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Hughes JW, Sisley EK, Hale OJ, Cooper HJ. Laser capture microdissection and native mass spectrometry for spatially-resolved analysis of intact protein assemblies in tissue. Chem Sci 2024; 15:5723-5729. [PMID: 38638209 PMCID: PMC11023061 DOI: 10.1039/d3sc04933g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/03/2024] [Indexed: 04/20/2024] Open
Abstract
Previously, we have shown that native ambient mass spectrometry imaging allows the spatial mapping of folded proteins and their complexes in thin tissue sections. Subsequent top-down native ambient mass spectrometry of adjacent tissue section enables protein identification. The challenges associated with protein identification by this approach are (i) the low abundance of proteins in tissue and associated long data acquisition timescales and (ii) irregular spatial distributions which hamper targeted sampling of the relevant tissue location. Here, we demonstrate that these challenges may be overcome through integration of laser capture microdissection in the workflow. We show identification of intact protein assemblies in rat liver tissue and apply the approach to identification of proteins in the granular layer of rat cerebellum.
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Affiliation(s)
- James W Hughes
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Emma K Sisley
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Oliver J Hale
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
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Leal-Galicia P, Chávez-Hernández ME, Mata F, Mata-Luévanos J, Rodríguez-Serrano LM, Tapia-de-Jesús A, Buenrostro-Jáuregui MH. Adult Neurogenesis: A Story Ranging from Controversial New Neurogenic Areas and Human Adult Neurogenesis to Molecular Regulation. Int J Mol Sci 2021; 22:11489. [PMID: 34768919 PMCID: PMC8584254 DOI: 10.3390/ijms222111489] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/16/2022] Open
Abstract
The generation of new neurons in the adult brain is a currently accepted phenomenon. Over the past few decades, the subventricular zone and the hippocampal dentate gyrus have been described as the two main neurogenic niches. Neurogenic niches generate new neurons through an asymmetric division process involving several developmental steps. This process occurs throughout life in several species, including humans. These new neurons possess unique properties that contribute to the local circuitry. Despite several efforts, no other neurogenic zones have been observed in many years; the lack of observation is probably due to technical issues. However, in recent years, more brain niches have been described, once again breaking the current paradigms. Currently, a debate in the scientific community about new neurogenic areas of the brain, namely, human adult neurogenesis, is ongoing. Thus, several open questions regarding new neurogenic niches, as well as this phenomenon in adult humans, their functional relevance, and their mechanisms, remain to be answered. In this review, we discuss the literature and provide a compressive overview of the known neurogenic zones, traditional zones, and newly described zones. Additionally, we will review the regulatory roles of some molecular mechanisms, such as miRNAs, neurotrophic factors, and neurotrophins. We also join the debate on human adult neurogenesis, and we will identify similarities and differences in the literature and summarize the knowledge regarding these interesting topics.
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Affiliation(s)
- Perla Leal-Galicia
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
| | - María Elena Chávez-Hernández
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
| | - Florencia Mata
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
| | - Jesús Mata-Luévanos
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
| | - Luis Miguel Rodríguez-Serrano
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
- Laboratorio de Neurobiología de la Alimentación, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
| | - Alejandro Tapia-de-Jesús
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
| | - Mario Humberto Buenrostro-Jáuregui
- Laboratorio de Neurociencias, Departamento de Psicología, Universidad Iberoamericana Ciudad de México, Ciudad de México 01219, Mexico; (M.E.C.-H.); (F.M.); (J.M.-L.); (L.M.R.-S.); (A.T.-d.-J.)
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Karachaliou CE, Kalbacher H, Voelter W, Tsitsilonis OE, Livaniou E. In Vitro Immunodetection of Prothymosin Alpha in Normal and Pathological Conditions. Curr Med Chem 2020; 27:4840-4854. [PMID: 31389310 DOI: 10.2174/0929867326666190807145212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/20/2019] [Accepted: 07/22/2019] [Indexed: 02/06/2023]
Abstract
Prothymosin alpha (ProTα) is a highly acidic polypeptide, ubiquitously expressed in almost all mammalian cells and tissues and consisting of 109 amino acids in humans. ProTα is known to act both, intracellularly, as an anti-apoptotic and proliferation mediator, and extracellularly, as a biologic response modifier mediating immune responses similar to molecules termed as "alarmins". Antibodies and immunochemical techniques for ProTα have played a leading role in the investigation of the biological role of ProTα, several aspects of which still remain unknown and contributed to unraveling the diagnostic and therapeutic potential of the polypeptide. This review deals with the so far reported antibodies along with the related immunodetection methodology for ProTα (immunoassays as well as immunohistochemical, immunocytological, immunoblotting, and immunoprecipitation techniques) and its application to biological samples of interest (tissue extracts and sections, cells, cell lysates and cell culture supernatants, body fluids), in health and disease states. In this context, literature information is critically discussed, and some concluding remarks are presented.
