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Veshchitskii A, Shkorbatova P, Merkulyeva N. Neurochemical atlas of the rabbit spinal cord. Brain Struct Funct 2024; 229:2011-2027. [PMID: 39115602 DOI: 10.1007/s00429-024-02842-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/15/2024] [Indexed: 10/18/2024]
Abstract
Complex neurophysiological and morphologic experiments require suitable animal models for investigation. The rabbit is one of the most successful models for studying spinal cord functions owing to its substantial size. However, achieving precise surgical access to specific spinal regions requires a thorough understanding of the spinal cord's cytoarchitectonic structure and its spatial relationship with the vertebrae. The comprehensive anatomo-neurochemical atlases of the spinal cord are invaluable for attaining such insight. While such atlases exist for some rodents and primates, none exist for rabbits. We have developed a spinal cord atlas for rabbits to bridge this gap. Utilizing various neurochemical markers-including antibodies to NeuN, calbindin 28 kDa, parvalbumin, choline acetyltransferase, nitric oxide synthase, and non-phosphorylated heavy-chain neurofilaments (SMI-32 antibody)-we present the visualization of diverse spinal neuronal populations, various spinal cord metrics, stereotaxic maps of transverse slices for each spinal segment, and a spatial map detailing the intricate relationship between the spinal cord and the vertebrae across its entire length.
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Affiliation(s)
- Aleksandr Veshchitskii
- Neuromorphology Lab, Pavlov Institute of Physiology Russian Academy of Sciences, Saint Petersburg, Russia, 199034
| | - Polina Shkorbatova
- Neuromorphology Lab, Pavlov Institute of Physiology Russian Academy of Sciences, Saint Petersburg, Russia, 199034
| | - Natalia Merkulyeva
- Neuromorphology Lab, Pavlov Institute of Physiology Russian Academy of Sciences, Saint Petersburg, Russia, 199034.
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2
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Wu CC, Meyer DN, Haimbaugh A, Baker TR. Implications of Lead (Pb)-Induced Transcriptomic and Phenotypic Alterations in the Aged Zebrafish ( Danio rerio). TOXICS 2024; 12:745. [PMID: 39453165 PMCID: PMC11511149 DOI: 10.3390/toxics12100745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 10/10/2024] [Accepted: 10/10/2024] [Indexed: 10/26/2024]
Abstract
Lead (Pb) is a well-known neurotoxin with established adverse effects on the neurological functions of children and younger adults, including motor, learning, and memory abilities. However, its potential impact on older adults has received less attention. Using the zebrafish model, our study aims to characterize the dose-response relationship between environmentally relevant Pb exposure levels and their effects on changes in behavior and transcriptomics during the geriatric periods. We exposed two-year-old zebrafish to waterborne lead acetate (1, 10, 100, 1000, or 10,000 µg/L) or a vehicle (DMSO) for 5 days. While lower concentrations (1-100 µg/L) reflect environmentally relevant Pb levels, higher concentrations (1000-10,000 µg/L) were included to assess acute toxicity under extreme exposure scenarios. We conducted adult behavior assessment to evaluate the locomotor activity following exposure. The same individual fish were subsequently sacrificed for brain dissection after a day of recovery in the aquatic system. RNA extraction and sequencing were then performed to evaluate the Pb-induced transcriptomic changes. Higher (1000-10,000 ug/L) Pb levels induced hyperactive locomotor patterns in aged zebrafish, while lower (10-100 ug/L) Pb levels resulted in the lowest locomotor activity compared to the control group. Exposure to 100 µg/L led to the highest number of differentially expressed genes (DEGs), while 10,000 µg/L induced larger fold changes in both directions. The neurological pathways impacted by Pb exposure include functions related to neurotransmission, such as cytoskeletal regulation and synaptogenesis, and oxidative stress response, such as mitochondrial dysfunction and downregulation of heat shock protein genes. These findings emphasize a U-shape dose-response relationship with Pb concentrations in locomotor activity and transcriptomic changes in the aging brain.
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Affiliation(s)
- Chia-Chen Wu
- Institute of Environmental Engineering, National Yang Ming Chiao Tung University, 1001, Daxue Rd, East District, Hsinchu City 300093, Taiwan;
- Department of Environmental and Global Health, University of Florida, 1225 Center Drive, Gainesville, FL 32610, USA; (D.N.M.)
| | - Danielle N. Meyer
- Department of Environmental and Global Health, University of Florida, 1225 Center Drive, Gainesville, FL 32610, USA; (D.N.M.)
- Department of Pharmacology, School of Medicine, Wayne State University, 540 E. Canfield, Detroit, MI 48201, USA
| | - Alex Haimbaugh
- Department of Environmental and Global Health, University of Florida, 1225 Center Drive, Gainesville, FL 32610, USA; (D.N.M.)
- Department of Pharmacology, School of Medicine, Wayne State University, 540 E. Canfield, Detroit, MI 48201, USA
| | - Tracie R. Baker
- Department of Environmental and Global Health, University of Florida, 1225 Center Drive, Gainesville, FL 32610, USA; (D.N.M.)
