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Khanal P, Patil VS, Bhattacharya K, Shrivastava AK, Bhandare VV. Exploring the globoid cell leukodystrophy protein network and therapeutic interventions. Sci Rep 2024; 14:18067. [PMID: 39103379 PMCID: PMC11300594 DOI: 10.1038/s41598-024-66437-8] [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: 02/25/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Globoid cell leukodystrophy is a severe rare disorder characterized by white matter degradation, resulting in a progressive loss of physical and mental abilities and has extremely limited therapeutic interventions. Therefore, this study aimed to delve into the Globoid cell leukodystrophy associated intricate network of differentially expressed genes (p < 0.05, |Fc|> 1) to identify potential druggable targets and possible therapeutic interventions using small molecules. The disease-associated neuronal protein circuit was constructed and analyzed, identifying 53 nodes (minimum edge cutoff 1), among which five (FOS, FOSB, GDNF, GFRA1, and JUN) were discerned as potential core protein nodes. Although our research enumerates the potential small molecules to target various protein nodes in the proposed disease network, we particularly underscore T-5224 to inhibit c-Jun activity as JUN was identified as one of the pivotal elements within the disease-associated neuronal protein circuit. The evaluation of T-5224 binding energy (- 11.0 kcal/mol) from docking study revealed that the compound to exhibit a notable affinity towards Jun/CRE complex. Moreover, the structural integrity of complex was affirmed through comprehensive molecular dynamics simulations, indicating a stable hydrophilic interaction between T-5224 and the Jun/CRE complex, thereby enhancing protein compactness and reducing solvent accessibility. This binding energy was further substantiated by free binding analysis, revealing a substantial thermodynamics complex state (- 448.00 ± 41.73 kJ/mol). Given that this investigation is confined to a computational framework, we additionally propose a hypothetical framework to ascertain the feasibility of inhibiting the Jun/CRE complex with T-5224 against Globoid cell leukodystrophy, employing a combination of in vitro and in vivo methodologies as a prospective avenue of this study.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India.
- Silicon Script Sciences Private Limited, Bharatpur, Ghorahi, Dang, Nepal.
| | - Vishal S Patil
- Department of Pharmacology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India
| | - Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, 781026, India
- Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam, 781035, India
| | - Amit Kumar Shrivastava
- Department of Pharmacology, Universal College of Medical Sciences, Ranigaon, Bhairahawa, Rupandehi, Nepal
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Li M, Li N, Shao F, Wang R, Chen M, Liu YJ, Zhao Y, Li R. Synthesis of a super-low detection limit fluorescent probe for Al 3+ and its application in fluorescence imaging of zebrafish and cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123676. [PMID: 38039642 DOI: 10.1016/j.saa.2023.123676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
A novel fluorescent probe N'-(2-hydroxybenzylidene)-indole-3-formylhydrazine (JHK) was designed and synthesized based on the condensation reaction of indole-3-formylhydrazine and salicylaldehyde. The probe JHK solution could highly selectively recognize Al3+ by the obvious fluorescence enhancement (288-fold) after adding Al3+. And the probe solution with Al3+ had a very high fluorescence quantum yield (89.29 %). The detection limit was calculated to be 1.135 nM, which was significantly lower than many reported detection limits, indicating that the probe JHK had pretty good sensitivity. The ratio of JHK to Al3+ (1:1) and the sensing mechanism were determined by Job's plot, 1H NMR spectra, FTIR spectra, ESI-MS and Gaussian calculation. The probe solution and medium-speed filter paper were successfully used to make test papers for more convenient detection of Al3+. Furthermore, the probe JHK had been successfully applied to the detection of Al3+ in real water, zebrafish and living cells.
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Affiliation(s)
- Min Li
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China
| | - Na Li
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China
| | - Feng Shao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China
| | - Rui Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China
| | - Miao Chen
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China
| | - Yuan-Jun Liu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China
| | - Yu Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, PR China.
| | - Rong Li
- Qingdao Women and Children 's Hospital, No. 217 Liaoyang West Road, Qingdao, Shandong 226034, PR China.
