1
|
Chong MC, Shah AD, Schittenhelm RB, Silva A, James PF, Wu SSX, Howitt J. Acute exercise-induced release of innate immune proteins via small extracellular vesicles changes with aerobic fitness and age. Acta Physiol (Oxf) 2024; 240:e14095. [PMID: 38243724 DOI: 10.1111/apha.14095] [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: 06/13/2023] [Revised: 10/04/2023] [Accepted: 01/01/2024] [Indexed: 01/21/2024]
Abstract
AIM Physical exercise triggers the secretion of small extracellular vesicles (sEVs) into the circulation in humans, enabling signalling crosstalk between tissues. Exercise-derived EVs and their cargo have been proposed to mediate adaptations to exercise; however, our understanding of how exercise-derived EV protein cargo is modulated by factors such as aerobic fitness and age of an individual is currently unknown. Here, we examined the circulating sEV proteome following aerobic exercise in healthy males of different ages and aerobic fitness to understand exercise-induced EV response during the aging process. METHODS Twenty-eight healthy men completed a bout of 20-min cycling exercise at 70% estimated VO2peak . Small EVs were isolated from blood samples collected before and immediately after exercise, and then quantified using particle analysis and Western blotting. Small EV proteome was examined using quantitative proteomic analysis. RESULTS We identified a significant increase in 13 proteins in small plasma EVs following moderate-to-vigorous intensity exercise. We observed distinct changes in sEV proteome after exercise in young, mature, unfit, and fit individuals, highlighting the impact of aerobic fitness and age on sEV protein secretion. Functional enrichment and pathway analysis identified that the majority of the significantly altered sEV proteins are associated with the innate immune system, including proteins known to be damage-associated molecular patterns (DAMPs). CONCLUSION Together, our findings suggest that exercise-evoked acute stress can positively challenge the innate immune system through the release of signalling molecules such as DAMPs in sEVs, proposing a novel EV-based mechanism for moderate-to-vigorous intensity exercise in immune surveillance pathways.
Collapse
Affiliation(s)
- Mee Chee Chong
- School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Anup D Shah
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria, Australia
| | - Anabel Silva
- Exopharm Limited, Melbourne, Victoria, Australia
| | | | - Sam Shi Xuan Wu
- School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Jason Howitt
- School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Iverson Health Innovation Institute, Swinburne University of Technology, Hawthorn, Victoria, Australia
| |
Collapse
|
2
|
Anuj A, Reuven N, Roberts SGE, Elson A. BASP1 down-regulates RANKL-induced osteoclastogenesis. Exp Cell Res 2023; 431:113758. [PMID: 37619639 DOI: 10.1016/j.yexcr.2023.113758] [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: 05/04/2023] [Revised: 07/03/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
The cytokine RANKL (Receptor Activator of NFκB Ligand) is the key driver of differentiation of monocytes/macrophages to form multi-nucleated, bone-resorbing osteoclasts, a process that is accompanied by significant changes in gene expression. We show that exposure to RANKL rapidly down-regulates expression of Brain Acid Soluble Protein 1 (BASP1) in cultured primary mouse bone marrow macrophages (BMMs), and that this reduced expression is causally linked to the osteoclastogenic process in vitro. Knocking down BASP1 expression in BMMs or eliminating its expression in these cells or in RAW 264.7 cells enhanced RANKL-induced osteoclastogenesis, promoted cell-cell fusion, and generated cultures containing larger osteoclasts with increased mineral degrading abilities relative to controls. Expression of exogenous BASP1 in BMMs undergoing osteoclastogenic differentiation produced the opposite effects. Upon exposure to RANKL, primary mouse BMMs in which BASP1 had been knocked down exhibited increased expression of the key osteoclastogenic transcription factor Nfatc1and of its downstream target genes Dc-stamp, Ctsk, Itgb3, and Mmp9 relative to controls. The knock-down cells also exhibited increased sensitivity to the pro-osteoclastogenic effects of RANKL. We conclude that BASP1 is a negative regulator of RANKL-induced osteoclastogenesis, which down-regulates the pro-osteoclastogenic gene expression pattern induced by this cytokine. Decreased expression of BASP1 upon exposure of BMMs to RANKL removes a negative regulator of osteoclastogenesis and promotes this process.
Collapse
Affiliation(s)
- Anuj Anuj
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nina Reuven
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Stefan G E Roberts
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel.
| |
Collapse
|
3
|
Brugmans AK, Walter C, Moreno N, Göbel C, Holdhof D, de Faria FW, Hotfilder M, Jeising D, Frühwald MC, Skryabin BV, Rozhdestvensky TS, Wachsmuth L, Faber C, Dugas M, Varghese J, Schüller U, Albert TK, Kerl K. A Carboxy-terminal Smarcb1 Point Mutation Induces Hydrocephalus Formation and Affects AP-1 and Neuronal Signalling Pathways in Mice. Cell Mol Neurobiol 2023; 43:3511-3526. [PMID: 37219662 PMCID: PMC10477118 DOI: 10.1007/s10571-023-01361-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023]
Abstract
The BAF (BRG1/BRM-associated factor) chromatin remodelling complex is essential for the regulation of DNA accessibility and gene expression during neuronal differentiation. Mutations of its core subunit SMARCB1 result in a broad spectrum of pathologies, including aggressive rhabdoid tumours or neurodevelopmental disorders. Other mouse models have addressed the influence of a homo- or heterozygous loss of Smarcb1, yet the impact of specific non-truncating mutations remains poorly understood. Here, we have established a new mouse model for the carboxy-terminal Smarcb1 c.1148del point mutation, which leads to the synthesis of elongated SMARCB1 proteins. We have investigated its impact on brain development in mice using magnetic resonance imaging, histology, and single-cell RNA sequencing. During adolescence, Smarcb11148del/1148del mice demonstrated rather slow weight gain and frequently developed hydrocephalus including enlarged lateral ventricles. In embryonic and neonatal stages, mutant brains did not differ anatomically and histologically from wild-type controls. Single-cell RNA sequencing of brains from newborn mutant mice revealed that a complete brain including all cell types of a physiologic mouse brain is formed despite the SMARCB1 mutation. However, neuronal signalling appeared disturbed in newborn mice, since genes of the AP-1 transcription factor family and neurite outgrowth-related transcripts were downregulated. These findings support the important role of SMARCB1 in neurodevelopment and extend the knowledge of different Smarcb1 mutations and their associated phenotypes.
Collapse
Affiliation(s)
- Aliska K Brugmans
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Carolin Walter
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
| | - Natalia Moreno
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Carolin Göbel
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
- Research Institute Children's Cancer Center, 20251, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Dörthe Holdhof
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
- Research Institute Children's Cancer Center, 20251, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Flavia W de Faria
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Marc Hotfilder
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Daniela Jeising
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Michael C Frühwald
- Swabian Children's Cancer Center, Paediatrics and Adolescent Medicine, University Medical Center Augsburg, 86156, Augsburg, Germany
| | - Boris V Skryabin
- Medical Faculty, Core Facility TRAnsgenic Animal and Genetic Engineering Models (TRAM), University of Münster, 48149, Münster, Germany
| | - Timofey S Rozhdestvensky
- Medical Faculty, Core Facility TRAnsgenic Animal and Genetic Engineering Models (TRAM), University of Münster, 48149, Münster, Germany
| | - Lydia Wachsmuth
- Clinic of Radiology, Translational Research Imaging Center (TRIC), University of Münster, 48149, Münster, Germany
| | - Cornelius Faber
- Clinic of Radiology, Translational Research Imaging Center (TRIC), University of Münster, 48149, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
- Institute of Medical Informatics, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
| | - Ulrich Schüller
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
- Research Institute Children's Cancer Center, 20251, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Thomas K Albert
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Kornelius Kerl
- Department of Paediatric Haematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany.
| |
Collapse
|
4
|
Dawson T, Rentia U, Sanford J, Cruchaga C, Kauwe JSK, Crandall KA. Locus specific endogenous retroviral expression associated with Alzheimer's disease. Front Aging Neurosci 2023; 15:1186470. [PMID: 37484691 PMCID: PMC10359044 DOI: 10.3389/fnagi.2023.1186470] [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: 03/14/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Human endogenous retroviruses (HERVs) are transcriptionally-active remnants of ancient retroviral infections that may play a role in Alzheimer's disease. Methods We combined two, publicly available RNA-Seq datasets with a third, novel dataset for a total cohort of 103 patients with Alzheimer's disease and 45 healthy controls. We use telescope to perform HERV quantification for these samples and simultaneously perform gene expression analysis. Results We identify differentially expressed genes and differentially expressed HERVs in Alzheimer's disease patients. Differentially expressed HERVs are scattered throughout the genome; many of them are members of the HERV-K superfamily. A number of HERVs are correlated with the expression of dysregulated genes in Alzheimer's and are physically proximal to genes which drive disease pathways. Discussion Dysregulated expression of ancient retroviral insertions in the human genome are present in Alzheimer's disease and show localization patterns that may explain how these elements drive pathogenic gene expression.
Collapse
Affiliation(s)
- Tyson Dawson
- Computational Biology Institute, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Uzma Rentia
- Computational Biology Institute, The George Washington University, Washington, DC, United States
| | - Jessie Sanford
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Keith A. Crandall
- Computational Biology Institute, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| |
Collapse
|
5
|
Ayupe AC, Choi JS, Beckedorff F, Catanuto P, Mccartan R, Levay K, Park KK. Single-Nucleus RNA Sequencing of Developing and Mature Superior Colliculus Identifies Neuronal Diversity and Candidate Mediators of Circuit Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526254. [PMID: 36778361 PMCID: PMC9915630 DOI: 10.1101/2023.02.01.526254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The superior colliculus (SC) is a sensorimotor structure in the midbrain that integrates input from multiple sensory modalities to initiate motor commands. It undergoes well-characterized steps of circuit assembly during development, rendering the mouse SC a popular model to study establishment and refinement of neural connectivity. Here we performed single nucleus RNA-sequencing analysis of the mouse SC isolated at various developmental time points. Our study provides a transcriptomic landscape of the cell types that comprise the SC across murine development with particular emphasis on neuronal heterogeneity. We used these data to identify Pax7 as a marker for an anatomically homogeneous population of GABAergic neurons. Lastly, we report a repertoire of genes differentially expressed across the different postnatal ages, many of which are known to regulate axon guidance and synapse formation. Our data provide a valuable resource for interrogating the mechanisms of circuit development, and identifying markers for manipulating specific SC neuronal populations and circuits.
Collapse
|
6
|
Li D, Cao R, Dong W, Cheng M, Pan X, Hu Z, Hao J. Identification of potential biomarkers for ankylosing spondylitis based on bioinformatics analysis. BMC Musculoskelet Disord 2023; 24:413. [PMID: 37226132 DOI: 10.1186/s12891-023-06550-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
OBJECTIVE The aim of this study was to search for key genes in ankylosing spondylitis (AS) through comprehensive bioinformatics analysis, thus providing some theoretical support for future diagnosis and treatment of AS and further research. METHODS Gene expression profiles were collected from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) by searching for the term "ankylosing spondylitis". Ultimately, two microarray datasets (GSE73754 and GSE11886) were downloaded from the GEO database. A bioinformatic approach was used to screen differentially expressed genes and perform functional enrichment analysis to obtain biological functions and signalling pathways associated with the disease. Weighted correlation network analysis (WGCNA) was used to further obtain key genes. Immune infiltration analysis was performed using the CIBERSORT algorithm to conduct a correlation analysis of key genes with immune cells. The GWAS data of AS were analysed to identify the pathogenic regions of key genes in AS. Finally, potential therapeutic agents for AS were predicted using these key genes. RESULTS A total of 7 potential biomarkers were identified: DYSF, BASP1, PYGL, SPI1, C5AR1, ANPEP and SORL1. ROC curves showed good prediction for each gene. T cell, CD4 naïve cell, and neutrophil levels were significantly higher in the disease group than in the paired normal group, and key gene expression was strongly correlated with immune cells. CMap results showed that the expression profiles of ibuprofen, forskolin, bongkrek-acid, and cimaterol showed the most significant negative correlation with the expression profiles of disease perturbations, suggesting that these drugs may play a role in AS treatment. CONCLUSION The potential biomarkers of AS screened in this study are closely related to the level of immune cell infiltration and play an important role in the immune microenvironment. This may provide help in the clinical diagnosis and treatment of AS and provide new ideas for further research.
Collapse
Affiliation(s)
- Dongxu Li
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Ruichao Cao
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Wei Dong
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Minghuang Cheng
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Xiaohan Pan
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Zhenming Hu
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China
| | - Jie Hao
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing, China.