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Affiliation(s)
- Chrysoula-Evangelia Karachaliou
- Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety (INRASTES), National Centre for Scientific Research "Demokritos", 15310 Agia Paraskevi, Athens, Greece
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tuebingen, 72076 Tuebingen, Germany
| | - Wolfgang Voelter
- Interfaculty Institute of Biochemistry, University of Tuebingen, 72076 Tuebingen, Germany
| | - Ourania E Tsitsilonis
- Department of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Evangelia Livaniou
- Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety (INRASTES), National Centre for Scientific Research "Demokritos", 15310 Agia Paraskevi, Athens, Greece
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Involvement of SNARE Protein Interaction for Non-classical Release of DAMPs/Alarmins Proteins, Prothymosin Alpha and S100A13. Cell Mol Neurobiol 2020; 41:1817-1828. [PMID: 32856232 DOI: 10.1007/s10571-020-00950-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/19/2020] [Indexed: 12/30/2022]
Abstract
Prothymosin alpha (ProTα) is involved in multiple cellular processes. Upon serum-free stress, ProTα lacking a signal peptide sequence is non-classically released from C6 glioma cells as a complex with Ca2+-binding cargo protein S100A13. Thus, ProTα and S100A13 are conceived to be members of damage-associated molecular patterns (DAMPs)/alarmins. However, it remains to be determined whether stress-induced release of ProTα and S100A13 involves SNARE proteins in the mechanisms underlying membrane tethering of the multiprotein complex. In the present study, we used C6 glioma cells as a model of ProTα release. In pull-down assay, p40 synaptotagmin-1 (Syt-1), a vesicular SNARE, formed a hetero-oligomeric complex with homodimeric S100A13 in a Ca2+-dependent manner. The interaction between p40 Syt-1 and S100A13 was also Ca2+-dependent in surface plasmon resonance (SPR). Immunoprecipitation using conditioned medium (CM) revealed that p40 Syt-1 was co-released with ProTα and S100A13 upon serum-free stress. In in situ proximity ligation assay (PLA), Syt-1 interacted with S100A13 upon serum-free stress in C6 glioma cells. The intracellular delivery of anti-Syt-1 IgG blocked serum free-induced release of ProTα and S100A13. Serum free-induced ProTα-EGFP release was significantly blocked by botulinum neurotoxin/C1 (BoNT/C1), which cleaves target SNARE syntaxin-1 (Stx-1). In immunocytochemistry, the cellular loss of ProTα-EGFP, S100A13, and Syt-1 was also blocked by BoNT/C1. Furthermore, the intracellular delivery of anti-Stx-1 IgG or Stx-1 siRNA treatment blocked Syt-1, S100A13 and ProTα release from C6 glioma cells. All these findings suggest that SNARE proteins play roles in stress-induced non-classical release of DAMPs/alarmins proteins, ProTα and S100A13 from C6 glioma cells.
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Sasaki K, Halder SK, Matsunaga H, Ueda H. Beneficial actions of prothymosin alpha-mimetic hexapeptide on central post-stroke pain, reduced social activity, learning-deficit and depression following cerebral ischemia in mice. Peptides 2020; 126:170265. [PMID: 31982448 DOI: 10.1016/j.peptides.2020.170265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 11/23/2022]
Abstract
Prothymosin alpha (ProTα)-mimetic hexapeptide (amino acid: NEVDQE, P6Q) inhibits cerebral or retinal ischemia-induced behavioral, electrophysiological and histological damage. P6Q also abolishes cerebral hemorrhage induced by ischemia with tissue plasminogen activator (tPA). In the present study we examined the beneficial effects of P6Q on other post-stroke prognostic psychology-related symptoms, which obstruct the motivation toward physical therapy. Intravenous (i.v.) administration with tPA (10 mg/kg) at 6 h after photochemically induced thrombosis (PIT) in mice resulted in bilateral central post-stroke pain in thermal and mechanical nociception tests and loss of social activity in the nest building test, both of which were significantly blocked by P6Q (30 mg/kg, i.v.) given at 5 h after PIT. P6Q (30 mg/kg, i.v.) also improved the memory-learning deficit in the step-through test and depression-like behavior in the tail suspension test when it was given 1 day after bilateral common carotid arteries occlusion (BCCAO) in mice. Thus, these studies suggest that P6Q could be a promising candidate to prevent negative prognostic psychological symptoms following focal and global ischemia.
