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Pal A, Noble MA, Morales M, Pal R, Baumgartner M, Yang JW, Yim KM, Uebbing S, Noonan JP. Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600691. [PMID: 39091792 PMCID: PMC11291010 DOI: 10.1101/2024.06.25.600691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.
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Mesías RE, Zaki Y, Guevara CA, Friedman LG, Hussein A, Therrien K, Magee AR, Tzavaras N, Del Valle P, Baxter MG, Huntley GW, Benson DL. Development and cadherin-mediated control of prefrontal corticostriatal projections in mice. iScience 2023; 26:108002. [PMID: 37854688 PMCID: PMC10579443 DOI: 10.1016/j.isci.2023.108002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/07/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023] Open
Abstract
Action-outcome associations depend on prefrontal cortex (PFC) projections to the dorsal striatum. To assess how these projections form, we measured PFC axon patterning, synapse formation, and functional maturation in the postnatally developing mouse striatum. Using Hotspot analysis, we show that PFC axons form an adult-like pattern of clustered terminations in the first postnatal week that remains largely stable thereafter. PFC-striatal synaptic strength is adult-like by P21, while excitatory synapse density increases until adulthood. We then tested how the targeted deletion of a candidate adhesion/guidance protein, Cadherin-8 (Cdh8), from corticostriatal neurons regulates pathway development. Mutant mice showed diminished PFC axon targeting and reduced spontaneous glutamatergic synaptic activity in the dorsal striatum. They also exhibited impaired behavioral performance in action-outcome learning. The data show that PFC-striatal axons form striatal territories through an early, directed growth model and they highlight essential contributions of Cdh8 to the anatomical and functional features critical for the formation of action-outcome associations.
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Affiliation(s)
- Roxana E. Mesías
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yosif Zaki
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher A. Guevara
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lauren G. Friedman
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ayan Hussein
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen Therrien
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandra R. Magee
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nikolaos Tzavaras
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela Del Valle
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark G. Baxter
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - George W. Huntley
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deanna L. Benson
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Mesías RE, Zaki Y, Guevara CA, Friedman LG, Hussein A, Therrien K, Magee AR, Tzavaras N, Valle PD, Baxter MG, Huntley GW, Benson DL. Development of prefrontal corticostriatal connectivity in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532475. [PMID: 36993639 PMCID: PMC10054964 DOI: 10.1101/2023.03.14.532475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rational decision making is grounded in learning to associate actions with outcomes, a process that depends on projections from prefrontal cortex to dorsomedial striatum. Symptoms associated with a variety of human pathological conditions ranging from schizophrenia and autism to Huntington's and Parkinson's disease point toward functional deficits in this projection, but its development is not well understood, making it difficult to investigate how perturbations in development of this circuitry could contribute to pathophysiology. We applied a novel strategy based on Hotspot Analysis to assess the developmental progression of anatomical positioning of prefrontal cortex to striatal projections. Corticostriatal axonal territories established at P7 expand in concert with striatal growth but remain largely unchanged in positioning through adulthood, indicating they are generated by directed, targeted growth and not modified extensively by postnatal experience. Consistent with these findings, corticostriatal synaptogenesis increased steadily from P7 to P56, with no evidence for widescale pruning. As corticostriatal synapse density increased over late postnatal ages, the strength of evoked PFC input onto dorsomedial striatal projection neurons also increased, but spontaneous glutamatergic synaptic activity was stable. Based on its pattern of expression, we asked whether the adhesion protein, Cdh8, influenced this progression. In mice lacking Cdh8 in PFC corticostriatal projection neurons, axon terminal fields in dorsal striatum shifted ventrally. Corticostriatal synaptogenesis was unimpeded, but spontaneous EPSC frequency declined and mice failed to learn to associate an action with an outcome. Collectively these findings show that corticostriatal axons grow to their target zone and are restrained from an early age, do not undergo postnatal synapse pruning as the most dominant models predict, and that a relatively modest shift in terminal arbor positioning and synapse function has an outsized, negative impact on corticostriatal-dependent behavior.