- Orthopedic Laboratory of Chongqing Medical University, Yuzhong, Chongqing, China.
| |
Collapse
|
7
|
A Proteome-Wide Effect of PHF8 Knockdown on Cortical Neurons Shows Downregulation of Parkinson's Disease-Associated Protein Alpha-Synuclein and Its Interactors. Biomedicines 2023; 11:biomedicines11020486. [PMID: 36831023 PMCID: PMC9953648 DOI: 10.3390/biomedicines11020486] [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: 01/11/2023] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Synaptic dysfunction may underlie the pathophysiology of Parkinson's disease (PD), a presently incurable condition characterized by motor and cognitive symptoms. Here, we used quantitative proteomics to study the role of PHD Finger Protein 8 (PHF8), a histone demethylating enzyme found to be mutated in X-linked intellectual disability and identified as a genetic marker of PD, in regulating the expression of PD-related synaptic plasticity proteins. Amongst the list of proteins found to be affected by PHF8 knockdown were Parkinson's-disease-associated SNCA (alpha synuclein) and PD-linked genes DNAJC6 (auxilin), SYNJ1 (synaptojanin 1), and the PD risk gene SH3GL2 (endophilin A1). Findings in this study show that depletion of PHF8 in cortical neurons affects the activity-induced expression of proteins involved in synaptic plasticity, synaptic structure, vesicular release and membrane trafficking, spanning the spectrum of pre-synaptic and post-synaptic transmission. Given that the depletion of even a single chromatin-modifying enzyme can affect synaptic protein expression in such a concerted manner, more in-depth studies will be needed to show whether such a mechanism can be exploited as a potential disease-modifying therapeutic drug target in PD.
Collapse
|
8
|
Li Z, Wang D, Guo W, Zhang S, Chen L, Zhang YH, Lu L, Pan X, Huang T, Cai YD. Identification of cortical interneuron cell markers in mouse embryos based on machine learning analysis of single-cell transcriptomics. Front Neurosci 2022; 16:841145. [PMID: 35911980 PMCID: PMC9337837 DOI: 10.3389/fnins.2022.841145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Mammalian cortical interneurons (CINs) could be classified into more than two dozen cell types that possess diverse electrophysiological and molecular characteristics, and participate in various essential biological processes in the human neural system. However, the mechanism to generate diversity in CINs remains controversial. This study aims to predict CIN diversity in mouse embryo by using single-cell transcriptomics and the machine learning methods. Data of 2,669 single-cell transcriptome sequencing results are employed. The 2,669 cells are classified into three categories, caudal ganglionic eminence (CGE) cells, dorsal medial ganglionic eminence (dMGE) cells, and ventral medial ganglionic eminence (vMGE) cells, corresponding to the three regions in the mouse subpallium where the cells are collected. Such transcriptomic profiles were first analyzed by the minimum redundancy and maximum relevance method. A feature list was obtained, which was further fed into the incremental feature selection, incorporating two classification algorithms (random forest and repeated incremental pruning to produce error reduction), to extract key genes and construct powerful classifiers and classification rules. The optimal classifier could achieve an MCC of 0.725, and category-specified prediction accuracies of 0.958, 0.760, and 0.737 for the CGE, dMGE, and vMGE cells, respectively. The related genes and rules may provide helpful information for deepening the understanding of CIN diversity.
Collapse
Affiliation(s)
- Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- State Key Laboratory of Oncology in South China, Department of Radiology, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shiqi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - Lin Lu
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, United States
| | - XiaoYong Pan
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- Yu-Dong Cai,
| |
Collapse
|
9
|
Bice AR, Xiao Q, Kong J, Yan P, Rosenthal ZP, Kraft AW, Smith KP, Wieloch T, Lee JM, Culver JP, Bauer AQ. Homotopic contralesional excitation suppresses spontaneous circuit repair and global network reconnections following ischemic stroke. eLife 2022; 11:e68852. [PMID: 35723585 PMCID: PMC9333991 DOI: 10.7554/elife.68852] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding circuit-level manipulations that affect the brain's capacity for plasticity will inform the design of targeted interventions that enhance recovery after stroke. Following stroke, increased contralesional activity (e.g. use of the unaffected limb) can negatively influence recovery, but it is unknown which specific neural connections exert this influence, and to what extent increased contralesional activity affects systems- and molecular-level biomarkers of recovery. Here, we combine optogenetic photostimulation with optical intrinsic signal imaging to examine how contralesional excitatory activity affects cortical remodeling after stroke in mice. Following photothrombosis of left primary somatosensory forepaw (S1FP) cortex, mice either recovered spontaneously or received chronic optogenetic excitation of right S1FP over the course of 4 weeks. Contralesional excitation suppressed perilesional S1FP remapping and was associated with abnormal patterns of stimulus-evoked activity in the unaffected limb. This maneuver also prevented the restoration of resting-state functional connectivity (RSFC) within the S1FP network, RSFC in several networks functionally distinct from somatomotor regions, and resulted in persistent limb-use asymmetry. In stimulated mice, perilesional tissue exhibited transcriptional changes in several genes relevant for recovery. Our results suggest that contralesional excitation impedes local and global circuit reconnection through suppression of cortical activity and several neuroplasticity-related genes after stroke, and highlight the importance of site selection for targeted therapeutic interventions after focal ischemia.
Collapse
Affiliation(s)
- Annie R Bice
- Department of Radiology, Washington University in St. LouisSaint LouisUnited States
| | - Qingli Xiao
- Department of Neurology, Washington University in St. LouisSaint LouisUnited States
| | - Justin Kong
- Department of Biology, Washington University in St. LouisSaint LouisUnited States
| | - Ping Yan
- Department of Neurology, Washington University in St. LouisSaint LouisUnited States
| | | | - Andrew W Kraft
- Department of Neurology, Washington University in St. LouisSaint LouisUnited States
| | - Karen P Smith
- Department of Neurology, Washington University in St. LouisSaint LouisUnited States
| | | | - Jin-Moo Lee
- Department of Neurology, Washington University in St. LouisSaint LouisUnited States
| | - Joseph P Culver
- Department of Radiology, Washington University in St. LouisSt. LouisUnited States
| | - Adam Q Bauer
- Department of Radiology, Washington University in St. LouisSaint LouisUnited States
| |
Collapse
|
10
|
Zhou R, Han B, Nowak R, Lu Y, Heller E, Xia C, Chishti AH, Fowler VM, Zhuang X. Proteomic and functional analyses of the periodic membrane skeleton in neurons. Nat Commun 2022; 13:3196. [PMID: 35680881 PMCID: PMC9184744 DOI: 10.1038/s41467-022-30720-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 05/09/2022] [Indexed: 12/29/2022] Open
Abstract
Actin, spectrin, and associated molecules form a membrane-associated periodic skeleton (MPS) in neurons. The molecular composition and functions of the MPS remain incompletely understood. Here, using co-immunoprecipitation and mass spectrometry, we identified hundreds of potential candidate MPS-interacting proteins that span diverse functional categories. We examined representative proteins in several of these categories using super-resolution imaging, including previously unknown MPS structural components, as well as motor proteins, cell adhesion molecules, ion channels, and signaling proteins, and observed periodic distributions characteristic of the MPS along the neurites for ~20 proteins. Genetic perturbations of the MPS and its interacting proteins further suggested functional roles of the MPS in axon-axon and axon-dendrite interactions and in axon diameter regulation, and implicated the involvement of MPS interactions with cell adhesion molecules and non-muscle myosin in these roles. These results provide insights into the interactome of the MPS and suggest previously unknown functions of the MPS in neurons.
Collapse
Affiliation(s)
- Ruobo Zhou
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Boran Han
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | - Roberta Nowak
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92307, USA
| | - Yunzhe Lu
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Evan Heller
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | - Chenglong Xia
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | - Athar H Chishti
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Velia M Fowler
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92307, USA
- Department of Biological Sciences, The University of Delaware, Newark, DE, 19716, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
11
|
A high-affinity cocaine binding site associated with the brain acid soluble protein 1. Proc Natl Acad Sci U S A 2022; 119:e2200545119. [PMID: 35412917 PMCID: PMC9169839 DOI: 10.1073/pnas.2200545119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cocaine is a monoamine transport inhibitor. Current models attributing pharmacologic actions of cocaine to inhibiting the activity of the amine transporters alone failed to translate to the clinic. Cocaine inhibition of the dopamine, serotonin, and norepinephrine transporters is relatively weak, suggesting that blockade of the amine transporters alone cannot account for the actions of cocaine, especially at low doses. There is evidence for significantly more potent actions of cocaine, suggesting the existence of a high-affinity receptor(s) for the drug. Identifying and characterizing such receptors will deepen our understanding of cocaine pharmacologic actions and pave the way for therapeutic development. Here we identify a high-affinity cocaine binding site associated with BASP1 that is involved in mediating the drug’s psychotropic actions. Cocaine exerts its stimulant effect by inhibiting dopamine (DA) reuptake, leading to increased dopamine signaling. This action is thought to reflect the binding of cocaine to the dopamine transporter (DAT) to inhibit its function. However, cocaine is a relatively weak inhibitor of DAT, and many DAT inhibitors do not share cocaine’s behavioral actions. Further, recent reports show more potent actions of the drug, implying the existence of a high-affinity receptor for cocaine. We now report high-affinity binding of cocaine associated with the brain acid soluble protein 1 (BASP1) with a dissociation constant (Kd) of 7 nM. Knocking down BASP1 in the striatum inhibits [3H]cocaine binding to striatal synaptosomes. Depleting BASP1 in the nucleus accumbens but not the dorsal striatum diminishes locomotor stimulation in mice. Our findings imply that BASP1 is a pharmacologically relevant receptor for cocaine.
Collapse
|
12
|
Mac Donald K, Iulianella A. The actin-cytoskeleton associating protein BASP1 regulates neural progenitor localization in the neural tube. Genesis 2021; 60:e23464. [PMID: 34897971 DOI: 10.1002/dvg.23464] [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: 08/06/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022]
Abstract
Brain acid soluble protein 1 (BASP1; previously NAP22 or CAP23) is an actin-associating protein that is highly expressed in the nervous system throughout development. While its roles at the neuromuscular junction and in certain non-neuronal tissues have been previously characterized, its function in the early neural tube is unclear. Using in ovo electroporation in the chicken (Gallus gallus) embryonic neural tube, we show that BASP1 overexpression resulted in the appearance of ectopic neural progenitor cells within the marginal zone of the neural tube. BASP1 knockdown did not affect the position of neural progenitors but did alter the complexity of axons developing from differentiated neurons. This suggests a role for BASP1 in regulating the apical polarity of progenitor cells and axon trajectories from developing neurons.
Collapse
Affiliation(s)
- Kaitlin Mac Donald
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University, Life Science Research Institute, Halifax, Nova Scotia, Canada
| | - Angelo Iulianella
- Department of Medical Neuroscience, and Brain Repair Centre, Faculty of Medicine, Dalhousie University, Life Science Research Institute, Halifax, Nova Scotia, Canada
| |
Collapse
|
13
|
Fernandes HJR, Patikas N, Foskolou S, Field SF, Park JE, Byrne ML, Bassett AR, Metzakopian E. Single-Cell Transcriptomics of Parkinson's Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses. Cell Rep 2021; 33:108263. [PMID: 33053338 DOI: 10.1016/j.celrep.2020.108263] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
The advent of induced pluripotent stem cell (iPSC)-derived neurons has revolutionized Parkinson's disease (PD) research, but single-cell transcriptomic analysis suggests unresolved cellular heterogeneity within these models. Here, we perform the largest single-cell transcriptomic study of human iPSC-derived dopaminergic neurons to elucidate gene expression dynamics in response to cytotoxic and genetic stressors. We identify multiple neuronal subtypes with transcriptionally distinct profiles and differential sensitivity to stress, highlighting cellular heterogeneity in dopamine in vitro models. We validate this disease model by showing robust expression of PD GWAS genes and overlap with postmortem adult substantia nigra neurons. Importantly, stress signatures are ameliorated using felodipine, an FDA-approved drug. Using isogenic SNCA-A53T mutants, we find perturbations in glycolysis, cholesterol metabolism, synaptic signaling, and ubiquitin-proteasomal degradation. Overall, our study reveals cell type-specific perturbations in human dopamine neurons, which will further our understanding of PD and have implications for cell replacement therapies.