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Affiliation(s)
- Keita Sasaki
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Sebok Kumar Halder
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Hayato Matsunaga
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Hiroshi Ueda
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Department of Molecular Pharmacology, Kyoto University Graduate School of Pharmaceutical Sciences, Kyoto 606-8501, Japan.
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Datta Chaudhuri A, Dasgheyb RM, DeVine LR, Bi H, Cole RN, Haughey NJ. Stimulus‐dependent modifications in astrocyte‐derived extracellular vesicle cargo regulate neuronal excitability. Glia 2019; 68:128-144. [DOI: 10.1002/glia.23708] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Amrita Datta Chaudhuri
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
| | - Raha M. Dasgheyb
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
| | - Lauren R. DeVine
- Department of Biological Chemistry, Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of Medicine Baltimore Maryland
| | - Honghao Bi
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
| | - Robert N. Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of Medicine Baltimore Maryland
| | - Norman J. Haughey
- Department of Neurology, Richard T Johnson Division of Neuroimmunology and Neurological InfectionsJohns Hopkins University School of Medicine Baltimore Maryland
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Ueda H, Sasaki K, Halder SK, Deguchi Y, Takao K, Miyakawa T, Tajima A. Prothymosin alpha-deficiency enhances anxiety-like behaviors and impairs learning/memory functions and neurogenesis. J Neurochem 2017; 141:124-136. [PMID: 28122138 DOI: 10.1111/jnc.13963] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 01/13/2017] [Accepted: 01/14/2017] [Indexed: 01/11/2023]
Abstract
Prothymosin alpha (ProTα) is expressed in various mammalian organs including the neuronal nuclei in the brain, and is involved in multiple functions, such as chromatin remodeling, transcriptional regulation, cell proliferation, and survival. ProTα has beneficial actions against ischemia-induced necrosis and apoptosis in the brain and retina. However, characterizing the physiological roles of endogenous ProTα in the brain without stress remains elusive. Here, we generated ProTα-deficiency mice to explore whether endogenous ProTα is involved in normal brain functions. We successfully generated heterozygous ProTα knockout (ProTα+/- ) mice, while all homozygous ProTα knockout (ProTα-/- ) offspring died at early embryonic stage, suggesting that ProTα has crucial roles in embryonic development. In the evaluation of different behavioral tests, ProTα+/- mice exhibited hypolocomotor activity in the open-field test and enhanced anxiety-like behaviors in the light/dark transition test and the novelty induced hypophagia test. ProTα+/- mice also showed impaired learning and memory in the step-through passive avoidance test and the KUROBOX test. Depression-like behaviors in ProTα+/- mice in the forced swim and tail suspension tests were comparable with that of wild-type mice. Furthermore, adult hippocampal neurogenesis was significantly decreased in ProTα+/- mice. ProTα+/- mice showed an impaired long-term potentiation induction in the evaluation of electrophysiological recordings from acute hippocampal slices. Microarray analysis revealed that the candidate genes related to anxiety, learning/memory-functions, and neurogenesis were down-regulated in ProTα+/- mice. Thus, this study suggests that ProTα has crucial physiological roles in the robustness of brain.