- Department of Pharmacology, School of Medicine, Wayne State University, 540 E. Canfield, Detroit, MI 48201, USA
- UF Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA
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3
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Vélez-López O, Carrasquillo-Carrión K, Cantres-Rosario YM, Machín-Martínez E, Álvarez-Ríos ME, Roche-Lima A, Tosado-Rodríguez EL, Meléndez LM. Analysis of Sigma-1 Receptor Antagonist BD1047 Effect on Upregulating Proteins in HIV-1-Infected Macrophages Exposed to Cocaine Using Quantitative Proteomics. Biomedicines 2024; 12:1934. [PMID: 39335448 PMCID: PMC11428496 DOI: 10.3390/biomedicines12091934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/30/2024] Open
Abstract
HIV-1 infects monocyte-derived macrophages (MDM) that migrate into the brain and secrete virus and neurotoxic molecules, including cathepsin B (CATB), causing cognitive dysfunction. Cocaine potentiates CATB secretion and neurotoxicity in HIV-infected MDM. Pretreatment with BD1047, a sigma-1 receptor antagonist, before cocaine exposure reduces HIV-1, CATB secretion, and neuronal apoptosis. We aimed to elucidate the intracellular pathways modulated by BD1047 in HIV-infected MDM exposed to cocaine. We hypothesized that the Sig1R antagonist BD1047, prior to cocaine, significantly deregulates proteins and pathways involved in HIV-1 replication and CATB secretion that lead to neurotoxicity. MDM culture lysates from HIV-1-infected women treated with BD1047 before cocaine were compared with untreated controls using TMT quantitative proteomics, bioinformatics, Lima statistics, and pathway analyses. Results demonstrate that pretreatment with BD1047 before cocaine dysregulated eighty (80) proteins when compared with the infected cocaine group. We found fifteen (15) proteins related to HIV-1 infection, CATB, and mitochondrial function. Upregulated proteins were related to oxidative phosphorylation (SLC25A-31), mitochondria (ATP5PD), ion transport (VDAC2-3), endoplasmic reticulum transport (PHB, TMED10, CANX), and cytoskeleton remodeling (TUB1A-C, ANXA1). BD1047 treatment protects HIV-1-infected MDM exposed to cocaine by upregulating proteins that reduce mitochondrial damage, ER transport, and exocytosis associated with CATB-induced neurotoxicity.
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Affiliation(s)
- Omar Vélez-López
- Department of Microbiology and Medical Zoology, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00936, USA;
| | - Kelvin Carrasquillo-Carrión
- Integrated Informatics, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00934, USA; (K.C.-C.); (A.R.-L.); (E.L.T.-R.)
| | - Yadira M. Cantres-Rosario
- Translational Proteomics, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00921, USA;
| | - Eraysy Machín-Martínez
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00921, USA; (E.M.-M.); (M.E.Á.-R.)
| | - Manuel E. Álvarez-Ríos
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00921, USA; (E.M.-M.); (M.E.Á.-R.)
| | - Abiel Roche-Lima
- Integrated Informatics, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00934, USA; (K.C.-C.); (A.R.-L.); (E.L.T.-R.)
| | - Eduardo L. Tosado-Rodríguez
- Integrated Informatics, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00934, USA; (K.C.-C.); (A.R.-L.); (E.L.T.-R.)
| | - Loyda M. Meléndez
- Department of Microbiology and Medical Zoology, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00936, USA;
- Translational Proteomics, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00921, USA;
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4
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Mack CM, Tsui-Bowen A, Smith AR, Jensen KF, Kodavanti PRS, Moser VC, Mundy WR, Shafer TJ, Herr DW. Identification of neural-relevant toxcast high-throughput assay intended gene targets: Applicability to neurotoxicity and neurotoxicant putative molecular initiating events. Neurotoxicology 2024; 103:256-265. [PMID: 38977203 DOI: 10.1016/j.neuro.2024.07.001] [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: 04/19/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
The US EPA's Toxicity Forecaster (ToxCast) is a suite of high-throughput in vitro assays to screen environmental toxicants and predict potential toxicity of uncharacterized chemicals. This work examines the relevance of ToxCast assay intended gene targets to putative molecular initiating events (MIEs) of neurotoxicants. This effort is needed as there is growing interest in the regulatory and scientific communities about developing new approach methodologies (NAMs) to screen large numbers of chemicals for neurotoxicity and developmental neurotoxicity. Assay gene function (GeneCards, NCBI-PUBMED) was used to categorize gene target neural relevance (1 = neural, 2 = neural development, 3 = general cellular process, 3 A = cellular process critical during neural development, 4 = unlikely significance). Of 481 unique gene targets, 80 = category 1 (16.6 %); 16 = category 2 (3.3 %); 303 = category 3 (63.0 %); 97 = category 3 A (20.2 %); 82 = category 4 (17.0 %). A representative list of neurotoxicants (548) was researched (ex. PUBMED, PubChem) for neurotoxicity associated MIEs/Key Events (KEs). MIEs were identified for 375 compounds, whereas only KEs for 173. ToxCast gene targets associated with MIEs were primarily neurotransmitter (ex. dopaminergic, GABA)receptors and ion channels (calcium, sodium, potassium). Conversely, numerous MIEs associated with neurotoxicity were absent. Oxidative stress (OS) mechanisms were 79.1 % of KEs. In summary, 40 % of ToxCast assay gene targets are relevant to neurotoxicity mechanisms. Additional receptor and ion channel subtypes and increased OS pathway coverage are identified for potential future assay inclusion to provide more complete coverage of neural and developmental neural targets in assessing neurotoxicity.
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Affiliation(s)
- Cina M Mack
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | | | - Alicia R Smith
- Oak Ridge Institute for Science Education, Oak Ridge, TN 37830, USA.
| | - Karl F Jensen
- US Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Prasada Rao S Kodavanti
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Virginia C Moser
- US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - William R Mundy
- US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Timothy J Shafer
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - David W Herr
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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5
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Feng T, Du H, Yang C, Wang Y, Hu F. Loss of TMEM106B exacerbates Tau pathology and neurodegeneration in PS19 mice. Acta Neuropathol 2024; 147:62. [PMID: 38526799 DOI: 10.1007/s00401-024-02702-4] [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: 10/02/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/27/2024]
Abstract
TMEM106B, a gene encoding a lysosome membrane protein, is tightly associated with brain aging, hypomyelinating leukodystrophy, and multiple neurodegenerative diseases, including frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Recently, TMEM106B polymorphisms have been associated with tauopathy in chronic traumatic encephalopathy (CTE) and FTLD-TDP patients. However, how TMEM106B influences Tau pathology and its associated neurodegeneration, is unclear. Here we show that loss of TMEM106B enhances the accumulation of pathological Tau, especially in the neuronal soma in the hippocampus, resulting in severe neuronal loss in the PS19 Tau transgenic mice. Moreover, Tmem106b-/- PS19 mice develop significantly increased abnormalities in the neuronal cytoskeleton, autophagy-lysosome activities, as well as glial activation, compared with PS19 and Tmem106b-/- mice. Together, our findings demonstrate that loss of TMEM106B drastically exacerbates Tau pathology and its associated disease phenotypes, and provide new insights into the roles of TMEM106B in neurodegenerative diseases.
