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Kiefer L, Gaudin S, Rajkumar SM, Servito GIF, Langen J, Mui MH, Nawsheen S, Canzio D. Tuning cohesin trajectories enables differential readout of the Pcdhα cluster across neurons. Science 2024; 385:eadm9802. [PMID: 39052779 DOI: 10.1126/science.adm9802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/16/2024] [Indexed: 07/27/2024]
Abstract
Expression of Protocadherin (Pcdh) genes is critical to the generation of neuron identity and wiring of the nervous system. Pcdhα genes are arranged in clusters and exhibit a range of expression profiles, from stochastic to deterministic. Because Pcdhα promoters have high sequence identity and share distal enhancers, how distinct neurons choose which gene to express remains unclear. We show that the interplay between multiple enhancers, epigenetics, and genome folding orchestrates differential readouts of the locus across neurons. The probability of Pcdhα promoter choice depends on enhancer/promoter encounters catalyzed by cohesin, whose extrusion trajectories determine the likelihood that an individual promoter can "escape" heterochromatin-mediated silencing. We propose that tunable locus-specific regulatory elements and cell type-specific cohesin activity underlie the generation of cellular diversity by Pcdh genes.
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Affiliation(s)
- Lea Kiefer
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Gaudin
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biology, Ecole Normale Supérieure de Lyon, 69432 Lyon, France
| | - Sandy M Rajkumar
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gabrielle Isabelle F Servito
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Langen
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael H Mui
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shayra Nawsheen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniele Canzio
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub Investigator, San Francisco, San Francisco, CA 94158, USA
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2
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Zhang J, Hu G, Lu Y, Ren H, Huang Y, Wen Y, Ji B, Wang D, Wang H, Liu H, Ma N, Zhang L, Pan G, Qu Y, Wang H, Zhang W, Miao Z, Yao H. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment. Nat Commun 2024; 15:5524. [PMID: 38951485 PMCID: PMC11217373 DOI: 10.1038/s41467-024-49684-1] [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: 05/12/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gongcheng Hu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yuli Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huawei Ren
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yin Huang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yulin Wen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Binrui Ji
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Diyang Wang
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Huisheng Liu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Ning Ma
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Guangjin Pan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Qu
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Hua Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Wei Zhang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Zhichao Miao
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
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El Kamouh M, Brionne A, Sayyari A, Laurent A, Labbé C. Cryopreservation effect on DNA methylation profile in rainbow trout spermatozoa. Sci Rep 2023; 13:19029. [PMID: 37923780 PMCID: PMC10624875 DOI: 10.1038/s41598-023-44803-2] [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: 08/11/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023] Open
Abstract
Spermatozoa are the cells that are most commonly used for cryopreservation of valuable genetic resources in aquaculture. It is known that fish spermatozoa transmit to the embryo not only their genetic but also their epigenetic profile, especially DNA methylation. Therefore, any alteration of the DNA methylation profile in spermatozoa induces the risk of transmitting epigenetic alterations to the offspring. The aim of this study was to assess the effect of cryopreservation on DNA methylation in rainbow trout spermatozoa. To trigger variable cellular response after freezing-thawing, spermatozoa from mature males were cryopreserved with dimethyl sulfoxide, methanol or glycerol as cryoprotectant. We observed that dimethyl sulfoxide was the best to preserve thawed spermatozoa functions. Methanol only slightly preserved all the cellular parameters, while glycerol failed to protect motility and fertilization ability. The consequences on DNA methylation were assessed using Reduced Representation Bisulfite Sequencing (RRBS). Sperm cryopreservation did not thoroughly impact DNA methylation, although 335-564 differentially methylated cytosines were characterized depending on the cryoprotectant. Very few of them were shared between cryoprotectants, and no correlation with the extent of cellular damage was found. Our study showed that DNA methylation was only slightly altered after sperm cryopreservation, and this may render further analysis of the risk for the progeny very challenging.
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Affiliation(s)
| | | | - Amin Sayyari
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Audrey Laurent
- INRAE, Fish Physiology and Genomics, UR 1037, Rennes, France.
| | - Catherine Labbé
- INRAE, Fish Physiology and Genomics, UR 1037, Rennes, France.
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4
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Kawamura N, Osuka T, Kaneko R, Kishi E, Higuchi R, Yoshimura Y, Hirabayashi T, Yagi T, Tarusawa E. Reciprocal Connections between Parvalbumin-Expressing Cells and Adjacent Pyramidal Cells Are Regulated by Clustered Protocadherin γ. eNeuro 2023; 10:ENEURO.0250-23.2023. [PMID: 37890993 PMCID: PMC10614112 DOI: 10.1523/eneuro.0250-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Functional neural circuits in the cerebral cortex are established through specific neural connections between excitatory and various inhibitory cell types. However, the molecular mechanisms underlying synaptic partner recognition remain unclear. In this study, we examined the impact of clustered protocadherin-γ (cPcdhγ) gene deletion in parvalbumin-positive (PV+) cells on intralaminar and translaminar neural circuits formed between PV+ and pyramidal (Pyr) cells in the primary visual cortex (V1) of male and female mice. First, we used whole-cell recordings and laser-scan photostimulation with caged glutamate to map excitatory inputs from layer 2/3 to layer 6. We found that cPcdhγ-deficient PV+ cells in layer 2/3 received normal translaminar inputs from Pyr cells through layers 2/3-6. Second, to further elucidate the effect on PV+-Pyr microcircuits within intralaminar layer 2/3, we conducted multiple whole-cell recordings. While the overall connection probability of PV+-Pyr cells remained largely unchanged, the connectivity of PV+-Pyr was significantly different between control and PV+-specific cPcdhγ-conditional knock-out (PV-cKO) mice. In control mice, the number of reciprocally connected PV+ cells was significantly higher than PV+ cells connected one way to Pyr cells, a difference that was not significant in PV-cKO mice. Interestingly, the proportion of highly reciprocally connected PV+ cells to Pyr cells with large unitary IPSC (uIPSC) amplitudes was reduced in PV-cKO mice. Conversely, the proportion of middle reciprocally connected PV+ cells to Pyr cells with large uIPSC amplitudes increased compared with control mice. This study demonstrated that cPcdhγ in PV+ cells modulates their reciprocity with Pyr cells in the cortex.
