1
|
Zhao Y, Kohl C, Rosebrock D, Hu Q, Hu Y, Vingron M. CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics. Nucleic Acids Res 2024; 52:e57. [PMID: 38850160 PMCID: PMC11260446 DOI: 10.1093/nar/gkae480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 04/10/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent visualization of cell clusters. The genes responsible for the clustering are only inferred in a subsequent step. Clustering cells and genes together would be the remit of biclustering algorithms, which are often bogged down by the size of single-cell data. Here we present 'Correspondence Analysis based Biclustering on Networks' (CAbiNet) for joint clustering and visualization of single-cell RNA-sequencing data. CAbiNet performs efficient co-clustering of cells and their respective marker genes and jointly visualizes the biclusters in a non-linear embedding for easy and interactive visual exploration of the data.
Collapse
Affiliation(s)
- Yan Zhao
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Clemens Kohl
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Daniel Rosebrock
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Qinan Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Yuhui Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| |
Collapse
|
2
|
Zhao B, Zhang H, Liu Y, Zu G, Zhang Y, Hu J, Liu S, You L. Forebrain excitatory neuron-specific loss of Brpf1 attenuates excitatory synaptic transmission and impairs spatial and fear memory. Neural Regen Res 2024; 19:1133-1141. [PMID: 37862219 PMCID: PMC10749587 DOI: 10.4103/1673-5374.385307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/10/2023] [Accepted: 07/19/2023] [Indexed: 10/22/2023] Open
Abstract
Bromodomain and plant homeodomain (PHD) finger containing protein 1 (Brpf1) is an activator and scaffold protein of a multiunit complex that includes other components involving lysine acetyltransferase (KAT) 6A/6B/7. Brpf1, KAT6A, and KAT6B mutations were identified as the causal genes of neurodevelopmental disorders leading to intellectual disability. Our previous work revealed strong and specific expression of Brpf1 in both the postnatal and adult forebrain, especially the hippocampus, which has essential roles in learning and memory. Here, we hypothesized that Brpf1 plays critical roles in the function of forebrain excitatory neurons, and that its deficiency leads to learning and memory deficits. To test this, we knocked out Brpf1 in forebrain excitatory neurons using CaMKIIa-Cre. We found that Brpf1 deficiency reduced the frequency of miniature excitatory postsynaptic currents and downregulated the expression of genes Pcdhgb1, Slc16a7, Robo3, and Rho, which are related to neural development, synapse function, and memory, thereby damaging spatial and fear memory in mice. These findings help explain the mechanisms of intellectual impairment in patients with BRPF1 mutation.
Collapse
Affiliation(s)
- Baicheng Zhao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hang Zhang
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ying Liu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuxiao Zhang
- Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
- Shanghai Changning Mental Health Center, Shanghai, China
- NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China
| | - Jiayi Hu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shuai Liu
- Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
- Shanghai Changning Mental Health Center, Shanghai, China
- NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai, China
| |
Collapse
|
3
|
Xu M, Li S, Xie X, Guo L, Yu D, Zhuo J, Lin J, Kol L, Gan L. ISL1 and POU4F1 Directly Interact to Regulate the Differentiation and Survival of Inner Ear Sensory Neurons. J Neurosci 2024; 44:e1718232024. [PMID: 38267260 PMCID: PMC10883659 DOI: 10.1523/jneurosci.1718-23.2024] [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: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
The inner ear sensory neurons play a pivotal role in auditory processing and balance control. Though significant progresses have been made, the underlying mechanisms controlling the differentiation and survival of the inner ear sensory neurons remain largely unknown. During development, ISL1 and POU4F transcription factors are co-expressed and are required for terminal differentiation, pathfinding, axon outgrowth and the survival of neurons in the central and peripheral nervous systems. However, little is understood about their functional relationship and regulatory mechanism in neural development. Here, we have knocked out Isl1 or Pou4f1 or both in mice of both sexes. In the absence of Isl1, the differentiation of cochleovestibular ganglion (CVG) neurons is disturbed and with that Isl1-deficient CVG neurons display defects in migration and axon pathfinding. Compound deletion of Isl1 and Pou4f1 causes a delay in CVG differentiation and results in a more severe CVG defect with a loss of nearly all of spiral ganglion neurons (SGNs). Moreover, ISL1 and POU4F1 interact directly in developing CVG neurons and act cooperatively as well as independently in regulating the expression of unique sets of CVG-specific genes crucial for CVG development and survival by binding to the cis-regulatory elements including the promoters of Fgf10, Pou4f2, and Epha5 and enhancers of Eya1 and Ntng2 These findings demonstrate that Isl1 and Pou4f1 are indispensable for CVG development and maintenance by acting epistatically to regulate genes essential for CVG development.