Collapse
Affiliation(s)
- Hugo J R Fernandes
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK; Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nikolaos Patikas
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Stefanie Foskolou
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK; Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sarah F Field
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Meg L Byrne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK.
| |
Collapse
|
14
|
Association between the expression of lncRNA BASP-AS1 and volume of right hippocampal tail moderated by episode duration in major depressive disorder: a CAN-BIND 1 report. Transl Psychiatry 2021; 11:469. [PMID: 34508068 PMCID: PMC8433329 DOI: 10.1038/s41398-021-01592-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023] Open
Abstract
The pathophysiology of major depressive disorder (MDD) encompasses an array of changes at molecular and neurobiological levels. As chronic stress promotes neurotoxicity there are alterations in the expression of genes and gene-regulatory molecules. The hippocampus is particularly sensitive to the effects of stress and its posterior volumes can deliver clinically valuable information about the outcomes of antidepressant treatment. In the present work, we analyzed individuals with MDD (N = 201) and healthy controls (HC = 104), as part of the CAN-BIND-1 study. We used magnetic resonance imaging (MRI) to measure hippocampal volumes, evaluated gene expression with RNA sequencing, and assessed DNA methylation with the (Infinium MethylationEpic Beadchip), in order to investigate the association between hippocampal volume and both RNA expression and DNA methylation. We identified 60 RNAs which were differentially expressed between groups. Of these, 21 displayed differential methylation, and seven displayed a correlation between methylation and expression. We found a negative association between expression of Brain Abundant Membrane Attached Signal Protein 1 antisense 1 RNA (BASP1-AS1) and right hippocampal tail volume in the MDD group (β = -0.218, p = 0.021). There was a moderating effect of the duration of the current episode on the association between the expression of BASP1-AS1 and right hippocampal tail volume in the MDD group (β = -0.48, 95% C.I. [-0.80, -0.16]. t = -2.95 p = 0.004). In conclusion, we found that overexpression of BASP1-AS1 was correlated with DNA methylation, and was negatively associated with right tail hippocampal volume in MDD.
Collapse
|
15
|
Liśkiewicz AD, Liśkiewicz D, Marczak Ł, Przybyła M, Grabowska K, Student S, Dębiec M, Sługocka A, Lewin-Kowalik J. Obesity-associated deterioration of the hippocampus is partially restored after weight loss. Brain Behav Immun 2021; 96:212-226. [PMID: 34087424 DOI: 10.1016/j.bbi.2021.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVE Obesity is a multidimensional condition that is treatable by the restoration of a lean phenotype; however, some obesity-related outcomes may persist after weight normalization. Among the organs of the human body, the brain possesses a relatively low regenerative capacity and could retain perturbations established as a result of developmental obesity. Calorie restriction (CR) or a restricted ketogenic diet (KD) are successfully used as weight loss approaches, but their impact on obesity-related effects in the brain have not been previously evaluated. METHODS We performed a series of experiments in a rat model of developmental obesity induced by a 12-week cafeteria diet, followed by CR to implement weight loss. First, we assessed the impact of obesity on neurogenesis (BrdU incorporation into the hippocampus), cognitive function (water maze), and concomitant changes in hippocampal protein expression (GC/MS-MS, western blot). Next, we repeated these experiments in a rat model of weight loss induced by CR. We also measured mitochondrial enzyme activity in rats after weight loss during the fed or fasting state. This study was extended by additional experiments with restricted KD used as a weight loss approach in order to compare the efficacy of two different nutritional interventions used in the treatment of obesity on hippocampal functions. By using a modified version of the water maze we evaluated cognitive abilities in rats subjected to weight loss by CR or a restricted KD. RESULTS In this study, obesity affected metabolic processes, upregulated hippocampal NF-κB, and induced proteomic differences which were associated with impaired cognition and neurogenesis. Weight loss improved neurogenesis and enhanced cognition. While the expression pattern of some proteins persisted after weight loss, most of the changes appeared de novo revealing metabolic adjustment by overactivation of citrate synthase and downregulation of ATP synthase. As a consequence of fasting, the activity of these enzymes indicated hippocampal adaptation to negative energy balance during the weight loss phase of CR. Moreover, the effects on cognitive abilities measured after weight loss were negatively correlated with the animal weight measured at the final stage of weight gain. This was alleviated by KD, which improved cognition when used as a weight loss approach. CONCLUSIONS The study shows that cognition and mitochondrial metabolism in the hippocampus are affected by CR- or KD-induced weight loss.
Collapse
Affiliation(s)
- Arkadiusz D Liśkiewicz
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice 40-752, Poland; Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education, Katowice 40-065, Poland.
| | - Daniela Liśkiewicz
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education, Katowice 40-065, Poland; Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice 40-752, Poland
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marta Przybyła
- Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice 40-752, Poland
| | - Konstancja Grabowska
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education, Katowice 40-065, Poland; Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice 40-752, Poland
| | - Sebastian Student
- Institute of Automatic Control, Silesian University of Technology, Gliwice 44-100, Poland; Biotechnology Centre, Silesian University of Technology, Gliwice 44-100, Poland
| | - Magdalena Dębiec
- Laboratory of Molecular Biology, Institute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education, Katowice 40-065, Poland
| | - Anna Sługocka
- Department for Experimental Medicine, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice 40-752, Poland
| | - Joanna Lewin-Kowalik
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice 40-752, Poland
| |
Collapse
|
16
|
The evolutionary acquisition and mode of functions of promoter-associated non-coding RNAs (pancRNAs) for mammalian development. Essays Biochem 2021; 65:697-708. [PMID: 34328174 DOI: 10.1042/ebc20200143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence has shown that many long non-coding RNAs (lncRNAs) are involved in gene regulation in a variety of ways such as transcriptional, post-transcriptional and epigenetic regulation. Promoter-associated non-coding RNAs (pancRNAs), which are categorized into the most abundant single-copy lncRNA biotype, play vital regulatory roles in finely tuning cellular specification at the epigenomic level. In short, pancRNAs can directly or indirectly regulate downstream genes to participate in the development of organisms in a cell-specific manner. In this review, we will introduce the evolutionarily acquired characteristics of pancRNAs as determined by comparative epigenomics and elaborate on the research progress on pancRNA-involving processes in mammalian embryonic development, including neural differentiation.
Collapse
|
17
|
Khajavi M, Zhou Y, Schiffer AJ, Bazinet L, Birsner AE, Zon L, D'Amato RJ. Identification of Basp1 as a novel angiogenesis-regulating gene by multi-model system studies. FASEB J 2021; 35:e21404. [PMID: 33899275 DOI: 10.1096/fj.202001936rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 01/23/2023]
Abstract
We have previously used the genetic diversity available in common inbred mouse strains to identify quantitative trait loci (QTLs) responsible for the differences in angiogenic response using the corneal micropocket neovascularization (CoNV) assay. Employing a mouse genome-wide association study (GWAS) approach, the region on chromosome 15 containing Basp1 was identified as being significantly associated with angiogenesis in inbred strains. Here, we developed a unique strategy to determine and verify the role of BASP1 in angiogenic pathways. Basp1 expression in cornea had a strong correlation with a haplotype shared by mouse strains with varied angiogenic phenotypes. In addition, inhibition of BASP1 demonstrated a dosage-dependent effect in both primary mouse brain endothelial and human microvascular endothelial cell (HMVEC) migration. To investigate its role in vivo, we knocked out basp1 in transgenic kdrl:zsGreen zebrafish embryos using a widely adopted CRISPR-Cas9 system. These embryos had severely disrupted vessel formation compared to control siblings. We further show that basp1 promotes angiogenesis by upregulating β-catenin gene and the Dll4/Notch1 signaling pathway. These results, to the best of our knowledge, provide the first in vivo evidence to indicate the role of Basp1 as an angiogenesis-regulating gene and opens the potential therapeutic avenues for a wide variety of systemic angiogenesis-dependent diseases.
Collapse
Affiliation(s)
- Mehrdad Khajavi
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Zhou
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Alex J Schiffer
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren Bazinet
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy E Birsner
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Robert J D'Amato
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
18
|
Manganas LN, Durá I, Osenberg S, Semerci F, Tosun M, Mishra R, Parkitny L, Encinas JM, Maletic-Savatic M. BASP1 labels neural stem cells in the neurogenic niches of mammalian brain. Sci Rep 2021; 11:5546. [PMID: 33692421 PMCID: PMC7970918 DOI: 10.1038/s41598-021-85129-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 02/04/2021] [Indexed: 11/08/2022] Open
Abstract
The mechanisms responsible for determining neural stem cell fate are numerous and complex. To begin to identify the specific components involved in these processes, we generated several mouse neural stem cell (NSC) antibodies against cultured mouse embryonic neurospheres. Our immunohistochemical data showed that the NSC-6 antibody recognized NSCs in the developing and postnatal murine brains as well as in human brain organoids. Mass spectrometry revealed the identity of the NSC-6 epitope as brain abundant, membrane-attached signal protein 1 (BASP1), a signaling protein that plays a key role in neurite outgrowth and plasticity. Western blot analysis using the NSC-6 antibody demonstrated multiple BASP1 isoforms with varying degrees of expression and correlating with distinct developmental stages. Herein, we describe the expression of BASP1 in NSCs in the developing and postnatal mammalian brains and human brain organoids, and demonstrate that the NSC-6 antibody may be a useful marker of these cells.
Collapse
Affiliation(s)
- Louis N Manganas
- Department of Neurology, Stony Brook University Medical Center, Stony Brook, NY, USA.
- Department of Neurology, Stony Brook University Medical Center, Health Sciences Center T-12, room 020, Stony Brook, NY, 11794, USA.
| | - Irene Durá
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Sivan Osenberg
- Departments of Pediatrics, Neurology and Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Fatih Semerci
- Departments of Pediatrics, Neurology and Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Mehmet Tosun
- Departments of Pediatrics, Neurology and Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Rachana Mishra
- Departments of Pediatrics, Neurology and Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Luke Parkitny
- Departments of Pediatrics, Neurology and Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Juan M Encinas
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- The Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
- Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mirjana Maletic-Savatic
- Department of Neurology, Stony Brook University Medical Center, Stony Brook, NY, USA.
- Departments of Pediatrics, Neurology and Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.
- Departments of Pediatrics, Neurology, and Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute at Texas Children Hospital, 1250 Moursund St., Rm 1250, Houston, TX, 77030, USA.
| |
Collapse
|
19
|
Jaikumarr Ram A, Girija As S, Jayaseelan VP, Arumugam P. Overexpression of BASP1 Indicates a Poor Prognosis in Head and Neck Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2020; 21:3435-3439. [PMID: 33247706 PMCID: PMC8033119 DOI: 10.31557/apjcp.2020.21.11.3435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 01/04/2023] Open
Abstract
Objective: Brain abundant membrane attached signal protein 1 (BASP1) was originally identified as a membrane and cytoplasmic protein. Recent studies have shown that BASP1 highly expressed in cancer and promoted the proliferation of cancer. However, the role of BASP1 in head and neck squamous cell carcinoma (HNSCC) is largely unknown. Here, we performed a systematic data analysis to examine whether BASP1 can function as prognostic marker in HNSCC. Methods: In this study, we used Oncomine, and UALCAN, databases to analyze the expression of BASP1 in HNSCC. We used Kaplan-Meier plotter to evaluate the effect of BASP1 on clinical prognosis. In addition, we also analyzed genetic alterations, interaction network, and functional enrichment of BASP1. Results: BASP1 mRNA expression level was remarkably increased in HNSCC than in normal tissues (P=1.624e-12). Moreover, high BASP1 expression was significantly related to poor survival (p=0.00056) in HNSCC patients. In addition, BASP1 gene amplified in 5% of HNSCC patients which contributes to the overexpression of BASP1. Conclusions: These findings suggest that BASP1 was frequently amplified which contributes to the overexpression of BASP1, thereby promoting HNSCC progression. Thus, these results indicate that BASP1 might serve as a biomarker to predict the progression and prognosis of HNSCC patients.
Collapse
Affiliation(s)
- Ashwin Jaikumarr Ram
- Department of Microbiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Smiline Girija As
- Department of Microbiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | | | - Paramasivam Arumugam
- BRULAC-DRC, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| |
Collapse
|
20
|
Chung D, Shum A, Caraveo G. GAP-43 and BASP1 in Axon Regeneration: Implications for the Treatment of Neurodegenerative Diseases. Front Cell Dev Biol 2020; 8:567537. [PMID: 33015061 PMCID: PMC7494789 DOI: 10.3389/fcell.2020.567537] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/14/2020] [Indexed: 01/06/2023] Open
Abstract
Growth-associated protein-43 (GAP-43) and brain acid-soluble protein 1 (BASP1) regulate actin dynamics and presynaptic vesicle cycling at axon terminals, thereby facilitating axonal growth, regeneration, and plasticity. These functions highly depend on changes in GAP-43 and BASP1 expression levels and post-translational modifications such as phosphorylation. Interestingly, examinations of GAP-43 and BASP1 in neurodegenerative diseases reveal alterations in their expression and phosphorylation profiles. This review provides an overview of the structural properties, regulations, and functions of GAP-43 and BASP1, highlighting their involvement in neural injury response and regeneration. By discussing GAP-43 and BASP1 in the context of neurodegenerative diseases, we also explore the therapeutic potential of modulating their activities to compensate for neuron loss in neurodegenerative diseases.