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Affiliation(s)
- Nanami Kawamura
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoki Osuka
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryosuke Kaneko
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Eri Kishi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryuon Higuchi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yumiko Yoshimura
- Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Department of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Takahiro Hirabayashi
- Clinical Medicine Research Laboratory, Shonan University of Medical Sciences, Totsuka-ku, Yokohama 244-0806, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Etsuko Tarusawa
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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5
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Hoshino N, Kanadome T, Takasugi T, Itoh M, Kaneko R, Inoue YU, Inoue T, Hirabayashi T, Watanabe M, Matsuda T, Nagai T, Tarusawa E, Yagi T. Visualization of trans homophilic interaction of clustered protocadherin in neurons. Proc Natl Acad Sci U S A 2023; 120:e2301003120. [PMID: 37695902 PMCID: PMC10515168 DOI: 10.1073/pnas.2301003120] [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: 01/17/2023] [Accepted: 07/20/2023] [Indexed: 09/13/2023] Open
Abstract
Clustered protocadherin (Pcdh) functions as a cell recognition molecule through the homophilic interaction in the central nervous system. However, its interactions have not yet been visualized in neurons. We previously reported PcdhγB2-Förster resonance energy transfer (FRET) probes to be applicable only to cell lines. Herein, we designed γB2-FRET probes by fusing FRET donor and acceptor fluorescent proteins to a single γB2 molecule and succeeded in visualizing γB2 homophilic interaction in cultured hippocampal neurons. The γB2-FRET probe localized in the soma and neurites, and FRET signals, which were observed at contact sites between neurites, eliminated by ethylene glycol tetraacetic acid (EGTA) addition. Live imaging revealed that the FRET-negative γB2 signals rapidly moved along neurites and soma, whereas the FRET-positive signals remained in place. We observed that the γB2 proteins at synapses rarely interact homophilically. The γB2-FRET probe might allow us to elucidate the function of the homophilic interaction and the cell recognition mechanism.
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Affiliation(s)
- Natsumi Hoshino
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Takashi Kanadome
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Ibaraki, Osaka567-0047, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama332-0012, Japan
| | - Tomomi Takasugi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Mizuho Itoh
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Ryosuke Kaneko
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Yukiko U. Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo187-8501, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo187-8501, Japan
| | - Takahiro Hirabayashi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
- Clinical Medicine Research Laboratory, Shonan University of Medical Sciences, Yokohama244-0806, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido060-8638, Japan
| | - Tomoki Matsuda
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Ibaraki, Osaka567-0047, Japan
| | - Takeharu Nagai
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Ibaraki, Osaka567-0047, Japan
| | - Etsuko Tarusawa
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
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6
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Kobayashi H, Takemoto K, Sanbo M, Hirabayashi M, Hirabayashi T, Hirayama T, Kiyonari H, Abe T, Yagi T. Isoform requirement of clustered protocadherin for preventing neuronal apoptosis and neonatal lethality. iScience 2023; 26:105766. [PMID: 36582829 PMCID: PMC9793319 DOI: 10.1016/j.isci.2022.105766] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/24/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Clustered protocadherin is a family of cell-surface recognition molecules implicated in neuronal connectivity that has a diverse isoform repertoire and homophilic binding specificity. Mice have 58 isoforms, encoded by Pcdhα, β, and γ gene clusters, and mutant mice lacking all isoforms died after birth, displaying massive neuronal apoptosis and synapse loss. The current hypothesis is that the three specific γC-type isoforms, especially γC4, are essential for the phenotype, raising the question about the necessity of isoform diversity. We generated TC mutant mice that expressed the three γC-type isoforms but lacked all the other 55 isoforms. The TC mutants died immediately after birth, showing massive neuronal death, and γC3 or γC4 expression did not prevent apoptosis. Restoring the α- and β-clusters with the three γC alleles rescued the phenotype, suggesting that along with the three γC-type isoforms, other isoforms are also required for the survival of neurons and individual mice.
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Affiliation(s)
- Hiroaki Kobayashi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Division of Biophysical Engineering, Department of Systems Science, School of Engineering Science, Osaka University, Toyonaka 565-8531, Japan
| | - Kenji Takemoto
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Makoto Sanbo
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Masumi Hirabayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Takahiro Hirabayashi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Department of Anatomy and Developmental Neurobiology, Tokushima University, Graduate School of Medical Science, Tokushima 770-8503, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 6500047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 6500047, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Division of Biophysical Engineering, Department of Systems Science, School of Engineering Science, Osaka University, Toyonaka 565-8531, Japan
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7
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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8
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Development of FRET-based indicators for visualizing homophilic trans interaction of a clustered protocadherin. Sci Rep 2021; 11:22237. [PMID: 34782670 PMCID: PMC8593154 DOI: 10.1038/s41598-021-01481-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022] Open
Abstract
Clustered protocadherins (Pcdhs), which are cell adhesion molecules, play a fundamental role in self-recognition and non-self-discrimination by conferring diversity on the cell surface. Although systematic cell-based aggregation assays provide information regarding the binding properties of Pcdhs, direct visualization of Pcdh trans interactions across cells remains challenging. Here, we present Förster resonance energy transfer (FRET)-based indicators for directly visualizing Pcdh trans interactions. We developed the indicators by individually inserting FRET donor and acceptor fluorescent proteins (FPs) into the ectodomain of Pcdh molecules. They enabled successful visualization of specific trans interactions of Pcdh and revealed that the Pcdh trans interaction is highly sensitive to changes in extracellular Ca2+ levels. We expect that FRET-based indicators for visualizing Pcdh trans interactions will provide a new approach for investigating the roles of Pcdh in self-recognition and non-self-discrimination processes.
