1
|
Gao Y, Shonai D, Trn M, Zhao J, Soderblom EJ, Garcia-Moreno SA, Gersbach CA, Wetsel WC, Dawson G, Velmeshev D, Jiang YH, Sloofman LG, Buxbaum JD, Soderling SH. Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions. Nat Commun 2024; 15:6801. [PMID: 39122707 PMCID: PMC11316102 DOI: 10.1038/s41467-024-51037-x] [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: 02/20/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
One of the main drivers of autism spectrum disorder is risk alleles within hundreds of genes, which may interact within shared but unknown protein complexes. Here we develop a scalable genome-editing-mediated approach to target 14 high-confidence autism risk genes within the mouse brain for proximity-based endogenous proteomics, achieving the identification of high-specificity spatial proteomes. The resulting native proximity proteomes are enriched for human genes dysregulated in the brain of autistic individuals, and reveal proximity interactions between proteins from high-confidence risk genes with those of lower-confidence that may provide new avenues to prioritize genetic risk. Importantly, the datasets are enriched for shared cellular functions and genetic interactions that may underlie the condition. We test this notion by spatial proteomics and CRISPR-based regulation of expression in two autism models, demonstrating functional interactions that modulate mechanisms of their dysregulation. Together, these results reveal native proteome networks in vivo relevant to autism, providing new inroads for understanding and manipulating the cellular drivers underpinning its etiology.
Collapse
Affiliation(s)
- Yudong Gao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Daichi Shonai
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Matthew Trn
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jieqing Zhao
- Department of Biology, Duke University, Durham, NC, USA
| | - Erik J Soderblom
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, NC, USA
| | | | - Charles A Gersbach
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - William C Wetsel
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Geraldine Dawson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Dmitry Velmeshev
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Laura G Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
2
|
Sharma N, Narang V, Sood A, Midha V, Senapati S. Reduced expression of Ankyrin-G and E-cadherin in duodenal mucosal biopsy of subjects with celiac disease. Pathol Res Pract 2024; 255:155164. [PMID: 38324966 DOI: 10.1016/j.prp.2024.155164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/09/2024]
Abstract
Confirmatory diagnosis of celiac disease (CD) include histopathology of duodenal biopsy and tissue trans-glutaminase-IgA. Identification of tissue-specific histological markers is warranted to improve the diagnosis. A genetic study in CD identified the association of ankyrin-G that connects E-cadherin with β2-spectrin in epithelial cells of the duodenal tissue. We attempted to investigate the differential expression of ankyrin-G, E-cadherin and β2-spectrin in duodenal biopsy of CD subjects compared to non-CD controls. Duodenal tissue was collected from 83 study participants, of which 50 were CD, and 33 were non-CD controls. Whole RNA was isolated from 32 CD and 23 non-CD controls from available tissues, and differential mRNA expression was measured using real-time PCR. Tissue sections from 18 CD cases and 10 non-CD controls were immunostained using monoclonal antibodies. Tissue immunohistochemistry were evaluated for differential expression and pattern of expression. RT-PCR revealed significantly reduced expression of ankyrin-G (fold change=0.63; p=0.03) and E-cadherin (fold change=0.50; p=0.02) among CD subjects compared to non-CD controls. Tissue immunohistochemistry confirmed the reduced expression of ankyrin-G and E-cadherin in CD. Differential expression is grossly limited within the outer columnar epithelial cell layer. Expression fold change of E-cadherin was seen to partially correlate with the serum tTG level (r=0.4; p=0.04). In CD, reduced expression of two key cytoskeletal proteins (ankyrin-G and E-cadherin) in duodenum mucosa was observed, which indicates its implication in disease biology and could be tested as a tissue-specific biomarker for CD. Functional studies may unravel the specific contribution of these proteins in CD pathophysiology.
