate process, whereas its relating molecular pathways are still poorly understood. LMO4, an LIM domain-only transcriptional regulator, is drawing an increasing amount of interest for its multiple roles regarding human embryonic development and the modulation of ototoxic side effects of cisplatin including cochlear apoptosis and hearing loss. The aim of the present study is to further explore the role of lmo4a in zebrafish inner ear development and thus explore its functional role. METHODS The Spatial Transcript Omics DataBase was referred to in order to evaluate the expression of lmo4a during the first 24 h of zebrafish development. In situ hybridization was applied to validate and extend the expression profile of lmo4a to 3 days post-fertilization. The morpholino (MO) knockdown and CRISPR/Cas9 knockout (KO) of lmo4a was applied. Morphological analyses of otic vesical, hair cells, statoacoustic ganglion and semicircular canals were conducted. The swimming pattern of lmo4a KO and MO zebrafish was tracked. In situ hybridization was further applied to verify the expression of genes of the related pathways. Rescue of the phenotype was attempted by blockage of the bmp pathway via heat shock and injection of Dorsomorphin. RESULTS lmo4a is constitutively expressed in the otic placode and otic vesicle during the early stages of zebrafish development. Knockdown and knockout of lmo4a both induced smaller otocysts, less hair cells, immature statoacoustic ganglion and malformed semicircular canals. Abnormal swimming patterns could be observed in both lmo4a MO and KO zebrafish. eya1 in preplacodal ectoderm patterning was downregulated. bmp2 and bmp4 expressions were found to be upregulated and extended in lmo4a morphants, and blockage of the Bmp pathway partially rescued the vestibular defects. CONCLUSIONS We concluded that lmo4a holds a regulative effect on the Bmp pathway and is required for the normal development of zebrafish inner ear. Our study pointed out the conservatism of LMO4 in inner ear development between mammals and zebrafish as well as shed more light on the molecular mechanisms behind it. Further research is needed to distinguish the relationships between lmo4 and the Bmp pathway, which may lead to diagnostic and therapeutic approaches towards human inner ear malformation.
Collapse
Affiliation(s)
- Le Sun
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, #1 Shuaifuyuan, Dongcheng District, Beijing 100730, China;
| | - Lu Ping
- Chinese Academy of Medical Sciences and Peking Union Medical College, #9 Dongdan Santiao, Dongcheng District, Beijing 100050, China;
| | - Ruzhen Gao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China;
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China;
| | - Xiaowei Chen
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, #1 Shuaifuyuan, Dongcheng District, Beijing 100730, China;
| |
Collapse
|
6
|
Wang J, Gu Y, Yan X, Zhang J, Wang J, Ding Y. USP38 inhibits colorectal cancer cell proliferation and migration via downregulating HMX3 ubiquitylation. Cell Cycle 2023; 22:1169-1181. [PMID: 36204976 PMCID: PMC10193867 DOI: 10.1080/15384101.2022.2042776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/10/2021] [Accepted: 01/04/2022] [Indexed: 11/03/2022] Open
Abstract
Accumulating evidence has shown that H6 Family Homeobox 3 (HMX3) plays a crucial role in nervous system regulation. However, the regulatory mechanism of HMX3 in colorectal cancer (CRC) has seldom been studied. Herein, HMX3 was significantly downregulated in CRC, as demonstrated by qRT-PCR and WB analysis on clinical samples and a panel of cell lines. Besides, it was found that the expression of HMX3 was negatively correlated with survival of CRC patients. The functional analyses (EdU staining, CCK-8, colony formation, Transwell, and wound scratch assays) showed that CRC cell proliferation, migration, and invasion were significantly suppressed by HMX3 overexpression, while enhanced by HMX3 knockdown. Moreover, in vivo experiment revealed HMX3 overexpression could also suppress tumor growth. Combining bioinformatics and WB analysis, we preliminarily uncovered that HMX3 was involved in apoptosis and KRAS signaling pathways. Mechanistically, Ubiquitin-specific protease 38 (USP38) was identified as a novel post-translational regulator of HMX3, which could directly interact with HMX3 to stabilize its protein expression via deubiquitination. Furthermore, the role of USP38 silencing in promoting cell proliferation, migration, and invasion of CRC cells was blocked by HMX3 overexpression. In conclusion, our findings suggested that USP38/HMX3 axis is a novel promising therapeutic candidate for CRC.
Collapse
Affiliation(s)
- Jun Wang
- Department of General Surgery, Huai’an People’s Hospital of Hongze District, Huai ‘An City, Jiangsu Province, China
| | - Yongxing Gu
- Department of General Surgery, Huai’an People’s Hospital of Hongze District, Huai ‘An City, Jiangsu Province, China
| | - Xueqin Yan
- Department of General Surgery, Huai’an People’s Hospital of Hongze District, Huai ‘An City, Jiangsu Province, China
| | - Jie Zhang
- Department of General Surgery, Huai’an People’s Hospital of Hongze District, Huai ‘An City, Jiangsu Province, China
| | - Jun Wang
- Department of General Surgery, Huai’an People’s Hospital of Hongze District, Huai ‘An City, Jiangsu Province, China
| | - Yong Ding
- Department of General Surgery, Huai’an People’s Hospital of Hongze District, Huai ‘An City, Jiangsu Province, China
| |
Collapse
|
7
|
Haws W, England S, Grieb G, Susana G, Hernandez S, Mirer H, Lewis K. Analyses of binding partners and functional domains for the developmentally essential protein Hmx3a/HMX3. Sci Rep 2023; 13:1151. [PMID: 36670152 PMCID: PMC9859826 DOI: 10.1038/s41598-023-27878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
HMX3 is a homeodomain protein with essential roles in CNS and ear development. Homeodomains are DNA-binding domains and hence homeodomain-containing proteins are usually assumed to be transcription factors. However, intriguingly, our recent data suggest that zebrafish Hmx3a may not require its homeodomain to function, raising the important question of what molecular interactions mediate its effects. To investigate this, we performed a yeast two-hybrid screen and identified 539 potential binding partners of mouse HMX3. Using co-immunoprecipitation, we tested whether a prioritized subset of these interactions are conserved in zebrafish and found that Tle3b, Azin1b, Prmt2, Hmgb1a, and Hmgn3 bind Hmx3a. Next, we tested whether these proteins bind the products of four distinct hmx3a mutant alleles that all lack the homeodomain. Embryos homozygous for two of these alleles develop abnormally and die, whereas zebrafish homozygous for the other two alleles are viable. We found that all four mutations abrogate binding to Prmt2 and Tle3b, whereas Azin1b binding was preserved in all cases. Interestingly, Hmgb1a and Hmgn3 had more affinity for products of the viable mutant alleles. These data shed light on how HMX3/Hmx3a might function at a molecular level and identify new targets for future study in these vital developmental processes.
Collapse
Affiliation(s)
- William Haws
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Samantha England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Gabriela Susana
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Sophie Hernandez
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Hunter Mirer
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Katharine Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| |
Collapse
|
8
|
Amasi-Hartoonian N, Pariante CM, Cattaneo A, Sforzini L. Understanding treatment-resistant depression using "omics" techniques: A systematic review. J Affect Disord 2022; 318:423-455. [PMID: 36103934 DOI: 10.1016/j.jad.2022.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Treatment-resistant depression (TRD) results in huge healthcare costs and poor patient clinical outcomes. Most studies have adopted a "candidate mechanism" approach to investigate TRD pathogenesis, however this is made more challenging due to the complex and heterogeneous nature of this condition. High-throughput "omics" technologies can provide a more holistic view and further insight into the underlying mechanisms involved in TRD development, expanding knowledge beyond already-identified mechanisms. This systematic review assessed the information from studies that examined TRD using hypothesis-free omics techniques. METHODS PubMed, MEDLINE, Embase, APA PsycInfo, Scopus and Web of Science databases were searched on July 2022. 37 human studies met the eligibility criteria, totalling 17,518 TRD patients, 571,402 healthy controls and 62,279 non-TRD depressed patients (including antidepressant responders and untreated MDD patients). RESULTS Significant findings were reported that implicate the role in TRD of various molecules, including polymorphisms, genes, mRNAs and microRNAs. The pathways most commonly reported by the identified studies were involved in immune system and inflammation, neuroplasticity, calcium signalling and neurotransmitters. LIMITATIONS Small sample sizes, variability in defining TRD, and heterogeneity in study design and methodology. CONCLUSIONS These findings provide insight into TRD pathophysiology, proposing future research directions for novel drug targets and potential biomarkers for clinical staging and response to antidepressants (citalopram/escitalopram in particular) and electroconvulsive therapy (ECT). Further validation is warranted in large prospective studies using standardised TRD criteria. A multi-omics and systems biology strategy with a collaborative effort will likely deliver robust findings for translation into the clinic.
Collapse
Affiliation(s)
- Nare Amasi-Hartoonian
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Department of Psychological Medicine, London, UK.
| | - Carmine Maria Pariante
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Department of Psychological Medicine, London, UK; National Institute for Health and Research Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, UK
| | - Annamaria Cattaneo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy; Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Luca Sforzini
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Department of Psychological Medicine, London, UK
| |
Collapse
|
9
|
Qi J, Ma L, Guo W. Recent advances in the regulation mechanism of SOX10. J Otol 2022; 17:247-252. [PMID: 36249926 PMCID: PMC9547104 DOI: 10.1016/j.joto.2022.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Neural crest (NC) is the primitive neural structure in embryonic stage, which develops from ectodermal neural plate cells and epithelial cells. When the neural fold forms into neural tube, neural crest also forms a cord like structure above the neural tube and below the ectoderm. Neural crest cells (NCC) have strong migration and proliferation abilities. A number of tissue cells differentiate from neural crest cells, such as melanocytes, central and peripheral neurons, glial cells, craniofacial cells, osteoblasts, chondrocytes and smooth muscle cells. The migration and differentiation of neural crest cells are regulated by a gene network where a variety of genes, transcriptional factors, signal pathways and growth factors are involved.