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9
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Aviña-Padilla K, Ramírez-Rafael JA, Herrera-Oropeza GE, Muley VY, Valdivia DI, Díaz-Valenzuela E, García-García A, Varela-Echavarría A, Hernández-Rosales M. Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role. Front Genet 2021; 12:654256. [PMID: 34306008 PMCID: PMC8302217 DOI: 10.3389/fgene.2021.654256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
The structure of eukaryotic genes is generally a combination of exons interrupted by intragenic non-coding DNA regions (introns) removed by RNA splicing to generate the mature mRNA. A fraction of genes, however, comprise a single coding exon with introns in their untranslated regions or are intronless genes (IGs), lacking introns entirely. The latter code for essential proteins involved in development, growth, and cell proliferation and their expression has been proposed to be highly specialized for neuro-specific functions and linked to cancer, neuropathies, and developmental disorders. The abundant presence of introns in eukaryotic genomes is pivotal for the precise control of gene expression. Notwithstanding, IGs exempting splicing events entail a higher transcriptional fidelity, making them even more valuable for regulatory roles. This work aimed to infer the functional role and evolutionary history of IGs centered on the mouse genome. IGs consist of a subgroup of genes with one exon including coding genes, non-coding genes, and pseudogenes, which conform approximately 6% of a total of 21,527 genes. To understand their prevalence, biological relevance, and evolution, we identified and studied 1,116 IG functional proteins validating their differential expression in transcriptomic data of embryonic mouse telencephalon. Our results showed that overall expression levels of IGs are lower than those of MEGs. However, strongly up-regulated IGs include transcription factors (TFs) such as the class 3 of POU (HMG Box), Neurog1, Olig1, and BHLHe22, BHLHe23, among other essential genes including the β-cluster of protocadherins. Most striking was the finding that IG-encoded BHLH TFs fit the criteria to be classified as microproteins. Finally, predicted protein orthologs in other six genomes confirmed high conservation of IGs associated with regulating neural processes and with chromatin organization and epigenetic regulation in Vertebrata. Moreover, this study highlights that IGs are essential modulators of regulatory processes, such as the Wnt signaling pathway and biological processes as pivotal as sensory organ developing at a transcriptional and post-translational level. Overall, our results suggest that IG proteins have specialized, prevalent, and unique biological roles and that functional divergence between IGs and MEGs is likely to be the result of specific evolutionary constraints.
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Affiliation(s)
- Katia Aviña-Padilla
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Centro de Investigacioìn y de Estudios Avanzados del IPN, Unidad Irapuato, Guanajuato, Mexico
| | | | - Gabriel Emilio Herrera-Oropeza
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, United Kingdom
| | | | - Dulce I. Valdivia
- Centro de Investigacioìn y de Estudios Avanzados del IPN, Unidad Irapuato, Guanajuato, Mexico
| | - Erik Díaz-Valenzuela
- Centro de Investigacioìn y de Estudios Avanzados del IPN, Unidad Irapuato, Guanajuato, Mexico
| | - Andrés García-García
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Querétaro, Mexico
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10
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Steffen DM, Ferri SL, Marcucci CG, Blocklinger KL, Molumby MJ, Abel T, Weiner JA. The γ-Protocadherins Interact Physically and Functionally with Neuroligin-2 to Negatively Regulate Inhibitory Synapse Density and Are Required for Normal Social Interaction. Mol Neurobiol 2021; 58:2574-2589. [PMID: 33471287 PMCID: PMC8137559 DOI: 10.1007/s12035-020-02263-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022]
Abstract
Cell adhesion molecules (CAMs) are key players in the formation of neural circuits during development. The γ-protocadherins (γ-Pcdhs), a family of 22 CAMs encoded by the Pcdhg gene cluster, are known to play important roles in dendrite arborization, axon targeting, and synapse development. We showed previously that multiple γ-Pcdhs interact physically with the autism-associated CAM neuroligin-1, and inhibit the latter's ability to promote excitatory synapse maturation. Here, we show that γ-Pcdhs can also interact physically with the related neuroligin-2, and inhibit this CAM's ability to promote inhibitory synapse development. In an artificial synapse assay, γ-Pcdhs co-expressed with neuroligin-2 in non-neuronal cells reduce inhibitory presynaptic maturation in contacting hippocampal axons. Mice lacking the γ-Pcdhs from the forebrain (including the cortex, the hippocampus, and portions of the amygdala) exhibit increased inhibitory synapse density and increased co-localization of neuroligin-2 with inhibitory postsynaptic markers in vivo. These Pcdhg mutants also exhibit defective social affiliation and an anxiety-like phenotype in behavioral assays. Together, these results suggest that γ-Pcdhs negatively regulate neuroligins to limit synapse density in a manner that is important for normal behavior.
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Affiliation(s)
- David M Steffen
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA, 52242, USA
| | - Sarah L Ferri
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Charles G Marcucci
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA, 52242, USA
| | - Kelsey L Blocklinger
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Michael J Molumby
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA, 52242, USA
| | - Ted Abel
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Joshua A Weiner
- Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biology, The University of Iowa, Iowa City, IA, 52242, USA.
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11
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Xu L, Zheng Y, Li X, Wang A, Huo D, Li Q, Wang S, Luo Z, Liu Y, Xu F, Wu X, Wu M, Zhou Y. Abnormal neocortex arealization and Sotos-like syndrome-associated behavior in Setd2 mutant mice. SCIENCE ADVANCES 2021; 7:7/1/eaba1180. [PMID: 33523829 PMCID: PMC7775761 DOI: 10.1126/sciadv.aba1180] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Proper formation of area identities of the cerebral cortex is crucial for cognitive functions and social behaviors of the brain. It remains largely unknown whether epigenetic mechanisms, including histone methylation, regulate cortical arealization. Here, we removed SETD2, the methyltransferase for histone 3 lysine-36 trimethylation (H3K36me3), in the developing dorsal forebrain in mice and showed that Setd2 is required for proper cortical arealization and the formation of cortico-thalamo-cortical circuits. Moreover, Setd2 conditional knockout mice exhibit defects in social interaction, motor learning, and spatial memory, reminiscent of patients with the Sotos-like syndrome bearing SETD2 mutations. SETD2 maintains the expression of clustered protocadherin (cPcdh) genes in an H3K36me3 methyltransferase-dependent manner. Aberrant cortical arealization was recapitulated in cPcdh heterozygous mice. Together, our study emphasizes epigenetic mechanisms underlying cortical arealization and pathogenesis of the Sotos-like syndrome.
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Affiliation(s)
- Lichao Xu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Yue Zheng
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Xuejing Li
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Andi Wang
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Dawei Huo
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China
| | - Qinglan Li
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Shikang Wang
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Zhiyuan Luo
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Ying Liu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Fuqiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xudong Wu
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China
| | - Min Wu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China.
| | - Yan Zhou
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China.
