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Dando O, McQueen J, Burr K, Kind PC, Chandran S, Hardingham GE, Qiu J. A comparison of basal and activity-dependent exon splicing in cortical-patterned neurons of human and mouse origin. Front Mol Neurosci 2024; 17:1392408. [PMID: 39268251 PMCID: PMC11390650 DOI: 10.3389/fnmol.2024.1392408] [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: 02/27/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024] Open
Abstract
Rodent studies have shown that alternative splicing in neurons plays important roles in development and maturity, and is regulatable by signals such as electrical activity. However, rodent-human similarities are less well explored. We compared basal and activity-dependent exon splicing in cortical-patterned human ESC-derived neurons with that in cortical mouse ESC-derived neurons, primary mouse cortical neurons at two developmental stages, and mouse hippocampal neurons, focussing on conserved orthologous exons. Both basal exon inclusion levels and activity-dependent changes in splicing showed human-mouse correlation. Conserved activity regulated exons are enriched in RBFOX, SAM68, NOVA and PTBP targets, and centered on cytoskeletal organization, mRNA processing, and synaptic signaling genes. However, human-mouse correlations were weaker than inter-mouse comparisons of neurons from different brain regions, developmental stages and origin (ESC vs. primary), suggestive of some inter-species divergence. The set of genes where activity-dependent splicing was observed only in human neurons were dominated by those involved in lipid biosynthesis, signaling and trafficking. Study of human exon splicing in mouse Tc1 neurons carrying human chromosome-21 showed that neuronal basal exon inclusion was influenced by cis-acting sequences, although may not be sufficient to confer activity-responsiveness in an allospecific environment. Overall, these comparisons suggest that neuronal alternative splicing should be confirmed in a human-relevant system even when exon structure is evolutionarily conserved.
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Affiliation(s)
- Owen Dando
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, United Kingdom
| | - Jamie McQueen
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, United Kingdom
| | - Karen Burr
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter C Kind
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharthan Chandran
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Centre for Clinical Brain Sciences, Edinburgh Medical School, Edinburgh, United Kingdom
| | - Giles E Hardingham
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, United Kingdom
| | - Jing Qiu
- Edinburgh Medical School, UK Dementia Research Institute at the University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, United Kingdom
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Mazuecos L, Artigas-Jerónimo S, Pintado C, Gómez O, Rubio B, Arribas C, Andrés A, Villar M, Gallardo N. Central leptin signaling deficiency induced by leptin receptor antagonist leads to hypothalamic proteomic remodeling. Life Sci 2024; 346:122649. [PMID: 38626868 DOI: 10.1016/j.lfs.2024.122649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
AIMS Leptin irresponsiveness, which is often associated with obesity, can have significant impacts on the hypothalamic proteome of individuals, including those who are lean. While mounting evidence on leptin irresponsiveness has focused on obese individuals, understanding the early molecular and proteomic changes associated with deficient hypothalamic leptin signaling in lean individuals is essential for early intervention and prevention of metabolic disorders. Leptin receptor antagonists block the binding of leptin to its receptors, potentially reducing its effects and used in cases where excessive leptin activity might be harmful. MATERIALS AND METHODS In this work, we blocked the central actions of leptin in lean male adult Wistar rat by chronically administering intracerebroventricularly the superactive leptin receptor antagonist (SLA) (D23L/L39A/D40A/F41A) and investigated its impact on the hypothalamic proteome using label-free sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for quantitative proteomics. KEY FINDINGS Our results show an accumulation of proteins involved in mRNA processing, mRNA stability, and translation in the hypothalamus of SLA-treated rats. Conversely, hypothalamic leptin signaling deficiency reduces the representation of proteins implicated in energy metabolism, neural circuitry, and neurotransmitter release. SIGNIFICANCE The alterations in the adult rat hypothalamic proteome contribute to dysregulate appetite, metabolism, and energy balance, which are key factors in the development and progression of obesity and related metabolic disorders. Additionally, using bioinformatic analysis, we identified a series of transcription factors that are potentially involved in the upstream regulatory mechanisms responsible for the observed signature.
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Affiliation(s)
- Lorena Mazuecos
- Biochemistry Section, Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Sara Artigas-Jerónimo
- Biochemistry Section, Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Cristina Pintado
- Biochemistry Section, Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Oscar Gómez
- Biochemistry Section, Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Blanca Rubio
- Biochemistry Section, Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Carmen Arribas
- Biochemistry Section, Faculty of Environmental Sciences and Biochemistry, University of Castilla-La Mancha, Avda. Carlos III s/n, 45071 Toledo, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Antonio Andrés
- Biochemistry Section, Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain
| | - Margarita Villar
- Biochemistry Section, Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain; SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain.
| | - Nilda Gallardo
- Biochemistry Section, Faculty of Sciences and Chemical Technologies, University of Castilla-La Mancha, Avda. Camilo Jose Cela 10, 13071 Ciudad Real, Spain; DOE, Regional Center for Biomedical Research (CRIB), Castilla-La Mancha, Spain.