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Wu W, Shen A, Lee I, Miranda EG, Spratt H, Pappolla M, Fang X, Bao X. Changes of tRNA-Derived Fragments by Alzheimer's Disease in Cerebrospinal Fluid and Blood Serum. J Alzheimers Dis 2023; 96:1285-1304. [PMID: 37980659 PMCID: PMC10832608 DOI: 10.3233/jad-230412] [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] [Indexed: 11/21/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common type of dementia, affecting individuals over 65. AD is also a multifactorial disease, with disease mechanisms incompletely characterized, and disease-modifying therapies are marginally effective. Biomarker signatures may shed light on the diagnosis, disease mechanisms, and the development of therapeutic targets. tRNA-derived RNA fragments (tRFs), a family of recently discovered small non-coding RNAs, have been found to be significantly enhanced in human AD hippocampus tissues. However, whether tRFs change in body fluids is unknown. OBJECTIVE To investigate whether tRFs in body fluids are impacted by AD. METHODS We first used T4 polynucleotide kinase-RNA-seq, a modified next-generation sequencing technique, to identify detectable tRFs in human cerebrospinal fluid and serum samples. The detectable tRFs were then compared in these fluids from control, AD, and mild cognitive impairment patients using tRF qRT-PCR. The stability of tRFs in serum was also investigated by checking the change in tRFs in response to protein digestion or exosome lysis. RESULTS Among various tRFs, tRF5-ProAGG seemed to be impacted by AD in both cerebrospinal fluid and serum. AD-impacted serum tRF5-ProAGG showed a correlation with the AD stage. Putative targets of tRF5-ProAGG in the hippocampus were also predicted by a computational algorithm, with some targets being validated experimentally and one of them being in a negative correlation with tRF5-ProAGG even using a small size of samples. CONCLUSIONS tRF5-ProAGG showed the potential as an AD biomarker and may play a role in disease progression.
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Affiliation(s)
- Wenzhe Wu
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, USA
| | - Audrey Shen
- Department of Human Physiology, Boston University, Boston, MA, USA
| | | | - Ernesto G. Miranda
- Department of Neurology and Mitchell Center for Neurodegenerative Diseases, The University of Texas Medical Branch, Galveston, TX
| | - Heidi Spratt
- Department of Biostatistics and Data Science, The University of Texas Medical Branch, Galveston, TX
- The Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX
| | - Miguel Pappolla
- Department of Neurology and Mitchell Center for Neurodegenerative Diseases, The University of Texas Medical Branch, Galveston, TX
| | - Xiang Fang
- Department of Neurology and Mitchell Center for Neurodegenerative Diseases, The University of Texas Medical Branch, Galveston, TX
| | - Xiaoyong Bao
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Biostatistics and Data Science, The University of Texas Medical Branch, Galveston, TX
- The Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX
- The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX
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5
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Vorperian SK, Moufarrej MN, Quake SR. Cell types of origin of the cell-free transcriptome. Nat Biotechnol 2022; 40:855-861. [PMID: 35132263 PMCID: PMC9200634 DOI: 10.1038/s41587-021-01188-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022]
Abstract
Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.
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Affiliation(s)
- Sevahn K Vorperian
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Mira N Moufarrej
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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6
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Wu N, Wang Y, Jia JY, Pan YH, Yuan XB. Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies. Neurosci Bull 2021; 38:29-46. [PMID: 34523068 PMCID: PMC8783018 DOI: 10.1007/s12264-021-00770-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022] Open
Abstract
A large number of putative risk genes for autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and causal relationships between their variation and autism traits have not been established. The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes (hcASDs). The results showed that three gene features - gene size, mRNA abundance, and guanine-cytosine content - affect the genome-wide co-expression profiles of hcASDs. To circumvent the interference of these features in gene co-expression analysis, we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as "matched-gene co-expression analysis" (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. The results of analysis of two recently-reported ASD candidate genes, CDH11 and CDH9, suggested the involvement of CDH11, but not CDH9, in ASD. Consistent with this prediction, behavioral studies showed that Cdh11-null mice, but not Cdh9-null mice, have multiple autism-like behavioral alterations. This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.
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Affiliation(s)
- Nan Wu
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yue Wang
- Hussman Institute for Autism, Baltimore, 21201, USA
| | - Jing-Yan Jia
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China.
| | - Xiao-Bing Yuan
- Key Laboratory of Brain Functional Genomics of Shanghai and the Ministry of Education, Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China. .,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, 21201, USA.
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7
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Takahashi M, Fukabori R, Kawasaki H, Kobayashi K, Kawakami K. The distribution of Cdh20 mRNA demarcates somatotopic subregions and subpopulations of spiny projection neurons in the rat dorsolateral striatum. J Comp Neurol 2021; 529:3655-3675. [PMID: 34240415 DOI: 10.1002/cne.25215] [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: 01/29/2021] [Revised: 06/21/2021] [Accepted: 07/02/2021] [Indexed: 11/07/2022]
Abstract
The dorsolateral striatum (DLS) of rodents is functionally subdivided into somatotopic subregions that represent each body part along both the dorsoventral and anteroposterior (A-P) axes and play crucial roles in sensorimotor functions via corticostriatal pathways. However, little is known about the spatial gene expression patterns and heterogeneity of spiny projection neurons (SPNs) within somatotopic subregions. Here, we show that the cell adhesion molecule gene Cdh20, which encodes a Type II cadherin, is expressed in discrete subregions covering the inner orofacial area and part of the forelimb area in the ventral domain of the DLS (v-DLS) in rats. Cdh20-expressing cells were localized in the v-DLS at the intermediate level of the striatum along the A-P axis and could be classified as direct-pathway SPNs or indirect-pathway SPNs. Unexpectedly, comprehensive analysis revealed that Cdh20 is expressed in SPNs in the rat DLS but not in the mouse DLS or the ferret putamen (Pu). Our observations reveal that Cdh20 expression demarcates somatotopic subregions and subpopulations of SPNs specifically in the rat DLS and suggest divergent regulation of genes differentially expressed in the v-DLS and Pu among mammals.