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
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12
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The γ-Protocadherins Regulate the Survival of GABAergic Interneurons during Developmental Cell Death. J Neurosci 2020; 40:8652-8668. [PMID: 33060174 DOI: 10.1523/jneurosci.1636-20.2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/23/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Inhibitory interneurons integrate into developing circuits in specific ratios and distributions. In the neocortex, inhibitory network formation occurs concurrently with the apoptotic elimination of a third of GABAergic interneurons. The cell surface molecules that select interneurons to survive or die are unknown. Here, we report that members of the clustered Protocadherins (cPCDHs) control GABAergic interneuron survival during developmentally-regulated cell death. Conditional deletion of the gene cluster encoding the γ-Protocadherins (Pcdhgs) from developing GABAergic neurons in mice of either sex causes a severe loss of inhibitory populations in multiple brain regions and results in neurologic deficits such as seizures. By focusing on the neocortex and the cerebellar cortex, we demonstrate that reductions of inhibitory interneurons result from elevated apoptosis during the critical postnatal period of programmed cell death (PCD). By contrast, cortical interneuron (cIN) populations are not affected by removal of Pcdhgs from pyramidal neurons or glial cells. Interneuron loss correlates with reduced AKT signaling in Pcdhg mutant interneurons, and is rescued by genetic blockade of the pro-apoptotic factor BAX. Together, these findings identify the PCDHGs as pro-survival transmembrane proteins that select inhibitory interneurons for survival and modulate the extent of PCD. We propose that the PCDHGs contribute to the formation of balanced inhibitory networks by controlling the size of GABAergic interneuron populations in the developing brain.SIGNIFICANCE STATEMENT A pivotal step for establishing appropriate excitatory-inhibitory ratios is adjustment of neuronal populations by cell death. In the mouse neocortex, a third of GABAergic interneurons are eliminated by BAX-dependent apoptosis during the first postnatal week. Interneuron cell death is modulated by neural activity and pro-survival pathways but the cell-surface molecules that select interneurons for survival or death are unknown. We demonstrate that members of the cadherin superfamily, the clustered γ-Protocadherins (PCDHGs), regulate the survival of inhibitory interneurons and the balance of cell death. Deletion of the Pcdhgs in mice causes inhibitory interneuron loss in the cortex and cerebellum, and leads to motor deficits and seizures. Our findings provide a molecular basis for controlling inhibitory interneuron population size during circuit formation.
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13
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Flaherty E, Maniatis T. The role of clustered protocadherins in neurodevelopment and neuropsychiatric diseases. Curr Opin Genet Dev 2020; 65:144-150. [PMID: 32679536 DOI: 10.1016/j.gde.2020.05.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/15/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022]
Abstract
During development, individual neurons extend highly branched arbors that innervate the surrounding territory, enabling the formation of appropriate synaptic connections. The clustered protocadherins (cPCDH), a family of diverse cell-surface homophilic proteins, provide each neuron with a cell specific identity required for distinguishing between self versus non-self. While only 52 unique cPcdh isoforms are encoded in the human genome, a combination of stochastic promoter choice and the formation of a protein lattice through engagement of adjacent cPCDH protein cis/trans-tetramers confer the high degree of cellular specificity required for self-recognition. Studies of mice bearing deletions of individual cPcdh gene clustees have identified deficits in circuit formation and behavior. In humans, single nucleotide variants scattered across the cPCDH locus have been identified, which associate with multiple neurodevelopmental disorders, including autism and schizophrenia. To advance our understanding of cPCDH stochastic choice and maintenance, function across cell types, and contribution to neuropsychiatric disease pathogenesis, hiPSC-based models have been developed. Ultimately, integration of human genetic data, biochemical assays, and functional studies is needed to uncover the mechanism underlying neurite repulsion, which has been implicated in neurodevelopmental disorders.
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Affiliation(s)
- Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, United States; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, United States
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, United States; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, United States; New York Genome Center, New York, NY 10013, United States.
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14
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Pancho A, Aerts T, Mitsogiannis MD, Seuntjens E. Protocadherins at the Crossroad of Signaling Pathways. Front Mol Neurosci 2020; 13:117. [PMID: 32694982 PMCID: PMC7339444 DOI: 10.3389/fnmol.2020.00117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022] Open
Abstract
Protocadherins (Pcdhs) are cell adhesion molecules that belong to the cadherin superfamily, and are subdivided into clustered (cPcdhs) and non-clustered Pcdhs (ncPcdhs) in vertebrates. In this review, we summarize their discovery, expression mechanisms, and roles in neuronal development and cancer, thereby highlighting the context-dependent nature of their actions. We furthermore provide an extensive overview of current structural knowledge, and its implications concerning extracellular interactions between cPcdhs, ncPcdhs, and classical cadherins. Next, we survey the known molecular action mechanisms of Pcdhs, emphasizing the regulatory functions of proteolytic processing and domain shedding. In addition, we outline the importance of Pcdh intracellular domains in the regulation of downstream signaling cascades, and we describe putative Pcdh interactions with intracellular molecules including components of the WAVE complex, the Wnt pathway, and apoptotic cascades. Our overview combines molecular interaction data from different contexts, such as neural development and cancer. This comprehensive approach reveals potential common Pcdh signaling hubs, and points out future directions for research. Functional studies of such key factors within the context of neural development might yield innovative insights into the molecular etiology of Pcdh-related neurodevelopmental disorders.
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Affiliation(s)
- Anna Pancho
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tania Aerts
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuela D Mitsogiannis
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
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15
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Asai H, Ohkawa N, Saitoh Y, Ghandour K, Murayama E, Nishizono H, Matsuo M, Hirayama T, Kaneko R, Muramatsu SI, Yagi T, Inokuchi K. Pcdhβ deficiency affects hippocampal CA1 ensemble activity and contextual fear discrimination. Mol Brain 2020; 13:7. [PMID: 31959219 PMCID: PMC6971911 DOI: 10.1186/s13041-020-0547-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/05/2020] [Indexed: 11/16/2022] Open
Abstract
Clustered protocadherins (Pcdhs), a large group of adhesion molecules, are important for axonal projections and dendritic spread, but little is known about how they influence neuronal activity. The Pcdhβ cluster is strongly expressed in the hippocampus, and in vivo Ca2+ imaging in Pcdhβ-deficient mice revealed altered activity of neuronal ensembles but not of individual cells in this region in freely moving animals. Specifically, Pcdhβ deficiency increased the number of large-size neuronal ensembles and the proportion of cells shared between ensembles. Furthermore, Pcdhβ-deficient mice exhibited reduced repetitive neuronal population activity during exploration of a novel context and were less able to discriminate contexts in a contextual fear conditioning paradigm. These results suggest that one function of Pcdhβs is to modulate neural ensemble activity in the hippocampus to promote context discrimination.