Collapse
Affiliation(s)
- Daayun Chung
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrew Shum
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Gabriela Caraveo
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| |
Collapse
|
21
|
Villa R, Fergnani VGC, Silipigni R, Guerneri S, Cinnante C, Guala A, Danesino C, Scola E, Conte G, Fumagalli M, Gangi S, Colombo L, Picciolini O, Ajmone PF, Accogli A, Madia F, Tassano E, Scala M, Capra V, Srour M, Spaccini L, Righini A, Greco D, Castiglia L, Romano C, Bedeschi MF. Structural brain anomalies in Cri-du-Chat syndrome: MRI findings in 14 patients and possible genotype-phenotype correlations. Eur J Paediatr Neurol 2020; 28:110-119. [PMID: 32800423 DOI: 10.1016/j.ejpn.2020.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/02/2020] [Accepted: 07/03/2020] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Cri-du-Chat Syndrome (CdCS) is a genetic condition due to deletions showing different breakpoints encompassing a critical region on the short arm of chromosome 5, located between p15.2 and p15.3, first defined by Niebuhr in 1978. The classic phenotype includes a characteristic cry, peculiar facies, microcephaly, growth retardation, hypotonia, speech and psychomotor delay and intellectual disability. A wide spectrum of clinical manifestations can be attributed to differences in size and localization of the 5p deletion. Several critical regions related to some of the main features (such as cry, peculiar facies, developmental delay) have been identified. The aim of this study is to further define the genotype-phenotype correlations in CdCS with particular regards to the specific neuroradiological findings. PATIENTS AND METHODS Fourteen patients with 5p deletions have been included in the present study. Neuroimaging studies were conducted using brain Magnetic Resonance Imaging (MRI). Genetic testing was performed by means of comparative genomic hybridization (CGH) array at 130 kb resolution. RESULTS MRI analyses showed that isolated pontine hypoplasia is the most common finding, followed by vermian hypoplasia, ventricular anomalies, abnormal basal angle, widening of cavum sellae, increased signal of white matter, corpus callosum anomalies, and anomalies of cortical development. Chromosomal microarray analysis identified deletions ranging in size from 11,6 to 33,8 Mb on the short arm of chromosome 5. Then, we took into consideration the overlapping and non-overlapping deleted regions. The goal was to establish a correlation between the deleted segments and the neuroradiological features of our patients. CONCLUSIONS Performing MRI on all the patients in our cohort, allowed us to expand the neuroradiological phenotype in CdCS. Moreover, possible critical regions associated to characteristic MRI findings have been identified.
Collapse
Affiliation(s)
- R Villa
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.
| | - V G C Fergnani
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.
| | - R Silipigni
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - S Guerneri
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - C Cinnante
- Neuroradiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - A Guala
- Department of Pediatrics, Castelli Hospital, Verbania, Italy.
| | - C Danesino
- Molecular Medicine Department, General Biology and Medical Genetics Unit, University of Pavia, Pavia, Italy.
| | - E Scola
- Neuroradiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - G Conte
- Neuroradiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - M Fumagalli
- NICU, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - S Gangi
- NICU, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - L Colombo
- NICU, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - O Picciolini
- Pediatric Physical Medicine & Rehabilitation Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - P F Ajmone
- Child and Adolescent Neuropsychiatric Service (UONPIA), Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.
| | - A Accogli
- DINOGMI, Università degli Studi di Genova, Italy; IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - F Madia
- IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - E Tassano
- IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - M Scala
- DINOGMI, Università degli Studi di Genova, Italy; IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - V Capra
- IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - M Srour
- Department of Pediatrics, Division of Pediatric Neurology, McGill University, Montreal, Canada; McGill University Health Center (MUHC) Research Institute, Montreal, Canada.
| | - L Spaccini
- Clinical Genetics Unit, Department of Obstetrics and Gynecology, V. Buzzi Children's Hospital, University of Milan, Italy.
| | - A Righini
- Department of Pediatric Radiology and Neuroradiology, V. Buzzi Children's Hospital, University of Milan, Italy.
| | - D Greco
- Oasi Research Institute, IRCCS, Troina, Italy.
| | - L Castiglia
- Oasi Research Institute, IRCCS, Troina, Italy.
| | - C Romano
- Oasi Research Institute, IRCCS, Troina, Italy.
| | - M F Bedeschi
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.
| |
Collapse
|
22
|
Prajapati B, Fatima M, Fatma M, Maddhesiya P, Arora H, Naskar T, Devasenapathy S, Seth P, Sinha S. Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation. Cell Death Discov 2020; 6:28. [PMID: 32351715 PMCID: PMC7181654 DOI: 10.1038/s41420-020-0263-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 03/19/2020] [Accepted: 04/02/2020] [Indexed: 02/08/2023] Open
Abstract
lncRNA genes can be genic or "intergenic". "Genic" RNAs can be further divided into six biotypes. Through genome-wide analysis of a publicly available data set on corticogenesis, we found that the divergent lncRNA (XH) biotype, comprising the lncRNA and the coding gene being in opposite directions in a head-to-head manner, was most prominent during neural commitment. Within this biotype, a coding gene/divergent RNA pair of the BASP1 gene and the uncharacterized RNA loc285696 (hitherto referred as BASP1-AS1) formed a major HUB gene during neuronal differentiation. Experimental validation during the in vitro differentiation of human neural progenitor cells (hNPCs) showed that BASP1-AS1 regulates the expression of its adjacent coding gene, BASP1. Both transcripts increased sharply on the first day of neuronal differentiation of hNPCs, to fall steadily thereafter, reaching very low levels in differentiated neurons. BASP1-AS1 RNA and the BASP1 gene formed a molecular complex that also included the transcription factor TCF12. TCF12 is coded by the DYX1 locus, associated with inherited dyslexia and neurodevelopmental defects. Knockdown of BASP1-AS1, BASP1, or TCF12 impaired the neuronal differentiation of hNPCs, as seen by reduction in DCX and TUJ1-positive cells and by reduced neurite length. There was also increased cell proliferation. A common set of critical genes was affected by the three molecules in the complex. Our study thus identified the role of the XH biotype and a novel mediator of neuronal differentiation-the complex of BASP1-AS1, BASP1, and TCF12. It also linked a neuronal differentiation pathway to inherited dyslexia.
Collapse
Affiliation(s)
| | - Mahar Fatima
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | - Mena Fatma
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | | | - Himali Arora
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | - Teesta Naskar
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | | | - Pankaj Seth
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | - Subrata Sinha
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029 India
| |
Collapse
|
23
|
The high-resolution proteomic analysis of protein composition of rat spleen lymphocytes stimulated by Concanavalin A; a comparison with morphine-treated cells. J Neuroimmunol 2020; 341:577191. [PMID: 32113006 DOI: 10.1016/j.jneuroim.2020.577191] [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: 11/13/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 11/23/2022]
Abstract
Morphine- and Concanavalin A-induced changes of protein composition of rat spleen lymphocytes were determined by high-resolution proteomic analysis, gel-free, label-free quantification, MaxLFQ. Stimulation by Con A resulted in a major reorganization of spleen cell protein composition evidenced by increased expression level of 94 proteins; 101 proteins were down-regulated (>2-fold). Interestingly, among proteins that were up-regulated to the largest extent were the prototypical brain proteins as a neuron specific enolase, synapsin-1, brain acid-soluble protein-1 and myelin basic protein. Morphine-induced change was limited to no more than 5 up-regulated and 18 down-regulated proteins (>2-fold).
Collapse
|
24
|
Wang Q, Luo Q, Yang Z, Zhao YH, Li J, Wang J, Piao J, Chen X. Weighted gene co-expression network analysis identified six hub genes associated with rupture of intracranial aneurysms. PLoS One 2020; 15:e0229308. [PMID: 32084215 PMCID: PMC7034829 DOI: 10.1371/journal.pone.0229308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Intracranial aneurysms (IAs) are characterized by localized dilation or ballooning of a cerebral artery. When IAs rupture, blood leaks into the space around the brain to create a subarachnoid hemorrhage. The latter is associated with a higher risk of disability and mortality. The aims of this study were to gain greater insight into the pathogenesis of ruptured IAs, and to clarify whether identified hub genes represent potential biological markers for assessing the likelihood of IA progression and rupture. Briefly, the GSE36791 and GSE73378 datasets from the National Center of Biotechnology Information Gene Expression Omnibus database were reanalyzed and subjected to a weighted gene co-expression network analysis to test the association between gene sets and clinical features. The clinical significance of these genes as potential biomarkers was also examined, with their expression validated by quantitative real-time PCR. A total of 14 co-expression modules and 238 hub genes were identified. In particular, three modules (labeled turquoise, blue, and brown) were found to highly correlate with IA rupture events. Additionally, six potential biomarkers were identified (BASP1, CEBPB, ECHDC2, GZMK, KLHL3, and SLC2A3), which are strongly associated with the progression and rupture of IAs. Taken together, these findings provide novel insights into potential molecular mechanisms responsible for IAs and they highlight the potential for these particular genes to serve as biomarkers for monitoring IA rupture.
Collapse
Affiliation(s)
- Qunhui Wang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
| | - Qi Luo
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
| | - Zhongxi Yang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
| | - Yu-Hao Zhao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
| | - Jiaqi Li
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
| | - Jian Wang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
| | - Jianmin Piao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
- * E-mail: (XC); (JP)
| | - Xuan Chen
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin, P. R. China
- * E-mail: (XC); (JP)
| |
Collapse
|
25
|
Hartl M, Puglisi K, Nist A, Raffeiner P, Bister K. The brain acid-soluble protein 1 (BASP1) interferes with the oncogenic capacity of MYC and its binding to calmodulin. Mol Oncol 2020; 14:625-644. [PMID: 31944520 PMCID: PMC7053243 DOI: 10.1002/1878-0261.12636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022] Open
Abstract
The MYC protein is a transcription factor with oncogenic potential controlling fundamental cellular processes such as cell proliferation, metabolism, differentiation, and apoptosis. The MYC gene is a major cancer driver, and elevated MYC protein levels are a hallmark of most human cancers. We have previously shown that the brain acid-soluble protein 1 gene (BASP1) is specifically downregulated by the v-myc oncogene and that ectopic BASP1 expression inhibits v-myc-induced cell transformation. The 11-amino acid effector domain of the BASP1 protein interacts with the calcium sensor calmodulin (CaM) and is mainly responsible for this inhibitory function. We also reported recently that CaM interacts with all MYC variant proteins and that ectopic CaM increases the transactivation and transformation potential of the v-Myc protein. Here, we show that the presence of excess BASP1 or of a synthetic BASP1 effector domain peptide leads to displacement of v-Myc from CaM. The protein stability of v-Myc is decreased in cells co-expressing v-Myc and BASP1, which may account for the inhibition of v-Myc. Furthermore, suppression of v-Myc-triggered transcriptional activation and cell transformation is compensated by ectopic CaM, suggesting that BASP1-mediated withdrawal of CaM from v-Myc is a crucial event in the inhibition. In view of the tumor-suppressive role of BASP1 which was recently also reported for human cancer, small compounds or peptides based on the BASP1 effector domain could be used in drug development strategies aimed at tumors with high MYC expression.