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Affiliation(s)
- Masanori Takahashi
- Graduate School of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan.,Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Ryoji Fukabori
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuto Kobayashi
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan
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Frei JA, Niescier RF, Bridi MS, Durens M, Nestor JE, Kilander MBC, Yuan X, Dykxhoorn DM, Nestor MW, Huang S, Blatt GJ, Lin YC. Regulation of Neural Circuit Development by Cadherin-11 Provides Implications for Autism. eNeuro 2021; 8:ENEURO.0066-21.2021. [PMID: 34135003 PMCID: PMC8266214 DOI: 10.1523/eneuro.0066-21.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurologic condition characterized by alterations in social interaction and communication, and restricted and/or repetitive behaviors. The classical Type II cadherins cadherin-8 (Cdh8, CDH8) and cadherin-11 (Cdh11, CDH11) have been implicated as autism risk gene candidates. To explore the role of cadherins in the etiology of autism, we investigated their expression patterns during mouse brain development and in autism-specific human tissue. In mice, expression of cadherin-8 and cadherin-11 was developmentally regulated and enriched in the cortex, hippocampus, and thalamus/striatum during the peak of dendrite formation and synaptogenesis. Both cadherins were expressed in synaptic compartments but only cadherin-8 associated with the excitatory synaptic marker neuroligin-1. Induced pluripotent stem cell (iPSC)-derived cortical neural precursor cells (NPCs) and cortical organoids generated from individuals with autism showed upregulated CDH8 expression levels, but downregulated CDH11. We used Cdh11 knock-out (KO) mice of both sexes to analyze the function of cadherin-11, which could help explain phenotypes observed in autism. Cdh11-/- hippocampal neurons exhibited increased dendritic complexity along with altered neuronal and synaptic activity. Similar to the expression profiles in human tissue, levels of cadherin-8 were significantly elevated in Cdh11 KO brains. Additionally, excitatory synaptic markers neuroligin-1 and postsynaptic density (PSD)-95 were both increased. Together, these results strongly suggest that cadherin-11 is involved in regulating the development of neuronal circuitry and that alterations in the expression levels of cadherin-11 may contribute to the etiology of autism.
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Affiliation(s)
- Jeannine A Frei
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Robert F Niescier
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Morgan S Bridi
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Madel Durens
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Jonathan E Nestor
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | | | - Xiaobing Yuan
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Science and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Michael W Nestor
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Shiyong Huang
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Gene J Blatt
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
| | - Yu-Chih Lin
- Program in Neuroscience, Hussman Institute for Autism, Baltimore, MD 21201
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9
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Sun YC, Chen X, Fischer S, Lu S, Zhan H, Gillis J, Zador AM. Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Nat Neurosci 2021; 24:873-885. [PMID: 33972801 PMCID: PMC8178227 DOI: 10.1038/s41593-021-00842-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Functional circuits consist of neurons with diverse axonal projections and gene expression. Understanding the molecular signature of projections requires high-throughput interrogation of both gene expression and projections to multiple targets in the same cells at cellular resolution, which is difficult to achieve using current technology. Here, we introduce BARseq2, a technique that simultaneously maps projections and detects multiplexed gene expression by in situ sequencing. We determined the expression of cadherins and cell-type markers in 29,933 cells and the projections of 3,164 cells in both the mouse motor cortex and auditory cortex. Associating gene expression and projections in 1,349 neurons revealed shared cadherin signatures of homologous projections across the two cortical areas. These cadherins were enriched across multiple branches of the transcriptomic taxonomy. By correlating multigene expression and projections to many targets in single neurons with high throughput, BARseq2 provides a potential path to uncovering the molecular logic underlying neuronal circuits.