Collapse
Affiliation(s)
- Mei Xu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
- Institution of Life Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Shuchun Li
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Xiaoling Xie
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Luming Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
- Institution of Life Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Dongliang Yu
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jiaping Zhuo
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Jacey Lin
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Lotem Kol
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Lin Gan
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Georgia 30912
| |
Collapse
|
4
|
Tang L, Wang Y, Xiang J, Yang D, Zhang Y, Xiang Q, Li J. lncRNA and circRNA expression profiles in the hippocampus of Aβ 25‑35‑induced AD mice treated with Tripterygium glycoside. Exp Ther Med 2023; 26:426. [PMID: 37602300 PMCID: PMC10433443 DOI: 10.3892/etm.2023.12125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/15/2023] [Indexed: 08/22/2023] Open
Abstract
Tripterygium glycosides (TG) have been reported to ameliorate Alzheimer's disease (AD), although the mechanism involved remains to be determined. In the present study, the lncRNA and circRNA expression profiles of an AD mouse model treated with TG were assessed using microarrays. lncRNAs, mRNAs, and circRNAs in the hippocampi of 3 AD+normal saline (NS) mice and 3 AD+TG mice were detected using microarrays. The most differentially expressed lncRNAs, mRNAs, and circRNAs were screened between the AD+NS and AD+TG groups. The differentially expressed lncRNAs and circRNAs were analyzed using GO enrichment and KEGG analyses. Co-expression analysis of lncRNAs, circRNAs, and mRNAs was performed by calculating the correlation coefficients. Protein-protein interaction (PPI) network analysis was performed on mRNAs using STRING. The lncRNA-target-transcription factor (TF) network was analyzed using the Network software. In total, 661 lncRNAs, 64 circRNAs, and 503 mRNAs were found to be differentially expressed in AD mice treated with TG. Pou4f1, Egr2, Mag, and Nr4a1 were the hub genes in the PPI network. The KEGG results showed that the mRNAs that were co-expressed with lncRNAs were enriched in the TNF, PI3K-Akt, and Wnt signaling pathways. LncRNA-target-TF network analysis indicated that TFs, including Cebpa, Zic2, and Rxra, were the most likely to regulate the detected lncRNAs. The circRNA-miRNA interaction network indicated that 275 miRNAs may bind to the 64 circRNAs. In conclusion, these findings provide a novel perspective on AD pathogenesis, and the detected lncRNAs, mRNAs, and circRNAs may serve as novel therapeutic targets for the management of AD.
Collapse
Affiliation(s)
- Liang Tang
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Department of Basic Biology, Wuzhou Medical College, Wuzhou, Guangxi Zhuang 543000, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- The Hunan Provincial University Key Laboratory of The Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical College, Changsha, Hunan 410219, P.R. China
| | - Yan Wang
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Department of Basic Biology, Wuzhou Medical College, Wuzhou, Guangxi Zhuang 543000, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
| | - Ju Xiang
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- The Hunan Provincial University Key Laboratory of The Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical College, Changsha, Hunan 410219, P.R. China
| | - Dawei Yang
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- The Hunan Provincial University Key Laboratory of The Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical College, Changsha, Hunan 410219, P.R. China
| | - Yan Zhang
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- The Hunan Provincial University Key Laboratory of The Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China
| | - Qin Xiang
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- The Hunan Provincial University Key Laboratory of The Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical College, Changsha, Hunan 410219, P.R. China
| | - Jianming Li
- Department of Basic Biology, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- Center for Neuroscience and Behavior, Changsha Medical College, Changsha, Hunan 410219, P.R. China
- The Hunan Provincial University Key Laboratory of The Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical College, Changsha, Hunan 410219, P.R. China
| |
Collapse
|
5
|
New Insights into the Identity of the DFNA58 Gene. Genes (Basel) 2022; 13:genes13122274. [PMID: 36553541 PMCID: PMC9777997 DOI: 10.3390/genes13122274] [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: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Hearing loss is the most common sensory deficit, affecting 466 million people worldwide. The vast and diverse genes involved reflect the complexity of auditory physiology, which requires the use of animal models in order to gain a fuller understanding. Among the loci with a yet-to-be validated gene is the DFNA58, in which ~200 Kb genomic duplication, including three protein-coding genes (PLEK, CNRIP1, and PPP3R1's exon1), was found to segregate with autosomal dominant hearing loss. Through whole genome sequencing, the duplication was found to be in tandem and inserted in an intergenic region, without the disruption of the topological domains. Reanalysis of transcriptomes data studies (zebrafish and mouse), and RT-qPCR analysis of adult zebrafish target organs, in order to access their orthologues expression, highlighted promising results with Cnrip1a, corroborated by zebrafish in situ hybridization and immunofluorescence. Mouse data also suggested Cnrip1 as the best candidate for a relevant role in auditory physiology, and its importance in hearing seems to have remained conserved but the cell type exerting its function might have changed, from hair cells to spiral ganglion neurons.
Collapse
|
6
|
Sanders TR, Kelley MW. Specification of neuronal subtypes in the spiral ganglion begins prior to birth in the mouse. Proc Natl Acad Sci U S A 2022; 119:e2203935119. [PMID: 36409884 PMCID: PMC9860252 DOI: 10.1073/pnas.2203935119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
The afferent innervation of the cochlea is comprised of spiral ganglion neurons (SGNs), which are characterized into four subtypes (Type 1A, B, and C and Type 2). However, little is known about the factors and/or processes that determine each subtype. Here, we present a transcriptional analysis of approximately 5,500 single murine SGNs collected across four developmental time points. All four subtypes are transcriptionally identifiable prior to the onset of coordinated spontaneous activity, indicating that the initial specification process is under genetic control. Trajectory analysis indicates that SGNs initially split into two precursor types (Type 1A/2 and Type 1B/C), followed by subsequent splits to give rise to four transcriptionally distinct subtypes. Differential gene expression, pseudotime, and regulon analyses were used to identify candidate transcription factors which may regulate the subtypes specification process. These results provide insights into SGN development and comprise a transcriptional atlas of SGN maturation across the prenatal period.
