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McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson J. Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573083. [PMID: 38187588 PMCID: PMC10769403 DOI: 10.1101/2023.12.22.573083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The understanding of how different cell types contribute to amyotrophic lateral sclerosis (ALS) pathogenesis is limited. Here we generated a single-nucleus transcriptomic and epigenomic atlas of the frontal cortex of ALS cases with C9orf72 (C9) hexanucleotide repeat expansions and sporadic ALS (sALS). Our findings reveal shared pathways in C9-ALS and sALS, characterized by synaptic dysfunction in excitatory neurons and a disease-associated state in microglia. The disease subtypes diverge with loss of astrocyte homeostasis in C9-ALS, and a more substantial disturbance of inhibitory neurons in sALS. Leveraging high depth 3'-end sequencing, we found a widespread switch towards distal polyadenylation (PA) site usage across ALS subtypes relative to controls. To explore this differential alternative PA (APA), we developed APA-Net, a deep neural network model that uses transcript sequence and expression levels of RNA-binding proteins (RBPs) to predict cell-type specific APA usage and RBP interactions likely to regulate APA across disease subtypes.
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2
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Cota P, Saber L, Taskin D, Jing C, Bastidas-Ponce A, Vanheusden M, Shahryari A, Sterr M, Burtscher I, Bakhti M, Lickert H. NEUROD2 function is dispensable for human pancreatic β cell specification. Front Endocrinol (Lausanne) 2023; 14:1286590. [PMID: 37955006 PMCID: PMC10634430 DOI: 10.3389/fendo.2023.1286590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction The molecular programs regulating human pancreatic endocrine cell induction and fate allocation are not well deciphered. Here, we investigated the spatiotemporal expression pattern and the function of the neurogenic differentiation factor 2 (NEUROD2) during human endocrinogenesis. Methods Using Crispr-Cas9 gene editing, we generated a reporter knock-in transcription factor (TF) knock-out human inducible pluripotent stem cell (iPSC) line in which the open reading frame of both NEUROD2 alleles are replaced by a nuclear histone 2B-Venus reporter (NEUROD2nVenus/nVenus). Results We identified a transient expression of NEUROD2 mRNA and its nuclear Venus reporter activity at the stage of human endocrine progenitor formation in an iPSC differentiation model. This expression profile is similar to what was previously reported in mice, uncovering an evolutionarily conserved gene expression pattern of NEUROD2 during endocrinogenesis. In vitro differentiation of the generated homozygous NEUROD2nVenus/nVenus iPSC line towards human endocrine lineages uncovered no significant impact upon the loss of NEUROD2 on endocrine cell induction. Moreover, analysis of endocrine cell specification revealed no striking changes in the generation of insulin-producing b cells and glucagon-secreting a cells upon lack of NEUROD2. Discussion Overall, our results suggest that NEUROD2 is expendable for human b cell formation in vitro.
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Affiliation(s)
- Perla Cota
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Lama Saber
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Damla Taskin
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Changying Jing
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Munich Medical Research School (MMRS), Ludwig Maximilian University (LMU), Munich, Germany
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthew Vanheusden
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Alireza Shahryari
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
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Sekine K, Onoguchi M, Hamada M. Transposons contribute to the acquisition of cell type-specific cis-elements in the brain. Commun Biol 2023; 6:631. [PMID: 37301950 PMCID: PMC10257727 DOI: 10.1038/s42003-023-04989-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Mammalian brains have evolved in stages over a long history to acquire higher functions. Recently, several transposable element (TE) families have been shown to evolve into cis-regulatory elements of brain-specific genes. However, it is not fully understood how TEs are important for gene regulatory networks. Here, we performed a single-cell level analysis using public data of scATAC-seq to discover TE-derived cis-elements that are important for specific cell types. Our results suggest that DNA elements derived from TEs, MER130 and MamRep434, can function as transcription factor-binding sites based on their internal motifs for Neurod2 and Lhx2, respectively, especially in glutamatergic neuronal progenitors. Furthermore, MER130- and MamRep434-derived cis-elements were amplified in the ancestors of Amniota and Eutheria, respectively. These results suggest that the acquisition of cis-elements with TEs occurred in different stages during evolution and may contribute to the acquisition of different functions or morphologies in the brain.
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Affiliation(s)
- Kotaro Sekine
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Masahiro Onoguchi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
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Zhao K, Bai X, Wang X, Cao Y, Zhang L, Li W, Wang S. Insight on the hub gene associated signatures and potential therapeutic agents in epilepsy and glioma. Brain Res Bull 2023; 199:110666. [PMID: 37192718 DOI: 10.1016/j.brainresbull.2023.110666] [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: 08/25/2022] [Revised: 04/04/2023] [Accepted: 05/13/2023] [Indexed: 05/18/2023]
Abstract
OBJECTIVE The relationship between epilepsy and glioma has long been widely recognized, but the mechanisms of interaction remain unclear. This study aimed to investigate the shared genetic signature and treatment strategies between epilepsy and glioma. METHODS We subjected hippocampal tissue samples from patients with epilepsy and glioma to transcriptomic analysis to identify differential genes and associated pathways, respectively. Weight gene co-expression network (WGCNA) analysis was performed to identify conserved modules in epilepsy and glioma and to obtain differentially expressed conserved genes. Prognostic and diagnostic models were built using lasso regression. We also focused on building transcription factor-gene interaction networks and assessing the proportion of immune invading cells in epilepsy patients. Finally, drug compounds were inferred using a drug signature database (DSigDB) based on core targets. RESULTS We discovered 88 differently conserved genes, most of which are involved in synaptic signaling and calcium ion pathways. We used lasso regression model to reduce 88 characteristic genes, and finally screened out 14 genes (EIF4A2, CEP170B, SNPH, EPHA4, KLK7, GNG3, MYOP, ANKRD29, RASD2, PRRT3, EFR3A, SGIP1, RAB6B, CNNM1) as the features of glioma prognosis model whose ROC curve is 0.9. Then, we developed a diagnosis model for epilepsy patients using 8 genes (PRRT3, RASD2, MYPOP, CNNM1, ANKRD29, GNG3, SGIP1, KLK7) with area under ROC curve (AUC) values near 1. According to the ssGSEA method, we observed an increase in activated B cells, eosinophils, follicular helper T cells and type 2T helper cells, and a decrease in monocytes in patients with epilepsy. Notably, the great majority of these immune cells showed a negative correlation with hub genes. To reveal the transcriptional-level regulation mechanism, we also built a TF-gene network. In addition, we discovered that patients with glioma-related epilepsy may benefit more from gabapentin and pregabalin. CONCLUSION This study reveals the modular conserved phenotypes of epilepsy and glioma and constructs effective diagnostic and prognostic markers. It provides new biological targets and ideas for the early diagnosis and effective treatment of epilepsy.