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Affiliation(s)
- Yu-Chi Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiaoyin Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | | | - Shaina Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Huiqing Zhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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10
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Remnestål J, Bergström S, Olofsson J, Sjöstedt E, Uhlén M, Blennow K, Zetterberg H, Zettergren A, Kern S, Skoog I, Nilsson P, Månberg A. Association of CSF proteins with tau and amyloid β levels in asymptomatic 70-year-olds. ALZHEIMERS RESEARCH & THERAPY 2021; 13:54. [PMID: 33653397 PMCID: PMC7923505 DOI: 10.1186/s13195-021-00789-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022]
Abstract
Background Increased knowledge of the evolution of molecular changes in neurodegenerative disorders such as Alzheimer’s disease (AD) is important for the understanding of disease pathophysiology and also crucial to be able to identify and validate disease biomarkers. While several biological changes that occur early in the disease development have already been recognized, the need for further characterization of the pathophysiological mechanisms behind AD still remains. Methods In this study, we investigated cerebrospinal fluid (CSF) levels of 104 proteins in 307 asymptomatic 70-year-olds from the H70 Gothenburg Birth Cohort Studies using a multiplexed antibody- and bead-based technology. Results The protein levels were first correlated with the core AD CSF biomarker concentrations of total tau, phospho-tau and amyloid beta (Aβ42) in all individuals. Sixty-three proteins showed significant correlations to either total tau, phospho-tau or Aβ42. Thereafter, individuals were divided based on CSF Aβ42/Aβ40 ratio and Clinical Dementia Rating (CDR) score to determine if early changes in pathology and cognition had an effect on the correlations. We compared the associations of the analysed proteins with CSF markers between groups and found 33 proteins displaying significantly different associations for amyloid-positive individuals and amyloid-negative individuals, as defined by the CSF Aβ42/Aβ40 ratio. No differences in the associations could be seen for individuals divided by CDR score. Conclusions We identified a series of transmembrane proteins, proteins associated with or anchored to the plasma membrane, and proteins involved in or connected to synaptic vesicle transport to be associated with CSF biomarkers of amyloid and tau pathology in AD. Further studies are needed to explore these proteins’ role in AD pathophysiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-021-00789-5.
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Affiliation(s)
- Julia Remnestål
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Jennie Olofsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Evelina Sjöstedt
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Mathias Uhlén
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Anna Zettergren
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
| | - Silke Kern
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - Ingmar Skoog
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden.
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11
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de Agustín-Durán D, Mateos-White I, Fabra-Beser J, Gil-Sanz C. Stick around: Cell-Cell Adhesion Molecules during Neocortical Development. Cells 2021; 10:118. [PMID: 33435191 PMCID: PMC7826847 DOI: 10.3390/cells10010118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/29/2020] [Accepted: 01/07/2021] [Indexed: 12/21/2022] Open
Abstract
The neocortex is an exquisitely organized structure achieved through complex cellular processes from the generation of neural cells to their integration into cortical circuits after complex migration processes. During this long journey, neural cells need to establish and release adhesive interactions through cell surface receptors known as cell adhesion molecules (CAMs). Several types of CAMs have been described regulating different aspects of neurodevelopment. Whereas some of them mediate interactions with the extracellular matrix, others allow contact with additional cells. In this review, we will focus on the role of two important families of cell-cell adhesion molecules (C-CAMs), classical cadherins and nectins, as well as in their effectors, in the control of fundamental processes related with corticogenesis, with special attention in the cooperative actions among the two families of C-CAMs.
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Affiliation(s)
| | | | | | - Cristina Gil-Sanz
- Neural Development Laboratory, Instituto Universitario de Biomedicina y Biotecnología (BIOTECMED) and Departamento de Biología Celular, Facultat de Biología, Universidad de Valencia, 46100 Burjassot, Spain; (D.d.A.-D.); (I.M.-W.); (J.F.-B.)
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12
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Knüfer A, Diana G, Walsh GS, Clarke JD, Guthrie S. Cadherins regulate nuclear topography and function of developing ocular motor circuitry. eLife 2020; 9:56725. [PMID: 33001027 PMCID: PMC7599068 DOI: 10.7554/elife.56725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 09/30/2020] [Indexed: 12/30/2022] Open
Abstract
In the vertebrate central nervous system, groups of functionally related neurons, including cranial motor neurons of the brainstem, are frequently organised as nuclei. The molecular mechanisms governing the emergence of nuclear topography and circuit function are poorly understood. Here we investigate the role of cadherin-mediated adhesion in the development of zebrafish ocular motor (sub)nuclei. We find that developing ocular motor (sub)nuclei differentially express classical cadherins. Perturbing cadherin function in these neurons results in distinct defects in neuronal positioning, including scattering of dorsal cells and defective contralateral migration of ventral subnuclei. In addition, we show that cadherin-mediated interactions between adjacent subnuclei are critical for subnucleus position. We also find that disrupting cadherin adhesivity in dorsal oculomotor neurons impairs the larval optokinetic reflex, suggesting that neuronal clustering is important for co-ordinating circuit function. Our findings reveal that cadherins regulate distinct aspects of cranial motor neuron positioning and establish subnuclear topography and motor function.