Collapse
Affiliation(s)
- Markus Hartl
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Austria
| | - Kane Puglisi
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Austria
| | - Andrea Nist
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Austria
| | - Philipp Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Austria
| |
Collapse
|
26
|
Srivastava AC, Thompson YG, Singhal J, Stellern J, Srivastava A, Du J, O'Connor TR, Riggs AD. Elimination of human folypolyglutamate synthetase alters programming and plasticity of somatic cells. FASEB J 2019; 33:13747-13761. [PMID: 31585510 DOI: 10.1096/fj.201901721r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Folates are vital cofactors for the regeneration of S-adenosyl methionine, which is the methyl source for DNA methylation, protein methylation, and other aspects of one-carbon (C1) metabolism. Thus, folates are critical for establishing and preserving epigenetic programming. Folypolyglutamate synthetase (FPGS) is known to play a crucial role in the maintenance of intracellular folate levels. Therefore, any modulation in FPGS is expected to alter DNA methylation and numerous other metabolic pathways. To explore the role of polyglutamylation of folate, we eliminated both isoforms of FPGS in human cells (293T), producing FPGS knockout (FPGSko) cells. The elimination of FPGS significantly decreased cell proliferation, with a major effect on oxidative phosphorylation and a lesser effect on glycolysis. We found a substantial reduction in global DNA methylation and noteworthy changes in gene expression related to C1 metabolism, cell division, DNA methylation, pluripotency, Glu metabolism, neurogenesis, and cardiogenesis. The expression levels of NANOG, octamer-binding transcription factor 4, and sex-determining region Y-box 2 levels were increased in the mutant, consistent with the transition to a stem cell-like state. Gene expression and metabolite data also indicate a major change in Glu and GABA metabolism. In the appropriate medium, FPGSko cells can differentiate to produce mainly cells with characteristics of either neural stem cells or cardiomyocytes.-Srivastava, A. C., Thompson, Y. G., Singhal, J., Stellern, J., Srivastava, A., Du, J., O'Connor, T. R., Riggs, A. D. Elimination of human folypolyglutamate synthetase alters programming and plasticity of somatic cells.
Collapse
Affiliation(s)
- Avinash C Srivastava
- Department of Diabetes Complications and Metabolism, City of Hope National Medical Center, Duarte, California, USA
| | | | - Jyotsana Singhal
- Department of Diabetes Complications and Metabolism, City of Hope National Medical Center, Duarte, California, USA
| | - Jordan Stellern
- Department of Cancer Biology, City of Hope National Medical Center, Duarte, California, USA
| | - Anviksha Srivastava
- Department of Cancer Biology, City of Hope National Medical Center, Duarte, California, USA
| | - Juan Du
- Integrative Genomics Core Facility, City of Hope National Medical Center, Duarte, California, USA
| | - Timothy R O'Connor
- Department of Cancer Biology, City of Hope National Medical Center, Duarte, California, USA
| | - Arthur D Riggs
- Department of Diabetes Complications and Metabolism, City of Hope National Medical Center, Duarte, California, USA
| |
Collapse
|
27
|
Ma NX, Yin JC, Chen G. Transcriptome Analysis of Small Molecule-Mediated Astrocyte-to-Neuron Reprogramming. Front Cell Dev Biol 2019; 7:82. [PMID: 31231645 PMCID: PMC6558402 DOI: 10.3389/fcell.2019.00082] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/01/2019] [Indexed: 12/21/2022] Open
Abstract
Chemical reprogramming of astrocytes into neurons represents a promising approach to regenerate new neurons for brain repair, but the underlying mechanisms driving this trans-differentiation process are not well understood. We have recently identified four small molecules – CHIR99021, DAPT, LDN193189, and SB431542 – that can efficiently reprogram cultured human fetal astrocytes into functional neurons. Here we employ the next generation of RNA-sequencing technology to investigate the transcriptome changes during the astrocyte-to-neuron (AtN) conversion process. We found that the four small molecules can rapidly activate the hedgehog signaling pathway while downregulating many glial genes such as FN1 and MYL9 within 24 h of treatment. Chemical reprogramming is mediated by several waves of differential gene expression, including upregulation of hedgehog, Wnt/β-catenin, and Notch signaling pathways, together with downregulation of TGF-β and JAK/STAT signaling pathways. Our gene network analyses reveal many well-connected hub genes such as repulsive guidance molecule A (RGMA), neuronatin (NNAT), neurogenin 2 (NEUROG2), NPTX2, MOXD1, JAG1, and GAP43, which may coordinate the chemical reprogramming process. Together, these findings provide critical insights into the molecular cascades triggered by a combination of small molecules that eventually leads to chemical conversion of astrocytes into neurons.
Collapse
Affiliation(s)
- Ning-Xin Ma
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Jiu-Chao Yin
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Gong Chen
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
28
|
Hartl M, Schneider R. A Unique Family of Neuronal Signaling Proteins Implicated in Oncogenesis and Tumor Suppression. Front Oncol 2019; 9:289. [PMID: 31058089 PMCID: PMC6478813 DOI: 10.3389/fonc.2019.00289] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/29/2019] [Indexed: 12/20/2022] Open
Abstract
The neuronal proteins GAP43 (neuromodulin), MARCKS, and BASP1 are highly expressed in the growth cones of nerve cells where they are involved in signal transmission and cytoskeleton organization. Although their primary structures are unrelated, these signaling proteins share several structural properties like fatty acid modification, and the presence of cationic effector domains. GAP43, MARCKS, and BASP1 bind to cell membrane phospholipids, a process reversibly regulated by protein kinase C-phosphorylation or by binding to the calcium sensor calmodulin (CaM). GAP43, MARCKS, and BASP1 are also expressed in non-neuronal cells, where they may have important functions to manage cytoskeleton architecture, and in case of MARCKS and BASP1 to act as cofactors in transcriptional regulation. During neoplastic cell transformation, the proteins reveal differential expression in normal vs. tumor cells, and display intrinsic tumor promoting or tumor suppressive activities. Whereas GAP43 and MARCKS are oncogenic, tumor suppressive functions have been ascribed to BASP1 and in part to MARCKS depending on the cell type. Like MARCKS, the myristoylated BASP1 protein is localized both in the cytoplasm and in the cell nucleus. Nuclear BASP1 participates in gene regulation converting the Wilms tumor transcription factor WT1 from an oncoprotein into a tumor suppressor. The BASP1 gene is downregulated in many human tumor cell lines particularly in those derived from leukemias, which display elevated levels of WT1 and of the major cancer driver MYC. BASP1 specifically inhibits MYC-induced cell transformation in cultured cells. The tumor suppressive functions of BASP1 and MARCKS could be exploited to expand the spectrum of future innovative therapeutic approaches to inhibit growth and viability of susceptible human tumors.
Collapse
Affiliation(s)
- Markus Hartl
- Center of Molecular Biosciences (CMBI), Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Rainer Schneider
- Center of Molecular Biosciences (CMBI), Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
29
|
Narbute K, Piļipenko V, Pupure J, Dzirkale Z, Jonavičė U, Tunaitis V, Kriaučiūnaitė K, Jarmalavičiūtė A, Jansone B, Kluša V, Pivoriūnas A. Intranasal Administration of Extracellular Vesicles Derived from Human Teeth Stem Cells Improves Motor Symptoms and Normalizes Tyrosine Hydroxylase Expression in the Substantia Nigra and Striatum of the 6-Hydroxydopamine-Treated Rats. Stem Cells Transl Med 2019; 8:490-499. [PMID: 30706999 PMCID: PMC6477008 DOI: 10.1002/sctm.18-0162] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder affecting millions of people worldwide. At present, there is no effective cure for PD; treatments are symptomatic and do not halt progression of neurodegeneration. Extracellular vesicles (EVs) can cross the blood-brain barrier and represent promising alternative to the classical treatment strategies. In the present study, we examined therapeutic effects of intranasal administration of EVs derived from human exfoliated deciduous teeth stem cells (SHEDs) on unilateral 6-hydroxydopamine (6-OHDA) medial forebrain bundle (MFB) rat model of PD. CatWalk gait tests revealed that EVs effectively suppressed 6-OHDA-induced gait impairments. All tested gait parameters (stand, stride length, step cycle, and duty cycle) were significantly improved in EV-treated animals when compared with 6-OHDA-lesion group rats. Furthermore, EVs slowed down numbers of 6-OHDA-induced contralateral rotations in apomorphine test. Improvements in motor function correlated with normalization of tyrosine hydroxylase expression in the striatum and substantia nigra. In conclusion, we demonstrated, for the first time, the therapeutic efficacy of intranasal administration of EVs derived from SHEDs in a rat model of PD induced by 6-OHDA intra-MFB lesion. Our findings could be potentially exploited for the development of new treatment strategies against PD.
Collapse
Affiliation(s)
- Karīna Narbute
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Vladimirs Piļipenko
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Jolanta Pupure
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Zane Dzirkale
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Ugnė Jonavičė
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Virginijus Tunaitis
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Karolina Kriaučiūnaitė
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Akvilė Jarmalavičiūtė
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Baiba Jansone
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Vija Kluša
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Augustas Pivoriūnas
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| |
Collapse
|
30
|
Methylation-associated silencing of BASP1 contributes to leukemogenesis in t(8;21) acute myeloid leukemia. Exp Mol Med 2018; 50:1-8. [PMID: 29674693 PMCID: PMC5938046 DOI: 10.1038/s12276-018-0067-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/06/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022] Open
Abstract
The AML1-ETO fusion protein (A/E), which results from the t(8;21) translocation, is considered to be a leukemia-initiating event. Identifying the mechanisms underlying the oncogenic activity of A/E remains a major challenge. In this study, we identified a specific down-regulation of brain acid-soluble protein 1 (BASP1) in t(8;21) acute myeloid leukemia (AML). A/E recognized AML1-binding sites and recruited DNA methyltransferase 3a (DNMT3a) to the BASP1 promoter sequence, which triggered DNA methylation-mediated silencing of BASP1. Ectopic expression of BASP1 inhibited proliferation and the colony-forming ability of A/E-positive AML cell lines and led to apoptosis and cell cycle arrest. The DNMT inhibitor decitabine up-regulated the expression of BASP1 in A/E-positive AML cell lines. In conclusion, our data suggest that BASP1 silencing via promoter methylation may be involved in A/E-mediated leukemogenesis and that BASP1 targeting may be an actionable therapeutic strategy in t(8;21) AML. A chromosomal rearrangement commonly observed in certain leukemias selectively inactivates a gene that otherwise thwarts cancerous growth. Between 7 and 12% of acute myeloid leukemia cases exhibit a dramatic alteration in chromosomal structure that results in the production of an abnormal fusion protein. Researchers led by Li Yu at the General Hospital of Shenzen University in China have learned that this protein promotes disease progression by switching off an important tumor suppressor. Yu and colleagues showed that it binds a genomic sequence that regulates the gene encoding a second protein called BASP1, dramatically reducing its production. This gene silencing facilitates tumor growth. Chemicals that reactivated BASP1 production slowed proliferation and initiated ‘self-destruct’ mechanisms in leukemia cells. These findings suggest that BASP1-oriented therapies could offer a fruitful avenue of treatment for some patients.
Collapse
|
31
|
Kurzbach D, Beier A, Vanas A, Flamm AG, Platzer G, Schwarz TC, Konrat R. NMR probing and visualization of correlated structural fluctuations in intrinsically disordered proteins. Phys Chem Chem Phys 2018; 19:10651-10656. [PMID: 28397898 DOI: 10.1039/c7cp00430c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel statistical analysis of paramagnetic relaxation enhancement (PRE) and paramagnetic relaxation interference (PRI) based nuclear magnetic resonance (NMR) data is proposed based on the computation of correlation matrices. The technique is demonstrated with an example of the intrinsically disordered proteins (IDPs) osteopontin (OPN) and brain acid soluble protein 1 (BASP1). The correlation analysis visualizes in detail the subtleties of conformational averaging in IDPs and highlights the presence of correlated structural fluctuations of individual sub-domains in IDPs.
Collapse
Affiliation(s)
- Dennis Kurzbach
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France.
| | | | | | | | | | | | | |
Collapse
|
32
|
Webber JP, Spary LK, Mason MD, Tabi Z, Brewis IA, Clayton A. Prostate stromal cell proteomics analysis discriminates normal from tumour reactive stromal phenotypes. Oncotarget 2018; 7:20124-39. [PMID: 26934553 PMCID: PMC4991442 DOI: 10.18632/oncotarget.7716] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/27/2016] [Indexed: 01/05/2023] Open
Abstract
Changes within interstitial stromal compartments often accompany carcinogenesis, and this is true of prostate cancer. Typically, the tissue becomes populated by myofibroblasts that can promote progression. Not all myofibroblasts exhibit the same negative influence, however, and identifying the aggressive form of myofibroblast may provide useful information at diagnosis. A means of molecularly defining such myofibroblasts is unknown. We compared protein profiles of normal and diseased stroma isolated from prostate cancer patients to identify discriminating hallmarks of disease-associated stroma. We included the stimulation of normal stromal cells with known myofibroblast inducers namely soluble TGFβ and exosome-associated-TGFβ and compared the function and protein profiles arising. In all 6-patients examined, diseased stroma exhibited a pro-angiogenic influence on endothelial cells, generating large multicellular vessel-like structures. Identical structures were apparent following stimulation of normal stroma with exosomes (5/6 patients), but TGFβ-stimulation generated a non-angiogenic stroma. Proteomics highlighted disease-related cytoskeleton alterations such as elevated Transgelin (TAGLN). Many of these were also changed following TGFβ or exosome stimulation and did not well discriminate the nature of the stimulus. Soluble TGFβ, however triggered differential expression of proteins related to mitochondrial function including voltage dependent ion channels VDAC1 and 2, and this was not found in the other stromal types studied. Surprisingly, Aldehyde Dehydrogenase (ALDH1A1), a stem-cell associated protein was detected in normal stromal cells and found to decrease in disease. In summary, we have discovered a set of proteins that contribute to defining disease-associated myofibroblasts, and emphasise the similarity between exosome-generated myofibroblasts and those naturally arising in situ.