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Affiliation(s)
- Kai Zhao
- Institute of Brain Trauma and Neurology, Pingjin Hospital, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, 300000, China
| | - Xuexue Bai
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Xiao Wang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Yiyao Cao
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Liu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Wei Li
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Shiyong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China.
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Sakpichaisakul K, Boonkrongsak R, Lertbutsayanukul P, Iemwimangsa N, Klumsathian S, Panthan B, Trachoo O. Epileptic spasms related to neuronal differentiation factor 2 (NEUROD2) mutation respond to combined vigabatrin and high dose prednisolone therapy. BMC Neurol 2022; 22:461. [PMID: 36494631 PMCID: PMC9733267 DOI: 10.1186/s12883-022-02992-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Epileptic spasms are a devastating form of early infantile epileptic encephalopathy (EIEE) with various etiologies. Early diagnosis and a shorter lead time to treatment are crucial to stop the seizures and optimize the neurodevelopmental outcome. Genetic testing has become an integral part of epilepsy care that directly guides management and family planning and discovers new targeted treatments. Neuronal differentiation Factor 2 (NEUROD2) variants have recently been a cause of neurodevelopmental disorders (NDDs) and EIEEs with distinctive features. However, there is limited information about the clinical and electroencephalographic response of epileptic spasm treatment in NEUROD2-related NDD syndrome. CASE PRESENTATION We report a female patient of Southeast Asian ethnicity with global developmental delay and epileptic spasms commencing in the first few months of life. A novel de novo heterozygous pathogenic NEUROD2 variant, p. E130Q, was subsequently identified by whole-exome sequencing. Electroencephalogram before treatment showed multifocal independent spikes predominantly in both posterior head regions and demonstrated marked improvement following combined vigabatrin and high-dose prednisolone treatment. However, multiple courses of relapse occurred after weaning off the antiseizure medication. CONCLUSIONS We propose that epileptic spasms related to de novo NEUROD2 pathogenic variant respond well to combined vigabatrin and high-dose prednisolone therapy. These findings may imply the benefit of using combination therapy to treat epileptic spasms in NEUROD2-related NDD syndrome.
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Affiliation(s)
- Kullasate Sakpichaisakul
- Department of Pediatrics, Queen Sirikit National Institute of Child Health, College of Medicine, Rangsit University, Bangkok, 10400, Thailand
| | - Rachata Boonkrongsak
- Department of Pediatrics, Queen Sirikit National Institute of Child Health, College of Medicine, Rangsit University, Bangkok, 10400, Thailand
| | | | - Nareenart Iemwimangsa
- Centre for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Sommon Klumsathian
- Centre for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | | | - Objoon Trachoo
- Centre for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok, 10400, Thailand.
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Leung HW, Foo G, VanDongen A. Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10081946. [PMID: 36009494 PMCID: PMC9405677 DOI: 10.3390/biomedicines10081946] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The immediate early gene Arc is a master regulator of synaptic function and a critical determinant of memory consolidation. Here, we show that Arc interacts with dynamic chromatin and closely associates with histone markers for active enhancers and transcription in cultured rat hippocampal neurons. Both these histone modifications, H3K27Ac and H3K9Ac, have recently been shown to be upregulated in late-onset Alzheimer’s disease (AD). When Arc induction by pharmacological network activation was prevented using a short hairpin RNA, the expression profile was altered for over 1900 genes, which included genes associated with synaptic function, neuronal plasticity, intrinsic excitability, and signalling pathways. Interestingly, about 100 Arc-dependent genes are associated with the pathophysiology of AD. When endogenous Arc expression was induced in HEK293T cells, the transcription of many neuronal genes was increased, suggesting that Arc can control expression in the absence of activated signalling pathways. Taken together, these data establish Arc as a master regulator of neuronal activity-dependent gene expression and suggest that it plays a significant role in the pathophysiology of AD.
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Affiliation(s)
| | - Gabriel Foo
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antonius VanDongen
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
- Correspondence:
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7
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Epigenetic genes and epilepsy - emerging mechanisms and clinical applications. Nat Rev Neurol 2022; 18:530-543. [PMID: 35859062 DOI: 10.1038/s41582-022-00693-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 12/21/2022]
Abstract
An increasing number of epilepsies are being attributed to variants in genes with epigenetic functions. The products of these genes include factors that regulate the structure and function of chromatin and the placing, reading and removal of epigenetic marks, as well as other epigenetic processes. In this Review, we provide an overview of the various epigenetic processes, structuring our discussion around five function-based categories: DNA methylation, histone modifications, histone-DNA crosstalk, non-coding RNAs and chromatin remodelling. We provide background information on each category, describing the general mechanism by which each process leads to altered gene expression. We also highlight key clinical and mechanistic aspects, providing examples of genes that strongly associate with epilepsy within each class. We consider the practical applications of these findings, including tissue-based and biofluid-based diagnostics and precision medicine-based treatments. We conclude that variants in epigenetic genes are increasingly found to be causally involved in the epilepsies, with implications for disease mechanisms, treatments and diagnostics.