Collapse
Affiliation(s)
- Jingcui Qi
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Ma
- PLA Rocket Force Characteristic Medical Center Department of Stomatology, China
| | - Weiwei Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
- Corresponding author. College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China.
| |
Collapse
|
10
|
Papadogiannis V, Pennati A, Parker HJ, Rothbächer U, Patthey C, Bronner ME, Shimeld SM. Hmx gene conservation identifies the origin of vertebrate cranial ganglia. Nature 2022; 605:701-705. [PMID: 35585239 DOI: 10.1038/s41586-022-04742-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/07/2022] [Indexed: 12/30/2022]
Abstract
The evolutionary origin of vertebrates included innovations in sensory processing associated with the acquisition of a predatory lifestyle1. Vertebrates perceive external stimuli through sensory systems serviced by cranial sensory ganglia, whose neurons arise predominantly from cranial placodes; however, the understanding of the evolutionary origin of placodes and cranial sensory ganglia is hampered by the anatomical differences between living lineages and the difficulty in assigning homology between cell types and structures. Here we show that the homeobox transcription factor Hmx is a constitutive component of vertebrate sensory ganglion development and that in the tunicate Ciona intestinalis, Hmx is necessary and sufficient to drive the differentiation programme of bipolar tail neurons, cells previously thought to be homologues of neural crest2,3. Using Ciona and lamprey transgenesis, we demonstrate that a unique, tandemly duplicated enhancer pair regulated Hmx expression in the stem-vertebrate lineage. We also show notably robust vertebrate Hmx enhancer function in Ciona, demonstrating that deep conservation of the upstream regulatory network spans the evolutionary origin of vertebrates. These experiments demonstrate regulatory and functional conservation between Ciona and vertebrate Hmx, and point to bipolar tail neurons as homologues of cranial sensory ganglia.
Collapse
Affiliation(s)
- Vasileios Papadogiannis
- Department of Zoology, University of Oxford, Oxford, UK.,Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes, Crete, Greece
| | - Alessandro Pennati
- Department of Zoology, University of Oxford, Oxford, UK.,Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Ute Rothbächer
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Cedric Patthey
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | |
Collapse
|
11
|
Li H, Liao S, Luo G, Li H, Wang S, Li Z, Luo X. An Association between EMX2 Variations and Mayer-Rokitansky-Küster-Hauser Syndrome: A Case-Control Study of Chinese Women. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:9975369. [PMID: 35463657 PMCID: PMC9020933 DOI: 10.1155/2022/9975369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 01/08/2023]
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by congenital malformations of Müllerian structures, including the uterus and upper two-thirds of the vagina in women. Until now, the etiology of this disease has remained unknown. We hypothesized that EMX2 (the human homologue of Drosophila empty spiracles gene (2) might be a candidate gene for MRKH syndrome because it plays an important role in the development of the urogenital system. Through sequence analysis of EMX2 in forty patients with MRKH syndrome and one hundred and forty healthy women controls, we identified eleven variations in total. Four novel variations were only found in MRKH patients, and seven single nucleotide polymorphisms were identified in both patients and controls. In silico analyses suggested that the novel variations in the 5'UTR (untranslated region) and 3'UTR might affect transcriptional activity of the EMX2 promoter or posttranscriptional processing. In conclusion, our study suggests an association between noncoding variations in the EMX2 gene and MRKH syndrome in a Chinese Han population.
Collapse
Affiliation(s)
- Haiping Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 511442, China
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511442, China
| | - Shi Liao
- Department of Gynecology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518005, China
| | - Guangnan Luo
- Department of Gynecology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518005, China
| | - Haixia Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Shuai Wang
- Department of Obstetrics and Gynecology, The Sixth Affiliated Hospital, South China University of Technology, Foshan, Guangdong 528237, China
| | - Zhimin Li
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511442, China
| | - Xiping Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 511442, China
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511442, China
| |
Collapse
|
12
|
Mackowetzky K, Yoon KH, Mackowetzky EJ, Waskiewicz AJ. Development and evolution of the vestibular apparatuses of the inner ear. J Anat 2021; 239:801-828. [PMID: 34047378 PMCID: PMC8450482 DOI: 10.1111/joa.13459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The vertebrate inner ear is a labyrinthine sensory organ responsible for perceiving sound and body motion. While a great deal of research has been invested in understanding the auditory system, a growing body of work has begun to delineate the complex developmental program behind the apparatuses of the inner ear involved with vestibular function. These animal studies have helped identify genes involved in inner ear development and model syndromes known to include vestibular dysfunction, paving the way for generating treatments for people suffering from these disorders. This review will provide an overview of known inner ear anatomy and function and summarize the exciting discoveries behind inner ear development and the evolution of its vestibular apparatuses.
Collapse
Affiliation(s)
- Kacey Mackowetzky
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin H. Yoon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Andrew J. Waskiewicz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children’s Health Research InstituteUniversity of AlbertaEdmontonAlbertaCanada
| |
Collapse
|
13
|
In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
Collapse
|
14
|
Chromatin remodelers and lineage-specific factors interact to target enhancers to establish proneurosensory fate within otic ectoderm. Proc Natl Acad Sci U S A 2021; 118:2025196118. [PMID: 33723076 DOI: 10.1073/pnas.2025196118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Specification of Sox2+ proneurosensory progenitors within otic ectoderm is a prerequisite for the production of sensory cells and neurons for hearing. However, the underlying molecular mechanisms driving this lineage specification remain unknown. Here, we show that the Brg1-based SWI/SNF chromatin-remodeling complex interacts with the neurosensory-specific transcriptional regulators Eya1/Six1 to induce Sox2 expression and promote proneurosensory-lineage specification. Ablation of the ATPase-subunit Brg1 or both Eya1/Six1 results in loss of Sox2 expression and lack of neurosensory identity, leading to abnormal apoptosis within the otic ectoderm. Brg1 binds to two of three distal 3' Sox2 enhancers occupied by Six1, and Brg1-binding to these regions depends on Eya1-Six1 activity. We demonstrate that the activity of these Sox2 enhancers in otic neurosensory cells specifically depends on binding to Six1. Furthermore, genome-wide and transcriptome profiling indicate that Brg1 may suppress apoptotic factor Map3k5 to inhibit apoptosis. Together, our findings reveal an essential role for Brg1, its downstream pathways, and their interactions with Six1/Eya1 in promoting proneurosensory fate induction in the otic ectoderm and subsequent neuronal lineage commitment and survival of otic cells.
Collapse
|
15
|
Kaiser M, Wojahn I, Rudat C, Lüdtke TH, Christoffels VM, Moon A, Kispert A, Trowe MO. Regulation of otocyst patterning by Tbx2 and Tbx3 is required for inner ear morphogenesis in the mouse. Development 2021; 148:dev.195651. [PMID: 33795231 DOI: 10.1242/dev.195651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 03/23/2021] [Indexed: 12/21/2022]
Abstract
All epithelial components of the inner ear, including sensory hair cells and innervating afferent neurons, arise by patterning and differentiation of epithelial progenitors residing in a simple sphere, the otocyst. Here, we identify the transcriptional repressors TBX2 and TBX3 as novel regulators of these processes in the mouse. Ablation of Tbx2 from the otocyst led to cochlear hypoplasia, whereas loss of Tbx3 was associated with vestibular malformations. The loss of function of both genes (Tbx2/3cDKO) prevented inner ear morphogenesis at midgestation, resulting in indiscernible cochlear and vestibular structures at birth. Morphogenetic impairment occurred concomitantly with increased apoptosis in ventral and lateral regions of Tbx2/3cDKO otocysts around E10.5. Expression analyses revealed partly disturbed regionalisation, and a posterior-ventral expansion of the neurogenic domain in Tbx2/3cDKO otocysts at this stage. We provide evidence that repression of FGF signalling by TBX2 is important to restrict neurogenesis to the anterior-ventral otocyst and implicate another T-box factor, TBX1, as a crucial mediator in this regulatory network.
Collapse
Affiliation(s)
- Marina Kaiser
- Institute for Molecular Biology, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Irina Wojahn
- Institute for Molecular Biology, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Carsten Rudat
- Institute for Molecular Biology, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Timo H Lüdtke
- Institute for Molecular Biology, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Vincent M Christoffels
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Anne Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA 17822, USA.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Andreas Kispert
- Institute for Molecular Biology, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| | - Mark-Oliver Trowe
- Institute for Molecular Biology, Medizinische Hochschule Hannover, 30625 Hannover, Germany
| |
Collapse
|
16
|
Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile. Mod Pathol 2021; 34:264-279. [PMID: 33051600 PMCID: PMC9361192 DOI: 10.1038/s41379-020-00659-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5-10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1 or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2 loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2 were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2-46 Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0-7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n = 16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n = 530) and glioblastoma (n = 171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n = 10), TSC cortical tubers (n = 15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3; and TFs IRF6 and EOMES were all expressed >12-fold higher in SEGAs (FDR/q-value < 0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2 loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1 or TSC2 and mTORC1 activation.