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Affiliation(s)
- Athene Knüfer
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Giovanni Diana
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Gregory S Walsh
- Department of Biology, Virginia Commonwealth University, Richmond, United States
| | - Jonathan Dw Clarke
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Sarah Guthrie
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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13
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Shiotani H, Miyata M, Kameyama T, Mandai K, Yamasaki M, Watanabe M, Mizutani K, Takai Y. Nectin‐2α is localized at cholinergic neuron dendrites and regulates synapse formation in the medial habenula. J Comp Neurol 2020; 529:450-477. [DOI: 10.1002/cne.24958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Hajime Shiotani
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology Kobe University Graduate School of Medicine Kobe Japan
| | - Muneaki Miyata
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology Kobe University Graduate School of Medicine Kobe Japan
| | - Takeshi Kameyama
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology Kobe University Graduate School of Medicine Kobe Japan
| | - Kenji Mandai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology Kobe University Graduate School of Medicine Kobe Japan
- Department of Molecular and Cellular Neurobiology Kitasato University Graduate School of Medical Sciences Sagamihara Japan
- Department of Biochemistry Kitasato University School of Medicine Sagamihara Japan
| | - Miwako Yamasaki
- Department of Anatomy, Faculty of Medicine Hokkaido University Sapporo Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine Hokkaido University Sapporo Japan
| | - Kiyohito Mizutani
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology Kobe University Graduate School of Medicine Kobe Japan
| | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology Kobe University Graduate School of Medicine Kobe Japan
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14
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Theisen JG, Sundaram V, Filchak MS, Chorich LP, Sullivan ME, Knight J, Kim HG, Layman LC. The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants. Sci Rep 2019; 9:20099. [PMID: 31882810 PMCID: PMC6934803 DOI: 10.1038/s41598-019-53500-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
Approximately 0.5-1.4% of natal males and 0.2-0.3% of natal females meet DSM-5 criteria for gender dysphoria, with many of these individuals self-describing as transgender men or women. Despite recent improvements both in social acceptance of transgender individuals as well as access to gender affirming therapy, progress in both areas has been hampered by poor understanding of the etiology of gender dysphoria. Prior studies have suggested a genetic contribution to gender dysphoria, but previously proposed candidate genes have not yet been verified in follow-up investigation. In this study, we expand on the topic of gender identity genomics by identifying rare variants in genes associated with sexually dimorphic brain development and exploring how they could contribute to gender dysphoria. To accomplish this, we performed whole exome sequencing on the genomic DNA of 13 transgender males and 17 transgender females. Whole exome sequencing revealed 120,582 genetic variants. After filtering, 441 variants in 421 genes remained for further consideration, including 21 nonsense, 28 frameshift, 13 splice-region, and 225 missense variants. Of these, 21 variants in 19 genes were found to have associations with previously described estrogen receptor activated pathways of sexually dimorphic brain development. These variants were confirmed by Sanger Sequencing. Our findings suggest a new avenue for investigation of genes involved in estrogen signaling pathways related to sexually dimorphic brain development and their relationship to gender dysphoria.
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Affiliation(s)
- J Graham Theisen
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States.
| | - Viji Sundaram
- Section of Reproductive Endocrinology & Infertility, Department of Obstetrics & Gynecology, University of California, San Francisco, San Francisco, California, United States
| | - Mary S Filchak
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Lynn P Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Megan E Sullivan
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - James Knight
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, United States
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States.
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15
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Yang G, Shcheglovitov A. Probing disrupted neurodevelopment in autism using human stem cell-derived neurons and organoids: An outlook into future diagnostics and drug development. Dev Dyn 2019; 249:6-33. [PMID: 31398277 DOI: 10.1002/dvdy.100] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/23/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022] Open
Abstract
Autism spectrum disorders (ASDs) represent a spectrum of neurodevelopmental disorders characterized by impaired social interaction, repetitive or restrictive behaviors, and problems with speech. According to a recent report by the Centers for Disease Control and Prevention, one in 68 children in the US is diagnosed with ASDs. Although ASD-related diagnostics and the knowledge of ASD-associated genetic abnormalities have improved in recent years, our understanding of the cellular and molecular pathways disrupted in ASD remains very limited. As a result, no specific therapies or medications are available for individuals with ASDs. In this review, we describe the neurodevelopmental processes that are likely affected in the brains of individuals with ASDs and discuss how patient-specific stem cell-derived neurons and organoids can be used for investigating these processes at the cellular and molecular levels. Finally, we propose a discovery pipeline to be used in the future for identifying the cellular and molecular deficits and developing novel personalized therapies for individuals with idiopathic ASDs.