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Wang L, Miao X, Nie R, Zhang Z, Zhang J, Cai J. MultiCapsNet: A General Framework for Data Integration and Interpretable Classification. Front Genet 2021; 12:767602. [PMID: 34899854 PMCID: PMC8652257 DOI: 10.3389/fgene.2021.767602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
The latest progresses of experimental biology have generated a large number of data with different formats and lengths. Deep learning is an ideal tool to deal with complex datasets, but its inherent “black box” nature needs more interpretability. At the same time, traditional interpretable machine learning methods, such as linear regression or random forest, could only deal with numerical features instead of modular features often encountered in the biological field. Here, we present MultiCapsNet (https://github.com/wanglf19/MultiCapsNet), a new deep learning model built on CapsNet and scCapsNet, which possesses the merits such as easy data integration and high model interpretability. To demonstrate the ability of this model as an interpretable classifier to deal with modular inputs, we test MultiCapsNet on three datasets with different data type and application scenarios. Firstly, on the labeled variant call dataset, MultiCapsNet shows a similar classification performance with neural network model, and provides importance scores for data sources directly without an extra importance determination step required by the neural network model. The importance scores generated by these two models are highly correlated. Secondly, on single cell RNA sequence (scRNA-seq) dataset, MultiCapsNet integrates information about protein-protein interaction (PPI), and protein-DNA interaction (PDI). The classification accuracy of MultiCapsNet is comparable to the neural network and random forest model. Meanwhile, MultiCapsNet reveals how each transcription factor (TF) or PPI cluster node contributes to classification of cell type. Thirdly, we made a comparison between MultiCapsNet and SCENIC. The results show several cell type relevant TFs identified by both methods, further proving the validity and interpretability of the MultiCapsNet.
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Affiliation(s)
- Lifei Wang
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China.,China National Center for Bioinformation, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuexia Miao
- China National Center for Bioinformation, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Rui Nie
- China National Center for Bioinformation, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- School of Systems Science, Beijing Normal University, Beijing, China
| | - Jiang Zhang
- School of Systems Science, Beijing Normal University, Beijing, China
| | - Jun Cai
- China National Center for Bioinformation, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Warnecke A, Harre J, Shew M, Mellott AJ, Majewski I, Durisin M, Staecker H. Successful Treatment of Noise-Induced Hearing Loss by Mesenchymal Stromal Cells: An RNAseq Analysis of Protective/Repair Pathways. Front Cell Neurosci 2021; 15:656930. [PMID: 34887728 PMCID: PMC8650824 DOI: 10.3389/fncel.2021.656930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are an adult derived stem cell-like population that has been shown to mediate repair in a wide range of degenerative disorders. The protective effects of MSCs are mainly mediated by the release of growth factors and cytokines thereby modulating the diseased environment and the immune system. Within the inner ear, MSCs have been shown protective against tissue damage induced by sound and a variety of ototoxins. To better understand the mechanism of action of MSCs in the inner ear, mice were exposed to narrow band noise. After exposure, MSCs derived from human umbilical cord Wharton's jelly were injected into the perilymph. Controls consisted of mice exposed to sound trauma only. Forty-eight hours post-cell delivery, total RNA was extracted from the cochlea and RNAseq performed to evaluate the gene expression induced by the cell therapy. Changes in gene expression were grouped together based on gene ontology classification. A separate cohort of animals was treated in a similar fashion and allowed to survive for 2 weeks post-cell therapy and hearing outcomes determined. Treatment with MSCs after severe sound trauma induced a moderate hearing protective effect. MSC treatment resulted in an up-regulation of genes related to immune modulation, hypoxia response, mitochondrial function and regulation of apoptosis. There was a down-regulation of genes related to synaptic remodeling, calcium homeostasis and the extracellular matrix. Application of MSCs may provide a novel approach to treating sound trauma induced hearing loss and may aid in the identification of novel strategies to protect hearing.
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Affiliation(s)
- Athanasia Warnecke
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation (EXC 2177/1), Oldenburg, Germany
| | - Jennifer Harre
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation (EXC 2177/1), Oldenburg, Germany
| | - Matthew Shew
- Department of Otolaryngology–Head & Neck Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | | | - Igor Majewski
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
| | - Martin Durisin
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
| | - Hinrich Staecker
- Department of Otolaryngology–Head & Neck Surgery, University of Kansas School of Medicine, Kansas City, KS, United States
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Qiu T, Yin H, Wang Y, Zhao C, Cai D. miR-153 attenuates the inflammatory response and oxidative stress induced by spinal cord injury by targeting of NEUROD2. Am J Transl Res 2021; 13:7968-7975. [PMID: 34377277 PMCID: PMC8340145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/23/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Spinal cord injury (SCI) is a common spine surgical injury that leads to loss of activities of daily living. NEUROD2, a member of the neuroD family, is newly known to play a crucial role in SCI progression. We aimed to investigate the underlying mechanism wherein miR-153 and NEUROD2 modulate the process of SCI. METHODS Expression of miR-153 and NEUROD2 in spinal cord in mice of SCI were analyzed employing western blot and qRT-PCR assays. Microglial cells were transfected with mimic of miR-153 or siRNA targeting NEUROD2 to determine the impact of miR-153 and NEUROD2 on SCI induced inflammatory reaction and oxidative stress. A luciferase reporter assay was conducted to verify the regulation of miR-153 on NERUOD2. RESULTS MiR-153 expression was decreased in injured spinal cord, while NERUOD2 was increased in a time-dependent manner. Addition of miR-153 mimic or silencing NERUOD2 might significantly inhibit the production of inflammation cytokines and attenuated oxidative stress in microglia cells of SCI. Luciferase reporter assay suggested that NERUOD2 was a direct target of miR-153. CONCLUSION We proved that miR-153 attenuated inflammatory response and oxidative stress induced by SCI by targeting of NEUROD2, indicating a protective role in SCI progression.
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Affiliation(s)
- Taibin Qiu
- Department of Orthopaedics, The Third Affiliated Hospital of Southern Medical UniversityGuangzhou, Guangdong Province, China
| | - Haidong Yin
- Department of Orthopaedics, Panyu Hospital of Chinese MedicineGuangzhou, Guangdong Province, China
| | - Yantao Wang
- Department of Orthopaedics, Panyu Hospital of Chinese MedicineGuangzhou, Guangdong Province, China
| | - Chang Zhao
- Department of Orthopaedics, The Third Affiliated Hospital of Southern Medical UniversityGuangzhou, Guangdong Province, China
| | - Daozhang Cai
- Department of Orthopaedics, The Third Affiliated Hospital of Southern Medical UniversityGuangzhou, Guangdong Province, China
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Tutukova S, Tarabykin V, Hernandez-Miranda LR. The Role of Neurod Genes in Brain Development, Function, and Disease. Front Mol Neurosci 2021; 14:662774. [PMID: 34177462 PMCID: PMC8221396 DOI: 10.3389/fnmol.2021.662774] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 01/14/2023] Open
Abstract
Transcriptional regulation is essential for the correct functioning of cells during development and in postnatal life. The basic Helix-loop-Helix (bHLH) superfamily of transcription factors is well conserved throughout evolution and plays critical roles in tissue development and tissue maintenance. A subgroup of this family, called neural lineage bHLH factors, is critical in the development and function of the central nervous system. In this review, we will focus on the function of one subgroup of neural lineage bHLH factors, the Neurod family. The Neurod family has four members: Neurod1, Neurod2, Neurod4, and Neurod6. Available evidence shows that these four factors are key during the development of the cerebral cortex but also in other regions of the central nervous system, such as the cerebellum, the brainstem, and the spinal cord. We will also discuss recent reports that link the dysfunction of these transcription factors to neurological disorders in humans.