Collapse
Affiliation(s)
- Tessa R. Sanders
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD20892
| | - Matthew W. Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD20892
| |
Collapse
|
7
|
Kelley MW. Cochlear Development; New Tools and Approaches. Front Cell Dev Biol 2022; 10:884240. [PMID: 35813214 PMCID: PMC9260282 DOI: 10.3389/fcell.2022.884240] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 12/21/2022] Open
Abstract
The sensory epithelium of the mammalian cochlea, the organ of Corti, is comprised of at least seven unique cell types including two functionally distinct types of mechanosensory hair cells. All of the cell types within the organ of Corti are believed to develop from a population of precursor cells referred to as prosensory cells. Results from previous studies have begun to identify the developmental processes, lineage restrictions and signaling networks that mediate the specification of many of these cell types, however, the small size of the organ and the limited number of each cell type has hampered progress. Recent technical advances, in particular relating to the ability to capture and characterize gene expression at the single cell level, have opened new avenues for understanding cellular specification in the organ of Corti. This review will cover our current understanding of cellular specification in the cochlea, discuss the most commonly used methods for single cell RNA sequencing and describe how results from a recent study using single cell sequencing provided new insights regarding cellular specification.
Collapse
|
8
|
Hosoya M, Fujioka M, Okahara J, Yoshimatsu S, Okano H, Ozawa H. Early development of the cochlea of the common marmoset, a non-human primate model. Neural Dev 2022; 17:6. [PMID: 35524278 PMCID: PMC9077934 DOI: 10.1186/s13064-022-00162-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
Background Fine-tuned cochlear development is essential for hearing. Owing to the difficulty in using early human fetal samples, most of our knowledge regarding cochlear development has been obtained from rodents. However, several inter-species differences in cochlear development between rodents and humans have been reported. To bridge these differences, we investigated early otic development of a non-human primate model animal, the common marmoset (Callithrix jacchus). Methods We examined 20 genes involved in early cochlear development and described the critical developmental steps for morphogenesis, which have been reported to vary between rodents and marmosets. Results The results revealed that several critical genes involved in prosensory epithelium specifications showed higher inter-species differences, suggesting that the molecular process for hair cell lineage acquisition in primates differs considerably from that of rodents. We also observed that the tempo of cochlear development was three times slower in the primate than in rodents. Conclusions Our data provide new insights into early cochlear development in primates and humans and imply that the procedures used for manipulating rodent cochlear sensory cells cannot be directly used for the research of primate cells due to the intrinsic inter-species differences in the cell fate determination program.
Collapse
Affiliation(s)
- Makoto Hosoya
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Masato Fujioka
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan. .,Department of Molecular Genetics, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan.
| | - Junko Okahara
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0193, Japan.,Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, 3-25-12 Tonomachi Kawasaki-ku Kawasaki, Kanagawa, 210-0821, Japan
| | - Sho Yoshimatsu
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0193, Japan.,Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0193, Japan.,Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Ozawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| |
Collapse
|
9
|
Almasoudi SH, Schlosser G. Otic Neurogenesis in Xenopus laevis: Proliferation, Differentiation, and the Role of Eya1. Front Neuroanat 2021; 15:722374. [PMID: 34616280 PMCID: PMC8488300 DOI: 10.3389/fnana.2021.722374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/27/2021] [Indexed: 11/15/2022] Open
Abstract
Using immunostaining and confocal microscopy, we here provide the first detailed description of otic neurogenesis in Xenopus laevis. We show that the otic vesicle comprises a pseudostratified epithelium with apicobasal polarity (apical enrichment of Par3, aPKC, phosphorylated Myosin light chain, N-cadherin) and interkinetic nuclear migration (apical localization of mitotic, pH3-positive cells). A Sox3-immunopositive neurosensory area in the ventromedial otic vesicle gives rise to neuroblasts, which delaminate through breaches in the basal lamina between stages 26/27 and 39. Delaminated cells congregate to form the vestibulocochlear ganglion, whose peripheral cells continue to proliferate (as judged by EdU incorporation), while central cells differentiate into Islet1/2-immunopositive neurons from stage 29 on and send out neurites at stage 31. The central part of the neurosensory area retains Sox3 but stops proliferating from stage 33, forming the first sensory areas (utricular/saccular maculae). The phosphatase and transcriptional coactivator Eya1 has previously been shown to play a central role for otic neurogenesis but the underlying mechanism is poorly understood. Using an antibody specifically raised against Xenopus Eya1, we characterize the subcellular localization of Eya1 proteins, their levels of expression as well as their distribution in relation to progenitor and neuronal differentiation markers during otic neurogenesis. We show that Eya1 protein localizes to both nuclei and cytoplasm in the otic epithelium, with levels of nuclear Eya1 declining in differentiating (Islet1/2+) vestibulocochlear ganglion neurons and in the developing sensory areas. Morpholino-based knockdown of Eya1 leads to reduction of proliferating, Sox3- and Islet1/2-immunopositive cells, redistribution of cell polarity proteins and loss of N-cadherin suggesting that Eya1 is required for maintenance of epithelial cells with apicobasal polarity, progenitor proliferation and neuronal differentiation during otic neurogenesis.