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Affiliation(s)
- Guang Yang
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah.,Neuroscience Graduate Program, University of Utah, Salt Lake City, Utah
| | - Alex Shcheglovitov
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah.,Neuroscience Graduate Program, University of Utah, Salt Lake City, Utah
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16
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Cadwell CR, Bhaduri A, Mostajo-Radji MA, Keefe MG, Nowakowski TJ. Development and Arealization of the Cerebral Cortex. Neuron 2019; 103:980-1004. [PMID: 31557462 PMCID: PMC9245854 DOI: 10.1016/j.neuron.2019.07.009] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/15/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Adult cortical areas consist of specialized cell types and circuits that support unique higher-order cognitive functions. How this regional diversity develops from an initially uniform neuroepithelium has been the subject of decades of seminal research, and emerging technologies, including single-cell transcriptomics, provide a new perspective on area-specific molecular diversity. Here, we review the early developmental processes that underlie cortical arealization, including both cortex intrinsic and extrinsic mechanisms as embodied by the protomap and protocortex hypotheses, respectively. We propose an integrated model of serial homology whereby intrinsic genetic programs and local factors establish early transcriptomic differences between excitatory neurons destined to give rise to broad "proto-regions," and activity-dependent mechanisms lead to progressive refinement and formation of sharp boundaries between functional areas. Finally, we explore the potential of these basic developmental processes to inform our understanding of the emergence of functional neural networks and circuit abnormalities in neurodevelopmental disorders.
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Affiliation(s)
- Cathryn R Cadwell
- Department of Anatomic Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94122, USA; The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mohammed A Mostajo-Radji
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94122, USA; The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew G Keefe
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA.
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17
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Fazel Darbandi S, Robinson Schwartz SE, Qi Q, Catta-Preta R, Pai ELL, Mandell JD, Everitt A, Rubin A, Krasnoff RA, Katzman S, Tastad D, Nord AS, Willsey AJ, Chen B, State MW, Sohal VS, Rubenstein JLR. Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity. Neuron 2018; 100:831-845.e7. [PMID: 30318412 PMCID: PMC6250594 DOI: 10.1016/j.neuron.2018.09.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
An understanding of how heterozygous loss-of-function mutations in autism spectrum disorder (ASD) risk genes, such as TBR1, contribute to ASD remains elusive. Conditional Tbr1 deletion during late mouse gestation in cortical layer 6 neurons (Tbr1layer6 mutants) provides novel insights into its function, including dendritic patterning, synaptogenesis, and cell-intrinsic physiology. These phenotypes occur in heterozygotes, providing insights into mechanisms that may underlie ASD pathophysiology. Restoring expression of Wnt7b largely rescues the synaptic deficit in Tbr1layer6 mutant neurons. Furthermore, Tbr1layer6 heterozygotes have increased anxiety-like behavior, a phenotype seen ASD. Integrating TBR1 chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data from layer 6 neurons and activity of TBR1-bound candidate enhancers provides evidence for how TBR1 regulates layer 6 properties. Moreover, several putative TBR1 targets are ASD risk genes, placing TBR1 in a central position both for ASD risk and for regulating transcriptional circuits that control multiple steps in layer 6 development essential for the assembly of neural circuits.
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Affiliation(s)
- Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah E Robinson Schwartz
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Qihao Qi
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey D Mandell
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anna Rubin
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca A Krasnoff
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sol Katzman
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Tastad
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew W State
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Vikaas S Sohal
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience and Sloan-Swartz Center for Theoretical Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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18
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Memi F, Killen AC, Barber M, Parnavelas JG, Andrews WD. Cadherin 8 regulates proliferation of cortical interneuron progenitors. Brain Struct Funct 2018; 224:277-292. [PMID: 30315415 PMCID: PMC6373371 DOI: 10.1007/s00429-018-1772-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/05/2018] [Indexed: 01/18/2023]
Abstract
Cortical interneurons are born in the ventral forebrain and migrate tangentially in two streams at the levels of the intermediate zone (IZ) and the pre-plate/marginal zone to the developing cortex where they switch to radial migration before settling in their final positions in the cortical plate. In a previous attempt to identify the molecules that regulate stream specification, we performed transcriptomic analysis of GFP-labelled interneurons taken from the two migratory streams during corticogenesis. A number of cadherins were found to be expressed differentially, with Cadherin-8 (Cdh8) selectively present in the IZ stream. We verified this expression pattern at the mRNA and protein levels on tissue sections and found approximately half of the interneurons of the IZ expressed Cdh8. Furthermore, this cadherin was also detected in the germinal zones of the subpallium, suggesting that it might be involved not only in the migration of interneurons but also in their generation. Quantitative analysis of cortical interneurons in animals lacking the cadherin at E18.5 revealed a significant increase in their numbers. Subsequent functional in vitro experiments showed that blocking Cdh8 function led to increased cell proliferation, with the opposite results observed with over-expression, supporting its role in interneuron generation.