Collapse
|
17
|
Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE. New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics 2021; 217:6117222. [PMID: 33681970 DOI: 10.1093/genetics/iyab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
Collapse
Affiliation(s)
- Manon Quiquand
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nan Qiao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chunyu Zhao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Matthew Slattery
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jackie J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
18
|
England SJ, Cerda GA, Kowalchuk A, Sorice T, Grieb G, Lewis KE. Hmx3a Has Essential Functions in Zebrafish Spinal Cord, Ear and Lateral Line Development. Genetics 2020; 216:1153-1185. [PMID: 33077489 PMCID: PMC7768253 DOI: 10.1534/genetics.120.303748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/14/2020] [Indexed: 11/30/2022] Open
Abstract
Transcription factors that contain a homeodomain DNA-binding domain have crucial functions in most aspects of cellular function and embryonic development in both animals and plants. Hmx proteins are a subfamily of NK homeodomain-containing proteins that have fundamental roles in development of sensory structures such as the eye and the ear. However, Hmx functions in spinal cord development have not been analyzed. Here, we show that zebrafish (Danio rerio) hmx2 and hmx3a are coexpressed in spinal dI2 and V1 interneurons, whereas hmx3b, hmx1, and hmx4 are not expressed in spinal cord. Using mutational analyses, we demonstrate that, in addition to its previously reported role in ear development, hmx3a is required for correct specification of a subset of spinal interneuron neurotransmitter phenotypes, as well as correct lateral line progression and survival to adulthood. Surprisingly, despite similar expression patterns of hmx2 and hmx3a during embryonic development, zebrafish hmx2 mutants are viable and have no obviously abnormal phenotypes in sensory structures or neurons that require hmx3a In addition, embryos homozygous for deletions of both hmx2 and hmx3a have identical phenotypes to severe hmx3a single mutants. However, mutating hmx2 in hypomorphic hmx3a mutants that usually develop normally, results in abnormal ear and lateral line phenotypes. This suggests that while hmx2 cannot compensate for loss of hmx3a, it does function in these developmental processes, although to a much lesser extent than hmx3a More surprisingly, our mutational analyses suggest that Hmx3a may not require its homeodomain DNA-binding domain for its roles in viability or embryonic development.
Collapse
Affiliation(s)
| | - Gustavo A Cerda
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3DY, UK
| | | | - Taylor Sorice
- Department of Biology, Syracuse University, New York 13244
| | - Ginny Grieb
- Department of Biology, Syracuse University, New York 13244
| | | |
Collapse
|
19
|
Vermeiren S, Bellefroid EJ, Desiderio S. Vertebrate Sensory Ganglia: Common and Divergent Features of the Transcriptional Programs Generating Their Functional Specialization. Front Cell Dev Biol 2020; 8:587699. [PMID: 33195244 PMCID: PMC7649826 DOI: 10.3389/fcell.2020.587699] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Sensory fibers of the peripheral nervous system carry sensation from specific sense structures or use different tissues and organs as receptive fields, and convey this information to the central nervous system. In the head of vertebrates, each cranial sensory ganglia and associated nerves perform specific functions. Sensory ganglia are composed of different types of specialized neurons in which two broad categories can be distinguished, somatosensory neurons relaying all sensations that are felt and visceral sensory neurons sensing the internal milieu and controlling body homeostasis. While in the trunk somatosensory neurons composing the dorsal root ganglia are derived exclusively from neural crest cells, somato- and visceral sensory neurons of cranial sensory ganglia have a dual origin, with contributions from both neural crest and placodes. As most studies on sensory neurogenesis have focused on dorsal root ganglia, our understanding of the molecular mechanisms underlying the embryonic development of the different cranial sensory ganglia remains today rudimentary. However, using single-cell RNA sequencing, recent studies have made significant advances in the characterization of the neuronal diversity of most sensory ganglia. Here we summarize the general anatomy, function and neuronal diversity of cranial sensory ganglia. We then provide an overview of our current knowledge of the transcriptional networks controlling neurogenesis and neuronal diversification in the developing sensory system, focusing on cranial sensory ganglia, highlighting specific aspects of their development and comparing it to that of trunk sensory ganglia.
Collapse
Affiliation(s)
- Simon Vermeiren
- ULB Neuroscience Institute, Université Libre de Bruxelles, Gosselies, Belgium
| | - Eric J Bellefroid
- ULB Neuroscience Institute, Université Libre de Bruxelles, Gosselies, Belgium
| | - Simon Desiderio
- Institute for Neurosciences of Montpellier, INSERM U1051, University of Montpellier, Montpellier, France
| |
Collapse
|
20
|
Nagel S, Pommerenke C, Meyer C, MacLeod RAF, Drexler HG. Aberrant expression of NKL homeobox genes HMX2 and HMX3 interferes with cell differentiation in acute myeloid leukemia. PLoS One 2020; 15:e0240120. [PMID: 33048949 PMCID: PMC7553312 DOI: 10.1371/journal.pone.0240120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
The NKL-code describes normal expression patterns of NKL homeobox genes in hematopoiesis. Aberrant expression of NKL homeobox gene subclass members have been reported in several hematopoietic malignancies including acute myeloid leukemia (AML). Here, we analyzed the oncogenic role of the HMX-group of NKL homeobox genes in AML. Public expression profiling data–available for HMX1 and HMX2—indicate aberrant activity of HMX2 in circa 2% AML patients overall, rising to 31% in those with KMT2A/MLL rearrangements whereas HMX1 expression remains inconspicuous. AML cell lines EOL-1, MV4-11 and MOLM-13 expressed both, HMX2 and neighboring HMX3 genes, and harbored KMT2A aberrations, suggesting their potential functional association. Surprisingly, knockdown experiments in these cell lines demonstrated that KMT2A inhibited HMX2/3 which, in turn, did not regulate KMT2A expression. Furthermore, karyotyping and genomic profiling analysis excluded rearrangements of the HMX2/3 locus in these cell lines. However, comparative expression profiling and subsequent functional analyses revealed that IRF8, IL7- and WNT-signalling activated HMX2/3 expression while TNFa/NFkB- signalling proved inhibitory. Whole genome sequencing of EOL-1 identified two mutations in the regulatory upstream regions of HMX2/3 resulting in generation of a consensus ETS-site and transformation of a former NFkB-site into an SP1-site. Reporter-gene assays demonstrated that both mutations contributed to HMX2/3 activation, modifying ETS1/ELK1- and TNFalpha-mediated gene regulation. Moreover, DMSO-induced eosinophilic differentiation of EOL-1 cells coincided with HMX2/3 downregulation while knockdown of HMX2 induced cell differentiation, collectively supporting a fundamental role for these genes in myeloid differentiation arrest. Finally, target genes of HMX2/3 were identified in EOL-1 and included suppression of differentiation gene EPX, and activation of fusion gene FIP1L1-PDGFRA and receptor-encoding gene HTR7, both of which enhanced oncogenic ERK-signalling. Taken together, our study documents a leukemic role for deregulated NKL homeobox genes HMX2 and HMX3 in AML, revealing molecular mechanisms of myeloid differentiation arrest.
Collapse
Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
21
|
Deol P, Kozlova E, Valdez M, Ho C, Yang EW, Richardson H, Gonzalez G, Truong E, Reid J, Valdez J, Deans JR, Martinez-Lomeli J, Evans JR, Jiang T, Sladek FM, Curras-Collazo MC. Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male Mice. Endocrinology 2020; 161:5698148. [PMID: 31912136 PMCID: PMC7041656 DOI: 10.1210/endocr/bqz044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/04/2020] [Indexed: 01/04/2023]
Abstract
Soybean oil consumption has increased greatly in the past half-century and is linked to obesity and diabetes. To test the hypothesis that soybean oil diet alters hypothalamic gene expression in conjunction with metabolic phenotype, we performed RNA sequencing analysis using male mice fed isocaloric, high-fat diets based on conventional soybean oil (high in linoleic acid, LA), a genetically modified, low-LA soybean oil (Plenish), and coconut oil (high in saturated fat, containing no LA). The 2 soybean oil diets had similar but nonidentical effects on the hypothalamic transcriptome, whereas the coconut oil diet had a negligible effect compared to a low-fat control diet. Dysregulated genes were associated with inflammation, neuroendocrine, neurochemical, and insulin signaling. Oxt was the only gene with metabolic, inflammation, and neurological relevance upregulated by both soybean oil diets compared to both control diets. Oxytocin immunoreactivity in the supraoptic and paraventricular nuclei of the hypothalamus was reduced, whereas plasma oxytocin and hypothalamic Oxt were increased. These central and peripheral effects of soybean oil diets were correlated with glucose intolerance but not body weight. Alterations in hypothalamic Oxt and plasma oxytocin were not observed in the coconut oil diet enriched in stigmasterol, a phytosterol found in soybean oil. We postulate that neither stigmasterol nor LA is responsible for effects of soybean oil diets on oxytocin and that Oxt messenger RNA levels could be associated with the diabetic state. Given the ubiquitous presence of soybean oil in the American diet, its observed effects on hypothalamic gene expression could have important public health ramifications.