Collapse
Affiliation(s)
| | - Gerhard Schlosser
- School of Natural Sciences, National University of Galway, Galway, Ireland
| |
Collapse
|
10
|
Combined Atoh1 and Neurod1 Deletion Reveals Autonomous Growth of Auditory Nerve Fibers. Mol Neurobiol 2020; 57:5307-5323. [PMID: 32880858 DOI: 10.1007/s12035-020-02092-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
Ear development requires the transcription factors ATOH1 for hair cell differentiation and NEUROD1 for sensory neuron development. In addition, NEUROD1 negatively regulates Atoh1 gene expression. As we previously showed that deletion of the Neurod1 gene in the cochlea results in axon guidance defects and excessive peripheral innervation of the sensory epithelium, we hypothesized that some of the innervation defects may be a result of abnormalities in NEUROD1 and ATOH1 interactions. To characterize the interdependency of ATOH1 and NEUROD1 in inner ear development, we generated a new Atoh1/Neurod1 double null conditional deletion mutant. Through careful comparison of the effects of single Atoh1 or Neurod1 gene deletion with combined double Atoh1 and Neurod1 deletion, we demonstrate that NEUROD1-ATOH1 interactions are not important for the Neurod1 null innervation phenotype. We report that neurons lacking Neurod1 can innervate the flat epithelium without any sensory hair cells or supporting cells left after Atoh1 deletion, indicating that neurons with Neurod1 deletion do not require the presence of hair cells for axon growth. Moreover, transcriptome analysis identified genes encoding axon guidance and neurite growth molecules that are dysregulated in the Neurod1 deletion mutant. Taken together, we demonstrate that much of the projections of NEUROD1-deprived inner ear sensory neurons are regulated cell-autonomously.
Collapse
|
11
|
Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep 2020; 26:2241-2256.e4. [PMID: 30784602 DOI: 10.1016/j.celrep.2019.01.095] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 12/12/2018] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
We used whole-organ mapping to study the locoregional molecular changes in a human bladder containing multifocal cancer. Widespread DNA methylation changes were identified in the entire mucosa, representing the initial field effect. The field effect was associated with subclonal low-allele frequency mutations and a small number of DNA copy alterations. A founder mutation in the RNA splicing gene, ACIN1, was identified in normal mucosa and expanded clonally with an additional 21 mutations in progression to carcinoma. The patterns of mutations and copy number changes in carcinoma in situ and foci of carcinoma were almost identical, confirming their clonal origins. The pathways affected by the DNA copy alterations and mutations, including the Kras pathway, were preceded by the field changes in DNA methylation, suggesting that they reinforced mechanisms that had already been initiated by methylation. The results demonstrate that DNA methylation can serve as the initiator of bladder carcinogenesis.
Collapse
|
12
|
He D, Guo R, Zheng D, Xu M, Li P, Guo L, Gan L. Transcription factor Isl1 is dispensable for the development of the mouse prosensory region. Cytotechnology 2020; 72:407-414. [PMID: 32219582 DOI: 10.1007/s10616-020-00387-7] [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: 10/13/2019] [Accepted: 02/28/2020] [Indexed: 01/17/2023] Open
Abstract
In order to identify genes involved in the development of inner ear hair cells, we investigated the role of the transcription factor Islet-class LIM-homeodomain (LIM-HD) 1 (Isl1) in the development of the mouse prosensory region. Isl1 was deleted using the Pax2-Cre system, and deletion of both alleles was verified using cochlea sections. Changes in the number of prosensory region cells were measured to determine the effect of Isl1 on the development of the mouse prosensory region. In order to test whether Isl1 formed a protein complex with Ldb1 and Gata3, co-immunoprecipitation experiments were performed in HEK293 cells using the Flag-tagged LIM-domain of Isl1, HA-tagged LID of Ldb1 and Myc-tagged C-terminal domain of Gata3. The expression of Gata3, Sox2, Jag1 and P27 proteins in the prosensory region were not affected in Isl1-/- prosensory cells. Thus, Isl1 did not form a protein complex with Gata3 through Ldb1 in the Isl1-/- cells. Our results suggest that Isl1 may be dispensable for the development of the mouse prosensory region.
Collapse
Affiliation(s)
- Daqiang He
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, 310018, Zhejiang, China
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Rui Guo
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dongwang Zheng
- Department of Reproductive Physiology, Zhejiang Academy of Medical Sciences, HangZhou Medical College, Hangzhou, 310000, Zhejiang, China
| | - Mei Xu
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, 310018, Zhejiang, China
| | - Ping Li
- HangZhou CalyGene Bitechnology Limited Company, Hangzhou, 310013, Zhejiang, China
| | - Luming Guo
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Lin Gan
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, 310018, Zhejiang, China.