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Affiliation(s)
- Svetlana Tutukova
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Victor Tarabykin
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Luis R Hernandez-Miranda
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
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12
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Safari MS, Obexer D, Baier-Bitterlich G, Zur Nedden S. PKN1 Is a Novel Regulator of Hippocampal GluA1 Levels. Front Synaptic Neurosci 2021; 13:640495. [PMID: 33613259 PMCID: PMC7892898 DOI: 10.3389/fnsyn.2021.640495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Alterations in the processes that control α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) expression, assembly and trafficking are closely linked to psychiatric and neurodegenerative disorders. We have recently shown that the serine/threonine kinase Protein kinase N1 (PKN1) is a developmentally active regulator of cerebellar synaptic maturation by inhibiting AKT and the neurogenic transcription factor neurogenic differentiation factor-2 (NeuroD2). NeuroD2 is involved in glutamatergic synaptic maturation by regulating expression levels of various synaptic proteins. Here we aimed to study the effect of Pkn1 knockout on AKT phosphorylation and NeuroD2 levels in the hippocampus and the subsequent expression levels of the NeuroD2 targets and AMPAR subunits: glutamate receptor 1 (GluA1) and GluA2/3. We show that PKN1 is expressed throughout the hippocampus. Interestingly, not only postnatal but also adult hippocampal phospho-AKT and NeuroD2 levels were significantly elevated upon Pkn1 knockout. Postnatal and adult Pkn1 -/- hippocampi showed enhanced expression of the AMPAR subunit GluA1, particularly in area CA1. Surprisingly, GluA2/3 levels were not different between both genotypes. In addition to higher protein levels, we also found an enhanced GluA1 content in the membrane fraction of postnatal and adult Pkn1 -/- animals, while GluA2/3 levels remained unchanged. This points toward a very specific regulation of GluA1 expression and/or trafficking by the novel PKN1-AKT-NeuroD2 axis. Considering the important role of GluA1 in hippocampal development as well as the pathophysiology of several disorders, ranging from Alzheimer's, to depression and schizophrenia, our results validate PKN1 for future studies into neurological disorders related to altered AMPAR subunit expression in the hippocampus.
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Affiliation(s)
- Motahareh Solina Safari
- CCB-Biocenter, Institute of Neurobiochemistry, Medical University of Innsbruck, Innsbruck, Austria
| | - Dido Obexer
- CCB-Biocenter, Institute of Neurobiochemistry, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Stephanie Zur Nedden
- CCB-Biocenter, Institute of Neurobiochemistry, Medical University of Innsbruck, Innsbruck, Austria
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13
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Mis EK, Sega AG, Signer RH, Cartwright T, Ji W, Martinez-Agosto JA, Nelson SF, Palmer CGS, Lee H, Mitzelfelt T, Konstantino M, Jeffries L, Khokha MK, Marco E, Martin MG, Lakhani SA. Expansion of NEUROD2 phenotypes to include developmental delay without seizures. Am J Med Genet A 2021; 185:1076-1080. [PMID: 33438828 DOI: 10.1002/ajmg.a.62064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/29/2020] [Accepted: 12/09/2020] [Indexed: 01/23/2023]
Abstract
De novo heterozygous variants in the brain-specific transcription factor Neuronal Differentiation Factor 2 (NEUROD2) have been recently associated with early-onset epileptic encephalopathy and developmental delay. Here, we report an adolescent with developmental delay without seizures who was found to have a novel de novo heterozygous NEUROD2 missense variant, p.(Leu163Pro). Functional testing using an in vivo assay of neuronal differentiation in Xenopus laevis tadpoles demonstrated that the patient variant of NEUROD2 displays minimal protein activity, strongly suggesting a loss of function effect. In contrast, a second rare NEUROD2 variant, p.(Ala235Thr), identified in an adolescent with developmental delay but lacking parental studies for inheritance, showed normal in vivo NEUROD2 activity. We thus provide clinical, genetic, and functional evidence that NEUROD2 variants can lead to developmental delay without accompanying early-onset seizures, and demonstrate how functional testing can complement genetic data when determining variant pathogenicity.
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Affiliation(s)
- Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Annalisa G Sega
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Rebecca H Signer
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA
| | | | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julian A Martinez-Agosto
- Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Stanley F Nelson
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA.,Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Christina G S Palmer
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Institute for Society and Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Hane Lee
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Thomas Mitzelfelt
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elysa Marco
- Cortica, San Rafael, California, USA.,Pediatric Brain Center, University of California San Francisco, San Francisco, California, USA
| | - Martin G Martin
- Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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14
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Disruption of NEUROD2 causes a neurodevelopmental syndrome with autistic features via cell-autonomous defects in forebrain glutamatergic neurons. Mol Psychiatry 2021; 26:6125-6148. [PMID: 34188164 PMCID: PMC8760061 DOI: 10.1038/s41380-021-01179-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
While the transcription factor NEUROD2 has recently been associated with epilepsy, its precise role during nervous system development remains unclear. Using a multi-scale approach, we set out to understand how Neurod2 deletion affects the development of the cerebral cortex in mice. In Neurod2 KO embryos, cortical projection neurons over-migrated, thereby altering the final size and position of layers. In juvenile and adults, spine density and turnover were dysregulated in apical but not basal compartments in layer 5 neurons. Patch-clamp recordings in layer 5 neurons of juvenile mice revealed increased intrinsic excitability. Bulk RNA sequencing showed dysregulated expression of many genes associated with neuronal excitability and synaptic function, whose human orthologs were strongly associated with autism spectrum disorders (ASD). At the behavior level, Neurod2 KO mice displayed social interaction deficits, stereotypies, hyperactivity, and occasionally spontaneous seizures. Mice heterozygous for Neurod2 had similar defects, indicating that Neurod2 is haploinsufficient. Finally, specific deletion of Neurod2 in forebrain excitatory neurons recapitulated cellular and behavioral phenotypes found in constitutive KO mice, revealing the region-specific contribution of dysfunctional Neurod2 in symptoms. Informed by these neurobehavioral features in mouse mutants, we identified eleven patients from eight families with a neurodevelopmental disorder including intellectual disability and ASD associated with NEUROD2 pathogenic mutations. Our findings demonstrate crucial roles for Neurod2 in neocortical development, whose alterations can cause neurodevelopmental disorders including intellectual disability and ASD.