Collapse
Affiliation(s)
- Jason P Webber
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Lisa K Spary
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Malcolm D Mason
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Zsuzsanna Tabi
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Ian A Brewis
- Institute of Translation, Innovation, Methodology and Engagement (TIME), Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Aled Clayton
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| |
Collapse
|
33
|
Caraveo G, Soste M, Cappelleti V, Fanning S, van Rossum DB, Whitesell L, Huang Y, Chung CY, Baru V, Zaichick S, Picotti P, Lindquist S. FKBP12 contributes to α-synuclein toxicity by regulating the calcineurin-dependent phosphoproteome. Proc Natl Acad Sci U S A 2017; 114:E11313-E11322. [PMID: 29229832 PMCID: PMC5748183 DOI: 10.1073/pnas.1711926115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Calcineurin is an essential Ca2+-dependent phosphatase. Increased calcineurin activity is associated with α-synuclein (α-syn) toxicity, a protein implicated in Parkinson's Disease (PD) and other neurodegenerative diseases. Calcineurin can be inhibited with Tacrolimus through the recruitment and inhibition of the 12-kDa cis-trans proline isomerase FK506-binding protein (FKBP12). Whether calcineurin/FKBP12 represents a native physiologically relevant assembly that occurs in the absence of pharmacological perturbation has remained elusive. We leveraged α-syn as a model to interrogate whether FKBP12 plays a role in regulating calcineurin activity in the absence of Tacrolimus. We show that FKBP12 profoundly affects the calcineurin-dependent phosphoproteome, promoting the dephosphorylation of a subset of proteins that contributes to α-syn toxicity. Using a rat model of PD, partial elimination of the functional interaction between FKBP12 and calcineurin, with low doses of the Food and Drug Administration (FDA)-approved compound Tacrolimus, blocks calcineurin's activity toward those proteins and protects against the toxic hallmarks of α-syn pathology. Thus, FKBP12 can endogenously regulate calcineurin activity with therapeutic implications for the treatment of PD.
Collapse
Affiliation(s)
- Gabriela Caraveo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142;
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | - Valentina Cappelleti
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
- Department of Computational Biology, Research and Innovation Centre, Foundation Edmund Mach, 38010 San Michele, Italy
| | - Saranna Fanning
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Damian B van Rossum
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA 17033
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Yanmei Huang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Chee Yeun Chung
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Valeriya Baru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Sofia Zaichick
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Paola Picotti
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
34
|
Replacing reprogramming factors with antibodies selected from combinatorial antibody libraries. Nat Biotechnol 2017; 35:960-968. [PMID: 28892074 DOI: 10.1038/nbt.3963] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 08/16/2017] [Indexed: 01/12/2023]
Abstract
The reprogramming of differentiated cells into induced pluripotent stem cells (iPSCs) is usually achieved by exogenous induction of transcription by factors acting in the nucleus. In contrast, during development, signaling pathways initiated at the membrane induce differentiation. The central idea of this study is to identify antibodies that can catalyze cellular de-differentiation and nuclear reprogramming by acting at the cell surface. We screen a lentiviral library encoding ∼100 million secreted and membrane-bound single-chain antibodies and identify antibodies that can replace either Sox2 and Myc (c-Myc) or Oct4 during reprogramming of mouse embryonic fibroblasts into iPSCs. We show that one Sox2-replacing antibody antagonizes the membrane-associated protein Basp1, thereby de-repressing nuclear factors WT1, Esrrb and Lin28a (Lin28) independent of Sox2. By manipulating this pathway, we identify three methods to generate iPSCs. Our results establish unbiased selection from autocrine combinatorial antibody libraries as a robust method to discover new biologics and uncover membrane-to-nucleus signaling pathways that regulate pluripotency and cell fate.
Collapse
|
35
|
Gollapalli K, Ghantasala S, Kumar S, Srivastava R, Rapole S, Moiyadi A, Epari S, Srivastava S. Subventricular zone involvement in Glioblastoma - A proteomic evaluation and clinicoradiological correlation. Sci Rep 2017; 7:1449. [PMID: 28469129 PMCID: PMC5431125 DOI: 10.1038/s41598-017-01202-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 03/27/2017] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma multiforme (GBM), the most malignant of all gliomas is characterized by a high degree of heterogeneity and poor response to treatment. The sub-ventricular zone (SVZ) is the major site of neurogenesis in the brain and is rich in neural stem cells. Based on the proximity of the GBM tumors to the SVZ, the tumors can be further classified into SVZ+ and SVZ−. The tumors located in close contact with the SVZ are classified as SVZ+, while the tumors located distantly from the SVZ are classified as SVZ−. To gain an insight into the increased aggressiveness of SVZ+ over SVZ− tumors, we have used proteomics techniques like 2D-DIGE and LC-MS/MS to investigate any possible proteomic differences between the two subtypes. Serum proteomic analysis revealed significant alterations of various acute phase proteins and lipid carrying proteins, while tissue proteomic analysis revealed significant alterations in cytoskeletal, lipid binding, chaperone and cell cycle regulating proteins, which are already known to be associated with disease pathobiology. These findings provide cues to molecular basis behind increased aggressiveness of SVZ+ GBM tumors over SVZ− GBM tumors and plausible therapeutic targets to improve treatment modalities for these highly invasive tumors.
Collapse
Affiliation(s)
| | | | - Sachendra Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | | | - Srikanth Rapole
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, India
| | - Aliasgar Moiyadi
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) and Tata Memorial Hospital, Tata Memorial Centre, Kharghar, Navi Mumbai, Mumbai, India
| | - Sridhar Epari
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) and Tata Memorial Hospital, Tata Memorial Centre, Kharghar, Navi Mumbai, Mumbai, India
| | | |
Collapse
|
36
|
Brethour D, Mehrabian M, Williams D, Wang X, Ghodrati F, Ehsani S, Rubie EA, Woodgett JR, Sevalle J, Xi Z, Rogaeva E, Schmitt-Ulms G. A ZIP6-ZIP10 heteromer controls NCAM1 phosphorylation and integration into focal adhesion complexes during epithelial-to-mesenchymal transition. Sci Rep 2017; 7:40313. [PMID: 28098160 PMCID: PMC5241876 DOI: 10.1038/srep40313] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023] Open
Abstract
The prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding the function of PrP. Building on data which suggested PrP and ZIP6 are critical during epithelial-to-mesenchymal transition (EMT), we investigated ZIP6 in an EMT paradigm using ZIP6 knockout cells, mass spectrometry and bioinformatic methods. Reminiscent of PrP, ZIP6 levels are five-fold upregulated during EMT and the protein forms a complex with NCAM1. ZIP6 also interacts with ZIP10 and the two ZIP transporters exhibit interdependency during their expression. ZIP6 contributes to the integration of NCAM1 in focal adhesion complexes but, unlike cells lacking PrP, ZIP6 deficiency does not abolish polysialylation of NCAM1. Instead, ZIP6 mediates phosphorylation of NCAM1 on a cluster of cytosolic acceptor sites. Substrate consensus motif features and in vitro phosphorylation data point toward GSK3 as the kinase responsible, and interface mapping experiments identified histidine-rich cytoplasmic loops within the ZIP6/ZIP10 heteromer as a novel scaffold for GSK3 binding. Our data suggests that PrP and ZIP6 inherited the ability to interact with NCAM1 from their common ZIP ancestors but have since diverged to control distinct posttranslational modifications of NCAM1.
Collapse
Affiliation(s)
- Dylan Brethour
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Department of Laboratory Medicine &Pathobiology, University of Toronto, Ontario, Canada
| | - Mohadeseh Mehrabian
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Department of Laboratory Medicine &Pathobiology, University of Toronto, Ontario, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Xinzhu Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Department of Laboratory Medicine &Pathobiology, University of Toronto, Ontario, Canada
| | - Farinaz Ghodrati
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Department of Laboratory Medicine &Pathobiology, University of Toronto, Ontario, Canada
| | - Sepehr Ehsani
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Elizabeth A Rubie
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jean Sevalle
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Zhengrui Xi
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Department of Neurology, University of Toronto, Ontario, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada.,Department of Laboratory Medicine &Pathobiology, University of Toronto, Ontario, Canada
| |
Collapse
|
37
|
Pires AO, Mendes-Pinheiro B, Teixeira FG, Anjo SI, Ribeiro-Samy S, Gomes ED, Serra SC, Silva NA, Manadas B, Sousa N, Salgado AJ. Unveiling the Differences of Secretome of Human Bone Marrow Mesenchymal Stem Cells, Adipose Tissue-Derived Stem Cells, and Human Umbilical Cord Perivascular Cells: A Proteomic Analysis. Stem Cells Dev 2016; 25:1073-83. [PMID: 27226274 DOI: 10.1089/scd.2016.0048] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The use of human mesenchymal stem cells (hMSCs) has emerged as a possible therapeutic strategy for CNS-related conditions. Research in the last decade strongly suggests that MSC-mediated benefits are closely related with their secretome. Studies published in recent years have shown that the secretome of hMSCs isolated from different tissue sources may present significant variation. With this in mind, the present work performed a comparative proteomic-based analysis through mass spectrometry on the secretome of hMSCs derived from bone marrow (BMSCs), adipose tissue (ASCs), and human umbilical cord perivascular cells (HUCPVCs). The results revealed that BMSCs, ASCs, and HUCPVCs differed in their secretion of neurotrophic, neurogenic, axon guidance, axon growth, and neurodifferentiative proteins, as well as proteins with neuroprotective actions against oxidative stress, apoptosis, and excitotoxicity, which have been shown to be involved in several CNS disorder/injury processes. Although important changes were observed within the secretome of the cell populations that were analyzed, all cell populations shared the capability of secreting important neuroregulatory molecules. The difference in their secretion pattern may indicate that their secretome is specific to a condition of the CNS. Nevertheless, the confirmation that the secretome of MSCs isolated from different tissue sources is rich in neuroregulatory molecules represents an important asset not only for the development of future neuroregenerative strategies but also for their use as a therapeutic option for human clinical trials.
Collapse
Affiliation(s)
- Ana O Pires
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Barbara Mendes-Pinheiro
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Fábio G Teixeira
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Sandra I Anjo
- 3 Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra , Coimbra, Portugal .,4 CNC-Center for Neurosciences and Cell Biology, University of Coimbra , Coimbra, Portugal
| | - Silvina Ribeiro-Samy
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Eduardo D Gomes
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Sofia C Serra
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Nuno A Silva
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Bruno Manadas
- 4 CNC-Center for Neurosciences and Cell Biology, University of Coimbra , Coimbra, Portugal
| | - Nuno Sousa
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Antonio J Salgado
- 1 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Braga, Portugal .,2 ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| |
Collapse
|
38
|
Forsova OS, Zakharov VV. High-order oligomers of intrinsically disordered brain proteins BASP1 and GAP-43 preserve the structural disorder. FEBS J 2016; 283:1550-69. [PMID: 26918762 DOI: 10.1111/febs.13692] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/26/2016] [Accepted: 02/23/2016] [Indexed: 11/30/2022]
Abstract
Brain acid-soluble protein-1 (BASP1) and growth-associated protein-43 (GAP-43) are presynaptic membrane proteins participating in axon guidance, neuroregeneration and synaptic plasticity. They are presumed to sequester phosphatidylinositol-4,5-bisphosphate (PIP2 ) in lipid rafts. Previously we have shown that the proteins form heterogeneously sized oligomers in the presence of anionic phospholipids or SDS at submicellar concentration. BASP1 and GAP-43 are intrinsically disordered proteins (IDPs). In light of this, we investigated the structure of their oligomers. Using partial cross-linking of the oligomers with glutaraldehyde, the aggregation numbers of BASP1 and GAP-43 were estimated as 10-14 and 6-7 monomer subunits, respectively. The cross-linking pattern indicated that the subunits are circularly arranged. The circular dichroism (CD) spectra of the monomers were characteristic of coil-like IDPs showing unordered structure with a high population of polyproline-II conformation. The oligomerization was accompanied by a minor CD spectral change attributable to formation of a small amount of α-helix. The number of residues in the α-helical conformation was estimated as 13 in BASP1 and 18 in GAP-43. However, the overall structure of the oligomers remained disordered, indicating a high degree of 'fuzziness'. This was confirmed by measuring the hydrodynamic dimensions of the oligomers using polyacrylamide gradient gel electrophoresis and size-exclusion chromatography, and by assaying their sensitivity to proteolytic digestion. There is evidence that the observed α-helical folding occurs within the basic effector domains, which are presumably tethered together via anionic molecules of SDS or PIP2 . We conclude that BASP1 and GAP-43 oligomers preserve a mostly disordered structure, which may be of great importance for their function in PIP2 signaling pathway.