Collapse
Affiliation(s)
- Nidhi Sharma
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Ghudda-151401, Bathinda, Punjab, India
| | - Vikram Narang
- Department of Pathology, Dayanand Medical College and Hospital, Ludhiana 141001, Punjab, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana 141001, Punjab, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana 141001, Punjab, India
| | - Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Ghudda-151401, Bathinda, Punjab, India.
| |
Collapse
|
3
|
Mulligan MR, Bicknell LS. The molecular genetics of nELAVL in brain development and disease. Eur J Hum Genet 2023; 31:1209-1217. [PMID: 37697079 PMCID: PMC10620143 DOI: 10.1038/s41431-023-01456-z] [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: 07/06/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Embryonic development requires tight control of gene expression levels, activity, and localisation. This control is coordinated by multiple levels of regulation on DNA, RNA and protein. RNA-binding proteins (RBPs) are recognised as key regulators of post-transcriptional gene regulation, where their binding controls splicing, polyadenylation, nuclear export, mRNA stability, translation rate and decay. In brain development, the ELAVL family of RNA binding proteins undertake essential functions across spatiotemporal windows to help regulate and specify transcriptomic programmes for cell specialisation. Despite their recognised importance in neural tissues, their molecular roles and connections to pathology are less explored. Here we provide an overview of the neuronal ELAVL family, noting commonalities and differences amongst different species, their molecular characteristics, and roles in the cell. We bring together the available molecular genetics evidence to link different ELAVL proteins to phenotypes and disease, in both the brain and beyond, including ELAVL2, which is the least studied ELAVL family member. We find that ELAVL-related pathology shares a common neurological theme, but different ELAVL proteins are more strongly connected to different phenotypes, reflecting their specialised expression across time and space.
Collapse
Affiliation(s)
- Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
4
|
Yang Y, Booker SA, Clegg JM, Quintana-Urzainqui I, Sumera A, Kozic Z, Dando O, Martin Lorenzo S, Herault Y, Kind PC, Price DJ, Pratt T. Identifying foetal forebrain interneurons as a target for monogenic autism risk factors and the polygenic 16p11.2 microdeletion. BMC Neurosci 2023; 24:5. [PMID: 36658491 PMCID: PMC9850541 DOI: 10.1186/s12868-022-00771-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Autism spectrum condition or 'autism' is associated with numerous genetic risk factors including the polygenic 16p11.2 microdeletion. The balance between excitatory and inhibitory neurons in the cerebral cortex is hypothesised to be critical for the aetiology of autism making improved understanding of how risk factors impact on the development of these cells an important area of research. In the current study we aim to combine bioinformatics analysis of human foetal cerebral cortex gene expression data with anatomical and electrophysiological analysis of a 16p11.2+/- rat model to investigate how genetic risk factors impact on inhibitory neuron development. METHODS We performed bioinformatics analysis of single cell transcriptomes from gestational week (GW) 8-26 human foetal prefrontal cortex and anatomical and electrophysiological analysis of 16p11.2+/- rat cerebral cortex and hippocampus at post-natal day (P) 21. RESULTS We identified a subset of human interneurons (INs) first appearing at GW23 with enriched expression of a large fraction of risk factor transcripts including those expressed from the 16p11.2 locus. This suggests the hypothesis that these foetal INs are vulnerable to mutations causing autism. We investigated this in a rat model of the 16p11.2 microdeletion. We found no change in the numbers or position of either excitatory or inhibitory neurons in the somatosensory cortex or CA1 of 16p11.2+/- rats but found that CA1 Sst INs were hyperexcitable with an enlarged axon initial segment, which was not the case for CA1 pyramidal cells. LIMITATIONS The human foetal gene expression data was acquired from cerebral cortex between gestational week (GW) 8 to 26. We cannot draw inferences about potential vulnerabilities to genetic autism risk factors for cells not present in the developing cerebral cortex at these stages. The analysis 16p11.2+/- rat phenotypes reported in the current study was restricted to 3-week old (P21) animals around the time of weaning and to a single interneuron cell-type while in human 16p11.2 microdeletion carriers symptoms likely involve multiple cell types and manifest in the first few years of life and on into adulthood. CONCLUSIONS We have identified developing interneurons in human foetal cerebral cortex as potentially vulnerable to monogenic autism risk factors and the 16p11.2 microdeletion and report interneuron phenotypes in post-natal 16p11.2+/- rats.