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Affiliation(s)
- Fani Memi
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Abigail C Killen
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Melissa Barber
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - John G Parnavelas
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| | - William D Andrews
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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19
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Shiotani H, Miyata M, Itoh Y, Wang S, Kaito A, Mizoguchi A, Yamasaki M, Watanabe M, Mandai K, Mochizuki H, Takai Y. Localization of nectin-2α at the boundary between the adjacent somata of the clustered cholinergic neurons and its regulatory role in the subcellular localization of the voltage-gated A-type K+channel Kv4.2 in the medial habenula. J Comp Neurol 2018. [DOI: 10.1002/cne.24425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hajime Shiotani
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology; Kobe University Graduate School of Medicine; Kobe Hyogo 650-0047 Japan
- Department of Neurology; Osaka University Graduate School of Medicine; Suita Osaka 565-0871 Japan
| | - Muneaki Miyata
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology; Kobe University Graduate School of Medicine; Kobe Hyogo 650-0047 Japan
| | - Yu Itoh
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology; Kobe University Graduate School of Medicine; Kobe Hyogo 650-0047 Japan
| | - Shujie Wang
- Department of Neural Regeneration and Cell Communication; Mie University Graduate School of Medicine; Tsu Mie 514-8507 Japan
| | - Aika Kaito
- Department of Neural Regeneration and Cell Communication; Mie University Graduate School of Medicine; Tsu Mie 514-8507 Japan
| | - Akira Mizoguchi
- Department of Neural Regeneration and Cell Communication; Mie University Graduate School of Medicine; Tsu Mie 514-8507 Japan
| | - Miwako Yamasaki
- Department of Anatomy, Faculty of Medicine; Hokkaido University; Sapporo Hokkaido 060-8638 Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine; Hokkaido University; Sapporo Hokkaido 060-8638 Japan
| | - Kenji Mandai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology; Kobe University Graduate School of Medicine; Kobe Hyogo 650-0047 Japan
| | - Hideki Mochizuki
- Department of Neurology; Osaka University Graduate School of Medicine; Suita Osaka 565-0871 Japan
| | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology; Kobe University Graduate School of Medicine; Kobe Hyogo 650-0047 Japan
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20
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Altered Development of Synapse Structure and Function in Striatum Caused by Parkinson's Disease-Linked LRRK2-G2019S Mutation. J Neurosci 2017; 36:7128-41. [PMID: 27383589 DOI: 10.1523/jneurosci.3314-15.2016] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 05/26/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) can cause Parkinson's disease (PD), and the most common disease-associated mutation, G2019S, increases kinase activity. Because LRRK2 expression levels rise during synaptogenesis and are highest in dorsal striatal spiny projection neurons (SPNs), we tested the hypothesis that the LRRK2-G2019S mutation would alter development of excitatory synaptic networks in dorsal striatum. To circumvent experimental confounds associated with LRRK2 overexpression, we used mice expressing LRRK2-G2019S or D2017A (kinase-dead) knockin mutations. In whole-cell recordings, G2019S SPNs exhibited a fourfold increase in sEPSC frequency compared with wild-type SPNs in postnatal day 21 mice. Such heightened neural activity was increased similarly in direct- and indirect-pathway SPNs, and action potential-dependent activity was particularly elevated. Excitatory synaptic activity in D2017A SPNs was similar to wild type, indicating a selective effect of G2019S. Acute exposure to LRRK2 kinase inhibitors normalized activity, supporting that excessive neural activity in G2019S SPNs is mediated directly and is kinase dependent. Although dendritic arborization and densities of excitatory presynaptic terminals and postsynaptic dendritic spines in G2019S SPNs were similar to wild type, G2019S SPNs displayed larger spines that were matched functionally by a shift toward larger postsynaptic response amplitudes. Acutely isolating striatum from overlying neocortex normalized sEPSC frequency in G2019S mutants, supporting that abnormal corticostriatal activity is involved. These findings indicate that the G2019S mutation imparts a gain-of-abnormal function to SPN activity and morphology during a stage of development when activity can permanently modify circuit structure and function. SIGNIFICANCE STATEMENT Mutations in the kinase domain of leucine-rich repeat kinase 2 (LRRK2) follow Parkinson's disease (PD) heritability. How such mutations affect brain function is poorly understood. LRRK2 expression levels rise after birth at a time when synapses are forming and are highest in dorsal striatum, suggesting that LRRK2 regulates development of striatal circuits. During a period of postnatal development when activity plays a large role in permanently shaping neural circuits, our data show how the most common PD-causing LRRK2 mutation dramatically alters excitatory synaptic activity and the shape of postsynaptic structures in striatum. These findings provide new insight into early functional and structural aberrations in striatal connectivity that may predispose striatal circuitry to both motor and nonmotor dysfunction later in life.