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Affiliation(s)
- Hiroshi Ueda
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Keita Sasaki
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Sebok Kumar Halder
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yuichi Deguchi
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Keizo Takao
- Section of Behavior Patterns, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, NINS, Okazaki, Aichi, Japan
| | - Tsuyoshi Miyakawa
- Section of Behavior Patterns, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, NINS, Okazaki, Aichi, Japan.,Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
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Moreira-Filho CA, Bando SY, Bertonha FB, Iamashita P, Silva FN, Costa LDF, Silva AV, Castro LHM, Wen HT. Community structure analysis of transcriptional networks reveals distinct molecular pathways for early- and late-onset temporal lobe epilepsy with childhood febrile seizures. PLoS One 2015; 10:e0128174. [PMID: 26011637 PMCID: PMC4444281 DOI: 10.1371/journal.pone.0128174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/24/2015] [Indexed: 12/21/2022] Open
Abstract
Age at epilepsy onset has a broad impact on brain plasticity and epilepsy pathomechanisms. Prolonged febrile seizures in early childhood (FS) constitute an initial precipitating insult (IPI) commonly associated with mesial temporal lobe epilepsy (MTLE). FS-MTLE patients may have early disease onset, i.e. just after the IPI, in early childhood, or late-onset, ranging from mid-adolescence to early adult life. The mechanisms governing early (E) or late (L) disease onset are largely unknown. In order to unveil the molecular pathways underlying E and L subtypes of FS-MTLE we investigated global gene expression in hippocampal CA3 explants of FS-MTLE patients submitted to hippocampectomy. Gene coexpression networks (GCNs) were obtained for the E and L patient groups. A network-based approach for GCN analysis was employed allowing: i) the visualization and analysis of differentially expressed (DE) and complete (CO) - all valid GO annotated transcripts - GCNs for the E and L groups; ii) the study of interactions between all the system's constituents based on community detection and coarse-grained community structure methods. We found that the E-DE communities with strongest connection weights harbor highly connected genes mainly related to neural excitability and febrile seizures, whereas in L-DE communities these genes are not only involved in network excitability but also playing roles in other epilepsy-related processes. Inversely, in E-CO the strongly connected communities are related to compensatory pathways (seizure inhibition, neuronal survival and responses to stress conditions) while in L-CO these communities harbor several genes related to pro-epileptic effects, seizure-related mechanisms and vulnerability to epilepsy. These results fit the concept, based on fMRI and behavioral studies, that early onset epilepsies, although impacting more severely the hippocampus, are associated to compensatory mechanisms, while in late MTLE development the brain is less able to generate adaptive mechanisms, what has implications for epilepsy management and drug discovery.
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Affiliation(s)
| | - Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Fernanda Bernardi Bertonha
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | | | | | | | - Luiz Henrique Martins Castro
- Department of Neurology, FMUSP, São Paulo, SP, Brazil
- Clinical Neurology Division, Hospital das Clínicas, FMUSP, São Paulo, SP, Brazil
| | - Hung-Tzu Wen
- Epilepsy Surgery Group, Hospital das Clínicas, FMUSP, São Paulo, SP, Brazil
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Halder SK, Matsunaga H, Ueda H. Neuron-specific non-classical release of prothymosin alpha: a novel neuroprotective damage-associated molecular patterns. J Neurochem 2012; 123:262-75. [PMID: 22853710 DOI: 10.1111/j.1471-4159.2012.07897.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 11/27/2022]
Abstract
Prothymosin alpha (ProTα), a nuclear protein devoid of signal sequence, has been shown to possess a number of cellular functions including cell survival. Most recently, we demonstrated that ProTα is localized in the nuclei of neurons, while it is found in both nuclei and cytoplasm in the astrocytes and microglia of adult brain. However, the cell type-specific non-classical release of ProTα under cerebral ischemia is yet unknown. In this study, we report that ProTα is non-classically released along with S100A13 from neurons in the hippocampus, striatum and somatosensory cortex at 3 h after cerebral ischemia, but amlexanox (an anti-allergic compound) reversibly blocks this neuronal ProTα release. We found that none of ProTα is released from astrocytes and microglia under ischemic stress. Indeed, ProTα intensity is increased gradually in astrocytes and microglia through 24 h after the cerebral ischemia. Interestingly, Z-Val-Ala-Asp fluoromethyl ketone, a caspase 3 inhibitor, pre-treatment induces ProTα release from astrocytes in the ischemic brain, but this release is reversibly blocked by amlexanox. However, Z-Val-Ala-Asp fluoromethyl ketone as well as amlexanox has no effect on ProTα distribution in microglia upon cerebral ischemia. Taken together, these results suggest that only neurons have machineries to release ProTα upon cerebral ischemic stress in vivo.
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Affiliation(s)
- Sebok Kumar Halder
- Department of Molecular Pharmacology and Neuroscience, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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