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15
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De Felice B, Montanino C, Oliva M, Bonavita S, Di Onofrio V, Coppola C. MicroRNA Expression Signature in Mild Cognitive Impairment Due to Alzheimer's Disease. Mol Neurobiol 2020; 57:4408-4416. [PMID: 32737762 PMCID: PMC7515963 DOI: 10.1007/s12035-020-02029-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023]
Abstract
Mild cognitive impairment (MCI) defines an intermediate state between normal ageing and dementia, including Alzheimer’s disease (AD). Identification of MCI subjects who will progress to AD (MCI-AD) is today of crucial importance, especially in light of the possible development of new pathogenic therapies. Several evidences suggest that miRNAs could play relevant roles in the biogenesis of AD, and the links between selected miRNAs and specific pathogenic aspects have been partly explored. In this study, we analysed the composition of microRNA transcriptome in blood, serum and cerebrospinal fluid samples from MCI-AD subjects, from an enriched small RNA library. Real-time qPCR from MCI-AD and AD patients and normal controls was performed to profile miRNA expression. In particular, four microRNAs, hsa-mir-5588-5p, hsa-mir-3658, hsa-mir-567 and hsa-mir-3908, among all selected microRNAs, are dysregulated. Hsa-mir-567 was found to be differentially expressed in cerebrospinal fluid samples, blood and serum from MCI-AD patients, showing the highest fold change and statistical significance. Target prediction analysis have been performed to evaluate mRNAs whose expression was controlled by miRNAs found to be dysregulated here, showing that hsa-mir-567 target genes are functionally active in neuronal cells. We propose that miRNA profiles found in samples from MCI-AD patients might be relevant for a better understanding of AD-related cognitive decline and could lead to set up suitable and potential biomarkers for MCI-AD progression to AD.
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Affiliation(s)
- Bruna De Felice
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100, Caserta, Italy.
| | - Concetta Montanino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100, Caserta, Italy
| | - Mariano Oliva
- Department of Advanced Medical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Simona Bonavita
- Department of Advanced Medical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Valeria Di Onofrio
- Department of Sciences and Technologies, University of Naples "Parthenope", Naples, Italy
| | - Cinzia Coppola
- Department of Advanced Medical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
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16
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Unterholzner J, Gryglewski G, Philippe C, Seiger R, Pichler V, Godbersen GM, Berroterán-Infante N, Murgaš M, Hahn A, Wadsak W, Mitterhauser M, Kasper S, Lanzenberger R. Topologically Guided Prioritization of Candidate Gene Transcripts Coexpressed with the 5-HT1A Receptor by Combining In Vivo PET and Allen Human Brain Atlas Data. Cereb Cortex 2020; 30:3771-3780. [PMID: 31989157 PMCID: PMC7232988 DOI: 10.1093/cercor/bhz341] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
The serotonin-1A receptor (5-HT1AR) represents a viable target in the treatment of disorders of the brain. However, development of psychiatric drugs continues to be hindered by the relative inaccessibility of brain tissue. Although the efficacy of drugs selective for the 5-HT1AR has not been proven, research continues to focus on drugs that influence this receptor subtype. To further knowledge on this topic, we investigated the topological coexpression patterns of the 5-HT1AR. We calculated Spearman’s rho for the correlation of positron emission tomography-binding potentials (BPND) of the 5-HT1AR assessed in 30 healthy subjects using the tracer [carbonyl-11C]WAY-100635 and predicted whole-brain mRNA expression of 18 686 genes. After applying a threshold of r > 0.3 in a leave-one-out cross-validation of the prediction of mRNA expression, genes with ρ ≥ 0.7 were considered to be relevant. In cortical regions, 199 genes showed high correlation with the BPND of the 5-HT1AR, in subcortical regions 194 genes. Using our approach, we could consolidate the role of BDNF and implicate new genes (AnxA8, NeuroD2) in serotonergic functioning. Despite its explorative nature, the analysis can be seen as a gene prioritization approach to reduce the number of genes potentially connected to 5-HT1AR functioning and guide future in vitro studies.
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Affiliation(s)
- Jakob Unterholzner
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Gregor Gryglewski
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Cecile Philippe
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Rene Seiger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Verena Pichler
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Godber M Godbersen
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Neydher Berroterán-Infante
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Matej Murgaš
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Andreas Hahn
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Wolfgang Wadsak
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Centre for Biomarker Research in Medicine (CBmed), Stiftingtalstrasse 5, 8010, Graz, Austria
| | - Markus Mitterhauser
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
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17
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Hahn MA, Jin SG, Li AX, Liu J, Huang Z, Wu X, Kim BW, Johnson J, Bilbao ADV, Tao S, Yim JA, Fong Y, Goebbels S, Schwab MH, Lu Q, Pfeifer GP. Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation. SCIENCE ADVANCES 2019; 5:eaax0080. [PMID: 31681843 PMCID: PMC6810389 DOI: 10.1126/sciadv.aax0080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/13/2019] [Indexed: 05/03/2023]
Abstract
The characteristics of DNA methylation changes that occur during neurogenesis in vivo remain unknown. We used whole-genome bisulfite sequencing to quantitate DNA cytosine modifications in differentiating neurons and their progenitors isolated from mouse brain at the peak of embryonic neurogenesis. Localized DNA hypomethylation was much more common than hypermethylation and often occurred at putative enhancers within genes that were upregulated in neurons and encoded proteins crucial for neuronal differentiation. The hypomethylated regions strongly overlapped with mapped binding sites of the key neuronal transcription factor NEUROD2. The 5-methylcytosine oxidase ten-eleven translocation 2 (TET2) interacted with NEUROD2, and its reaction product 5-hydroxymethylcytosine accumulated at the demethylated regions. NEUROD2-targeted differentially methylated regions retained higher methylation levels in Neurod2 knockout mice, and inducible expression of NEUROD2 caused TET2-associated demethylation at its in vivo binding sites. The data suggest that the reorganization of DNA methylation in developing neurons involves NEUROD2 and TET2-mediated DNA demethylation.