Collapse
Affiliation(s)
- Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Elena Kozlova
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
| | - Matthew Valdez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
| | - Catherine Ho
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Ei-Wen Yang
- Department of Computer Science and Engineering, University of California Riverside, California
| | - Holly Richardson
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Gwendolyn Gonzalez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Edward Truong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jack Reid
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Joseph Valdez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jonathan R Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jose Martinez-Lomeli
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jane R Evans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California Riverside, California
| | - Frances M Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Margarita C Curras-Collazo
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
- Correspondence: Margarita C. Curras-Collazo, PhD, FAPS, Department of Molecular, Cell and Systems Biology, University of California, 2110 Biological Sciences Building, Riverside, California 92521. E-mail:
| |
Collapse
|
22
|
Kojima K, Nishida AT, Tashiro K, Hirota K, Nishio T, Murata M, Kato N, Kawaguchi S, Zine A, Ito J, Van De Water TR. Isolation and Characterization of Mammalian Otic Progenitor Cells that Can Differentiate into Both Sensory Epithelial and Neuronal Cell Lineages. Anat Rec (Hoboken) 2020; 303:451-460. [PMID: 31943808 DOI: 10.1002/ar.24335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023]
Abstract
The mammalian inner ear mediates hearing and balance and during development generates both cochleo-vestibular ganglion neurons and sensory epithelial receptor cells, that is, hair cells and support cells. Cell marking experiments have shown that both hair cells and support cells can originate from a common progenitor. Here, we demonstrate the lineage potential of individual otic epithelial cell clones using three cell lines established by a combination of limiting dilution and gene-marking techniques from an embryonic day 12 (E12) rat otocyst. Cell-type specific marker analyses of these clonal lines under proliferation and differentiation culture conditions demonstrate that during differentiation immature cell markers (Nanog and Nestin) were downregulated and hair cell (Myosin VIIa and Math1), support cell (p27Kip1 and cytokeratin) and neuronal cell (NF-H and NeuroD) markers were upregulated. Our results suggest that the otic epithelium of the E12 mammalian inner ear possess multipotent progenitor cells able to generate cell types of both sensory epithelial and neural cell lineages when cultured under a differentiation culture condition. Understanding the molecular mechanisms of proliferation and differentiation of multipotent otic progenitor cells may provide insights that could contribute to the development of a novel cell therapy with a potential to initiate or stimulate the sensorineural repair of damaged inner ear sensory receptors. Anat Rec, 303:451-460, 2020. © 2019 American Association for Anatomy.
Collapse
Affiliation(s)
- Ken Kojima
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,University of Miami Ear Institute, Department of Otolaryngology, University of Miami School of Medicine, Miami, Florida.,Department of Integrative Brain Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akiko T Nishida
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Molecular Biology and Genetics, Kyoto University, Kyoto, Japan
| | - Kei Tashiro
- Center for Molecular Biology and Genetics, Kyoto University, Kyoto, Japan
| | - Kiichi Hirota
- BioMedical Special Research Unit, Human Stress Signal Research Center, National Institute of Advanced Industrial Science and Technology, Ikeda, Japan
| | - Takeshi Nishio
- Department of Integrative Brain Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Miyahiko Murata
- Department of Integrative Brain Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuo Kato
- Department of Integrative Brain Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Saburo Kawaguchi
- Department of Integrative Brain Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Azel Zine
- Institute of Neuroscience, INSERM U. 583, University of Montpellier I, Montpellier, France
| | - Juichi Ito
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thomas R Van De Water
- University of Miami Ear Institute, Department of Otolaryngology, University of Miami School of Medicine, Miami, Florida
| |
Collapse
|
23
|
Wigmore EM, Hafferty JD, Hall LS, Howard DM, Clarke TK, Fabbri C, Lewis CM, Uher R, Navrady LB, Adams MJ, Zeng Y, Campbell A, Gibson J, Thomson PA, Hayward C, Smith BH, Hocking LJ, Padmanabhan S, Deary IJ, Porteous DJ, Mors O, Mattheisen M, Nicodemus KK, McIntosh AM. Genome-wide association study of antidepressant treatment resistance in a population-based cohort using health service prescription data and meta-analysis with GENDEP. THE PHARMACOGENOMICS JOURNAL 2020; 20:329-341. [PMID: 30700811 PMCID: PMC7096334 DOI: 10.1038/s41397-019-0067-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/20/2018] [Accepted: 12/20/2018] [Indexed: 02/08/2023]
Abstract
Antidepressants demonstrate modest response rates in the treatment of major depressive disorder (MDD). Despite previous genome-wide association studies (GWAS) of antidepressant treatment response, the underlying genetic factors are unknown. Using prescription data in a population and family-based cohort (Generation Scotland: Scottish Family Health Study; GS:SFHS), we sought to define a measure of (a) antidepressant treatment resistance and (b) stages of antidepressant resistance by inferring antidepressant switching as non-response to treatment. GWAS were conducted separately for antidepressant treatment resistance in GS:SFHS and the Genome-based Therapeutic Drugs for Depression (GENDEP) study and then meta-analysed (meta-analysis n = 4213, cases = 358). For stages of antidepressant resistance, a GWAS on GS:SFHS only was performed (n = 3452). Additionally, we conducted gene-set enrichment, polygenic risk scoring (PRS) and genetic correlation analysis. We did not identify any significant loci, genes or gene sets associated with antidepressant treatment resistance or stages of resistance. Significant positive genetic correlations of antidepressant treatment resistance and stages of resistance with neuroticism, psychological distress, schizotypy and mood disorder traits were identified. These findings suggest that larger sample sizes are needed to identify the genetic architecture of antidepressant treatment response, and that population-based observational studies may provide a tractable approach to achieving the necessary statistical power.
Collapse
Affiliation(s)
- Eleanor M. Wigmore
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Jonathan D. Hafferty
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Lynsey S. Hall
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - David M. Howard
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Toni-Kim Clarke
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Chiara Fabbri
- 0000 0001 2322 6764grid.13097.3cMRC SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, England ,0000 0004 1757 1758grid.6292.fDepartment of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Cathryn M. Lewis
- 0000 0001 2322 6764grid.13097.3cMRC SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, England
| | - Rudolf Uher
- 0000 0001 2322 6764grid.13097.3cMRC SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, England ,0000 0004 1936 8200grid.55602.34Department of Psychiatry, Dalhousie University, Halifax, NS Canada
| | - Lauren B. Navrady
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Mark J. Adams
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Yanni Zeng
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Archie Campbell
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and
Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Jude Gibson
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK
| | - Pippa A. Thomson
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and
Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- 0000 0004 1936 7988grid.4305.2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine,
Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Blair H. Smith
- 0000 0004 0397 2876grid.8241.fDivision of Population Health Sciences, University of Dundee, Dundee, UK
| | - Lynne J. Hocking
- 0000 0004 1936 7291grid.7107.1Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
| | - Sandosh Padmanabhan
- 0000 0001 2193 314Xgrid.8756.cInstitute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Ian J. Deary
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - David J. Porteous
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and
Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Ole Mors
- 0000 0004 0512 597Xgrid.154185.cPsychosis Research Unit, Aarhus University Hospital, Risskov, Denmark ,0000 0000 9817 5300grid.452548.aiPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric
Research, Aarhus, Denmark
| | - Manuel Mattheisen
- 0000 0000 9817 5300grid.452548.aiPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric
Research, Aarhus, Denmark ,0000 0001 1956 2722grid.7048.bDepartment of Biomedicine and Centre for Integrative Sequencing
(iSEQ), Aarhus University, Aarhus, Denmark ,0000 0004 1937 0626grid.4714.6Centre for Psychiatry Research, Department of Clinical
Neuroscience, Karolinska Institutet, Stockholm, Sweden ,0000 0001 2326 2191grid.425979.4Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Kristin K. Nicodemus
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and
Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andrew M. McIntosh
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, EH10 5HF Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
24
|
Muthu V, Rohacek AM, Yao Y, Rakowiecki SM, Brown AS, Zhao YT, Meyers J, Won KJ, Ramdas S, Brown CD, Peterson KA, Epstein DJ. Genomic architecture of Shh-dependent cochlear morphogenesis. Development 2019; 146:dev.181339. [PMID: 31488567 DOI: 10.1242/dev.181339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022]
Abstract
The mammalian cochlea develops from a ventral outgrowth of the otic vesicle in response to Shh signaling. Mouse embryos lacking Shh or its essential signal transduction components display cochlear agenesis; however, a detailed understanding of the transcriptional network mediating this process is unclear. Here, we describe an integrated genomic approach to identify Shh-dependent genes and associated regulatory sequences that promote cochlear duct morphogenesis. A comparative transcriptome analysis of otic vesicles from mouse mutants exhibiting loss (Smoecko ) and gain (Shh-P1) of Shh signaling reveal a set of Shh-responsive genes partitioned into four expression categories in the ventral half of the otic vesicle. This target gene classification scheme provides novel insight into several unanticipated roles for Shh, including priming the cochlear epithelium for subsequent sensory development. We also mapped regions of open chromatin in the inner ear by ATAC-seq that, in combination with Gli2 ChIP-seq, identified inner ear enhancers in the vicinity of Shh-responsive genes. These datasets are useful entry points for deciphering Shh-dependent regulatory mechanisms involved in cochlear duct morphogenesis and establishment of its constituent cell types.