| |
Collapse
|
13
|
Li X, Bi Z, Sun Y, Li C, Li Y, Liu Z. In vivo ectopic Ngn1 and Neurod1 convert neonatal cochlear glial cells into spiral ganglion neurons. FASEB J 2020; 34:4764-4782. [PMID: 32027432 DOI: 10.1096/fj.201902118r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Damage or degeneration of inner ear spiral ganglion neurons (SGNs) causes hearing impairment. Previous in vitro studies indicate that cochlear glial cells can be reprogrammed into SGNs, however, it remains unknown whether this can occur in vivo. Here, we show that neonatal glial cells can be converted, in vivo, into SGNs (defined as new SGNs) by simultaneous induction of Neurog1 (Ngn1) and Neurod1. New SGNs express SGN markers, Tuj1, Map2, Prox1, Mafb and Gata3, and reduce glial cell marker Sox10 and Scn7a. The heterogeneity within new SGNs is illustrated by immunostaining and transcriptomic assays. Transcriptomes analysis indicates that well reprogrammed SGNs are similar to type I SGNs. In addition, reprogramming efficiency is positively correlated with the dosage of Ngn1 and Neurod1, but declined with aging. Taken together, our in vivo data demonstrates the plasticity of cochlear neonatal glial cells and the capacity of Ngn1 and Neurod1 to reprogram glial cells into SGNs. Looking ahead, we expect that combination of Neurog1 and Neurod1 along with other factors will further boost the percentage of fully converted (Mafb+/Gata3+) new SGNs.
Collapse
Affiliation(s)
- Xiang Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Zhenghong Bi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yidi Sun
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yixue Li
- University of Chinese Academy of Sciences, Shanghai, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhiyong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| |
Collapse
|
14
|
Law S, Stout M, Rensch A, Rowsell JM. Expression of MYOSIN VIIA in developing mouse cochleovestibular ganglion neurons. Gene Expr Patterns 2020; 35:119092. [PMID: 31918020 DOI: 10.1016/j.gep.2019.119092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 10/25/2022]
Abstract
Myosins make up a large super family of motor proteins responsible for actin-based motility in most eukaryotic cells. Myosin VIIA is essential for the development and function of sensory hair cells in the inner ear. The role of Myosin VIIA in the development of cochleovestibular ganglion (CVG) neurons in the mouse is largely unknown. Neurons of the CVG innervate sensory hair cells of the cochlea and vestibular organs to transmit hearing and balance information respectively to the brain. The aim of this study was to characterize the expression of MYOSIN VIIA in the CVG of mouse embryos. Spatiotemporal expression of MYOSIN VIIA was characterized in embryonic (E) mouse inner ear neurons from E9.5 to postnatal (P) day 0. At early stages, when otic neurons begin to delaminate to form the CVG, MYOSIN VIIA was co-expressed with TuJ1, ISLET1 and NEUROD in the otic epithelium and CVG. When CVG neurons were migrating and exiting mitosis, MYSOSIN VIIA was downregulated in a subset of neurons, which were NEUROD-negative and GATA3-positive. After segregation of the CVG, MYOSIN VIIA was observed in a subset of vestibular neurons marked by TUJ1 and absent in cochlear neurons, marked by GATA3. The differential expression of MYOSIN VIIA may indicate a role in inner ear neuron migration and specific labeling of vestibular neurons.
Collapse
Affiliation(s)
- Sarah Law
- Department of Biology, Saint Mary's College, Notre Dame, IN, 46556, USA.
| | - Molly Stout
- Department of Biology, Saint Mary's College, Notre Dame, IN, 46556, USA.
| | - Amanda Rensch
- Department of Biology, Saint Mary's College, Notre Dame, IN, 46556, USA.
| | - Jennifer M Rowsell
- Department of Biology, Saint Mary's College, Notre Dame, IN, 46556, USA.
| |
Collapse
|
15
|
Pou4f1 Defines a Subgroup of Type I Spiral Ganglion Neurons and Is Necessary for Normal Inner Hair Cell Presynaptic Ca 2+ Signaling. J Neurosci 2019; 39:5284-5298. [PMID: 31085606 DOI: 10.1523/jneurosci.2728-18.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 02/02/2023] Open
Abstract
Acoustic signals are relayed from the ear to the brain via spiral ganglion neurons (SGNs) that receive auditory information from the cochlear inner hair cells (IHCs) and transmit that information to the cochlear nucleus of the brainstem. Physiologically distinct classes of SGNs have been characterized by their spontaneous firing rate and responses to sound and those physiological distinctions are thought to correspond to stereotyped synaptic positions on the IHC. More recently, single-cell profiling has identified multiple groups of SGNs based on transcriptional profiling; however, correlations between any of these groups and distinct neuronal physiology have not been determined. In this study, we show that expression of the POU (Pit-Oct-Unc) transcription factor Pou4f1 in type I SGNs in mice of both sexes correlates with a synaptic location on the modiolar side of IHCs. Conditional deletion of Pou4f1 in SGNs beginning in mice at embryonic day 13 rescues the early path-finding and apoptotic phenotypes reported for germline deletion of Pou4f1, resulting in a phenotypically normal development of SGN patterning. However, conditional deletion of Pou4f1 in SGNs alters the activation of Ca2+ channels in IHCs primarily by increasing their voltage sensitivity. Moreover, the modiolar to pillar gradient of active zone Ca2+ influx strength is eliminated. These results demonstrate that a subset of modiolar-targeted SGNs retain expression of Pou4f1 beyond the onset of hearing and suggest that this transcription factor plays an instructive role in presynaptic Ca2+ signaling in IHCs.SIGNIFICANCE STATEMENT Physiologically distinct classes of type I spiral ganglion neurons (SGNs) are necessary to encode sound intensities spanning the audible range. Although anatomical studies have demonstrated structural correlates for some physiologically defined classes of type I SGNs, an understanding of the molecular pathways that specify each type is only now emerging. Here, we demonstrate that expression of the transcription factor Pou4f1 corresponds to a distinct subgroup of type I SGNs that synapse on the modiolar side of inner hair cells. The conditional deletion of Pou4f1 after SGN formation does not disrupt ganglion size or morphology, change the distribution of IHC synaptic locations, or affect the creation of synapses, but it does influence the voltage dependence and strength of Ca2+ influx at presynaptic active zones in inner hair cells.