Collapse
Affiliation(s)
- Yifei Yang
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Department of Brain Sciences, Imperial College London, London, W12 0NN, United Kingdom
| | - Sam A Booker
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - James M Clegg
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - Idoia Quintana-Urzainqui
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69012, Heidelberg, Germany
| | - Anna Sumera
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - Zrinko Kozic
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - Owen Dando
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - Sandra Martin Lorenzo
- CNRS, Université de Strasbourg, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Yann Herault
- CNRS, Université de Strasbourg, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Peter C Kind
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - David J Price
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom
| | - Thomas Pratt
- Simons Initiative for the Developing Brain, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom. .,Centre for Discovery Brain Sciences, The University of Edinburgh, 15 George Square, Edinburgh, EH8 9XD, United Kingdom.
| |
Collapse
|
5
|
Nagata KI. Pathophysiological Mechanism of Neurodevelopmental Disorders-Overview. Cells 2022; 11:cells11244082. [PMID: 36552846 PMCID: PMC9776511 DOI: 10.3390/cells11244082] [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: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Technological advancements in next-generation DNA sequencing have enabled elucidation of many genetic causes of neurodevelopmental disorders (NDDs) over the last two decades [...].
Collapse
Affiliation(s)
- Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai 480-0392, Japan
| |
Collapse
|
6
|
Dziadkowiak E, Nowakowska-Kotas M, Budrewicz S, Koszewicz M. Pathology of Initial Axon Segments in Chronic Inflammatory Demyelinating Polyradiculoneuropathy and Related Disorders. Int J Mol Sci 2022; 23:13621. [PMID: 36362407 PMCID: PMC9658771 DOI: 10.3390/ijms232113621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 07/30/2023] Open
Abstract
The diagnosis of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is based on a combination of clinical, electrodiagnostic and laboratory features. The different entities of the disease include chronic immune sensory polyradiculopathy (CISP) and autoimmune nodopathies. It is debatable whether CIDP occurring in the course of other conditions, i.e., monoclonal IgG or IgA gammopathy, should be treated as a separate disease entity from idiopathic CIDP. This study aims to evaluate the molecular differences of the nodes of Ranvier and the initial axon segment (AIS) and juxtaparanode region (JXP) as the potential cause of phenotypic variation of CIDP while also seeking new pathomechanisms since JXP is sequestered behind the paranode and autoantibodies may not access the site easily. The authors initially present the structure of the different parts of the neuron and its functional significance, then discuss the problem of whether damage to the juxtaparanodal region, Schwann cells and axons could cause CIDP or if these damages should be separated as separate disease entities. In particular, AIS's importance for modulating neural excitability and carrying out transport along the axon is highlighted. The disclosure of specific pathomechanisms, including novel target antigens, in the heterogeneous CIDP syndrome is important for diagnosing and treating these patients.
Collapse
|
7
|
Alexandrov YI, Pletnikov MV. Neuronal metabolism in learning and memory: The anticipatory activity perspective. Neurosci Biobehav Rev 2022; 137:104664. [PMID: 35439520 DOI: 10.1016/j.neubiorev.2022.104664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 12/20/2022]
Abstract
Current research on the molecular mechanisms of learning and memory is based on the "stimulus-response" paradigm, in which the neural circuits connecting environmental events with behavioral responses are strengthened. By contrast, cognitive and systems neuroscience emphasize the intrinsic activity of the brain that integrates information, establishes anticipatory actions, executes adaptive actions, and assesses the outcome via regulatory feedback mechanisms. We believe that the difference in the perspectives of systems and molecular studies is a major roadblock to further progress toward understanding the mechanisms of learning and memory. Here, we briefly overview the current studies in molecular mechanisms of learning and memory and propose that studying the predictive properties of neuronal metabolism will significantly advance our knowledge of how intrinsic, predictive activity of neurons shapes a new learning event. We further suggest that predictive metabolic changes in the brain may also take place in non-neuronal cells, including those of peripheral tissues. Finally, we present a path forward toward more in-depth studies of the role of cell metabolism in learning and memory.
Collapse
Affiliation(s)
- Yuri I Alexandrov
- V. B. Shvyrkov Laboratory for the Neural Bases of the Mind, Institute of Psychology, the Russian Academy of Sciences, Moscow, Russia; Department of Psychology, Institute for Cognitive Neuroscience, HSE University, Moscow, Russia.
| | - Mikhail V Pletnikov
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| |
Collapse
|