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Das S, Li Z, Wachter A, Alla S, Noori A, Abdourahman A, Tamm JA, Woodbury ME, Talanian RV, Biber K, Karran EH, Hyman BT, Serrano‐Pozo A. Distinct transcriptomic responses to Aβ plaques, neurofibrillary tangles, and APOE in Alzheimer's disease. Alzheimers Dement 2024; 20:74-90. [PMID: 37461318 PMCID: PMC10792109 DOI: 10.1002/alz.13387] [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: 03/14/2023] [Revised: 06/07/2023] [Accepted: 06/11/2023] [Indexed: 07/28/2023]
Abstract
INTRODUCTION Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE-linked differences remain unclear. METHODS We performed laser capture microdissection of amyloid beta (Aβ) plaques, the 50 μm halo around them, tangles with the 50 μm halo around them, and areas distant (> 50 μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing. RESULTS Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque > peri-plaque > tangle > distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques. DISCUSSION Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.
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Affiliation(s)
- Sudeshna Das
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Zhaozhi Li
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
| | - Astrid Wachter
- AbbVie Deutschland GmbH & Co. KGGenomics Research CenterLudwigshafenGermany
| | - Srinija Alla
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
| | - Ayush Noori
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
| | | | - Joseph A. Tamm
- AbbVie, Cambridge Research CenterCambridgeMassachusettsUSA
| | | | | | - Knut Biber
- AbbVie Deutschland GmbH & Co. KGNeuroscience Research CenterLudwigshafenGermany
| | - Eric H. Karran
- AbbVie, Cambridge Research CenterCambridgeMassachusettsUSA
| | - Bradley T. Hyman
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alberto Serrano‐Pozo
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
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Das S, Li Z, Wachter A, Alla S, Noori A, Abdourahman A, Tamm JA, Woodbury ME, Talanian RV, Biber K, Karran EH, Hyman BT, Serrano-Pozo A. Distinct Transcriptomic Responses to Aβ plaques, Neurofibrillary Tangles, and APOE in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533303. [PMID: 36993332 PMCID: PMC10055287 DOI: 10.1101/2023.03.20.533303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
INTRODUCTION Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE -linked differences remain unclear. METHODS We performed laser capture microdissection of Aβ plaques, the 50μm halo around them, tangles with the 50μm halo around them, and areas distant (>50μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing. RESULTS Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque>peri-plaque>tangle>distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques. DISCUSSION Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.
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Affiliation(s)
- Sudeshna Das
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
- Harvard Medical School, Boston, MA 02115
| | - Zhaozhi Li
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
| | - Astrid Wachter
- AbbVie Deutschland GmbH & Co. KG, Genomics Research Center, Knollstrasse, 67061 Ludwigshafen
| | - Srinija Alla
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
| | - Ayush Noori
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
| | - Aicha Abdourahman
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Joseph A. Tamm
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Maya E. Woodbury
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Robert V. Talanian
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Knut Biber
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Research Center, Knollstrasse, 67061 Ludwigshafen
| | - Eric H. Karran
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Bradley T. Hyman
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
- Harvard Medical School, Boston, MA 02115
| | - Alberto Serrano-Pozo
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
- Harvard Medical School, Boston, MA 02115
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Hou X, Hou J, Huang G. Bi-dimensional principal gene feature selection from big gene expression data. PLoS One 2022; 17:e0278583. [PMID: 36477666 PMCID: PMC9728919 DOI: 10.1371/journal.pone.0278583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
Gene expression sample data, which usually contains massive expression profiles of genes, is commonly used for disease related gene analysis. The selection of relevant genes from huge amount of genes is always a fundamental process in applications of gene expression data. As more and more genes have been detected, the size of gene expression data becomes larger and larger; this challenges the computing efficiency for extracting the relevant and important genes from gene expression data. In this paper, we provide a novel Bi-dimensional Principal Feature Selection (BPFS) method for efficiently extracting critical genes from big gene expression data. It applies the principal component analysis (PCA) method on sample and gene domains successively, aiming at extracting the relevant gene features and reducing redundancies while losing less information. The experimental results on four real-world cancer gene expression datasets show that the proposed BPFS method greatly reduces the data size and achieves a nearly double processing speed compared to the counterpart methods, while maintaining better accuracy and effectiveness.