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21
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Nibbeling EAR, Delnooz CCS, de Koning TJ, Sinke RJ, Jinnah HA, Tijssen MAJ, Verbeek DS. Using the shared genetics of dystonia and ataxia to unravel their pathogenesis. Neurosci Biobehav Rev 2017; 75:22-39. [PMID: 28143763 DOI: 10.1016/j.neubiorev.2017.01.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/09/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022]
Abstract
In this review we explore the similarities between spinocerebellar ataxias and dystonias, and suggest potentially shared molecular pathways using a gene co-expression network approach. The spinocerebellar ataxias are a group of neurodegenerative disorders characterized by coordination problems caused mainly by atrophy of the cerebellum. The dystonias are another group of neurological movement disorders linked to basal ganglia dysfunction, although evidence is now pointing to cerebellar involvement as well. Our gene co-expression network approach identified 99 shared genes and showed the involvement of two major pathways: synaptic transmission and neurodevelopment. These pathways overlapped in the two disorders, with a large role for GABAergic signaling in both. The overlapping pathways may provide novel targets for disease therapies. We need to prioritize variants obtained by whole exome sequencing in the genes associated with these pathways in the search for new pathogenic variants, which can than be used to help in the genetic counseling of patients and their families.
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Affiliation(s)
- Esther A R Nibbeling
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cathérine C S Delnooz
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Hyder A Jinnah
- Departments of Neurology, Human Genetics and Pediatrics, Emory Clinic, Atlanta, USA
| | - Marina A J Tijssen
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, The Netherlands
| | - Dineke S Verbeek
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
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22
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Lin YC, Frei JA, Kilander MBC, Shen W, Blatt GJ. A Subset of Autism-Associated Genes Regulate the Structural Stability of Neurons. Front Cell Neurosci 2016; 10:263. [PMID: 27909399 PMCID: PMC5112273 DOI: 10.3389/fncel.2016.00263] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a range of neurological conditions that affect individuals’ ability to communicate and interact with others. People with ASD often exhibit marked qualitative difficulties in social interaction, communication, and behavior. Alterations in neurite arborization and dendritic spine morphology, including size, shape, and number, are hallmarks of almost all neurological conditions, including ASD. As experimental evidence emerges in recent years, it becomes clear that although there is broad heterogeneity of identified autism risk genes, many of them converge into similar cellular pathways, including those regulating neurite outgrowth, synapse formation and spine stability, and synaptic plasticity. These mechanisms together regulate the structural stability of neurons and are vulnerable targets in ASD. In this review, we discuss the current understanding of those autism risk genes that affect the structural connectivity of neurons. We sub-categorize them into (1) cytoskeletal regulators, e.g., motors and small RhoGTPase regulators; (2) adhesion molecules, e.g., cadherins, NCAM, and neurexin superfamily; (3) cell surface receptors, e.g., glutamatergic receptors and receptor tyrosine kinases; (4) signaling molecules, e.g., protein kinases and phosphatases; and (5) synaptic proteins, e.g., vesicle and scaffolding proteins. Although the roles of some of these genes in maintaining neuronal structural stability are well studied, how mutations contribute to the autism phenotype is still largely unknown. Investigating whether and how the neuronal structure and function are affected when these genes are mutated will provide insights toward developing effective interventions aimed at improving the lives of people with autism and their families.
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Affiliation(s)
- Yu-Chih Lin
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Jeannine A Frei
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Michaela B C Kilander
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Wenjuan Shen
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Gene J Blatt
- Laboratory of Autism Neurocircuitry, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
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23
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Friedman LG, Benson DL, Huntley GW. Cadherin-based transsynaptic networks in establishing and modifying neural connectivity. Curr Top Dev Biol 2015; 112:415-65. [PMID: 25733148 DOI: 10.1016/bs.ctdb.2014.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is tacitly understood that cell adhesion molecules (CAMs) are critically important for the development of cells, circuits, and synapses in the brain. What is less clear is what CAMs continue to contribute to brain structure and function after the early period of development. Here, we focus on the cadherin family of CAMs to first briefly recap their multidimensional roles in neural development and then to highlight emerging data showing that with maturity, cadherins become largely dispensible for maintaining neuronal and synaptic structure, instead displaying new and narrower roles at mature synapses where they critically regulate dynamic aspects of synaptic signaling, structural plasticity, and cognitive function. At mature synapses, cadherins are an integral component of multiprotein networks, modifying synaptic signaling, morphology, and plasticity through collaborative interactions with other CAM family members as well as a variety of neurotransmitter receptors, scaffolding proteins, and other effector molecules. Such recognition of the ever-evolving functions of synaptic cadherins may yield insight into the pathophysiology of brain disorders in which cadherins have been implicated and that manifest at different times of life.
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Affiliation(s)
- Lauren G Friedman
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Deanna L Benson
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - George W Huntley
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
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