Collapse
Affiliation(s)
- Victor Muthu
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex M Rohacek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yao Yao
- Department of Animal and Dairy Science, Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Staci M Rakowiecki
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander S Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ying-Tao Zhao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Meyers
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- Biotech Research and Innovation Centre (BRIC), Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Shweta Ramdas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
25
|
Skarp S, Kanervo L, Kotimäki J, Sorri M, Männikkö M, Hietikko E. Whole-exome sequencing suggests multiallelic inheritance for childhood-onset Ménière's disease. Ann Hum Genet 2019; 83:389-396. [PMID: 31106404 DOI: 10.1111/ahg.12327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 01/22/2023]
Abstract
The genetic background of Ménière's disease (MD) was studied in one patient with childhood-onset MD and his grandfather affected with middle age-onset MD. Whole-exome sequencing was performed and the data were compared to 76 exomes from unrelated subjects without MD. Thirteen rare inner ear expressed variants with pathogenic estimations were observed in the case of childhood-onset MD. These variants were in genes involved in the formation of cell membranes or the cytoskeleton and in genes participating in cell death or gene-regulation pathways. His grandfather shared two of the variants: p.Y273N in HMX2 and p.L229F in TMEM55B. HMX2 p.Y273N was considered the more likely candidate for MD, as the gene is known to affect both hearing and vestibular function. The variant in the HMX2 gene may affect inner ear development and structural integrity and thus might predispose to the onset of MD. As there was a significant difference in onset between the patients, an accumulation of defects in several pathways is probably responsible for the exceptionally early onset of the disease, and the genetic etiology of childhood-onset MD is most likely multifactorial. This is the first molecular genetic study of childhood-onset MD.
Collapse
Affiliation(s)
- Sini Skarp
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Laura Kanervo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jouko Kotimäki
- Department of Otorhinolaryngology, Kainuu Central Hospital, Kajaani, Finland
| | - Martti Sorri
- Department of Otorhinolaryngology and Head and Neck Surgery, Oulu University Hospital, Finland & PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Minna Männikkö
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Hietikko
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| |
Collapse
|
26
|
Hartwell RD, England SJ, Monk NAM, van Hateren NJ, Baxendale S, Marzo M, Lewis KE, Whitfield TT. Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression. PLoS Genet 2019; 15:e1008051. [PMID: 31022185 PMCID: PMC6504108 DOI: 10.1371/journal.pgen.1008051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/07/2019] [Accepted: 02/27/2019] [Indexed: 12/16/2022] Open
Abstract
In the zebrafish, Fgf and Hh signalling assign anterior and posterior identity, respectively, to the poles of the developing ear. Mis-expression of fgf3 or inhibition of Hh signalling results in double-anterior ears, including ectopic expression of hmx3a. To understand how this double-anterior pattern is established, we characterised transcriptional responses in Fgf gain-of-signalling or Hh loss-of-signalling backgrounds. Mis-expression of fgf3 resulted in rapid expansion of anterior otic markers, refining over time to give the duplicated pattern. Response to Hh inhibition was very different: initial anteroposterior asymmetry was retained, with de novo duplicate expression domains appearing later. We show that Hmx3a is required for normal anterior otic patterning, and that otic patterning defects in hmx3a-/- mutants are a close phenocopy to those seen in fgf3-/- mutants. However, neither loss nor gain of hmx3a function was sufficient to generate full ear duplications. Using our data to infer a transcriptional regulatory network required for acquisition of otic anterior identity, we can recapitulate both the wild-type and the double-anterior pattern in a mathematical model. Understanding how signalling molecules impart information to developing organ systems, and how this is interpreted through networks of gene activity, is a key goal of developmental genetic analysis. In the developing zebrafish inner ear, differences in gene expression arise between the anterior and posterior poles of the ear placode, ensuring that sensory structures in the ear develop in their correct positions. If signalling pathways are disrupted, a mirror-image ear can result, developing with two anterior poles. We have used genetic, pharmacological and mathematical modelling approaches to decipher the pathway of gene action required to specify anterior structures in the zebrafish ear. Patterns of gene expression are dynamic and plastic, with two different routes leading to the formation of duplicate anterior structures. Expression of the hmx3a gene is an early response to the anterior signalling molecule Fgf3, but is not sufficient to drive the formation of ectopic anterior structures at the posterior of the ear. The hmx3a gene codes for a protein that regulates other genes, and in humans, mutation of HMX genes results in diseases affecting inner ear function. Our work provides a framework for understanding the dynamics of early patterning events in the developing inner ear.
Collapse
Affiliation(s)
- Ryan D. Hartwell
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Samantha J. England
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Nicholas A. M. Monk
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
| | - Nicholas J. van Hateren
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Sarah Baxendale
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Mar Marzo
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Katharine E. Lewis
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Tanya T. Whitfield
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| |
Collapse
|
27
|
Hwang CH, Keller J, Renner C, Ohta S, Wu DK. Genetic interactions support an inhibitory relationship between bone morphogenetic protein 2 and netrin 1 during semicircular canal formation. Development 2019; 146:dev.174748. [PMID: 30770380 PMCID: PMC6398446 DOI: 10.1242/dev.174748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022]
Abstract
The semicircular canals of the mammalian inner ear are derived from epithelial pouches in which epithelial cells in the central region of each pouch undergo resorption, leaving behind the region at the rim to form a tube-shaped canal. Lack of proliferation at the rim and/or over-clearing of epithelial cells in the center of the pouch can obliterate canal formation. Otic-specific knockout of bone morphogenetic protein 2 (Bmp2) results in absence of all three semicircular canals; however, the common crus and ampullae housing the sensory tissue (crista) are intact. The lack of Bmp2 causes Ntn1 (which encodes netrin 1), which is required for canal resorption, to be ectopically expressed at the canal rim. Ectopic Ntn1 results in reduction of Dlx5 and Lmo4, which are required for rim formation. These phenotypes can be partially rescued by removing one allele of Ntn1 in the Bmp2 mutants, indicating that Bmp2 normally negatively regulates Ntn1 for canal formation. Additionally, non-resorption of the canal pouch in Ntn1−/− mutants is partially rescued by removing one allele of Bmp2. Thus, reciprocal inhibition between Bmp2 and netrin 1 is involved in canal formation of the vestibule. Summary:Bmp2-conditional mutant analyses support the hypothesis that presumptive crista induces canal genesis zone in the canal pouch to express Bmp2, which promotes canal formation by restricting Ntn1 expression to the resorption domain.
Collapse
Affiliation(s)
- Chan Ho Hwang
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - James Keller
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Charles Renner
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Sho Ohta
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Doris K Wu
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| |
Collapse
|
28
|
Fanis P, Skordis N, Toumba M, Papaioannou N, Makris A, Kyriakou A, Neocleous V, Phylactou LA. Central Precocious Puberty Caused by Novel Mutations in the Promoter and 5'-UTR Region of the Imprinted MKRN3 Gene. Front Endocrinol (Lausanne) 2019; 10:677. [PMID: 31636607 PMCID: PMC6787840 DOI: 10.3389/fendo.2019.00677] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Central Precocious Puberty (CPP) is clinically defined by the development of secondary sexual characteristics before the age of 8 years in girls and 9 years in boys. To date, mutations in the coding region of KISS1, KISS1R, PROKR2, DLK1, and MKRN3 genes have been reported as causative for CPP. This study investigated the presence of causative mutations in both the promoter and the 5'-UTR regions of the MKRN3 gene. Methods: Sanger DNA sequencing was used for screening the proximal promoter and 5'-UTR region of the MKRN3 gene in a group of 73 index girls with CPP. Mutations identified were cloned in luciferase reporter gene vectors and transiently transfected in GN11 cells in order to check for changes in the activity of the MKRN3 promoter. GN11 cells were previously checked for Mkrn3 expression using lentivirus mediated knock-down. In silico analysis was implemented for the detection of changes in the mRNA secondary structure of the mutated MKRN3 5'-UTR. Results: Three novel heterozygous mutations (-166, -865, -886 nt upstream to the transcription start site) located in the proximal promoter region of the MKRN3 gene were identified in six non-related girls with CPP. Four of these girls shared the -865 mutation, one the -166, and another one the -886. A 5'-UTR (+13 nt downstream to the transcription start site) novel mutation was also identified in a girl with similar clinical phenotype. Gene reporter assay evaluated the identified promoter mutations and demonstrated a significant reduction of MKRN3 promoter activity in transfected GN11 cells. In silico analysis for the mutated 5'-UTR predicted a significant change of the mRNA secondary structure. The minimum free energy (MFE) of the mutated 5'-UTR was higher when compared to the corresponding wild-type indicating less stable RNA secondary structure. Conclusion: Our findings demonstrated novel genetic alterations in the promoter and 5'-UTR regulatory regions of the MKRN3 gene. These changes add to another region to check for the etiology of CPP.
Collapse
Affiliation(s)
- Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Pediatric Endocrine Clinic, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Department of Pediatrics, Iasis Hospital, Paphos, Cyprus
| | - Nikoletta Papaioannou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Anestis Makris
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Andreas Kyriakou
- Developmental Endocrinology Research Group, School of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- *Correspondence: Leonidas A. Phylactou
| |
Collapse
|
29
|
Development of neuroendocrine neurons in the mammalian hypothalamus. Cell Tissue Res 2018; 375:23-39. [PMID: 29869716 DOI: 10.1007/s00441-018-2859-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/11/2018] [Indexed: 12/21/2022]
Abstract
The neuroendocrine system consists of a heterogeneous collection of (mostly) neuropeptidergic neurons found in four hypothalamic nuclei and sharing the ability to secrete neurohormones (all of them neuropeptides except dopamine) into the bloodstream. There are, however, abundant hypothalamic non-neuroendocrine neuropeptidergic neurons developing in parallel with the neuroendocrine system, so that both cannot be entirely disentangled. This heterogeneity results from the workings of a network of transcription factors many of which are already known. Olig2 and Fezf2 expressed in the progenitors, acting through mantle-expressed Otp and Sim1, Sim2 and Pou3f2 (Brn2), regulate production of magnocellular and anterior parvocellular neurons. Nkx2-1, Rax, Ascl1, Neurog3 and Dbx1 expressed in the progenitors, acting through mantle-expressed Isl1, Dlx1, Gsx1, Bsx, Hmx2/3, Ikzf1, Nr5a2 (LH-1) and Nr5a1 (SF-1) are responsible for tuberal parvocellular (arcuate nucleus) and other neuropeptidergic neurons. The existence of multiple progenitor domains whose progeny undergoes intricate tangential migrations as one source of complexity in the neuropeptidergic hypothalamus is the focus of much attention. How neurosecretory cells target axons to the medial eminence and posterior hypophysis is gradually becoming clear and exciting progress has been made on the mechanisms underlying neurovascular interface formation. While rat neuroanatomy and targeted mutations in mice have yielded fundamental knowledge about the neuroendocrine system in mammals, experiments on chick and zebrafish are providing key information about cellular and molecular mechanisms. Looking forward, data from every source will be necessary to unravel the ways in which the environment affects neuroendocrine development with consequences for adult health and disease.