Collapse
|
16
|
Viventi S, Dottori M. Modelling the dorsal root ganglia using human pluripotent stem cells: A platform to study peripheral neuropathies. Int J Biochem Cell Biol 2018; 100:61-68. [PMID: 29772357 DOI: 10.1016/j.biocel.2018.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 12/28/2022]
Abstract
Sensory neurons of the dorsal root ganglia (DRG) are the primary responders to stimuli inducing feelings of touch, pain, temperature, vibration, pressure and muscle tension. They consist of multiple subpopulations based on their morphology, molecular and functional properties. Our understanding of DRG sensory neurons has been predominantly driven by rodent studies and using transformed cell lines, whereas less is known about human sensory DRG neurons simply because of limited availability of human tissue. Although these previous studies have been fundamental for our understanding of the sensory system, it is imperative to profile human DRG subpopulations as it is becoming evident that human sensory neurons do not share the identical molecular and functional properties found in other species. Furthermore, there are wide range of diseases and disorders that directly/indirectly cause sensory neuronal degeneration or dysfunctionality. Having an in vitro source of human DRG sensory neurons is paramount for studying their development, unique neuronal properties and for accelerating regenerative therapies to treat sensory neuropathies. Here we review the major studies describing generation of DRG sensory neurons from human pluripotent stem cells and fibroblasts and the gaps that need to be addressed for using in vitro-generated human DRG neurons to model human DRG tissue.
Collapse
Affiliation(s)
- Serena Viventi
- Department of Biomedical Engineering, University of Melbourne, Australia
| | - Mirella Dottori
- Department of Biomedical Engineering, University of Melbourne, Australia; Illawarra Health and Medical Research Institute, Centre for Molecular and Medical Bioscience, University of Wollongong, Australia.
| |
Collapse
|
17
|
Abstract
Neurons of the cochleovestibular ganglion (CVG) transmit hearing and balance information to the brain. During development, a select population of early otic progenitors express NEUROG1, delaminate from the otocyst, and coalesce to form the neurons that innervate all inner ear sensory regions. At present, the selection process that determines which otic progenitors activate NEUROG1 and adopt a neuroblast fate is incompletely understood. The transcription factor SOX2 has been implicated in otic neurogenesis, but its requirement in the specification of the CVG neurons has not been established. Here we tested SOX2's requirement during inner ear neuronal specification using a conditional deletion paradigm in the mouse. SOX2 deficiency at otocyst stages caused a near-absence of NEUROG1-expressing neuroblasts, increased cell death in the neurosensory epithelium, and significantly reduced the CVG volume. Interestingly, a milder decrease in neurogenesis was observed in heterozygotes, indicating SOX2 levels are important. Moreover, fate-mapping experiments revealed that the timing of SOX2 expression did not parallel the established vestibular-then-auditory sequence. These results demonstrate that SOX2 is required for the initial events in otic neuronal specification including expression of NEUROG1, although fate-mapping results suggest SOX2 may be required as a competence factor rather than a direct initiator of the neural fate.
Collapse
Affiliation(s)
- Aleta R Steevens
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Jenna C Glatzer
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Amy E Kiernan
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY, USA. .,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA.
| |
Collapse
|
18
|
Zheng D, Yang X, Sheng D, Yu D, Liang G, Guo L, Xu M, Hu X, He D, Yang Y, Wang Y. Pou4f2-GFP knock-in mouse line: A model for studying retinal ganglion cell development. Genesis 2016; 54:534-541. [PMID: 27532212 DOI: 10.1002/dvg.22960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/27/2016] [Accepted: 07/27/2016] [Indexed: 01/10/2023]
Abstract
Pou4f2 acts as a key node in the comprehensive and step-wise gene regulatory network (GRN) and regulates the development of retinal ganglion cells (RGCs). Accordingly, deletion of Pou4f2 results in RGC axon defects and apoptosis. To investigate the GRN involved in RGC regeneration, we generated a mouse line with a POU4F2-green fluorescent protein (GFP) fusion protein expressed in RGCs. Co-localization of POU4F2 and GFP in the retina and brain of Pou4f2-GFP/+ heterozygote mice was confirmed using immunofluorescence analysis. Compared with those in wild-type mice, the expression patterns of POU4F2 and POU4F1 and the co-expression patterns of ISL1 and POU4F2 were unaffected in Pou4f2-GFP/GFP homozygote mice. Moreover, the quantification of RGCs showed no significant difference between Pou4f2-GFP/GFP homozygote and wild-type mice. These results demonstrated that the development of RGCs in Pou4f2-GFP/GFP homozygote mice was the same as in wild-type mice. Thus, the present Pou4f2-GFP knock-in mouse line is a useful tool for further studies on the differentiation and regeneration of RGCs.