Collapse
Affiliation(s)
- Oksana S Forsova
- Molecular and Radiation Biophysics Division, B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre 'Kurchatov Institute', Gatchina, Russia.,Laboratory of Natural Polymers, Institute of Macromolecular Compounds, Russian Academy of Sciences, St Petersburg, Russia
| | - Vladislav V Zakharov
- Molecular and Radiation Biophysics Division, B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre 'Kurchatov Institute', Gatchina, Russia.,Laboratory of Natural Polymers, Institute of Macromolecular Compounds, Russian Academy of Sciences, St Petersburg, Russia.,Department of Biophysics, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St Petersburg Polytechnic University, Russia
| |
Collapse
|
39
|
Murphy S, Zweyer M, Henry M, Meleady P, Mundegar RR, Swandulla D, Ohlendieck K. Label-free mass spectrometric analysis reveals complex changes in the brain proteome from the mdx-4cv mouse model of Duchenne muscular dystrophy. Clin Proteomics 2015; 12:27. [PMID: 26604869 PMCID: PMC4657206 DOI: 10.1186/s12014-015-9099-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/13/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND X-linked muscular dystrophy is a primary disease of the neuromuscular system. Primary abnormalities in the Dmd gene result in the absence of the full-length isoform of the membrane cytoskeletal protein dystrophin. Besides progressive skeletal muscle wasting and cardio-respiratory complications, developmental cognitive deficits and behavioural abnormalities are clinical features of Duchenne muscular dystrophy. In order to better understand the mechanisms that underlie impaired brain functions in Duchenne patients, we have carried out a proteomic analysis of total brain extracts from the mdx-4cv mouse model of dystrophinopathy. RESULTS The comparative proteomic profiling of the mdx-4cv brain revealed a significant increase in 39 proteins and a decrease in 7 proteins. Interesting brain tissue-associated proteins with an increased concentration in the mdx-4cv animal model were represented by the glial fibrillary acidic protein GFAP, the neuronal Ca(2+)-binding protein calretinin, annexin AnxA5, vimentin, the neuron-specific enzyme ubiquitin carboxyl-terminal hydrolase isozyme L1, the dendritic spine protein drebrin, the cytomatrix protein bassoon of the nerve terminal active zone, and the synapse-associated protein SAP97. Decreased proteins were identified as the nervous system-specific proteins syntaxin-1B and syntaxin-binding protein 1, as well as the plasma membrane Ca(2+)-transporting ATPase PMCA2 that is mostly found in the brain cortex. The differential expression patterns of GFAP, vimentin, PMCA2 and AnxA5 were confirmed by immunoblotting. Increased GFAP levels were also verified by immunofluorescence microscopy. CONCLUSIONS The large number of mass spectrometrically identified proteins with an altered abundance suggests complex changes in the mdx-4cv brain proteome. Increased levels of the glial fibrillary acidic protein, an intermediate filament component that is uniquely associated with astrocytes in the central nervous system, imply neurodegeneration-associated astrogliosis. The up-regulation of annexin and vimentin probably represent compensatory mechanisms involved in membrane repair and cytoskeletal stabilization in the absence of brain dystrophin. Differential alterations in the Ca(2+)-binding protein calretinin and the Ca(2+)-pumping protein PMCA2 suggest altered Ca(2+)-handling mechanisms in the Dp427-deficient brain. In addition, the proteomic findings demonstrated metabolic adaptations and functional changes in the central nervous system from the dystrophic phenotype. Candidate proteins can now be evaluated for their suitability as proteomic biomarkers and their potential in predictive, diagnostic, prognostic and/or therapy-monitoring approaches to treat brain abnormalities in dystrophinopathies.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Rustam R Mundegar
- Department of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Dieter Swandulla
- Department of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare Ireland
| |
Collapse
|
40
|
Chen HJ, Shen YC, Shiao YJ, Liou KT, Hsu WH, Hsieh PH, Lee CY, Chen YR, Lin YL. Multiplex Brain Proteomic Analysis Revealed the Molecular Therapeutic Effects of Buyang Huanwu Decoction on Cerebral Ischemic Stroke Mice. PLoS One 2015; 10:e0140823. [PMID: 26492191 PMCID: PMC4619651 DOI: 10.1371/journal.pone.0140823] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/29/2015] [Indexed: 11/18/2022] Open
Abstract
Stroke is the second-leading cause of death worldwide, and tissue plasminogen activator (TPA) is the only drug used for a limited group of stroke patients in the acute phase. Buyang Huanwu Decoction (BHD), a traditional Chinese medicine prescription, has long been used for improving neurological functional recovery in stroke. In this study, we characterized the therapeutic effect of TPA and BHD in a cerebral ischemia/reperfusion (CIR) injury mouse model using multiplex proteomics approach. After the iTRAQ-based proteomics analysis, 1310 proteins were identified from the mouse brain with <1% false discovery rate. Among them, 877 quantitative proteins, 10.26% (90/877), 1.71% (15/877), and 2.62% (23/877) of the proteins was significantly changed in the CIR, BHD treatment, and TPA treatment, respectively. Functional categorization analysis showed that BHD treatment preserved the integrity of the blood–brain barrier (BBB) (Alb, Fga, and Trf), suppressed excitotoxicity (Grm5, Gnai, and Gdi), and enhanced energy metabolism (Bdh), thereby revealing its multiple effects on ischemic stroke mice. Moreover, the neurogenesis marker doublecortin was upregulated, and the activity of glycogen synthase kinase 3 (GSK-3) and Tau was inhibited, which represented the neuroprotective effects. However, TPA treatment deteriorated BBB breakdown. This study highlights the potential of BHD in clinical applications for ischemic stroke.
Collapse
Affiliation(s)
- Hong-Jhang Chen
- National Research Institute of Chinese Medicine, Taipei, Taiwan
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yuh-Chiang Shen
- National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Young-Ji Shiao
- National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Kuo-Tong Liou
- Department of Chinese Martial Arts and Graduate Institute of Sport Coaching Science, Chinese Culture University, Taipei, Taiwan
| | - Wei-Hsiang Hsu
- National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Pei-Hsuan Hsieh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Ying Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail: (YLL); (YRC)
| | - Yun-Lian Lin
- National Research Institute of Chinese Medicine, Taipei, Taiwan
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
- School of Pharmacy, National Taiwan University, Taipei, Taiwan
- * E-mail: (YLL); (YRC)
| |
Collapse
|
41
|
Partridge MA, Gopinath S, Myers SJ, Coorssen JR. An initial top-down proteomic analysis of the standard cuprizone mouse model of multiple sclerosis. J Chem Biol 2015; 9:9-18. [PMID: 26855677 DOI: 10.1007/s12154-015-0138-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/28/2015] [Indexed: 11/29/2022] Open
Abstract
An initial proteomic analysis of the cuprizone mouse model to characterise the breadth of toxicity by assessing cortex, skeletal muscle, spleen and peripheral blood mononuclear cells. Cuprizone treated vs. control mice for an initial characterisation. Select tissues from each group were pooled, analysed in triplicate using two-dimensional gel electrophoresis (2DE) and deep imaging and altered protein species identified using liquid chromatography tandem mass spectrometry (LC/MS/MS). Forty-three proteins were found to be uniquely detectable or undetectable in the cuprizone treatment group across the tissues analysed. Protein species identified in the cortex may potentially be linked to axonal damage in this model, and those in the spleen and peripheral blood mononuclear cells to the minimal peripheral immune cell infiltration into the central nervous system during cuprizone mediated demyelination. Primary oligodendrocytosis has been observed in type III lesions in multiple sclerosis. However, the underlying mechanisms are poorly understood. Cuprizone treatment results in oligodendrocyte apoptosis and secondary demyelination. This initial analysis identified proteins likely related to axonal damage; these may link primary oligodendrocytosis and secondary axonal damage. Furthermore, this appears to be the first study of the cuprizone model to also identify alterations in the proteomes of skeletal muscle, spleen and peripheral blood mononuclear cells. Notably, protein disulphide isomerase was not detected in the cuprizone cohort; its absence has been linked to reduced major histocompatibility class I assembly and reduced antigen presentation. Overall, the results suggest that, like experimental autoimmune encephalomyelitis, results from the standard cuprizone model should be carefully considered relative to clinical multiple sclerosis.
Collapse
Affiliation(s)
- Melissa A Partridge
- Department of Molecular Physiology, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia
| | - Sumana Gopinath
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Department of Neurology, Campbelltown Hospital, Campbelltown, NSW Australia
| | - Simon J Myers
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Neuro-Cell Biology Laboratory, School of Science and Health, University of Western Sydney, Penrith, NSW Australia
| | - Jens R Coorssen
- Department of Molecular Physiology, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia
| |
Collapse
|
42
|
Geist L, Henen MA, Haiderer S, Schwarz TC, Kurzbach D, Zawadzka-Kazimierczuk A, Saxena S, Zerko S, Koźmiński W, Hinderberger D, Konrat R. Protonation-dependent conformational variability of intrinsically disordered proteins. Protein Sci 2014; 22:1196-205. [PMID: 23821606 DOI: 10.1002/pro.2304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 11/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity and undergo rearrangements of the time-averaged conformational ensemble on changes of environmental conditions (e.g., in ionic strength, pH, molecular crowding). In contrast to stably folded proteins, IDPs often form compact conformations at acidic pH. The biological relevance of this process was, for example, demonstrated by nuclear magnetic resonance studies of the aggregation prone (low pH) state of α-synuclein. In this study, we report a large-scale analysis of the pH dependence of disordered proteins using the recently developed meta-structure approach. The meta-structure analysis of a large set of IDPs revealed a significant tendency of IDPs to form α-helical secondary structure elements and to preferentially fold into more compact structures under acidic conditions. The predictive validity of this novel approach was demonstrated with applications to the tumor-suppressor BASP1 and the transcription factor Tcf4.
Collapse
Affiliation(s)
- Leonhard Geist
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Laßek M, Weingarten J, Volknandt W. The synaptic proteome. Cell Tissue Res 2014; 359:255-65. [PMID: 25038742 DOI: 10.1007/s00441-014-1943-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/04/2014] [Indexed: 11/29/2022]
Abstract
Synapses are focal hot spots for signal transduction and plasticity in the brain. A synapse comprises an axon terminus, the presynapse, the synaptic cleft containing extracellular matrix proteins as well as adhesion molecules, and the postsynaptic density as target structure for chemical signaling. The proteomes of the presynaptic and postsynaptic active zones control neurotransmitter release and perception. These tasks demand short- and long-term structural and functional dynamics of the synapse mediated by its proteinaceous inventory. This review addresses subcellular fractionation protocols and the related proteomic approaches to the various synaptic subcompartments with an emphasis on the presynaptic active zone (PAZ). Furthermore, it discusses major constituents of the PAZ including the amyloid precursor protein family members. Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the pre- and postsynapse. The identification of protein candidates of the synapse provides the basis for further analyzing the interaction of synaptic proteins with their targets, and the effect of their deletion opens novel insights into the functional role of these proteins in neuronal communication. The knowledge of the molecular interactome is also a prerequisite for understanding numerous neurodegenerative diseases.