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Affiliation(s)
- Xiaoqian Hou
- School of Information Technology, Deakin University, Melbourne, Victoria, Australia
| | - Jingyu Hou
- School of Information Technology, Deakin University, Melbourne, Victoria, Australia
| | - Guangyan Huang
- School of Information Technology, Deakin University, Melbourne, Victoria, Australia
- * E-mail:
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Milani M, Mammarella E, Rossi S, Miele C, Lattante S, Sabatelli M, Cozzolino M, D'Ambrosi N, Apolloni S. Targeting S100A4 with niclosamide attenuates inflammatory and profibrotic pathways in models of amyotrophic lateral sclerosis. J Neuroinflammation 2021; 18:132. [PMID: 34118929 PMCID: PMC8196441 DOI: 10.1186/s12974-021-02184-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/28/2021] [Indexed: 12/23/2022] Open
Abstract
Background An increasing number of studies evidences that amyotrophic lateral sclerosis (ALS) is characterized by extensive alterations in different cell types and in different regions besides the CNS. We previously reported the upregulation in ALS models of a gene called fibroblast-specific protein-1 or S100A4, recognized as a pro-inflammatory and profibrotic factor. Since inflammation and fibrosis are often mutual-sustaining events that contribute to establish a hostile environment for organ functions, the comprehension of the elements responsible for these interconnected pathways is crucial to disclose novel aspects involved in ALS pathology. Methods Here, we employed fibroblasts derived from ALS patients harboring the C9orf72 hexanucleotide repeat expansion and ALS patients with no mutations in known ALS-associated genes and we downregulated S100A4 using siRNA or the S100A4 transcriptional inhibitor niclosamide. Mice overexpressing human FUS were adopted to assess the effects of niclosamide in vivo on ALS pathology. Results We demonstrated that S100A4 underlies impaired autophagy and a profibrotic phenotype, which characterize ALS fibroblasts. Indeed, its inhibition reduces inflammatory, autophagic, and profibrotic pathways in ALS fibroblasts, and interferes with different markers known as pathogenic in the disease, such as mTOR, SQSTM1/p62, STAT3, α-SMA, and NF-κB. Importantly, niclosamide in vivo treatment of ALS-FUS mice reduces the expression of S100A4, α-SMA, and PDGFRβ in the spinal cord, as well as gliosis in central and peripheral nervous tissues, together with axonal impairment and displays beneficial effects on muscle atrophy, by promoting muscle regeneration and reducing fibrosis. Conclusion Our findings show that S100A4 has a role in ALS-related mechanisms, and that drugs such as niclosamide which are able to target inflammatory and fibrotic pathways could represent promising pharmacological tools for ALS. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-021-02184-1.
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Affiliation(s)
- Martina Milani
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Rome, Italy
| | - Eleonora Mammarella
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Rome, Italy
| | - Simona Rossi
- Institute of Translational Pharmacology, CNR, 00133, Rome, Italy
| | - Chiara Miele
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Rome, Italy
| | - Serena Lattante
- Unità Operativa Complessa di Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.,Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Mario Sabatelli
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.,Centro Clinico NEMO, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.,Sezione di Neurologia, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Mauro Cozzolino
- Institute of Translational Pharmacology, CNR, 00133, Rome, Italy
| | - Nadia D'Ambrosi
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Rome, Italy.
| | - Savina Apolloni
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Rome, Italy.
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S100A4 in the Physiology and Pathology of the Central and Peripheral Nervous System. Cells 2021; 10:cells10040798. [PMID: 33918416 PMCID: PMC8066633 DOI: 10.3390/cells10040798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
S100A4 is a member of the large family of S100 proteins, exerting a broad range of intracellular and extracellular functions that vary upon different cellular contexts. While S100A4 has long been implicated mainly in tumorigenesis and metastatization, mounting evidence shows that S100A4 is a key player in promoting pro-inflammatory phenotypes and organ pro-fibrotic pathways in the liver, kidney, lung, heart, tendons, and synovial tissues. Regarding the nervous system, there is still limited information concerning S100A4 presence and function. It was observed that S100A4 exerts physiological roles contributing to neurogenesis, cellular motility and chemotaxis, cell differentiation, and cell-to cell communication. Furthermore, S100A4 is likely to participate to numerous pathological processes of the nervous system by affecting the functions of astrocytes, microglia, infiltrating cells and neurons and thereby modulating inflammation and immune reactions, fibrosis as well as neuronal plasticity and survival. This review summarizes the current state of knowledge concerning the localization, deregulation, and possible functions of S100A4 in the physiology of the central and peripheral nervous system. Furthermore, we highlight S100A4 as a gene involved in the pathogenesis of neurological disorders such as brain tumors, neurodegenerative diseases, and acute injuries.
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