Collapse
Affiliation(s)
- Dongwang Zheng
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoyan Yang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Shanghai Chenpartner Company Limited, Shanghai, China
| | - Donglai Sheng
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Dongliang Yu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Guoqing Liang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Luming Guo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mei Xu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xu Hu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Daqiang He
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yang Yang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuying Wang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
| |
Collapse
|
19
|
Xu H, Yi Q, Yang C, Wang Y, Tian J, Zhu J. Histone modifications interact with DNA methylation at the GATA4 promoter during differentiation of mesenchymal stem cells into cardiomyocyte-like cells. Cell Prolif 2016; 49:315-29. [PMID: 27117983 DOI: 10.1111/cpr.12253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/29/2016] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES A previous study of ours confirmed that Islet-1 specifically induces differentiation of MSCs into cardiomyocytes, and that one of the mechanisms underlying that process is regulation of histone acetylation. Here, we further explore the mechanism of MSC differentiation into cardiomyocytes from the perspective of interactions between epigenetic modifications. MATERIALS AND METHODS We used lentiviral vectors to overexpress Islet-1 in MSCs, and ChIP-qPCR, MSP and BSP were performed to detect levels of histone acetylation/methylation and DNA methylation in the GATA4 and Nkx2.5 promoters. To further explore relationships between these epigenetic modifications, we used 5-aza or TSA to interfere with DNA methylation and histone acetylation, respectively, and detected effects on the other two modifications. RESULTS Histone acetylation level increased and its methylation level decreased at GATA4 and Nkx2.5 promoters; DNA methylation level was reduced at the GATA4 promoter but did not change at the Nkx2.5 promoter. Furthermore, 5-aza increased histone acetylation level and reduced its methylation level at the GATA4 promoter but had no effect on the Nkx2.5 promoter; TSA reduced histone methylation and DNA methylation levels at the GATA4 promoter, but it only reduced histone methylation level at the Nkx2.5 promoter. CONCLUSIONS Histone acetylation/methylation and DNA methylation were both involved in regulating GATA4 expression, but Nkx2.5 expression was not regulated by DNA methylation. These three modifications had high correlation with each other during regulation of GATA4 and produced a regulation loop at the GATA4 promoter.
Collapse
Affiliation(s)
- Hao Xu
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, 400014, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Qin Yi
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, 400014, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Chunmei Yang
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, 400014, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Yue Wang
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, 400014, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Jie Tian
- Cardiovascular Department (Internal Medicine), Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Jing Zhu
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, 400014, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| |
Collapse
|
20
|
Goodrich LV. Early Development of the Spiral Ganglion. THE PRIMARY AUDITORY NEURONS OF THE MAMMALIAN COCHLEA 2016. [DOI: 10.1007/978-1-4939-3031-9_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
21
|
Lorenzen SM, Duggan A, Osipovich AB, Magnuson MA, García-Añoveros J. Insm1 promotes neurogenic proliferation in delaminated otic progenitors. Mech Dev 2015; 138 Pt 3:233-45. [PMID: 26545349 DOI: 10.1016/j.mod.2015.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/02/2015] [Accepted: 11/02/2015] [Indexed: 01/12/2023]
Abstract
INSM1 is a zinc-finger protein expressed throughout the developing nervous system in late neuronal progenitors and nascent neurons. In the embryonic cortex and olfactory epithelium, Insm1 may promote the transition of progenitors from apical, proliferative, and uncommitted to basal, terminally-dividing and neuron producing. In the otocyst, delaminating and delaminated progenitors express Insm1, whereas apically-dividing progenitors do not. This expression pattern is analogous to that in embryonic olfactory epithelium and cortex (basal/subventricular progenitors). Lineage analysis confirms that auditory and vestibular neurons originate from Insm1-expressing cells. In the absence of Insm1, otic ganglia are smaller, with 40% fewer neurons. Accounting for the decrease in neurons, delaminated progenitors undergo fewer mitoses, but there is no change in apoptosis. We conclude that in the embryonic inner ear, Insm1 promotes proliferation of delaminated neuronal progenitors and hence the production of neurons, a similar function to that in other embryonic neural epithelia. Unexpectedly, we also found that differentiating, but not mature, outer hair cells express Insm1, whereas inner hair cells do not. Insm1 is the earliest known gene expressed in outer versus inner hair cells, demonstrating that nascent outer hair cells initiate a unique differentiation program in the embryo, much earlier than previously believed.