Collapse
|
30
|
Lee B, Kim J, An T, Kim S, Patel EM, Raber J, Lee SK, Lee S, Lee JW. Dlx1/2 and Otp coordinate the production of hypothalamic GHRH- and AgRP-neurons. Nat Commun 2018; 9:2026. [PMID: 29795232 PMCID: PMC5966420 DOI: 10.1038/s41467-018-04377-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/23/2018] [Indexed: 01/07/2023] Open
Abstract
Despite critical roles of the hypothalamic arcuate neurons in controlling the growth and energy homeostasis, the gene regulatory network directing their development remains unclear. Here we report that the transcription factors Dlx1/2 and Otp coordinate the balanced generation of the two functionally related neurons in the hypothalamic arcuate nucleus, GHRH-neurons promoting the growth and AgRP-neurons controlling the feeding and energy expenditure. Dlx1/2-deficient mice show a loss-of-GHRH-neurons and an increase of AgRP-neurons, and consistently develop dwarfism and consume less energy. These results indicate that Dlx1/2 are crucial for specifying the GHRH-neuronal identity and, simultaneously, for suppressing AgRP-neuronal fate. We further show that Otp is required for the generation of AgRP-neurons and that Dlx1/2 repress the expression of Otp by directly binding the Otp gene. Together, our study demonstrates that the identity of GHRH- and AgRP-neurons is synchronously specified and segregated by the Dlx1/2-Otp gene regulatory axis.
Collapse
Affiliation(s)
- Bora Lee
- Center for Neuroscience, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Janghyun Kim
- Neuroscience Section, Papé Family Pediatrics Research Center, Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Taekyeong An
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, 06978, Korea
| | - Sangsoo Kim
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, 06978, Korea
| | - Esha M Patel
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
- Departments of Neurology and Radiation Medicine, and Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Soo-Kyung Lee
- Neuroscience Section, Papé Family Pediatrics Research Center, Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
- Vollum Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Seunghee Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Jae W Lee
- Neuroscience Section, Papé Family Pediatrics Research Center, Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA.
| |
Collapse
|
31
|
Mann ZF, Gálvez H, Pedreno D, Chen Z, Chrysostomou E, Żak M, Kang M, Canden E, Daudet N. Shaping of inner ear sensory organs through antagonistic interactions between Notch signalling and Lmx1a. eLife 2017; 6:e33323. [PMID: 29199954 PMCID: PMC5724992 DOI: 10.7554/elife.33323] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/02/2017] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of formation of the distinct sensory organs of the inner ear and the non-sensory domains that separate them are still unclear. Here, we show that several sensory patches arise by progressive segregation from a common prosensory domain in the embryonic chicken and mouse otocyst. This process is regulated by mutually antagonistic signals: Notch signalling and Lmx1a. Notch-mediated lateral induction promotes prosensory fate. Some of the early Notch-active cells, however, are normally diverted from this fate and increasing lateral induction produces misshapen or fused sensory organs in the chick. Conversely Lmx1a (or cLmx1b in the chick) allows sensory organ segregation by antagonizing lateral induction and promoting commitment to the non-sensory fate. Our findings highlight the dynamic nature of sensory patch formation and the labile character of the sensory-competent progenitors, which could have facilitated the emergence of new inner ear organs and their functional diversification in the course of evolution.
Collapse
Affiliation(s)
- Zoe F Mann
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| | - Héctor Gálvez
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| | - David Pedreno
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| | - Ziqi Chen
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| | | | - Magdalena Żak
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| | - Miso Kang
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| | | | - Nicolas Daudet
- The Ear InstituteUniversity College LondonLondonUnited Kingdom
| |
Collapse
|
32
|
Xie Y, Dorsky RI. Development of the hypothalamus: conservation, modification and innovation. Development 2017; 144:1588-1599. [PMID: 28465334 DOI: 10.1242/dev.139055] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The hypothalamus, which regulates fundamental aspects of physiological homeostasis and behavior, is a brain region that exhibits highly conserved anatomy across vertebrate species. Its development involves conserved basic mechanisms of induction and patterning, combined with a more plastic process of neuronal fate specification, to produce brain circuits that mediate physiology and behavior according to the needs of each species. Here, we review the factors involved in the induction, patterning and neuronal differentiation of the hypothalamus, highlighting recent evidence that illustrates how changes in Wnt/β-catenin signaling during development may lead to species-specific form and function of this important brain structure.
Collapse
Affiliation(s)
- Yuanyuan Xie
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Richard I Dorsky
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
33
|
Sculpting the labyrinth: Morphogenesis of the developing inner ear. Semin Cell Dev Biol 2017; 65:47-59. [DOI: 10.1016/j.semcdb.2016.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/26/2016] [Accepted: 09/25/2016] [Indexed: 01/23/2023]
|
34
|
Nesan D, Kurrasch DM. Genetic programs of the developing tuberal hypothalamus and potential mechanisms of their disruption by environmental factors. Mol Cell Endocrinol 2016; 438:3-17. [PMID: 27720896 DOI: 10.1016/j.mce.2016.09.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/22/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
The hypothalamus is a critical regulator of body homeostasis, influencing the autonomic nervous system and releasing trophic hormones to modulate the endocrine system. The developmental mechanisms that govern formation of the mature hypothalamus are becoming increasingly understood as research in this area grows, leading us to gain appreciation for how these developmental programs are susceptible to disruption by maternal exposure to endocrine disrupting chemicals or other environmental factors in utero. These vulnerabilities, combined with the prominent roles of the various hypothalamic nuclei in regulating appetite, reproductive behaviour, mood, and other physiologies, create a window whereby early developmental disruption can have potent long-term effects. Here we broadly outline our current understanding of hypothalamic development, with a particular focus on the tuberal hypothalamus, including what is know about nuclear coalescing and maturation. We finish by discussing how exposure to environmental or maternally-derived factors can perhaps disrupt these hypothalamic developmental programs, and potentially lead to neuroendocrine disease states.
Collapse
Affiliation(s)
- Dinushan Nesan
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deborah M Kurrasch
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
35
|
SHH ventralizes the otocyst by maintaining basal PKA activity and regulating GLI3 signaling. Dev Biol 2016; 420:100-109. [PMID: 27720745 DOI: 10.1016/j.ydbio.2016.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 02/07/2023]
Abstract
During development of the inner ear, secreted morphogens act coordinately to establish otocyst dorsoventral polarity. Among these, Sonic hedgehog (SHH) plays a critical role in determining ventral polarity. However, how this extracellular signal is transduced intracellularly to establish ventral polarity is unknown. In this study, we show that cAMP dependent protein kinase A (PKA) is a key intracellular factor mediating SHH signaling through regulation of GLI3 processing. Gain-of-function experiments using targeted gene transfection by sonoporation or electroporation revealed that SHH signaling inactivates PKA, maintaining a basal level of PKA activity in the ventral otocyst. This, in turn, suppresses partial proteolytic processing of GLI3FL, resulting in a low GLI3R/GLI3FL ratio in the ventral otocyst and the expression of ventral-specific genes required for ventral otocyst morphogenesis. Thus, we identify a molecular mechanism that links extracellular and intracellular signaling, determines early ventral polarity of the inner ear, and has implications for understanding the integration of polarity signals in multiple organ rudiments regulated by gradients of signaling molecules.
Collapse
|
36
|
Lee B, Lee S, Lee SK, Lee JW. The LIM-homeobox transcription factor Isl1 plays crucial roles in the development of multiple arcuate nucleus neurons. Development 2016; 143:3763-3773. [PMID: 27578785 DOI: 10.1242/dev.133967] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 08/22/2016] [Indexed: 12/24/2022]
Abstract
Neurons in the hypothalamic arcuate nucleus relay and translate important cues from the periphery into the central nervous system. However, the gene regulatory program directing their development remains poorly understood. Here, we report that the LIM-homeodomain transcription factor Isl1 is expressed in several subpopulations of developing arcuate neurons and plays crucial roles in their fate specification. Mice with conditional deletion of the Isl1 gene in developing hypothalamus display severe deficits in both feeding and linear growth. Consistent with these results, their arcuate nucleus fails to express key fate markers of Isl1-expressing neurons that regulate feeding and growth. These include the orexigenic neuropeptides AgRP and NPY for specifying AgRP-neurons, the anorexigenic neuropeptide αMSH for POMC-neurons, and two growth-stimulatory peptides, growth hormone-releasing hormone (GHRH) for GHRH-neurons and somatostatin (Sst) for Sst-neurons. Finally, we show that Isl1 directly enhances the expression of AgRP by cooperating with the key orexigenic transcription factors glucocorticoid receptor and brain-specific homeobox factor. Our results identify Isl1 as a crucial transcription factor that plays essential roles in the gene regulatory program directing development of multiple arcuate neuronal subpopulations.