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Affiliation(s)
- Tuancheng Feng
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, 345 Weill Hall, Ithaca, NY, 14853, USA
| | - Huan Du
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, 345 Weill Hall, Ithaca, NY, 14853, USA
| | - Cha Yang
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, 345 Weill Hall, Ithaca, NY, 14853, USA
| | - Ya Wang
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, 345 Weill Hall, Ithaca, NY, 14853, USA
| | - Fenghua Hu
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, 345 Weill Hall, Ithaca, NY, 14853, USA.
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6
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Geraci J, Bhargava R, Qorri B, Leonchyk P, Cook D, Cook M, Sie F, Pani L. Machine learning hypothesis-generation for patient stratification and target discovery in rare disease: our experience with Open Science in ALS. Front Comput Neurosci 2024; 17:1199736. [PMID: 38260713 PMCID: PMC10801647 DOI: 10.3389/fncom.2023.1199736] [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: 04/03/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Advances in machine learning (ML) methodologies, combined with multidisciplinary collaborations across biological and physical sciences, has the potential to propel drug discovery and development. Open Science fosters this collaboration by releasing datasets and methods into the public space; however, further education and widespread acceptance and adoption of Open Science approaches are necessary to tackle the plethora of known disease states. Motivation In addition to providing much needed insights into potential therapeutic protein targets, we also aim to demonstrate that small patient datasets have the potential to provide insights that usually require many samples (>5,000). There are many such datasets available and novel advancements in ML can provide valuable insights from these patient datasets. Problem statement Using a public dataset made available by patient advocacy group AnswerALS and a multidisciplinary Open Science approach with a systems biology augmented ML technology, we aim to validate previously reported drug targets in ALS and provide novel insights about ALS subpopulations and potential drug targets using a unique combination of ML methods and graph theory. Methodology We use NetraAI to generate hypotheses about specific patient subpopulations, which were then refined and validated through a combination of ML techniques, systems biology methods, and expert input. Results We extracted 8 target classes, each comprising of several genes that shed light into ALS pathophysiology and represent new avenues for treatment. These target classes are broadly categorized as inflammation, epigenetic, heat shock, neuromuscular junction, autophagy, apoptosis, axonal transport, and excitotoxicity. These findings are not mutually exclusive, and instead represent a systematic view of ALS pathophysiology. Based on these findings, we suggest that simultaneous targeting of ALS has the potential to mitigate ALS progression, with the plausibility of maintaining and sustaining an improved quality of life (QoL) for ALS patients. Even further, we identified subpopulations based on disease onset. Conclusion In the spirit of Open Science, this work aims to bridge the knowledge gap in ALS pathophysiology to aid in diagnostic, prognostic, and therapeutic strategies and pave the way for the development of personalized treatments tailored to the individual's needs.
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Affiliation(s)
- Joseph Geraci
- NetraMark Corp, Toronto, ON, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
- Centre for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
- Arthur C. Clarke Center for Human Imagination, School of Physical Sciences, University of California San Diego, San Diego, CA, United States
| | - Ravi Bhargava
- Department of Biomedical and Molecular Science, Queens University, Kingston, ON, Canada
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | | | | | - Douglas Cook
- NetraMark Corp, Toronto, ON, Canada
- Department of Surgery, Queen's University, Kingston, ON, Canada
| | - Moses Cook
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fanny Sie
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | - Luca Pani
- NetraMark Corp, Toronto, ON, Canada
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Coral Gables, FL, United States
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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7
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Feng T, Du H, Hu F. Loss of TMEM106B exacerbates Tau pathology and neurodegeneration in PS19 mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566707. [PMID: 38014238 PMCID: PMC10680640 DOI: 10.1101/2023.11.11.566707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
TMEM106B, a gene encoding a lysosome membrane protein, is tightly associated with brain aging, hypomyelinating leukodystrophy, and multiple neurodegenerative diseases, including frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Recently, TMEM106B polymorphisms have been associated with tauopathy in chronic traumatic encephalopathy (CTE) and FTLD-TDP patients. However, how TMEM106B influences Tau pathology and its associated neurodegeneration, is unclear. Here we show that loss of TMEM106B enhances the accumulation of pathological Tau, especially in the neuronal soma in the hippocampus, resulting in severe neuronal loss in the PS19 Tau transgenic mice. Moreover, Tmem106b-/- PS19 mice develop significantly increased disruption of the neuronal cytoskeleton, autophagy-lysosomal function, and lysosomal trafficking along the axon as well as enhanced gliosis compared with PS19 and Tmem106b-/- mice. Together, our findings demonstrate that loss of TMEM106B drastically exacerbates Tau pathology and its associated disease phenotypes, and provide new insights into the roles of TMEM106B in neurodegenerative diseases.