Collapse
Affiliation(s)
- Sarah M Lorenzen
- Department of Anesthesiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anne Duggan
- Department of Anesthesiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anna B Osipovich
- Center for Stem Cell Biology, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mark A Magnuson
- Center for Stem Cell Biology, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jaime García-Añoveros
- Department of Anesthesiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Departments of Neurology and Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| |
Collapse
|
22
|
Sajgo S, Ali S, Popescu O, Badea TC. Dynamic expression of transcription factor Brn3b during mouse cranial nerve development. J Comp Neurol 2015; 524:1033-61. [PMID: 26356988 DOI: 10.1002/cne.23890] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/18/2015] [Accepted: 08/31/2015] [Indexed: 01/23/2023]
Abstract
During development, transcription factor combinatorial codes define a large variety of morphologically and physiologically distinct neurons. Such a combinatorial code has been proposed for the differentiation of projection neurons of the somatic and visceral components of cranial nerves. It is possible that individual neuronal cell types are not specified by unique transcription factors but rather emerge through the intersection of their expression domains. Brn3a, Brn3b, and Brn3c, in combination with each other and/or transcription factors of other families, can define subgroups of retinal ganglion cells (RGC), spiral and vestibular ganglia, inner ear and vestibular hair cell neurons in the vestibuloacoustic system, and groups of somatosensory neurons in the dorsal root ganglia. The present study investigates the expression and potential role of the Brn3b transcription factor in cranial nerves and associated nuclei of the brainstem. We report the dynamic expression of Brn3b in the somatosensory component of cranial nerves II, V, VII, and VIII and visceromotor nuclei of nerves VII, IX, and X as well as other brainstem nuclei during different stages of development into adult stage. We find that genetically identified Brn3b(KO) RGC axons show correct but delayed pathfinding during the early stages of embryonic development. However, loss of Brn3b does not affect the anatomy of the other cranial nerves normally expressing this transcription factor.
Collapse
Affiliation(s)
- Szilard Sajgo
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, 20892.,Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Science, Babes-Bolyai University, Cluj-Napoca, Cluj, 400084, Romania
| | - Seid Ali
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Octavian Popescu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Science, Babes-Bolyai University, Cluj-Napoca, Cluj, 400084, Romania.,Institute of Biology, Romanian Academy, Bucharest, 060031, Romania
| | | |
Collapse
|
23
|
Nguyen K, Hall AL, Jones JM. Expression of myosin VIIA in the developing chick inner ear neurons. Gene Expr Patterns 2015. [DOI: 10.1016/j.gep.2015.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
24
|
Expression and function of the LIM-homeodomain transcription factor Islet-1 in the developing and mature vertebrate retina. Exp Eye Res 2015; 138:22-31. [DOI: 10.1016/j.exer.2015.06.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 11/19/2022]
|
25
|
Saritas-Yildirim B, Childers CP, Elsik CG, Silva EM. Identification of REST targets in the Xenopus tropicalis genome. BMC Genomics 2015; 16:380. [PMID: 25971704 PMCID: PMC4430910 DOI: 10.1186/s12864-015-1591-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 04/28/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A major role of REST (repressor element-1 silencing transcription factor) is to inhibit the expression of neuronal genes in neural stem cells and non-neuronal cells by binding to a 21 bp consensus sequence and recruiting epigenetic and regulatory cofactors to gene regulatory regions. In neural stem cells, REST silences differentiation-promoting genes to prevent their premature expression and is central to the regulation of neurogenesis and the balance of neural stem cells and neurons. RESULTS To understand the role of REST in vertebrate neurogenesis, we performed a genome-wide screen for REST targets in Xenopus tropicalis. We identified 742 neuron-restrictive silencer elements (NRSE) associated with 1396 genes that are enriched in neuronal function. Comparative analyses revealed that characteristics of NRSE motifs in frog are similar to those in mammals in terms of the distance to target genes, frequency of motifs and the repertoire of putative target genes. In addition, we identified four F-box ubiquitin ligases as putative REST targets and determined that they are expressed in neuronal tissues during Xenopus development. CONCLUSION We identified a conserved core of putative target genes in human, mouse and frog that may be fundamental to REST function in vertebrates. We demonstrate that NRSE sites are associated with both protein-coding genes and lncRNAs in the human genome. Furthermore, we demonstrate that REST binding sites are abundant in low gene-occupancy regions of the human genome but this is not due to an increased association with non-coding RNAs. Our findings identify novel targets of REST and broaden the known mechanism of REST-mediated silencing in neurogenesis.
Collapse
Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
| | - Christopher P Childers
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Christine G Elsik
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. .,Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
| |
Collapse
|
26
|
Chen L, Chu C, Kong X, Huang T, Cai YD. Discovery of new candidate genes related to brain development using protein interaction information. PLoS One 2015; 10:e0118003. [PMID: 25635857 PMCID: PMC4311913 DOI: 10.1371/journal.pone.0118003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/03/2015] [Indexed: 12/18/2022] Open
Abstract
Human brain development is a dramatic process composed of a series of complex and fine-tuned spatiotemporal gene expressions. A good comprehension of this process can assist us in developing the potential of our brain. However, we have only limited knowledge about the genes and gene functions that are involved in this biological process. Therefore, a substantial demand remains to discover new brain development-related genes and identify their biological functions. In this study, we aimed to discover new brain-development related genes by building a computational method. We referred to a series of computational methods used to discover new disease-related genes and developed a similar method. In this method, the shortest path algorithm was executed on a weighted graph that was constructed using protein-protein interactions. New candidate genes fell on at least one of the shortest paths connecting two known genes that are related to brain development. A randomization test was then adopted to filter positive discoveries. Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development.
Collapse
Affiliation(s)
- Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People’s Republic of China
| | - Chen Chu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People’s Republic of China
| | - Xiangyin Kong
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People’s Republic of China
- * E-mail: (TH); (YDC)
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai 200444, People’s Republic of China
- * E-mail: (TH); (YDC)
| |
Collapse
|