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Affiliation(s)
- Maria A. Hahn
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Arthur X. Li
- Department of Information Sciences, City of Hope, Duarte, CA 91010
| | - Jiancheng Liu
- Department of Developmental and Stem Cell Biology, City of Hope, Duarte, CA 91010, USA
| | - Zhijun Huang
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Byung-Wook Kim
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Jennifer Johnson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Shu Tao
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Jacob A. Yim
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Yuman Fong
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Sandra Goebbels
- Max Planck Institute of Experimental Medicine, Department of Neurogenetics, D-37075 Göttingen, Germany
| | - Markus H. Schwab
- Max Planck Institute of Experimental Medicine, Department of Neurogenetics, D-37075 Göttingen, Germany
- Cellular Neurophysiology and Center for Systems Neuroscience (ZSN), Hannover Medical School, 30625 Hannover, Germany
| | - Qiang Lu
- Department of Developmental and Stem Cell Biology, City of Hope, Duarte, CA 91010, USA
- Corresponding author. (G.P.P.); (Q.L.)
| | - Gerd P. Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Corresponding author. (G.P.P.); (Q.L.)
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18
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Sega AG, Mis EK, Lindstrom K, Mercimek-Andrews S, Ji W, Cho MT, Juusola J, Konstantino M, Jeffries L, Khokha MK, Lakhani SA. De novo pathogenic variants in neuronal differentiation factor 2 (NEUROD2) cause a form of early infantile epileptic encephalopathy. J Med Genet 2018; 56:113-122. [PMID: 30323019 DOI: 10.1136/jmedgenet-2018-105322] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/08/2018] [Accepted: 09/22/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Early infantile epileptic encephalopathies are severe disorders consisting of early-onset refractory seizures accompanied often by significant developmental delay. The increasing availability of next-generation sequencing has facilitated the recognition of single gene mutations as an underlying aetiology of some forms of early infantile epileptic encephalopathies. OBJECTIVES This study was designed to identify candidate genes as a potential cause of early infantile epileptic encephalopathy, and then to provide genetic and functional evidence supporting patient variants as causative. METHODS We used whole exome sequencing to identify candidate genes. To model the disease and assess the functional effects of patient variants on candidate protein function, we used in vivo CRISPR/Cas9-mediated genome editing and protein overexpression in frog tadpoles. RESULTS We identified novel de novo variants in neuronal differentiation factor 2 (NEUROD2) in two unrelated children with early infantile epileptic encephalopathy. Depleting neurod2 with CRISPR/Cas9-mediated genome editing induced spontaneous seizures in tadpoles, mimicking the patients' condition. Overexpression of wild-type NEUROD2 induced ectopic neurons in tadpoles; however, patient variants were markedly less effective, suggesting that both variants are dysfunctional and likely pathogenic. CONCLUSION This study provides clinical and functional support for NEUROD2 variants as a cause of early infantile epileptic encephalopathy, the first evidence of human disease caused by NEUROD2 variants.
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Affiliation(s)
- Annalisa G Sega
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Saadet Mercimek-Andrews
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Saquib Ali Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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19
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Martini-Stoica H, Cole AL, Swartzlander DB, Chen F, Wan YW, Bajaj L, Bader DA, Lee VMY, Trojanowski JQ, Liu Z, Sardiello M, Zheng H. TFEB enhances astroglial uptake of extracellular tau species and reduces tau spreading. J Exp Med 2018; 215:2355-2377. [PMID: 30108137 PMCID: PMC6122971 DOI: 10.1084/jem.20172158] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/11/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
Martini-Stoica et al. demonstrate that the TFEB-mediated lysosomal pathway in astrocytes is increased in tauopathy and plays a functional role in modulating extracellular tau and the propagation of neuronal tau pathology in a mouse model of tau spreading. The progression of tau pathology in Alzheimer’s disease follows a stereotyped pattern, and recent evidence suggests a role of synaptic connections in this process. Astrocytes are well positioned at the neuronal synapse to capture and degrade extracellular tau as it transits the synapse and hence could potentially have the ability to inhibit tau spreading and delay disease progression. Our study shows increased expression and activity of Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis, in response to tau pathology in both human brains with dementia and transgenic mouse models. Exogenous TFEB expression in primary astrocytes enhances tau fibril uptake and lysosomal activity, while TFEB knockout has the reverse effect. In vivo, induced TFEB expression in astrocytes reduces pathology in the hippocampus of PS19 tauopathy mice, as well as prominently attenuates tau spreading from the ipsilateral to the contralateral hippocampus in a mouse model of tau spreading. Our study suggests that astrocytic TFEB plays a functional role in modulating extracellular tau and the propagation of neuronal tau pathology in tauopathies such as Alzheimer’s disease.