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Affiliation(s)
- Tuancheng Feng
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Huan Du
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Fenghua Hu
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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8
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Zoroddu S, Sanna L, Bordoni V, Lyu W, Murineddu G, Pinna GA, Forcales SV, Sala A, Kelvin DJ, Bagella L. RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines. Int J Mol Sci 2023; 24:11263. [PMID: 37511023 PMCID: PMC10379353 DOI: 10.3390/ijms241411263] [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: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
1,3,4-Oxadiazole derivatives are among the most studied anticancer drugs. Previous studies have analyzed the action of different 1,3,4-oxadiazole derivatives and their effects on cancer cells. This study investigated the characterization of two new compounds named 6 and 14 on HeLa and PC-3 cancer cell lines. Based on the previously obtained IC50, cell cycle effects were monitored by flow cytometry. RNA sequencing (RNAseq) was performed to identify differentially expressed genes, followed by functional annotation using gene ontology (GO), KEGG signaling pathway enrichment, and protein-protein interaction (PPI) network analyses. The tubulin polymerization assay was used to analyze the interaction of both compounds with tubulin. The results showed that 6 and 14 strongly inhibited the proliferation of cancer cells by arresting them in the G2/M phase of the cell cycle. Transcriptome analysis showed that exposure of HeLa and PC-3 cells to the compounds caused a marked reprograming of gene expression. Functional enrichment analysis indicated that differentially expressed genes were significantly enriched throughout the cell cycle and cancer-related biological processes. Furthermore, PPI network, hub gene, and CMap analyses revealed that compounds 14 and 6 shared target genes with established microtubule inhibitors, indicating points of similarity between the two molecules and microtubule inhibitors in terms of the mechanism of action. They were also able to influence the polymerization process of tubulin, suggesting the potential of these new compounds to be used as efficient chemotherapeutic agents.
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Affiliation(s)
- Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Luca Sanna
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Valentina Bordoni
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Weidong Lyu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, China
| | - Gabriele Murineddu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Gerard A Pinna
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Sonia Vanina Forcales
- Department of Pathology and Experimental Therapeutics, School of Medicine, Health Science Campus of Bellvitge, University of Barcelona, Carrer de la Feixa Llarga, s/n, Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Arturo Sala
- Centre for Inflammation Research and Translational Medicine (CIRTM), Department of Life Sciences, Brunel University, London UB8 3PH, UK
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, China
- Department of Microbiology and Immunology, Dalhousie University, 6299 South St, Halifax, NS B3H 4R2, Canada
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Centre for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Zocchi R, Bellacchio E, Piccione M, Scardigli R, D’Oria V, Petrini S, Baranano K, Bertini E, Sferra A. Novel loss of function mutation in TUBA1A gene compromises tubulin stability and proteostasis causing spastic paraplegia and ataxia. Front Cell Neurosci 2023; 17:1162363. [PMID: 37435044 PMCID: PMC10332271 DOI: 10.3389/fncel.2023.1162363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Microtubules are dynamic cytoskeletal structures involved in several cellular functions, such as intracellular trafficking, cell division and motility. More than other cell types, neurons rely on the proper functioning of microtubules to conduct their activities and achieve complex morphologies. Pathogenic variants in genes encoding for α and β-tubulins, the structural subunits of microtubules, give rise to a wide class of neurological disorders collectively known as "tubulinopathies" and mainly involving a wide and overlapping range of brain malformations resulting from defective neuronal proliferation, migration, differentiation and axon guidance. Although tubulin mutations have been classically linked to neurodevelopmental defects, growing evidence demonstrates that perturbations of tubulin functions and activities may also drive neurodegeneration. In this study, we causally link the previously unreported missense mutation p.I384N in TUBA1A, one of the neuron-specific α-tubulin isotype I, to a neurodegenerative disorder characterized by progressive spastic paraplegia and ataxia. We demonstrate that, in contrast to the p.R402H substitution, which is one of the most recurrent TUBA1A pathogenic variants associated to lissencephaly, the present mutation impairs TUBA1A stability, reducing the abundance of TUBA1A available in the cell and preventing its incorporation into microtubules. We also show that the isoleucine at position 384 is an amino acid residue, which is critical for α-tubulin stability, since the introduction of the p.I384N substitution in three different tubulin paralogs reduces their protein level and assembly into microtubules, increasing their propensity to aggregation. Moreover, we demonstrate that the inhibition of the proteasome degradative systems increases the protein levels of TUBA1A mutant, promoting the formation of tubulin aggregates that, as their size increases, coalesce into inclusions that precipitate within the insoluble cellular fraction. Overall, our data describe a novel pathogenic effect of p.I384N mutation that differs from the previously described substitutions in TUBA1A, and expand both phenotypic and mutational spectrum related to this gene.
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Affiliation(s)
- Riccardo Zocchi
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Emanuele Bellacchio
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Michela Piccione
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCSS, Rome, Italy
| | - Raffaella Scardigli
- Consiglio Nazionale delle Ricerche (CNR), Institute of Translational Pharmacology (IFT), Rome, Italy
- European Brain Research Institute (EBRI) “Rita Levi-Montalcini,” Rome, Italy
| | - Valentina D’Oria
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCSS, Rome, Italy
| | - Stefania Petrini
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCSS, Rome, Italy
| | - Kristin Baranano
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Enrico Bertini
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonella Sferra
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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10
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Zocchi R, Compagnucci C, Bertini E, Sferra A. Deciphering the Tubulin Language: Molecular Determinants and Readout Mechanisms of the Tubulin Code in Neurons. Int J Mol Sci 2023; 24:ijms24032781. [PMID: 36769099 PMCID: PMC9917122 DOI: 10.3390/ijms24032781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/17/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Microtubules (MTs) are dynamic components of the cell cytoskeleton involved in several cellular functions, such as structural support, migration and intracellular trafficking. Despite their high similarity, MTs have functional heterogeneity that is generated by the incorporation into the MT lattice of different tubulin gene products and by their post-translational modifications (PTMs). Such regulations, besides modulating the tubulin composition of MTs, create on their surface a "biochemical code" that is translated, through the action of protein effectors, into specific MT-based functions. This code, known as "tubulin code", plays an important role in neuronal cells, whose highly specialized morphologies and activities depend on the correct functioning of the MT cytoskeleton and on its interplay with a myriad of MT-interacting proteins. In recent years, a growing number of mutations in genes encoding for tubulins, MT-interacting proteins and enzymes that post-translationally modify MTs, which are the main players of the tubulin code, have been linked to neurodegenerative processes or abnormalities in neural migration, differentiation and connectivity. Nevertheless, the exact molecular mechanisms through which the cell writes and, downstream, MT-interacting proteins decipher the tubulin code are still largely uncharted. The purpose of this review is to describe the molecular determinants and the readout mechanisms of the tubulin code, and briefly elucidate how they coordinate MT behavior during critical neuronal events, such as neuron migration, maturation and axonal transport.