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Affiliation(s)
- Hirotaka Asai
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, 930-0194, Japan
| | - Noriaki Ohkawa
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, 930-0194, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), JST, Saitama, 332-0012, Japan
| | - Yoshito Saitoh
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, 930-0194, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), JST, Saitama, 332-0012, Japan
| | - Khaled Ghandour
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, 930-0194, Japan
| | - Emi Murayama
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, 930-0194, Japan
| | - Hirofumi Nishizono
- Division of Animal Experimental Laboratory, Life Science Research Center, University of Toyama, Toyama, 930-0194, Japan
| | - Mina Matsuo
- Division of Animal Experimental Laboratory, Life Science Research Center, University of Toyama, Toyama, 930-0194, Japan
| | - Teruyoshi Hirayama
- Department of Anatomy and Developmental Neurobiology, Tokushima University, Tokushima, 770-8501, Japan
| | - Ryosuke Kaneko
- Bioresource Center, Gunma University Graduate School of Medicine, Gunma, 371-8511, Japan
| | - Shin-Ichi Muramatsu
- Division of Neurology, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan.,Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
| | - Kaoru Inokuchi
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, 930-0194, Japan.
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16
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Garrett AM, Bosch PJ, Steffen DM, Fuller LC, Marcucci CG, Koch AA, Bais P, Weiner JA, Burgess RW. CRISPR/Cas9 interrogation of the mouse Pcdhg gene cluster reveals a crucial isoform-specific role for Pcdhgc4. PLoS Genet 2019; 15:e1008554. [PMID: 31877124 PMCID: PMC6957209 DOI: 10.1371/journal.pgen.1008554] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/13/2020] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
The mammalian Pcdhg gene cluster encodes a family of 22 cell adhesion molecules, the gamma-Protocadherins (γ-Pcdhs), critical for neuronal survival and neural circuit formation. The extent to which isoform diversity–a γ-Pcdh hallmark–is required for their functions remains unclear. We used a CRISPR/Cas9 approach to reduce isoform diversity, targeting each Pcdhg variable exon with pooled sgRNAs to generate an allelic series of 26 mouse lines with 1 to 21 isoforms disrupted via discrete indels at guide sites and/or larger deletions/rearrangements. Analysis of 5 mutant lines indicates that postnatal viability and neuronal survival do not require isoform diversity. Surprisingly, given reports that it might not independently engage in trans-interactions, we find that γC4, encoded by Pcdhgc4, is the only critical isoform. Because the human orthologue is the only PCDHG gene constrained in humans, our results indicate a conserved γC4 function that likely involves distinct molecular mechanisms. The γ-Protocadherins (γ-Pcdhs) are a family of 22 molecules that serve many crucial functions during neural development. They can combine to form multimers at the cell surface, such that each combination specifically recognizes the same combination at the surface of other cells. In this way, 22 molecules can generate thousands of distinct recognition complexes. To test the extent to which molecular diversity is required for the γ-Pcdhs to serve their many functions, we used CRISPR/Cas9 gene editing to make a series of mouse mutants in which different combinations of the γ-Pcdhs are disrupted. We report 25 new mouse lines with between 1 and 21 intact members of the γ-Pcdh family. Further, we found that for the critical function of neuronal survival–and consequently the survival of the animal–the molecular diversity was not essential. Rather, a single member of the family called γC4 was the only one necessary or sufficient for this function; databases of human genome sequences suggest that this important role is conserved. These new strains will be invaluable for disentangling the role of molecular diversity in the γ-Pcdhs’ functions, and as we have already found, will help identify specific functions for specific γ-Pcdh family members.
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Affiliation(s)
- Andrew M. Garrett
- Department of Pharmacology and Department of Ophthalmology, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail: (AMG); (JAW); (RWB)
| | - Peter J. Bosch
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - David M. Steffen
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Leah C. Fuller
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Charles G. Marcucci
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexis A. Koch
- Department of Pharmacology and Department of Ophthalmology, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Preeti Bais
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Joshua A. Weiner
- Department of Biology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (AMG); (JAW); (RWB)
| | - Robert W. Burgess
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail: (AMG); (JAW); (RWB)
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17
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Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells. Nat Genet 2019; 51:1691-1701. [PMID: 31740836 PMCID: PMC7061033 DOI: 10.1038/s41588-019-0526-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/30/2019] [Indexed: 01/09/2023]
Abstract
In the mammalian genome, the clustered protocadherin (cPcdh) locus is a paradigm of stochastic gene expression with the potential to generate a unique cPcdh combination in every neuron. Here, we report a chromatin-based mechanism emerging during the transition from the naive to the primed states of cell pluripotency that reduces by orders of magnitude the combinatorial potential in the human cPcdh locus. This mechanism selectively increases the frequency of stochastic selection of a small subset of cPcdh genes after neuronal differentiation in monolayers, months-old organoids, and engrafted cells in the rat spinal cord. Signs of these frequent selections can be observed in the brain throughout fetal development and disappear after birth, unless there is a condition of delayed maturation such as Down Syndrome. We therefore propose that a pattern of limited cPcdh diversity is maintained while human neurons still retain fetal-like levels of maturation. Short and long-term cultures of human stem cell-derived neurons reveal that a pattern of restricted selection of clustered protocadherin isoforms, pre-established in pluripotent cells, distinguishes immature from mature neurons.