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Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
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Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
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Bhat VD, Jayaraj J, Babu K. RNA and neuronal function: the importance of post-transcriptional regulation. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac011. [PMID: 38596700 PMCID: PMC10913846 DOI: 10.1093/oons/kvac011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/03/2022] [Accepted: 05/28/2022] [Indexed: 04/11/2024]
Abstract
The brain represents an organ with a particularly high diversity of genes that undergo post-transcriptional gene regulation through multiple mechanisms that affect RNA metabolism and, consequently, brain function. This vast regulatory process in the brain allows for a tight spatiotemporal control over protein expression, a necessary factor due to the unique morphologies of neurons. The numerous mechanisms of post-transcriptional regulation or translational control of gene expression in the brain include alternative splicing, RNA editing, mRNA stability and transport. A large number of trans-elements such as RNA-binding proteins and micro RNAs bind to specific cis-elements on transcripts to dictate the fate of mRNAs including its stability, localization, activation and degradation. Several trans-elements are exemplary regulators of translation, employing multiple cofactors and regulatory machinery so as to influence mRNA fate. Networks of regulatory trans-elements exert control over key neuronal processes such as neurogenesis, synaptic transmission and plasticity. Perturbations in these networks may directly or indirectly cause neuropsychiatric and neurodegenerative disorders. We will be reviewing multiple mechanisms of gene regulation by trans-elements occurring specifically in neurons.
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Affiliation(s)
- Vandita D Bhat
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Jagannath Jayaraj
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Kavita Babu
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
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Usui N, Tian X, Harigai W, Togawa S, Utsunomiya R, Doi T, Miyoshi K, Shinoda K, Tanaka J, Shimada S, Katayama T, Yoshimura T. Length impairments of the axon initial segment in rodent models of attention-deficit hyperactivity disorder and autism spectrum disorder. Neurochem Int 2021; 153:105273. [PMID: 34971749 DOI: 10.1016/j.neuint.2021.105273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/25/2022]
Abstract
The axon initial segment (AIS) is a structural neuronal compartment of the proximal axon that plays key roles in sodium channel clustering, action potential initiation, and signal propagation of neuronal outputs. Mutations in constitutive genes of the AIS, such as ANK3, have been identified in patients with neurodevelopmental disorders. Nevertheless, morphological changes in the AIS in neurodevelopmental disorders have not been characterized. In this study, we investigated the length of the AIS in rodent models of attention-deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). We observed abnormalities in AIS length in both animal models. In ADHD model rodents, we observed shorter AIS length in layer 2/3 (L2/3) neurons of the medial prefrontal cortex (mPFC) and primary somatosensory barrel field (S1BF). Further, we observed shorter AIS length in S1BF L5 neurons. In ASD model mice, we observed shorter AIS length in L2/3 and L5 neurons of the S1BF. These results suggest that impairments in AIS length are common phenomena in neurodevelopmental disorders such as ADHD and ASD and may be conserved across species. Our findings provide novel insight into the potential contribution of the AIS to the pathophysiology and pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, 565-0871, Japan; United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Suita, 565-0871, Japan; Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Hirakata, 573-0022, Japan.
| | - Xiaoye Tian
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan
| | - Wakana Harigai
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan
| | - Shogo Togawa
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, 565-0871, Japan; Division of Neuroanatomy, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, Yamaguchi, 755-8505, Japan
| | - Ryo Utsunomiya
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Ehime, 791-0295, Japan
| | - Tomomi Doi
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Ehime, 791-0295, Japan
| | - Ko Miyoshi
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan
| | - Koh Shinoda
- Division of Neuroanatomy, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, Yamaguchi, 755-8505, Japan
| | - Junya Tanaka
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Ehime, 791-0295, Japan
| | - Shoichi Shimada
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, 565-0871, Japan; United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan; Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Hirakata, 573-0022, Japan
| | - Taiichi Katayama
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan
| | - Takeshi Yoshimura
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan.
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Li J, Chen K, Zhu R, Zhang M. Structural Basis Underlying Strong Interactions between Ankyrins and Spectrins. J Mol Biol 2020; 432:3838-3850. [DOI: 10.1016/j.jmb.2020.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023]
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