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Affiliation(s)
- Riccardo Zocchi
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
| | - Claudia Compagnucci
- Molecular Genetics and Functional Genomics, Bambino Gesù Children’s Research Hospital, IRCCS, 00146 Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
- Correspondence: (E.B.); or (A.S.); Tel.: +39-06-6859-2104 (E.B. & A.S.)
| | - Antonella Sferra
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
- Correspondence: (E.B.); or (A.S.); Tel.: +39-06-6859-2104 (E.B. & A.S.)
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11
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Hoff KJ, Neumann AJ, Moore JK. The molecular biology of tubulinopathies: Understanding the impact of variants on tubulin structure and microtubule regulation. Front Cell Neurosci 2022; 16:1023267. [PMID: 36406756 PMCID: PMC9666403 DOI: 10.3389/fncel.2022.1023267] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Heterozygous, missense mutations in both α- and β-tubulin genes have been linked to an array of neurodevelopment disorders, commonly referred to as "tubulinopathies." To date, tubulinopathy mutations have been identified in three β-tubulin isotypes and one α-tubulin isotype. These mutations occur throughout the different genetic domains and protein structures of these tubulin isotypes, and the field is working to address how this molecular-level diversity results in different cellular and tissue-level pathologies. Studies from many groups have focused on elucidating the consequences of individual mutations; however, the field lacks comprehensive models for the molecular etiology of different types of tubulinopathies, presenting a major gap in diagnosis and treatment. This review highlights recent advances in understanding tubulin structural dynamics, the roles microtubule-associated proteins (MAPs) play in microtubule regulation, and how these are inextricably linked. We emphasize the value of investigating interactions between tubulin structures, microtubules, and MAPs to understand and predict the impact of tubulinopathy mutations at the cell and tissue levels. Microtubule regulation is multifaceted and provides a complex set of controls for generating a functional cytoskeleton at the right place and right time during neurodevelopment. Understanding how tubulinopathy mutations disrupt distinct subsets of those controls, and how that ultimately disrupts neurodevelopment, will be important for establishing mechanistic themes among tubulinopathies that may lead to insights in other neurodevelopment disorders and normal neurodevelopment.
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Affiliation(s)
| | | | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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12
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Zheng L, Liang P, Long C, Li H, Li H, Liang Y, He X, Xi Q, Xing Y, Zuo Y. EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis. Nucleic Acids Res 2022; 51:D924-D932. [PMID: 36189903 PMCID: PMC9825456 DOI: 10.1093/nar/gkac848] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/06/2022] [Accepted: 09/21/2022] [Indexed: 01/30/2023] Open
Abstract
The emerging importance of embryonic development research rapidly increases the volume for a professional resource related to multi-omics data. However, the lack of global embryogenesis repository and systematic analysis tools limits the preceding in stem cell research, human congenital diseases and assisted reproduction. Here, we developed the EmAtlas, which collects the most comprehensive multi-omics data and provides multi-scale tools to explore spatiotemporal activation during mammalian embryogenesis. EmAtlas contains data on multiple types of gene expression, chromatin accessibility, DNA methylation, nucleosome occupancy, histone modifications, and transcription factors, which displays the complete spatiotemporal landscape in mouse and human across several time points, involving gametogenesis, preimplantation, even fetus and neonate, and each tissue involves various cell types. To characterize signatures involved in the tissue, cell, genome, gene and protein levels during mammalian embryogenesis, analysis tools on these five scales were developed. Additionally, we proposed EmRanger to deliver extensive development-related biological background annotations. Users can utilize these tools to analyze, browse, visualize, and download data owing to the user-friendly interface. EmAtlas is freely accessible at http://bioinfor.imu.edu.cn/ematlas.
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Affiliation(s)
- Lei Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Pengfei Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Haicheng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yuchao Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xiang He
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Qilemuge Xi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongqiang Xing
- Correspondence may also be addressed to Yongqiang Xing. Tel: +86 472 5951944; Fax: +86 472 5951944;
| | - Yongchun Zuo
- To whom correspondence should be addressed. Tel: +86 471 5227683; Fax: +86 471 5227683;
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13
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Gelon PA, Dutchak PA, Sephton CF. Synaptic dysfunction in ALS and FTD: anatomical and molecular changes provide insights into mechanisms of disease. Front Mol Neurosci 2022; 15:1000183. [PMID: 36263379 PMCID: PMC9575515 DOI: 10.3389/fnmol.2022.1000183] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022] Open
Abstract
Synaptic loss is a pathological feature of all neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS is a disease of the cortical and spinal motor neurons resulting in fatal paralysis due to denervation of muscles. FTD is a form of dementia that primarily affects brain regions controlling cognition, language and behavior. Once classified as two distinct diseases, ALS and FTD are now considered as part of a common disease spectrum based on overlapping clinical, pathological and genetic evidence. At the cellular level, aggregation of common proteins and overlapping gene susceptibilities are shared in both ALS and FTD. Despite the convergence of these two fields of research, the underlying disease mechanisms remain elusive. However, recent discovers from ALS and FTD patient studies and models of ALS/FTD strongly suggests that synaptic dysfunction is an early event in the disease process and a unifying hallmark of these diseases. This review provides a summary of the reported anatomical and cellular changes that occur in cortical and spinal motor neurons in ALS and FTD tissues and models of disease. We also highlight studies that identify changes in the proteome and transcriptome of ALS and FTD models and provide a conceptual overview of the processes that contribute to synaptic dysfunction in these diseases. Due to space limitations and the vast number of publications in the ALS and FTD fields, many articles have not been discussed in this review. As such, this review focuses on the three most common shared mutations in ALS and FTD, the hexanucleuotide repeat expansion within intron 1 of chromosome 9 open reading frame 72 (C9ORF72), transactive response DNA binding protein 43 (TARDBP or TDP-43) and fused in sarcoma (FUS), with the intention of highlighting common pathways that promote synaptic dysfunction in the ALS-FTD disease spectrum.