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18
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Miralles CP, Taylor MJ, Bear J, Fekete CD, George S, Li Y, Bonhomme B, Chiou TT, De Blas AL. Expression of protocadherin-γC4 protein in the rat brain. J Comp Neurol 2019; 528:840-864. [PMID: 31609469 DOI: 10.1002/cne.24783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/26/2022]
Abstract
It has been proposed that the combinatorial expression of γ-protocadherins (Pcdh-γs) and other clustered protocadherins (Pcdhs) provides a code of molecular identity and individuality to neurons, which plays a major role in the establishment of specific synaptic connectivity and formation of neuronal circuits. Particular attention has been directed to the Pcdh-γ family, for which experimental evidence derived from Pcdh-γ-deficient mice shows that they are involved in dendrite self-avoidance, synapse development, dendritic arborization, spine maturation, and prevention of apoptosis of some neurons. Moreover, a triple-mutant mouse deficient in the three C-type members of the Pcdh-γ family (Pcdh-γC3, Pcdh-γC4, and Pcdh-γC5) shows a phenotype similar to the mouse deficient in whole Pcdh-γ family, indicating that the latter is largely due to the absence of C-type Pcdh-γs. The role of each individual C-type Pcdh-γ is not known. We have developed a specific antibody to Pcdh-γC4 to reveal the expression of this protein in the rat brain. The results show that although Pcdh-γC4 is expressed at higher levels in the embryo and earlier postnatal weeks, it is also expressed in the adult rat brain. Pcdh-γC4 is expressed in both neurons and astrocytes. In the adult brain, the regional distribution of Pcdh-γC4 immunoreactivity is similar to that of Pcdh-γC4 mRNA, being highest in the olfactory bulb, dentate gyrus, and cerebellum. Pcdh-γC4 forms puncta that are frequently apposed to glutamatergic and GABAergic synapses. They are also frequently associated with neuron-astrocyte contacts. The results provide new insights into the cell recognition function of Pcdh-γC4 in neurons and astrocytes.
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Affiliation(s)
- Celia P Miralles
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Michael J Taylor
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - John Bear
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Christopher D Fekete
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Shanu George
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Yanfang Li
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Bevan Bonhomme
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Tzu-Ting Chiou
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Angel L De Blas
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
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19
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Mountoufaris G, Canzio D, Nwakeze CL, Chen WV, Maniatis T. Writing, Reading, and Translating the Clustered Protocadherin Cell Surface Recognition Code for Neural Circuit Assembly. Annu Rev Cell Dev Biol 2019; 34:471-493. [PMID: 30296392 DOI: 10.1146/annurev-cellbio-100616-060701] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability of neurites of individual neurons to distinguish between themselves and neurites from other neurons and to avoid self (self-avoidance) plays a key role in neural circuit assembly in both invertebrates and vertebrates. Similarly, when individual neurons of the same type project into receptive fields of the brain, they must avoid each other to maximize target coverage (tiling). Counterintuitively, these processes are driven by highly specific homophilic interactions between cell surface proteins that lead to neurite repulsion rather than adhesion. Among these proteins in vertebrates are the clustered protocadherins (Pcdhs), and key to their function is the generation of enormous cell surface structural diversity. Here we review recent advances in understanding how a Pcdh cell surface code is generated by stochastic promoter choice; how this code is amplified and read by homophilic interactions between Pcdh complexes at the surface of neurons; and, finally, how the Pcdh code is translated to cellular function, which mediates self-avoidance and tiling and thus plays a central role in the development of complex neural circuits. Not surprisingly, Pcdh mutations that diminish homophilic interactions lead to wiring defects and abnormal behavior in mice, and sequence variants in the Pcdh gene cluster are associated with autism spectrum disorders in family-based genetic studies in humans.
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Affiliation(s)
- George Mountoufaris
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA; .,Current address: Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA;
| | - Chiamaka L Nwakeze
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA;
| | - Weisheng V Chen
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA; .,Current address: Leveragen, Inc., Cambridge, Massachusetts 02139, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA;
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20
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Kim S, Wyckoff J, Morris AT, Succop A, Avery A, Duncan GE, Jazwinski SM. DNA methylation associated with healthy aging of elderly twins. GeroScience 2018; 40:469-484. [PMID: 30136078 PMCID: PMC6294724 DOI: 10.1007/s11357-018-0040-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/09/2018] [Indexed: 12/21/2022] Open
Abstract
Variation in healthy aging and lifespan is ascribed more to various non-genetic factors than to inherited genetic determinants, and a major goal in aging research is to reveal the epigenetic basis of aging. One approach to this goal is to find genomic sites or regions where DNA methylation correlates with biological age. Using health data from 134 elderly twins, we calculated a frailty index as a quantitative indicator of biological age, and by applying the Infinium HumanMethylation450K BeadChip technology to their leukocyte DNA samples, we obtained quantitative DNA methylation data on genome-wide CpG sites. We analyzed the health and epigenome data by taking two independent associative approaches: the parametric regression-based approach and a non-parametric machine learning approach followed by GO ontology analysis. Our results indicate that DNA methylation at CpG sites in the promoter region of PCDHGA3 is associated with biological age. PCDHGA3 belongs to clustered protocadherin genes, which are all located in a single locus on chromosome 5 in human. Previous studies of the clustered protocadherin genes showed that (1) DNA methylation is associated with age or age-related phenotypes; (2) DNA methylation can modulate gene expression; (3) dysregulated gene expression is associated with various pathologies; and (4) DNA methylation patterns at this locus are associated with adverse lifetime experiences. All these observations suggest that DNA methylation at the clustered protocadherin genes, including PCDHGA3, is a key mediator of healthy aging.
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Affiliation(s)
- Sangkyu Kim
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.