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Affiliation(s)
- Heidi Martini-Stoica
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX.,Interdepartmental Program of Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX
| | - Allysa L Cole
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | | | - Fading Chen
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lakshya Bajaj
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - David A Bader
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Virginia M Y Lee
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Marco Sardiello
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Hui Zheng
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX .,Interdepartmental Program of Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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20
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Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Z. Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. Front Mol Neurosci 2018; 11:219. [PMID: 29997476 PMCID: PMC6028693 DOI: 10.3389/fnmol.2018.00219] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/06/2018] [Indexed: 12/23/2022] Open
Abstract
Orofacial pain and headache disorders are among the most debilitating pain conditions. While the pathophysiological basis of these disorders may be diverse, it is generally accepted that a common mechanism behind the arising pain is the sensitization of extra- and intracranial trigeminal primary afferents. In the present study we investigated gene expression changes in the trigeminal ganglia (TRG), trigeminal nucleus caudalis (TNC) and peripheral blood mononuclear cells (PBMC) evoked by Complete Freund's Adjuvant (CFA)-induced orofacial inflammation in rats, as a model of trigeminal sensitization. Microarray analysis revealed 512 differentially expressed genes between the ipsi- and contralateral TRG samples 7 days after CFA injection. Time-dependent expression changes of G-protein coupled receptor 39 (Gpr39), kisspeptin-1 receptor (Kiss1r), kisspeptin (Kiss1), as well as synaptic plasticity-associated Lkaaear1 (Lkr) and Neurod2 mRNA were described on the basis of qPCR results. The greatest alterations were observed on day 3 ipsilaterally, when orofacial mechanical allodynia reached its maximum. This corresponded well with patterns of neuronal (Fosb), microglia (Iba1), and astrocyte (Gfap) activation markers in both TRG and TNC, and interestingly also in PBMCs. This is the first description of up- and downregulated genes both in primary and secondary sensory neurones of the trigeminovascular system that might play important roles in neuroinflammatory activation mechanisms. We are the first to show transcriptomic alterations in the PBMCs that are similar to the neuronal changes. These results open new perspectives and initiate further investigations in the research of trigeminal pain disorders.
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Affiliation(s)
- Timea Aczél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | - József Kun
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
| | - Éva Szőke
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
| | - Tibor Rauch
- Section of Molecular Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Sini Junttila
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Attila Gyenesei
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Kata Bölcskei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
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21
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zur Nedden S, Eith R, Schwarzer C, Zanetti L, Seitter H, Fresser F, Koschak A, Cameron AJ, Parker PJ, Baier G, Baier-Bitterlich G. Protein kinase N1 critically regulates cerebellar development and long-term function. J Clin Invest 2018; 128:2076-2088. [PMID: 29494346 PMCID: PMC5919825 DOI: 10.1172/jci96165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 02/27/2018] [Indexed: 01/16/2023] Open
Abstract
Increasing evidence suggests that synapse dysfunctions are a major determinant of several neurodevelopmental and neurodegenerative diseases. Here we identify protein kinase N1 (PKN1) as a novel key player in fine-tuning the balance between axonal outgrowth and presynaptic differentiation in the parallel fiber-forming (PF-forming) cerebellar granule cells (Cgcs). Postnatal Pkn1-/- animals showed a defective PF-Purkinje cell (PF-PC) synapse formation. In vitro, Pkn1-/- Cgcs exhibited deregulated axonal outgrowth, elevated AKT phosphorylation, and higher levels of neuronal differentiation-2 (NeuroD2), a transcription factor preventing presynaptic maturation. Concomitantly, Pkn1-/- Cgcs had a reduced density of presynaptic sites. By inhibiting AKT with MK-2206 and siRNA-mediated knockdown, we found that AKT hyperactivation is responsible for the elongated axons, higher NeuroD2 levels, and reduced density of presynaptic specifications in Pkn1-/- Cgcs. In line with our in vitro data, Pkn1-/- mice showed AKT hyperactivation, elevated NeuroD2 levels, and reduced expression of PF-PC synaptic markers during stages of PF maturation in vivo. The long-term effect of Pkn1 knockout was further seen in cerebellar atrophy and mild ataxia. In summary, our results demonstrate that PKN1 functions as a developmentally active gatekeeper of AKT activity, thereby fine-tuning axonal outgrowth and presynaptic differentiation of Cgcs and subsequently the correct PF-PC synapse formation.
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Affiliation(s)
| | | | - Christoph Schwarzer
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lucia Zanetti
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Hartwig Seitter
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Friedrich Fresser
- Department for Pharmacology and Genetics, Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Koschak
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Angus J.M. Cameron
- Kinase Biology Laboratory, John Vane Science Centre, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Peter J. Parker
- Francis Crick Institute, London, United Kingdom
- Division of Cancer Studies, King’s College London, London, United Kingdom
| | - Gottfried Baier
- Department for Pharmacology and Genetics, Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
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22
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Dennis DJ, Han S, Schuurmans C. bHLH transcription factors in neural development, disease, and reprogramming. Brain Res 2018; 1705:48-65. [PMID: 29544733 DOI: 10.1016/j.brainres.2018.03.013] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 01/16/2023]
Abstract
The formation of functional neural circuits in the vertebrate central nervous system (CNS) requires that appropriate numbers of the correct types of neuronal and glial cells are generated in their proper places and times during development. In the embryonic CNS, multipotent progenitor cells first acquire regional identities, and then undergo precisely choreographed temporal identity transitions (i.e. time-dependent changes in their identity) that determine how many neuronal and glial cells of each type they will generate. Transcription factors of the basic-helix-loop-helix (bHLH) family have emerged as key determinants of neural cell fate specification and differentiation, ensuring that appropriate numbers of specific neuronal and glial cell types are produced. Recent studies have further revealed that the functions of these bHLH factors are strictly regulated. Given their essential developmental roles, it is not surprising that bHLH mutations and de-regulated expression are associated with various neurological diseases and cancers. Moreover, the powerful ability of bHLH factors to direct neuronal and glial cell fate specification and differentiation has been exploited in the relatively new field of cellular reprogramming, in which pluripotent stem cells or somatic stem cells are converted to neural lineages, often with a transcription factor-based lineage conversion strategy that includes one or more of the bHLH genes. These concepts are reviewed herein.