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Multiple roles for the cytoskeleton in ALS. Exp Neurol 2022; 355:114143. [PMID: 35714755 PMCID: PMC10163623 DOI: 10.1016/j.expneurol.2022.114143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by more than sixty genes identified through classic linkage analysis and new sequencing methods. Yet no clear mechanism of onset, cure, or effective treatment is known. Popular discourse classifies the proteins encoded from ALS-related genes into four disrupted processes: proteostasis, mitochondrial function and ROS, nucleic acid regulation, and cytoskeletal dynamics. Surprisingly, the mechanisms detailing the contribution of the neuronal cytoskeletal in ALS are the least explored, despite involvement in these cell processes. Eight genes directly regulate properties of cytoskeleton function and are essential for the health and survival of motor neurons, including: TUBA4A, SPAST, KIF5A, DCTN1, NF, PRPH, ALS2, and PFN1. Here we review the properties and studies exploring the contribution of each of these genes to ALS.
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15
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Stanton-Turcotte D, Hsu K, Moore SA, Yamada M, Fawcett JP, Iulianella A. Mllt11 Regulates Migration and Neurite Outgrowth of Cortical Projection Neurons during Development. J Neurosci 2022; 42:3931-3948. [PMID: 35379703 PMCID: PMC9097781 DOI: 10.1523/jneurosci.0124-22.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 11/22/2022] Open
Abstract
The formation of connections within the mammalian neocortex is highly regulated by both extracellular guidance mechanisms and intrinsic gene expression programs. There are two types of cortical projection neurons (CPNs): those that project locally and interhemispherically and those that project to subcerebral structures such as the thalamus, hindbrain, and spinal cord. The regulation of cortical projection morphologies is not yet fully understood at the molecular level. Here, we report a role for Mllt11 (Myeloid/lymphoid or mixed-lineage leukemia; translocated to chromosome 11/All1 Fused Gene From Chromosome 1q) in the migration and neurite outgrowth of callosal projection neurons during mouse brain formation. We show that Mllt11 expression is exclusive to developing neurons and is enriched in the developing cortical plate (CP) during the formation of the superficial cortical layers. In cultured primary cortical neurons, Mllt11 is detected in varicosities and growth cones as well as the soma. Using conditional loss-of-function and gain-of-function analysis we show that Mllt11 is required for neuritogenesis and proper migration of upper layer CPNs. Loss of Mllt11 in the superficial cortex of male and female neonates leads to a severe reduction in fibers crossing the corpus callosum (CC), a progressive loss in the maintenance of upper layer projection neuron gene expression, and reduced complexity of dendritic arborization. Proteomic analysis revealed that Mllt11 associates with stabilized microtubules, and Mllt11 loss affected microtubule staining in callosal axons. Taken together, our findings support a role for Mllt11 in promoting the formation of mature upper-layer neuron morphologies and connectivity in the cerebral cortex.SIGNIFICANCE STATEMENT The regulation of cortical projection neuron (CPN) morphologies is an area of active investigation since the time of Cajal. Yet the molecular mechanisms of how the complex dendritic and axonal morphologies of projection neurons are formed remains incompletely understood. Although conditional mutagenesis analysis in the mouse, coupled with overexpression assays in the developing fetal brain, we show that a novel protein called Mllt11 is sufficient and necessary to regulate the dendritic and axonal characteristics of callosal projection neurons in the developing mammalian neocortex. Furthermore, we show that Mllt11 interacts with microtubules, likely accounting for its role in neuritogenesis.