| | - Jennifer Wyckoff
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Anne-T Morris
- Virginia Commonwealth University, Mid-Atlantic Twin Registry, Richmond, VA, USA
| | | | - Ally Avery
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - Glen E Duncan
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
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21
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Kaur G, Helmer RA, Smith LA, Martinez-Zaguilan R, Dufour JM, Chilton BS. Alternative splicing of helicase-like transcription factor (Hltf): Intron retention-dependent activation of immune tolerance at the feto-maternal interface. PLoS One 2018; 13:e0200211. [PMID: 29975766 PMCID: PMC6033450 DOI: 10.1371/journal.pone.0200211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Hltf is regulated by intron retention, and global Hltf-deletion causes perinatal lethality from hypoglycemia. In heart, full-length Hltf is a transcriptional regulator of Hif-1α that controls transport systems. Thus, we tested the hypothesis that Hltf deletion from placenta caused or exacerbated neonatal hypoglycemia via Hif-1α regulation of nutrient transporters. RNA-seq data analyses identified significant changes in transcript expression and alternative splicing (AS) in E18.5 placentome. iPathwayGuide was used for gene ontology (GO) analysis of biological processes, molecular functions and cellular components. Elim pruning algorithm identified hierarchical relationships. The methylome was interrogated by Methyl-MiniSeq Epiquest analysis. GO analysis identified gene enrichment within biological processes. Protein expression was visualized with immunohistochemistry. Although two Hltf mRNA isoforms are quantifiable in most murine tissues, only the truncated Hltf isoform is expressed in placenta. The responsible intron retention event occurs in the absence of DNA methylation. iPathwayGuide analysis identified 157 target genes of 11,538 total genes with measured expression. These were obtained using a threshold of 0.05 for statistical significance (p-value) and a long fold change of expression with absolute value of at least 0.6. Hltf deletion altered transcription of trophoblast lineage-specific genes, and increased transcription of the Cxcr7 (p = 0.004) gene whose protein product is a co-receptor for human and simian immunodeficiency viruses. Concomitant increased Cxcr7 protein was identified with immunolabeling. Hltf deletion had no effect on transcription or site-specific methylation patterns of Hif-1α, the major glucose transporters, or System A amino acid transporters. There was no measureable evidence of uteroplacental dysfunction or fetal compromise. iPathGuide analysis revealed Hltf suppresses cytolysis (10/21 genes; p-value 1.900e-12; p-value correction: Elim pruning; GO:019835) including the perforin-granzyme pathway in uterine natural killer cells. Our findings 1) prove the truncated Hltf protein isoform is a transcription factor, 2) establish a functional link between AS of Hltf and immunosuppression at the feto-maternal interface, 3) correlate intron retention with the absence of DNA methylation, and 4) underscore the importance of differential splicing analysis to identify Hltf's functional diversity.
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Affiliation(s)
- Gurvinder Kaur
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Lisa A. Smith
- Department of Pathology, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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22
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Ing-Esteves S, Kostadinov D, Marocha J, Sing AD, Joseph KS, Laboulaye MA, Sanes JR, Lefebvre JL. Combinatorial Effects of Alpha- and Gamma-Protocadherins on Neuronal Survival and Dendritic Self-Avoidance. J Neurosci 2018; 38:2713-2729. [PMID: 29439167 PMCID: PMC5852656 DOI: 10.1523/jneurosci.3035-17.2018] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/12/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
The clustered protocadherins (Pcdhs) comprise 58 cadherin-related proteins encoded by three tandemly arrayed gene clusters, Pcdh-α, Pcdh-β, and Pcdh-γ (Pcdha, Pcdhb, and Pcdhg, respectively). Pcdh isoforms from different clusters are combinatorially expressed in neurons. They form multimers that interact homophilically and mediate a variety of developmental processes, including neuronal survival, synaptic maintenance, axonal tiling, and dendritic self-avoidance. Most studies have analyzed clusters individually. Here, we assessed functional interactions between Pcdha and Pcdhg clusters. To circumvent neonatal lethality associated with deletion of Pcdhgs, we used Crispr-Cas9 genome editing in mice to combine a constitutive Pcdha mutant allele with a conditional Pcdhg allele. We analyzed roles of Pcdhas and Pcdhgs in the retina and cerebellum from mice (both sexes) lacking one or both clusters. In retina, Pcdhgs are essential for survival of inner retinal neurons and dendritic self-avoidance of starburst amacrine cells, whereas Pcdhas are dispensable for both processes. Deletion of both Pcdha and Pcdhg clusters led to far more dramatic defects in survival and self-avoidance than Pcdhg deletion alone. Comparisons of an allelic series of mutants support the conclusion that Pcdhas and Pcdhgs function together in a dose-dependent and cell-type-specific manner to provide a critical threshold of Pcdh activity. In the cerebellum, Pcdhas and Pcdhgs also cooperate to mediate self-avoidance of Purkinje cell dendrites, with modest but significant defects in either single mutant and dramatic defects in the double mutant. Together, our results demonstrate complex patterns of redundancy between Pcdh clusters and the importance of Pcdh cluster diversity in postnatal CNS development.SIGNIFICANCE STATEMENT The formation of neural circuits requires diversification and combinatorial actions of cell surface proteins. Prominent among them are the clustered protocadherins (Pcdhs), a family of ∼60 neuronal recognition molecules. Pcdhs are encoded by three closely linked gene clusters called Pcdh-α, Pcdh-β, and Pcdh-γ. The Pcdhs mediate a variety of developmental processes, including neuronal survival, synaptic maintenance, and spatial patterning of axons and dendrites. Most studies to date have been limited to single clusters. Here, we used genome editing to assess interactions between Pcdh-α and Pcdh-γ gene clusters. We examined two regions of the CNS, the retina and cerebellum and show that the 14 α-Pcdhs and 22 γ-Pcdhs act synergistically to mediate neuronal survival and dendrite patterning.
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Affiliation(s)
- Samantha Ing-Esteves
- Program for Neurosciences and Mental Health, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada and
| | - Dimitar Kostadinov
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
| | - Julie Marocha
- Program for Neurosciences and Mental Health, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada and
| | - Anson D Sing
- Program for Neurosciences and Mental Health, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada and
| | - Kezia S Joseph
- Program for Neurosciences and Mental Health, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada and
| | - Mallory A Laboulaye
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
| | - Julie L Lefebvre
- Program for Neurosciences and Mental Health, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada and
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
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23
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Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family. EBioMedicine 2018; 28:168-179. [PMID: 29409727 PMCID: PMC5835549 DOI: 10.1016/j.ebiom.2017.12.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9 Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A > C [p.Ile154Leu], c.541G > A [p.Ala181Thr], c.2036G > C [p.Arg679Pro] and c.2059A > G [p.Lys687Glu]) result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading. A set of seventeen common variations on chr5q31.3 co-segregate with dyslexia Ancestral risk forms are conserved throughoutNeanderthals to primates while non-risks are preponderant in modern humans p.Ile154Leu and p.Ala181Thr, present in interacting interface of EC2: EC3 Species specific isoform identity of p.Ile154Leu, p.Arg679Pro and p.Lys687Glu
Worldwide epidemiological data suggests that one in every ten children is affected with dyslexia which is an alarming number and possesses a serious burden on mental health. We identified single nucleotide variations on protocadherin gamma (PCDHG) gene cluster co-segregate with dyslexia in a multiincident family. The described variants present on the interacting domain of protocadherin gamma reiterates the underlying dysregulated functional connectivity in dyslexia pathophysiology. This finding may help toward understanding the basic molecular mechanisms of dyslexia, and may help in identifying points of therapeutic intervention.