Collapse
Affiliation(s)
- Bora Lee
- Neuroscience Section, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Seunghee Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Soo-Kyung Lee
- Neuroscience Section, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA.,Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jae W Lee
- Neuroscience Section, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA .,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
37
|
Ohta S, Wang B, Mansour SL, Schoenwolf GC. BMP regulates regional gene expression in the dorsal otocyst through canonical and non-canonical intracellular pathways. Development 2016; 143:2228-37. [PMID: 27151948 DOI: 10.1242/dev.137133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/27/2016] [Indexed: 12/13/2022]
Abstract
The inner ear consists of two otocyst-derived, structurally and functionally distinct components: the dorsal vestibular and ventral auditory compartments. BMP signaling is required to form the vestibular compartment, but how it complements other required signaling molecules and acts intracellularly is unknown. Using spatially and temporally controlled delivery of signaling pathway regulators to developing chick otocysts, we show that BMP signaling regulates the expression of Dlx5 and Hmx3, both of which encode transcription factors essential for vestibular formation. However, although BMP regulates Dlx5 through the canonical SMAD pathway, surprisingly, it regulates Hmx3 through a non-canonical pathway involving both an increase in cAMP-dependent protein kinase A activity and the GLI3R to GLI3A ratio. Thus, both canonical and non-canonical BMP signaling establish the precise spatiotemporal expression of Dlx5 and Hmx3 during dorsal vestibular development. The identification of the non-canonical pathway suggests an intersection point between BMP and SHH signaling, which is required for ventral auditory development.
Collapse
Affiliation(s)
- Sho Ohta
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| | - Baolin Wang
- Department of Cell and Developmental Biology and Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Suzanne L Mansour
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
| | - Gary C Schoenwolf
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| |
Collapse
|
38
|
Abstract
The neuroendocrine hypothalamus is composed of the tuberal and anterodorsal hypothalamus, together with the median eminence/neurohypophysis. It centrally governs wide-ranging physiological processes, including homeostasis of energy balance, circadian rhythms and stress responses, as well as growth and reproductive behaviours. Homeostasis is maintained by integrating sensory inputs and effecting responses via autonomic, endocrine and behavioural outputs, over diverse time-scales and throughout the lifecourse of an individual. Here, we summarize studies that begin to reveal how different territories and cell types within the neuroendocrine hypothalamus are assembled in an integrated manner to enable function, thus supporting the organism's ability to survive and thrive. We discuss how signaling pathways and transcription factors dictate the appearance and regionalization of the hypothalamic primordium, the maintenance of progenitor cells, and their specification and differentiation into neurons. We comment on recent studies that harness such programmes for the directed differentiation of human ES/iPS cells. We summarize how developmental plasticity is maintained even into adulthood and how integration between the hypothalamus and peripheral body is established in the median eminence and neurohypophysis. Analysis of model organisms, including mouse, chick and zebrafish, provides a picture of how complex, yet elegantly coordinated, developmental programmes build glial and neuronal cells around the third ventricle of the brain. Such conserved processes enable the hypothalamus to mediate its function as a central integrating and response-control mediator for the homeostatic processes that are critical to life. Early indications suggest that deregulation of these events may underlie multifaceted pathological conditions and dysfunctional physiology in humans, such as obesity.
Collapse
Affiliation(s)
- Sarah Burbridge
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Iain Stewart
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Marysia Placzek
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
39
|
Bedont JL, Newman EA, Blackshaw S. Patterning, specification, and differentiation in the developing hypothalamus. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:445-68. [PMID: 25820448 DOI: 10.1002/wdev.187] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 12/21/2022]
Abstract
Owing to its complex structure and highly diverse cell populations, the study of hypothalamic development has historically lagged behind that of other brain regions. However, in recent years, a greatly expanded understanding of hypothalamic gene expression during development has opened up new avenues of investigation. In this review, we synthesize existing work to present a holistic picture of hypothalamic development from early induction and patterning through nuclear specification and differentiation, with a particular emphasis on determination of cell fate. We will also touch on special topics in the field including the prosomere model, adult neurogenesis, and integration of migratory cells originating outside the hypothalamic neuroepithelium, and how these topics relate to our broader theme.
Collapse
Affiliation(s)
- Joseph L Bedont
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth A Newman
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
40
|
Díaz C, Morales-Delgado N, Puelles L. Ontogenesis of peptidergic neurons within the genoarchitectonic map of the mouse hypothalamus. Front Neuroanat 2015; 8:162. [PMID: 25628541 PMCID: PMC4290630 DOI: 10.3389/fnana.2014.00162] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/12/2014] [Indexed: 11/13/2022] Open
Abstract
During early development, the hypothalamic primordium undergoes anteroposterior and dorsoventral regionalization into diverse progenitor domains, each characterized by a differential gene expression code. The types of neurons produced selectively in each of these distinct progenitor domains are still poorly understood. Recent analysis of the ontogeny of peptidergic neuronal populations expressing Sst, Ghrh, Crh and Trh mRNAs in the mouse hypothalamus showed that these cell types originate from particular dorsoventral domains, characterized by specific combinations of gene markers. Such analysis implies that the differentiation of diverse peptidergic cell populations depends on the molecular environment where they are born. Moreover, a number of these peptidergic neurons were observed to migrate radially and/or tangentially, invading different adult locations, often intermingled with other cell types. This suggests that a developmental approach is absolutely necessary for the understanding of their adult distribution. In this essay, we examine comparatively the ontogenetic hypothalamic topography of twelve additional peptidergic populations documented in the Allen Developmental Mouse Brain Atlas, and discuss shared vs. variant aspects in their apparent origins, migrations and final distribution, in the context of the respective genoarchitectonic backgrounds. This analysis should aid ulterior attempts to explain causally the development of neuronal diversity in the hypothalamus, and contribute to our understanding of its topographic complexity in the adult.
Collapse
Affiliation(s)
- Carmen Díaz
- Department of Medical Sciences, School of Medicine and Institute for Research in Neurological Disabilities, University of Castilla-La Mancha Albacete, Spain
| | - Nicanor Morales-Delgado
- Department of Human Anatomy and Psychobiology, University of Murcia, School of Medicine and IMIB (Instituto Murciano de Investigación Biosanitaria) Murcia, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, University of Murcia, School of Medicine and IMIB (Instituto Murciano de Investigación Biosanitaria) Murcia, Spain
| |
Collapse
|
41
|
Davies KTJ, Tsagkogeorga G, Rossiter SJ. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals. BMC Evol Biol 2014; 14:261. [PMID: 25523630 PMCID: PMC4302572 DOI: 10.1186/s12862-014-0261-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/08/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. RESULTS Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found. CONCLUSIONS Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.
Collapse
Affiliation(s)
- Kalina T J Davies
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Georgia Tsagkogeorga
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| |
Collapse
|
42
|
Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol 2014; 31:2672-88. [PMID: 25016582 PMCID: PMC4166925 DOI: 10.1093/molbev/msu213] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). Transcription factor proteins that bind these CRMs may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using protein-binding microarray, surface plasmon resonance, and in vivo reporter assays, we demonstrate an important difference in DNA-binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. Although both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in GRNs through modification of binding to secondary sites.
Collapse
Affiliation(s)
| | - Lisa Brubaker
- Department of Biological Sciences, Carnegie Mellon University
| | - Anastasia Vedenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Anisha Gupta
- Department of Chemistry, Carnegie Mellon University
| | | | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | |
Collapse
|
43
|
Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet 2014; 10:e1004461. [PMID: 25010687 PMCID: PMC4091791 DOI: 10.1371/journal.pgen.1004461] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.
Collapse
Affiliation(s)
- Julien Bryois
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - John P. Kemp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Department of Pathology and Genetics, Stanford University, Stanford, California, United States of America
| | | | - Karen M. Ho
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kindom
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
- Center of Excellence for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
| |
Collapse
|
44
|
Identification of a SNP in a regulatory region of GJB2 associated with idiopathic nonsyndromic autosomal recessive hearing loss in a multicenter study. Otol Neurotol 2013; 34:650-6. [PMID: 23640091 DOI: 10.1097/mao.0b013e31828d6501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
HYPOTHESIS Additional genetic changes in the regulatory region of the human GJB2 gene encoding the gap junction protein (Connexin 26) may contribute to sensorineural hearing loss. BACKGROUND Mutations in GJB2 cause up to 50% of autosomal recessive nonsyndromic hearing impairment (NSHI). METHODS In the present study, we screened the putative 5' GJB2 regulatory region for novel alterations. RESULTS In idiopathic familial cases of NSHI lacking known pathogenic alterations in GJB2, we identified a T→C transition (refSNP: rs117685390) in a putative transcription factor binding sequence 228 bp proximal to the transcriptional start site at a homozygous frequency of 0.125 (n = 40), significantly overrepresented in comparison to the homozygous allele frequencies of 0.043 in the normal-hearing Caucasian population (n = 211; p < 0.001). In a NSHI family, inheritance of the rs117685390 C allele segregated on independent chromosomes with NSHI in conjunction with heterozygous inheritance of c.35delG, the most common Caucasian mutation in the GJB2 coding region. In a patient group (n = 32) bearing heterozygous pathogenic c.35delG mutations, - rs117685390 C allele homozygosity was also highly overrepresented (0.25; p < 0.001) and not exclusively linked to the c.35delG mutation in cis in patients homozygous for c.35delG. However, in the majority of NSHI homozygous c.35delG chromosomes examined (91/94), c.35delG homozygosity was linked to the rs117685390 C allele in cis. CONCLUSION These results suggest that the rs117685390 C allele could represent a biomarker for the development of NSHI in Caucasian populations and may be included in risk assessment for the development of NSHI.