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Affiliation(s)
- Daniel J Dennis
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N3M5, Canada
| | - Sisu Han
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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23
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Spellmann I, Riedel M, Städtler J, Zill P, Obermeier M, Cerovecki A, Dehning S, Schennach R, Epple M, Opgen-Rhein M, Müller N, Bondy B, Möller HJ, Musil R. Associations of NEUROD2 polymorphisms and change of cognitive dysfunctions in schizophrenia and schizoaffective disorder after eight weeks of antipsychotic treatment. Cogn Neuropsychiatry 2017; 22:280-297. [PMID: 28470106 DOI: 10.1080/13546805.2017.1322502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION NEUROD2 is a neurospecific helix-loop-helix transcription factor which has an impact on the regulation of glutamatergic and GABAergic genes. We investigated an association of NEUROD2 with neurocognitive dysfunctions in schizophrenia and schizoaffective disorder patients before and during treatment with different second-generation antipsychotics. METHODS Patients were genotyped for four different polymorphisms of the NEUROD2 gene ((rs9889354(A/G), rs1877032(C/T), rs12453682(C/T) and rs11078918(C/G)). Cognitive function was assessed at baseline and week 8. Results of individual neuropsychological tests were assigned to six cognitive domains (reaction time and quality; executive function; working, verbal and visual memory) and a general cognitive index. RESULTS 167 patients were included in the study. The NEUROD2 exonic polymorphism rs11078918 showed significant associations with verbal memory and executive functions, whereas the NEUROD2 polymorphism rs12453682 was significantly associated with working and verbal memory, executive functions and with a cognitive index. Significant associations were found at baseline and after eight weeks. Moreover, significant associations between the change in neuropsychological test results during antipsychotic treatment and the NEUROD2 polymorphisms rs11078918 and rs12453682 were observed. CONCLUSIONS Our findings suggest that the NEUROD2 gene could play a role in the pathophysiology of neurocognitive dysfunctions as well as in the change of cognitive symptoms under antipsychotic treatment in schizophrenia and schizoaffective disorder.
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Affiliation(s)
- Ilja Spellmann
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Michael Riedel
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Julia Städtler
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Peter Zill
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Michael Obermeier
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Anja Cerovecki
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Sandra Dehning
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Rebecca Schennach
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Maria Epple
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Markus Opgen-Rhein
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Norbert Müller
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Brigitta Bondy
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Hans-Jürgen Möller
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Richard Musil
- a Department of Psychiatry and Psychotherapy , Ludwig-Maximilians-University Munich , Munich , Germany
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24
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Chen F, Hall BJ. Synaptic activity suppresses expression of neurogenic differentiation factor 2 in an NMDA receptor-dependent manner. Synapse 2017; 71. [PMID: 28524267 DOI: 10.1002/syn.21986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/03/2017] [Accepted: 05/14/2017] [Indexed: 01/16/2023]
Abstract
Neurogenic differentiation factor 2 (NeuroD2) is a highly expressed transcription factor in the developing central nervous system. In newborn neurons, NeuroD2-mediated gene expression promotes differentiation, maturation, and survival. In addition to these early, cell-intrinsic developmental processes, NeuroD2 in postmitotic neurons also regulates synapse growth and ion channel expression to control excitability. While NeuroD2 transactivation can be induced in an activity-dependent manner, little is known about how expression of NeuroD2 itself is regulated. Using genome-wide, mRNA-based microarray analysis, we found that NeuroD2 is actually one of hundreds of genes whose mRNA levels are suppressed by synaptic activity, in a manner dependent upon N-methyl d-aspartate receptor (NMDAR) activation. We confirmed this observation both in vitro and in vivo and provide evidence that this happens at the level of transcription and not mRNA stability. Our experiments further indicate that suppression of NeuroD2 message by NMDARs likely involves both CaMKII and MAPK but not voltage-gated calcium channels, in contrast to its mechanism of transactivation. We predict from these data that NMDARs may transduce information about the level of synaptic activity a developing neuron receives, to down-regulate NeuroD2 and allow proper maturation of cortical circuits by suppressing expression of neurite and synaptic growth promoting gene products.
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Affiliation(s)
- Fading Chen
- The Department of Cell and Molecular Biology, Tulane University, School of Science and Engineering, New Orleans, Louisiana 70118
| | - Benjamin J Hall
- The Department of Cell and Molecular Biology, Tulane University, School of Science and Engineering, New Orleans, Louisiana 70118.,The Neuroscience Program, Tulane University, School of Science and Engineering, New Orleans, Louisiana 70118.,Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
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25
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NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. eNeuro 2017; 4:eN-NWR-0255-16. [PMID: 28303257 PMCID: PMC5343279 DOI: 10.1523/eneuro.0255-16.2017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/18/2017] [Accepted: 01/25/2017] [Indexed: 12/26/2022] Open
Abstract
Calcium signaling controls many key processes in neurons, including gene expression, axon guidance, and synaptic plasticity. In contrast to calcium influx through voltage- or neurotransmitter-gated channels, regulatory pathways that control store-operated calcium entry (SOCE) in neurons are poorly understood. Here, we report a transcriptional control of Stim1 (stromal interaction molecule 1) gene, which is a major sensor of endoplasmic reticulum (ER) calcium levels and a regulator of SOCE. By using a genome-wide chromatin immunoprecipitation and sequencing approach in mice, we find that NEUROD2, a neurogenic transcription factor, binds to an intronic element within the Stim1 gene. We show that NEUROD2 limits Stim1 expression in cortical neurons and consequently fine-tunes the SOCE response upon depletion of ER calcium. Our findings reveal a novel mechanism that regulates neuronal calcium homeostasis during cortical development.
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26
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Shen L, Lin Y, Sun Z, Yuan X, Chen L, Shen B. Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers. Sci Rep 2016; 6:39663. [PMID: 28000768 PMCID: PMC5175196 DOI: 10.1038/srep39663] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/24/2016] [Indexed: 01/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a severe neurodevelopmental disease with a high incidence and effective biomarkers are urgently needed for its diagnosis. A few previous studies have reported the detection of miRNA biomarkers for autism diagnosis, especially those based on bioinformatics approaches. In this study, we developed a knowledge-guided bioinformatics model for identifying autism miRNA biomarkers. We downloaded gene expression microarray data from the GEO Database and extracted genes with expression levels that differed in ASD and the controls. We then constructed an autism-specific miRNA-mRNA network and inferred candidate autism biomarker miRNAs based on their regulatory modes and functions. We defined a novel parameter called the autism gene percentage as autism-specific knowledge to further facilitate the identification of autism-specific biomarker miRNAs. Finally, 11 miRNAs were screened as putative autism biomarkers, where eight miRNAs (72.7%) were significantly dysregulated in ASD samples according to previous reports. Functional enrichment results indicated that the targets of the identified miRNAs were enriched in autism-associated pathways, such as Wnt signaling (in KEGG and IPA), cell cycle (in KEGG), and glioblastoma multiforme signaling (in IPA), thereby supporting the predictive power of our model.
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Affiliation(s)
- Li Shen
- Center for Systems Biology, Soochow University, Suzhou, 215006, China.,Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Zhandong Sun
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Xuye Yuan
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Luonan Chen
- Key laboratory of Systems Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
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