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24
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Dantoft W, Martínez-Vicente P, Jafali J, Pérez-Martínez L, Martin K, Kotzamanis K, Craigon M, Auer M, Young NT, Walsh P, Marchant A, Angulo A, Forster T, Ghazal P. Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses. Front Immunol 2017; 8:1146. [PMID: 28993767 PMCID: PMC5622154 DOI: 10.3389/fimmu.2017.01146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/30/2017] [Indexed: 12/12/2022] Open
Abstract
Neonates and especially premature infants are highly susceptible to infection but still can have a remarkable resilience that is poorly understood. The view that neonates have an incomplete or deficient immune system is changing. Human neonatal studies are challenging, and elucidating host protective responses and underlying cognate pathway biology, in the context of viral infection in early life, remains to be fully explored. In both resource rich and poor settings, human cytomegalovirus (HCMV) is the most common cause of congenital infection. By using unbiased systems analyses of transcriptomic resources for HCMV neonatal infection, we find the systemic response of a preterm congenital HCMV infection, involves a focused IFN regulatory response associated with dendritic cells. Further analysis of transcriptional-programming of neonatal dendritic cells in response to HCMV infection in culture revealed an early dominant IFN-chemokine regulatory subnetworks, and at later times the plasticity of pathways implicated in cell-cycle control and lipid metabolism. Further, we identify previously unknown suppressed networks associated with infection, including a select group of GPCRs. Functional siRNA viral growth screen targeting 516-GPCRs and subsequent validation identified novel GPCR-dependent antiviral (ADORA1) and proviral (GPR146, RGS16, PTAFR, SCTR, GPR84, GPR85, NMUR2, FZ10, RDS, CCL17, and SORT1) roles. By contrast a gene family cluster of protocadherins is significantly differentially induced in neonatal cells, suggestive of possible immunomodulatory roles. Unexpectedly, programming responses of adult and neonatal dendritic cells, upon HCMV infection, demonstrated comparable quantitative and qualitative responses showing that functionally, neonatal dendritic cell are not overly compromised. However, a delay in responses of neonatal cells for IFN subnetworks in comparison with adult-derived cells are notable, suggestive of subtle plasticity differences. These findings support a set-point control mechanism rather than immaturity for explaining not only neonatal susceptibility but also resilience to infection. In summary, our findings show that neonatal HCMV infection leads to a highly plastic and functional robust programming of dendritic cells in vivo and in vitro. In comparison with adults, a minimal number of subtle quantitative and temporal differences may contribute to variability in host susceptibility and resilience, in a context dependent manner.
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Affiliation(s)
- Widad Dantoft
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Pablo Martínez-Vicente
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - James Jafali
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lara Pérez-Martínez
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Quantitative Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kim Martin
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Synexa Life Sciences, Cape Town, South Africa
| | - Konstantinos Kotzamanis
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Marie Craigon
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Manfred Auer
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.,SynthSys-Centre for Synthetic and Systems Biology, School of Engineering, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil T Young
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Paul Walsh
- NSilico Life Science and Department of Computing, Institute of Technology, Cork, Ireland
| | - Arnaud Marchant
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Thorsten Forster
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Ghazal
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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25
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Mah KM, Weiner JA. Regulation of Wnt signaling by protocadherins. Semin Cell Dev Biol 2017; 69:158-171. [PMID: 28774578 PMCID: PMC5586504 DOI: 10.1016/j.semcdb.2017.07.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/21/2017] [Accepted: 07/28/2017] [Indexed: 12/23/2022]
Abstract
The ∼70 protocadherins comprise the largest group within the cadherin superfamily. Their diversity, the complexity of the mechanisms through which their genes are regulated, and their many critical functions in nervous system development have engendered a growing interest in elucidating the intracellular signaling pathways through which they act. Recently, multiple protocadherins across several subfamilies have been implicated as modulators of Wnt signaling pathways, and through this as potential tumor suppressors. Here, we review the extant data on the regulation by protocadherins of Wnt signaling pathways and components, and highlight some key unanswered questions that could shape future research.
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Affiliation(s)
- Kar Men Mah
- Department of Biology, The University of Iowa, Iowa City, IA, USA.
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, IA, USA; Department of Psychiatry, The University of Iowa, Iowa City, IA, USA; Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, USA.
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26
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Hirayama T, Yagi T. Regulation of clustered protocadherin genes in individual neurons. Semin Cell Dev Biol 2017; 69:122-130. [PMID: 28591566 DOI: 10.1016/j.semcdb.2017.05.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 02/06/2023]
Abstract
Individual neurons are basic functional units in the complex system of the brain. One aspect of neuronal individuality is generated by stochastic and combinatorial expression of diverse clustered protocadherins (Pcdhs), encoded by the Pcdha, Pcdhb, and Pcdhg gene clusters, that are critical for several aspects of neural circuit formation. Each clustered Pcdh gene has its own promoter containing conserved sequences and is transcribed by a promoter choice mechanism involving interaction between the promoter and enhancers. A CTCF/Cohesin complex induces this interaction by configuration of DNA-looping in the chromatin structure. At the same time, the semi-stochastic expression of clustered Pcdh genes is regulated in individual neurons by DNA methylation: the methyltransferase Dnmt3b regulates methylation state of individual clustered Pcdh genes during early embryonic stages prior to the establishment of neural stem cells. Several other factors, including Smchd1, also contribute to the regulation of clustered Pcdh gene expression. In addition, psychiatric diseases and early life experiences of individuals can influence expression of clustered Pcdh genes in the brain, through epigenetic alterations. Clustered Pcdh gene expression is thus a significant and highly regulated step in establishing neuronal individuality and generating functional neural circuits in the brain.
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Affiliation(s)
- Teruyoshi Hirayama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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