Collapse
Affiliation(s)
- Melanie Laßek
- Molecular and Cellular Neurobiology, Goethe University, Frankfurt, Germany
| | | | | |
Collapse
|
44
|
Cadet JL, Brannock C, Jayanthi S, Krasnova IN. Transcriptional and epigenetic substrates of methamphetamine addiction and withdrawal: evidence from a long-access self-administration model in the rat. Mol Neurobiol 2014; 51:696-717. [PMID: 24939695 PMCID: PMC4359351 DOI: 10.1007/s12035-014-8776-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/01/2014] [Indexed: 01/06/2023]
Abstract
Methamphetamine use disorder is a chronic neuropsychiatric disorder characterized by recurrent binge episodes, intervals of abstinence, and relapses to drug use. Humans addicted to methamphetamine experience various degrees of cognitive deficits and other neurological abnormalities that complicate their activities of daily living and their participation in treatment programs. Importantly, models of methamphetamine addiction in rodents have shown that animals will readily learn to give themselves methamphetamine. Rats also accelerate their intake over time. Microarray studies have also shown that methamphetamine taking is associated with major transcriptional changes in the striatum measured within a short or longer time after cessation of drug taking. After a 2-h withdrawal time, there was increased expression of genes that participate in transcription regulation. These included cyclic AMP response element binding (CREB), ETS domain-containing protein (ELK1), and members of the FOS family of transcription factors. Other genes of interest include brain-derived neurotrophic factor (BDNF), tyrosine kinase receptor, type 2 (TrkB), and synaptophysin. Methamphetamine-induced transcription was found to be regulated via phosphorylated CREB-dependent events. After a 30-day withdrawal from methamphetamine self-administration, however, there was mostly decreased expression of transcription factors including junD. There was also downregulation of genes whose protein products are constituents of chromatin-remodeling complexes. Altogether, these genome-wide results show that methamphetamine abuse might be associated with altered regulation of a diversity of gene networks that impact cellular and synaptic functions. These transcriptional changes might serve as triggers for the neuropsychiatric presentations of humans who abuse this drug. Better understanding of the way that gene products interact to cause methamphetamine addiction will help to develop better pharmacological treatment of methamphetamine addicts.
Collapse
Affiliation(s)
- Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH, DHHS, 251 Bayview Boulevard, Baltimore, MD, 21224, USA,
| | | | | | | |
Collapse
|
45
|
Laßek M, Weingarten J, Volknandt W. The Proteome of the Murine Presynaptic Active Zone. Proteomes 2014; 2:243-257. [PMID: 28250380 PMCID: PMC5302740 DOI: 10.3390/proteomes2020243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/09/2014] [Accepted: 04/21/2014] [Indexed: 01/09/2023] Open
Abstract
The proteome of the presynaptic active zone controls neurotransmitter release and the short- and long-term structural and functional dynamics of the nerve terminal. The proteinaceous inventory of the presynaptic active zone has recently been reported. This review will evaluate the subcellular fractionation protocols and the proteomic approaches employed. A breakthrough for the identification of the proteome of the presynaptic active zone was the successful employment of antibodies directed against a cytosolic epitope of membrane integral synaptic vesicle proteins for the immunopurification of synaptic vesicles docked to the presynaptic plasma membrane. Combining immunopurification and subsequent analytical mass spectrometry, hundreds of proteins, including synaptic vesicle proteins, components of the presynaptic fusion and retrieval machinery, proteins involved in intracellular and extracellular signaling and a large variety of adhesion molecules, were identified. Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the presynapse. This review will critically discuss both the experimental approaches and prominent protein candidates identified. Many proteins have not previously been assigned to the presynaptic release sites and may be directly involved in the short- and long-term structural modulation of the presynaptic compartment. The identification of proteinaceous constituents of the presynaptic active zone provides the basis for further analyzing the interaction of presynaptic proteins with their targets and opens novel insights into the functional role of these proteins in neuronal communication.
Collapse
Affiliation(s)
- Melanie Laßek
- Institute for Cell Biology and Neuroscience, Department Molecular and Cellular Neurobiology, Max von Laue Str. 13, 60438 Frankfurt am Main, Germany.
| | - Jens Weingarten
- Institute for Cell Biology and Neuroscience, Department Molecular and Cellular Neurobiology, Max von Laue Str. 13, 60438 Frankfurt am Main, Germany.
| | - Walter Volknandt
- Institute for Cell Biology and Neuroscience, Department Molecular and Cellular Neurobiology, Max von Laue Str. 13, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
46
|
Weingarten J, Lassek M, Mueller BF, Rohmer M, Lunger I, Baeumlisberger D, Dudek S, Gogesch P, Karas M, Volknandt W. The proteome of the presynaptic active zone from mouse brain. Mol Cell Neurosci 2014; 59:106-18. [PMID: 24534009 DOI: 10.1016/j.mcn.2014.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 01/07/2023] Open
Abstract
Neurotransmitter release as well as the structural and functional dynamics of the presynaptic active zone is controlled by proteinaceous components. Here we describe for the first time an experimental approach for the isolation of the presynaptic active zone from individual mouse brains, a prerequisite for understanding the functional inventory of the presynaptic protein network and for the later analysis of changes occurring in mutant mice. Using a monoclonal antibody against the ubiquitous synaptic vesicle protein SV2 we immunopurified synaptic vesicles docked to the presynaptic plasma membrane. Enrichment studies by means of Western blot analysis and mass spectrometry identified 485 proteins belonging to an impressive variety of functional categories. Our data suggest that presynaptic active zones represent focal hot spots that are not only involved in the regulation of neurotransmitter release but also in multiple structural and functional alterations the adult nerve terminal undergoes during neural activity in adult CNS. They furthermore open new avenues for characterizing alterations in the active zone proteome of mutant mice and their corresponding controls, including the various mouse models of neurological diseases.
Collapse
Affiliation(s)
- Jens Weingarten
- Institute for Cell Biology and Neuroscience, Biologicum, Goethe-University, Frankfurt am Main, Germany
| | - Melanie Lassek
- Institute for Cell Biology and Neuroscience, Biologicum, Goethe-University, Frankfurt am Main, Germany
| | - Benjamin F Mueller
- Institute of Pharmaceutical Chemistry, Cluster of Excellence "Macromolecular Complexes", Goethe-University, Frankfurt am Main, Germany
| | - Marion Rohmer
- Institute of Pharmaceutical Chemistry, Cluster of Excellence "Macromolecular Complexes", Goethe-University, Frankfurt am Main, Germany
| | - Ilaria Lunger
- Institute for Cell Biology and Neuroscience, Biologicum, Goethe-University, Frankfurt am Main, Germany
| | | | - Simone Dudek
- Institute for Cell Biology and Neuroscience, Biologicum, Goethe-University, Frankfurt am Main, Germany
| | - Patricia Gogesch
- Institute for Cell Biology and Neuroscience, Biologicum, Goethe-University, Frankfurt am Main, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Cluster of Excellence "Macromolecular Complexes", Goethe-University, Frankfurt am Main, Germany
| | - Walter Volknandt
- Institute for Cell Biology and Neuroscience, Biologicum, Goethe-University, Frankfurt am Main, Germany.
| |
Collapse
|
47
|
Geist L, Zawadzka-Kazimierczuk A, Saxena S, Żerko S, Koźmiński W, Konrat R. ¹H, ¹³C and ¹⁵N resonance assignments of human BASP1. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:315-319. [PMID: 23179057 PMCID: PMC3758512 DOI: 10.1007/s12104-012-9436-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 10/31/2012] [Indexed: 05/30/2023]
Abstract
Brain acid-soluble protein 1 (BASP1, CAP-23, NAP-22) appears to be implicated in diverse cellular processes. An N-terminally myristoylated form of BASP1 has been discovered to participate in the regulation of actin cytoskeleton dynamics in neurons, whereas non-myristoylated nuclear BASP1 acts as co-suppressor of the potent transcription regulator WT1 (Wilms' Tumor suppressor protein 1). Here we report NMR chemical shift assignment of recombinant human BASP1 fused to an N-terminal cleavable His6-tag.
Collapse
Affiliation(s)
- Leonhard Geist
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | | | - Saurabh Saxena
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Szymon Żerko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Robert Konrat
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| |
Collapse
|
48
|
Kropotova E, Klementiev B, Mosevitsky M. BASP1 and its N-end fragments (BNEMFs) dynamics in rat brain during development. Neurochem Res 2013; 38:1278-84. [PMID: 23579388 DOI: 10.1007/s11064-013-1035-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 10/27/2022]
Abstract
Protein BASP1 was discovered in brains of mammals and birds. In presynaptic area of synapses, BASP1 is attached to plasma membrane owing to N-terminal myristoylation as well as to the positively charged "effecter domain". BASP1 interactions with other proteins as well as with lipids contribute to membrane traffic, axon outgrowth and synaptic plasticity. BASP1 is present also in other tissues, where it was found not only in cytoplasm, but also in nucleus. Nuclear BASP1 suppresses activity of transcription factor WT1 and acts as tumor suppressor. BASP1 deficiency in a cell leads to its transformation. Previously it was shown that in BASP1 samples prepared from different animals and different tissues, six BASP1 N-end myristoylated fragments (BNEMFs) are present. Together, they amount to 30 % of the whole molecules. BNEMFs presence in different species and tissues demonstrates their physiological significance. However BNEMFs remain unexplored. In this paper, the time of appearance and dynamics of both BASP1 and BNEMFs during rat development from embryo to adult animals were determined. In rat brain, the amounts of all BASP1 forms per cell systematically increase during development and remain at the highest levels in adult animals. BNEMFs appear during embryogenesis non-simultaneously and accumulate with different dynamics. These results say for formation of six BNEMFs in the course of different processes and, possibly, using different mechanisms.
Collapse
Affiliation(s)
- Ekaterina Kropotova
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, National Kurchatov Research Center, Leningrad District, 188300 Gatchina, Orlova Roscha, Russian Federation
| | | | | |
Collapse
|
49
|
Dimatelis JJ, Russell VA, Stein DJ, Daniels WM. Effects of maternal separation and methamphetamine exposure on protein expression in the nucleus accumbens shell and core. Metab Brain Dis 2012; 27:363-75. [PMID: 22451087 DOI: 10.1007/s11011-012-9295-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 03/15/2012] [Indexed: 12/14/2022]
Abstract
Early life adversity has been suggested to predispose an individual to later drug abuse. The core and shell sub-regions of the nucleus accumbens are differentially affected by both stressors and methamphetamine. This study aimed to characterize and quantify methamphetamine-induced protein expression in the shell and core of the nucleus accumbens in animals exposed to maternal separation during early development. Isobaric tagging (iTRAQ) which enables simultaneous identification and quantification of peptides with tandem mass spectrometry (MS/MS) was used. We found that maternal separation altered more proteins involved in structure and redox regulation in the shell than in the core of the nucleus accumbens, and that maternal separation and methamphetamine had differential effects on signaling proteins in the shell and core. Compared to maternal separation or methamphetamine alone, the maternal separation/methamphetamine combination altered more proteins involved in energy metabolism, redox regulatory processes and neurotrophic proteins. Methamphetamine treatment of rats subjected to maternal separation caused a reduction of cytoskeletal proteins in the shell and altered cytoskeletal, signaling, energy metabolism and redox proteins in the core. Comparison of maternal separation/methamphetamine to methamphetamine alone resulted in decreased cytoskeletal proteins in both the shell and core and increased neurotrophic proteins in the core. This study confirms that both early life stress and methamphetamine differentially affect the shell and core of the nucleus accumbens and demonstrates that the combination of early life adversity and later methamphetamine use results in more proteins being affected in the nucleus accumbens than either treatment alone.
Collapse
Affiliation(s)
- J J Dimatelis
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925 Cape Town, South Africa.
| | | | | | | |
Collapse
|
50
|
Repression of transcription by WT1-BASP1 requires the myristoylation of BASP1 and the PIP2-dependent recruitment of histone deacetylase. Cell Rep 2012; 2:462-9. [PMID: 22939983 DOI: 10.1016/j.celrep.2012.08.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/14/2012] [Accepted: 08/10/2012] [Indexed: 11/20/2022] Open
Abstract
The Wilms' tumor 1 protein WT1 is a transcriptional regulator that is involved in cell growth and differentiation. The transcriptional corepressor BASP1 interacts with WT1 and converts WT1 from a transcriptional activator to a repressor. Here, we demonstrate that the N-terminal myristoylation of BASP1 is required in order to elicit transcriptional repression at WT1 target genes. We show that myristoylated BASP1 binds to nuclear PIP2, which leads to the recruitment of PIP2 to the promoter regions of WT1-dependent target genes. BASP1's myristoylation and association with PIP2 are required for the interaction of BASP1 with HDAC1, which mediates the recruitment of HDAC1 to the promoter and elicits transcriptional repression. Our findings uncover a role for myristoylation in transcription, as well as a critical function for PIP2 in gene-specific transcriptional repression through the recruitment of histone deacetylase.
Collapse
|