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Affiliation(s)
- Danielle Stanton-Turcotte
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University. Life Science Research Institute, Halifax, Nova Scotia B3H-4R2, Canada
| | - Karolynn Hsu
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University. Life Science Research Institute, Halifax, Nova Scotia B3H-4R2, Canada
| | - Samantha A Moore
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University. Life Science Research Institute, Halifax, Nova Scotia B3H-4R2, Canada
| | - Makiko Yamada
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University. Life Science Research Institute, Halifax, Nova Scotia B3H-4R2, Canada
| | - James P Fawcett
- Departments of Phamacology, Surgery, and Brain Repair Centre, Faculty of Medicine, Dalhousie University. Life Science Research Institute, Halifax, Nova Scotia B3H-4R2, Canada
| | - Angelo Iulianella
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University. Life Science Research Institute, Halifax, Nova Scotia B3H-4R2, Canada
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16
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Hoff KJ, Aiken JE, Gutierrez MA, Franco SJ, Moore JK. Tubulinopathy mutations in TUBA1A that disrupt neuronal morphogenesis and migration override XMAP215/Stu2 regulation of microtubule dynamics. eLife 2022; 11:76189. [PMID: 35511030 PMCID: PMC9236607 DOI: 10.7554/elife.76189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Heterozygous, missense mutations in α- or β-tubulin genes are associated with a wide range of human brain malformations, known as tubulinopathies. We seek to understand whether a mutation’s impact at the molecular and cellular levels scale with the severity of brain malformation. Here, we focus on two mutations at the valine 409 residue of TUBA1A, V409I, and V409A, identified in patients with pachygyria or lissencephaly, respectively. We find that ectopic expression of TUBA1A-V409I/A mutants disrupt neuronal migration in mice and promote excessive neurite branching and a decrease in the number of neurite retraction events in primary rat neuronal cultures. These neuronal phenotypes are accompanied by increased microtubule acetylation and polymerization rates. To determine the molecular mechanisms, we modeled the V409I/A mutants in budding yeast and found that they promote intrinsically faster microtubule polymerization rates in cells and in reconstitution experiments with purified tubulin. In addition, V409I/A mutants decrease the recruitment of XMAP215/Stu2 to plus ends in budding yeast and ablate tubulin binding to TOG (tumor overexpressed gene) domains. In each assay tested, the TUBA1A-V409I mutant exhibits an intermediate phenotype between wild type and the more severe TUBA1A-V409A, reflecting the severity observed in brain malformations. Together, our data support a model in which the V409I/A mutations disrupt microtubule regulation typically conferred by XMAP215 proteins during neuronal morphogenesis and migration, and this impact on tubulin activity at the molecular level scales with the impact at the cellular and tissue levels. Proteins are molecules made up of long chains of building blocks called amino acids. When a mutation changes one of these amino acids, it can lead to the protein malfunctioning, which can have many effects at the cell and tissue level. Given that human proteins are made up of 20 different amino acids, each building block in a protein could mutate to any of the other 19 amino acids, and each mutations could have different effects. Tubulins are proteins that form microtubules, thin tubes that help give cells their shape and allow them to migrate. These proteins are added or removed to microtubules depending on the cell’s needs, meaning that microtubules can grow or shrink depending on the situation. Mutations in the tubulin proteins have been linked to malformations of varying severities involving the formation of ridges and folds on the surface of the brain, including lissencephaly, pachygyria or polymicrogyria. Hoff et al. wanted to establish links between tubulin mutations and the effects observed at both cell and tissue level in the brain. They focused on two mutations in the tubulin protein TUBA1A that affect the amino acid in position 409 in the protein, which is normally a valine. One of the mutations turns this valine into an amino acid called isoleucine. This mutation is associated with pachygyria, which leads to the brain developing few ridges that are broad and flat. The second mutation turns the valine into an alanine, and is linked to lissencephaly, a more severe condition in which the brain develops no ridges, appearing smooth. Hoff et al. found that both mutations interfere with the development of the brain by stopping neurons from migrating properly, which prevents them from forming the folds in the brain correctly. At the cellular level, the mutations lead to tubulins becoming harder to remove from microtubules, making microtubules more stable than usual. This results in longer microtubules that are harder for the cell to shorten or destroy as needed. Additionally, Hoff et al. showed that the mutant versions of TUBA1A have weaker interactions with a protein called XMAP215, which controls the addition of tubulin to microtubules. This causes the microtubules to grow uncontrollably. Hoff et al. also established that the magnitude of the effects of each mutation on microtubule growth scale with the severity of the disorder they cause. Specifically, cells in which TUBA1A is not mutated have microtubules that grow at a normal rate, and lead to typical brain development. Meanwhile, cells carrying the mutation that turns a valine into an alanine, which is linked to the more severe condition lissencephaly, have microtubules that grow very fast. Finally, cells in which the valine is mutated to an isoleucine – the mutation associated with the less severe malformation pachygyria – have microtubules that grow at an intermediate rate. These findings provide a link between mutations in tubulin proteins and larger effects on cell movement that lead to brain malformations. Additionally, they also link the severity of the malformation to the severity of the microtubule defect caused by each mutation. Further work could examine whether microtubule stabilization is also seen in other similar diseases, which, in the long term, could reveal ways to detect and treat these illnesses.
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Affiliation(s)
- Katelyn J Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Jayne E Aiken
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Mark A Gutierrez
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Santos J Franco
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Jeffrey K Moore
- University of Colorado School of Medicine, Aurora, United States
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17
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Abstract
The microtubule cytoskeleton is assembled from the α- and β-tubulin subunits of the canonical tubulin heterodimer, which polymerizes into microtubules, and a small number of other family members, such as γ-tubulin, with specialized functions. Overall, microtubule function involves the collective action of multiple α- and β-tubulin isotypes. However, despite 40 years of awareness that most eukaryotes harbor multiple tubulin isotypes, their role in the microtubule cytoskeleton has remained relatively unclear. Various model organisms offer specific advantages for gaining insight into the role of tubulin isotypes. Whereas simple unicellular organisms such as yeast provide experimental tractability that can facilitate deeper access to mechanistic details, more complex organisms, such as the fruit fly, nematode and mouse, can be used to discern potential specialized functions of tissue- and structure-specific isotypes. Here, we review the role of α- and β-tubulin isotypes in microtubule function and in associated tubulinopathies with an emphasis on the advances gained using model organisms. Overall, we argue that studying tubulin isotypes in a range of organisms can reveal the fundamental mechanisms by which they mediate microtubule function. It will also provide valuable perspectives on how these mechanisms underlie the functional and biological diversity of the cytoskeleton.