Collapse
|
45
|
Geng FS, Abbas L, Baxendale S, Holdsworth CJ, Swanson AG, Slanchev K, Hammerschmidt M, Topczewski J, Whitfield TT. Semicircular canal morphogenesis in the zebrafish inner ear requires the function of gpr126 (lauscher), an adhesion class G protein-coupled receptor gene. Development 2013; 140:4362-74. [PMID: 24067352 PMCID: PMC4007713 DOI: 10.1242/dev.098061] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Morphogenesis of the semicircular canal ducts in the vertebrate inner ear is a dramatic example of epithelial remodelling in the embryo, and failure of normal canal development results in vestibular dysfunction. In zebrafish and Xenopus, semicircular canal ducts develop when projections of epithelium, driven by extracellular matrix production, push into the otic vesicle and fuse to form pillars. We show that in the zebrafish, extracellular matrix gene expression is high during projection outgrowth and then rapidly downregulated after fusion. Enzymatic disruption of hyaluronan in the projections leads to their collapse and a failure to form pillars: as a result, the ears swell. We have cloned a zebrafish mutant, lauscher (lau), identified by its swollen ear phenotype. The primary defect in the ear is abnormal projection outgrowth and a failure of fusion to form the semicircular canal pillars. Otic expression of extracellular matrix components is highly disrupted: several genes fail to become downregulated and remain expressed at abnormally high levels into late larval stages. The lau mutations disrupt gpr126, an adhesion class G protein-coupled receptor gene. Expression of gpr126 is similar to that of sox10, an ear and neural crest marker, and is partially dependent on sox10 activity. Fusion of canal projections and downregulation of otic versican expression in a hypomorphic lau allele can be restored by cAMP agonists. We propose that Gpr126 acts through a cAMP-mediated pathway to control the outgrowth and adhesion of canal projections in the zebrafish ear via the regulation of extracellular matrix gene expression.
Collapse
Affiliation(s)
- Fan-Suo Geng
- MRC Centre for Developmental and Biomedical Genetics and Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Morales-Delgado N, Castro-Robles B, Ferrán JL, Martinez-de-la-Torre M, Puelles L, Díaz C. Regionalized differentiation of CRH, TRH, and GHRH peptidergic neurons in the mouse hypothalamus. Brain Struct Funct 2013; 219:1083-111. [PMID: 24337236 PMCID: PMC4013449 DOI: 10.1007/s00429-013-0554-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/11/2013] [Indexed: 01/25/2023]
Abstract
According to the updated prosomeric model, the hypothalamus is subdivided rostrocaudally into terminal and peduncular parts, and dorsoventrally into alar, basal, and floor longitudinal zones. In this context, we examined the ontogeny of peptidergic cell populations expressing Crh, Trh, and Ghrh mRNAs in the mouse hypothalamus, comparing their distribution relative to the major progenitor domains characterized by molecular markers such as Otp, Sim1, Dlx5, Arx, Gsh1, and Nkx2.1. All three neuronal types originate mainly in the peduncular paraventricular domain and less importantly at the terminal paraventricular domain; both are characteristic alar Otp/Sim1-positive areas. Trh and Ghrh cells appeared specifically at the ventral subdomain of the cited areas after E10.5. Additional Ghrh cells emerged separately at the tuberal arcuate area, characterized by Nkx2.1 expression. Crh-positive cells emerged instead in the central part of the peduncular paraventricular domain at E13.5 and remained there. In contrast, as development progresses (E13.5-E18.5) many alar Ghrh and Trh cells translocate into the alar subparaventricular area, and often also into underlying basal neighborhoods expressing Nkx2.1 and/or Dlx5, such as the tuberal and retrotuberal areas, becoming partly or totally depleted at the original birth sites. Our data correlate a topologic map of molecularly defined hypothalamic progenitor areas with three types of specific neurons, each with restricted spatial origins and differential migratory behavior during prenatal hypothalamic development. The study may be useful for detailed causal analysis of the respective differential specification mechanisms. The postulated migrations also contribute to our understanding of adult hypothalamic complexity.
Collapse
Affiliation(s)
- Nicanor Morales-Delgado
- Department of Medical Sciences, School of Medicine, Regional Centre for Biomedical Research and Institute for Research in Neurological Disabilities, University of Castilla-La Mancha, Calle Almansa, 14, 02006, Albacete, Spain
| | | | | | | | | | | |
Collapse
|
47
|
Munnamalai V, Fekete DM. Wnt signaling during cochlear development. Semin Cell Dev Biol 2013; 24:480-9. [PMID: 23548730 DOI: 10.1016/j.semcdb.2013.03.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/30/2013] [Accepted: 03/21/2013] [Indexed: 02/07/2023]
Abstract
Wnt signaling is a hallmark of all embryonic development with multiple roles at multiple developmental time points. Wnt signaling is also important in the development of several organs, one of which is the inner ear, where it participates in otic specification, the formation of vestibular structures, and the development of the cochlea. In particular, we focus on Wnt signaling in the auditory organ, the cochlea. Attempting to dissect the multiple Wnt signaling pathways in the mammalian cochlea is a challenging task due to limited expression data, particularly at proliferating stages. To offer predictions about Wnt activity, we compare cochlear development with that of other biological systems such as Xenopus retina, brain, cancer cells and osteoblasts. Wnts are likely to regulate development through crosstalk with other signaling pathways, particularly Notch and FGF, leading to changes in the expression of Sox2 and proneural (pro-hair cell) genes. In this review we have consolidated the known signaling pathways in the cochlea with known developmental roles of Wnts from other systems to generate a potential timeline of cochlear development.
Collapse
Affiliation(s)
- Vidhya Munnamalai
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA.
| | | |
Collapse
|
48
|
Buniello A, Hardisty-Hughes RE, Pass JC, Bober E, Smith RJ, Steel KP. Headbobber: a combined morphogenetic and cochleosaccular mouse model to study 10qter deletions in human deafness. PLoS One 2013; 8:e56274. [PMID: 23457544 PMCID: PMC3572983 DOI: 10.1371/journal.pone.0056274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/08/2013] [Indexed: 02/07/2023] Open
Abstract
The recessive mouse mutant headbobber (hb) displays the characteristic behavioural traits associated with vestibular defects including headbobbing, circling and deafness. This mutation was caused by the insertion of a transgene into distal chromosome 7 affecting expression of native genes. We show that the inner ear of hb/hb mutants lacks semicircular canals and cristae, and the saccule and utricle are fused together in a single utriculosaccular sac. Moreover, we detect severe abnormalities of the cochlear sensory hair cells, the stria vascularis looks severely disorganised, Reissner's membrane is collapsed and no endocochlear potential is detected. Myo7a and Kcnj10 expression analysis show a lack of the melanocyte-like intermediate cells in hb/hb stria vascularis, which can explain the absence of endocochlear potential. We use Trp2 as a marker of melanoblasts migrating from the neural crest at E12.5 and show that they do not interdigitate into the developing strial epithelium, associated with abnormal persistence of the basal lamina in the hb/hb cochlea. We perform array CGH, deep sequencing as well as an extensive expression analysis of candidate genes in the headbobber region of hb/hb and littermate controls, and conclude that the headbobber phenotype is caused by: 1) effect of a 648 kb deletion on distal Chr7, resulting in the loss of three protein coding genes (Gpr26, Cpmx2 and Chst15) with expression in the inner ear but unknown function; and 2) indirect, long range effect of the deletion on the expression of neighboring genes on Chr7, associated with downregulation of Hmx3, Hmx2 and Nkx1.2 homeobox transcription factors. Interestingly, deletions of the orthologous region in humans, affecting the same genes, have been reported in nineteen patients with common features including sensorineural hearing loss and vestibular problems. Therefore, we propose that headbobber is a useful model to gain insight into the mechanisms underlying deafness in human 10qter deletion syndrome.
Collapse
Affiliation(s)
- Annalisa Buniello
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | | | - Johanna C. Pass
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Eva Bober
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Karen P. Steel
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
- MRC Institute of Hearing Research, Nottingham, United Kingdom
- * E-mail:
| |
Collapse
|
49
|
|
50
|
Spirov AV, Sabirov MA, Holloway DM. In silico evolution of gene cooption in pattern-forming gene networks. ScientificWorldJournal 2012; 2012:560101. [PMID: 23365523 PMCID: PMC3540831 DOI: 10.1100/2012/560101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/13/2012] [Indexed: 11/17/2022] Open
Abstract
Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC), we investigate how cooption affects the evolvability, outgrowth and robustness of GRNs. We use a data-driven model of insect segmentation, for the fruit fly Drosophila, and evaluate fitness by robustness to maternal variability—a major constraint in biological development. We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection. Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. With the transposon mechanism, we find co-evolutionary oscillations between genes and their transposons. These oscillations may offer a new technique in EC for overcoming premature convergence. Finally, we comment on how a differential equations (in contrast to Boolean) approach is necessary for addressing realistic continuous variation in biochemical parameters.
Collapse
Affiliation(s)
- Alexander V Spirov
- Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, NY 11794, USA.
| | | | | |
Collapse
|