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Affiliation(s)
- Emmanuel T Nsamba
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Mohan L Gupta
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
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18
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Buscaglia G, Northington KR, Aiken J, Hoff KJ, Bates EA. Bridging the Gap: The Importance of TUBA1A α-Tubulin in Forming Midline Commissures. Front Cell Dev Biol 2022; 9:789438. [PMID: 35127710 PMCID: PMC8807549 DOI: 10.3389/fcell.2021.789438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Developing neurons undergo dramatic morphological changes to appropriately migrate and extend axons to make synaptic connections. The microtubule cytoskeleton, made of α/β-tubulin dimers, drives neurite outgrowth, promotes neuronal growth cone responses, and facilitates intracellular transport of critical cargoes during neurodevelopment. TUBA1A constitutes the majority of α-tubulin in the developing brain and mutations to TUBA1A in humans cause severe brain malformations accompanied by varying neurological defects, collectively termed tubulinopathies. Studies of TUBA1A function in mammalian cells have been limited by the presence of multiple genes encoding highly similar tubulin proteins, which leads to α-tubulin antibody promiscuity and makes genetic manipulation challenging. Here, we test mutant tubulin levels and assembly activity and analyze the impact of TUBA1A reduction on growth cone composition, neurite extension, and commissural axon architecture during brain development. We present a novel tagging method for studying and manipulating TUBA1A in cells without impairing tubulin function. Using this tool, we show that a TUBA1A loss-of-function mutation TUBA1A N102D (TUBA1A ND ), reduces TUBA1A protein levels and prevents incorporation of TUBA1A into microtubule polymers. Reduced Tuba1a α-tubulin in heterozygous Tuba1a ND/+ mice leads to grossly normal brain formation except a significant impact on axon extension and impaired formation of forebrain commissures. Neurons with reduced Tuba1a as a result of the Tuba1a ND mutation exhibit slower neuron outgrowth compared to controls. Neurons deficient in Tuba1a failed to localize microtubule associated protein-1b (Map1b) to the developing growth cone, likely impacting stabilization of microtubules. Overall, we show that reduced Tuba1a is sufficient to support neuronal migration and cortex development but not commissure formation, and provide mechanistic insight as to how TUBA1A tunes microtubule function to support neurodevelopment.
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Affiliation(s)
- Georgia Buscaglia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kyle R. Northington
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jayne Aiken
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Katelyn J. Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Emily A. Bates
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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19
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Park K, Hoff KJ, Wethekam L, Stence N, Saenz M, Moore JK. Kinetically Stabilizing Mutations in Beta Tubulins Create Isotype-Specific Brain Malformations. Front Cell Dev Biol 2021; 9:765992. [PMID: 34869359 PMCID: PMC8637541 DOI: 10.3389/fcell.2021.765992] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in the family of genes encoding the tubulin subunits of microtubules are associated with a spectrum of human brain malformations known as tubulinopathies. How these mutations impact tubulin activity to give rise to distinct developmental consequences is poorly understood. Here we report two patients exhibiting brain malformations characteristic of tubulinopathies and heterozygous T178M missense mutations in different β-tubulin genes, TUBB2A or TUBB3. RNAseq analysis indicates that both TUBB2A and TUBB3 are expressed in the brain during development, but only TUBB2A maintains high expression in neurons into adulthood. The T178 residue is highly conserved in β-tubulins and located in the exchangeable GTP-binding pocket of β-tubulin. To determine the impact of T178M on β-tubulin function we created an analogous mutation in the β-tubulin of budding yeast and show that the substitution acts dominantly to produce kinetically stabilized microtubules that assemble and disassemble slowly, with fewer transitions between these states. In vitro experiments with purified mutant tubulin demonstrate that T178M decreases the intrinsic assembly activity of β-tubulin and forms microtubules that rarely transition to disassembly. We provide evidence that the T178M substitution disrupts GTPase-dependent conformational changes in tubulin, providing a mechanistic explanation for kinetic stabilization. Our findings demonstrate the importance of tubulin’s GTPase activity during brain development, and indicate that tubulin isotypes play different, important roles during brain development.
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Affiliation(s)
- Kristen Park
- Department of Pediatrics and Neurology, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Katelyn J Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Linnea Wethekam
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nicholas Stence
- Section of Pediatric Radiology, Department of Radiology, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Margarita Saenz
- Section of Genetics, Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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20
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Novel proteins associated with chronic intermittent hypoxia and obstructive sleep apnea: From rat model to clinical evidence. PLoS One 2021; 16:e0253943. [PMID: 34185819 PMCID: PMC8241050 DOI: 10.1371/journal.pone.0253943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To screen for obstructive sleep apnea (OSA) biomarkers, isobaric tags for relative and absolute quantitation (iTRAQ)-labeled quantitative proteomics assay was used to identify differentially expressed proteins (DEPs) during chronic intermittent hypoxia (CIH). METHOD The iTRAQ technique was applied to compare DEPs in the serum of a CIH rat model and control group. Biological analysis of DEPs was performed using Gene Ontology and Kyoto Encyclopedia to explore related biological functions and signaling pathways. Enzyme-linked immunosorbent assay (ELISA) was performed to validate their expression in sera from patients with OSA and CIH rats. RESULTS Twenty-three DEPs (fold change ≥1.2 or ≤0.833, p<0.05) were identified, and two DEPs (unique peptides>3 and higher coverage) were further verified by ELISA in the CIH rat model and OSA subject: apolipoprotein A-IV (APOA4, p<0.05) and Tubulin alpha-1A chain (TUBA1A, p<0.05). Both groups showed significant differences in the expression levels of DEPs between the CIH and control groups and the severe OSA and non-OSA groups. APOA4 was found to be upregulated and TUBA1A downregulated in both the sera from OSA patients and CIH rats, on comparing proteomics results with clinical results. There were two pathways that involved three DEPs, the mitogen-activated protein kinase (MAPK) signaling pathway (p<0.05) and cytokine-cytokine receptor interaction (p<0.05). CONCLUSION APOA4 and TUBA1A may be potential novel biomarkers for CIH and OSA, and may play an important role in the development of OSA complications.
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