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Cui J, Wen D, Wang L, Meng C, Wang Y, Zhao Z, Wu C. CRISPR/Cas9-induced asap1a and asap1b co-knockout mutant zebrafish displayed abnormal embryonic development and impaired neutrophil migration. Gene Expr Patterns 2023; 49:119331. [PMID: 37390886 DOI: 10.1016/j.gep.2023.119331] [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: 04/13/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
ASAP1 (Arf-GAP with SH3 domain, the ankyrin repeat and the PH domain) is the GTPase activating protein of the small G protein Arf. To understand more about the physiological functions of ASAP1 in vivo, we chose to use the zebrafish as an animal model, and analyzed the characterization of asap1 using loss-of-function studies. Here, two isoforms in zebrafish, asap1a and asap1b, were found to be homologous to human ASAP1, and the gene knockout zebrafish lines for asap1a and asap1b were established using the CRISPR/Cas9 technique with different insertions and deletions of bases. Zebrafish with asap1a and asap1b co-knockout showed a significant reduction in survival and hatching rates, as well as an increase in malformation rates during the early stages of development, while the asap1a or asap1b single knockout mutants did not affect the growth and development of individual zebrafish. Exploring the gene expression compensation between asap1a and asap1b using qRT-PCR, we found that asap1b had increased expression when asap1a was knocked out, showing a clear compensatory effect against asap1a knockout; In turn, asap1a did not have detectable compensating expression after asap1b knockout. Furthermore, the co-knockout homozygous mutants displayed impaired neutrophil migration to Mycobacterium marinum infection, and showed an increased bacterial load. Together, these are the first inherited asap1a and/or asap1b mutant zebrafish lines by the CRISPR/Cas9 gene editing approach, and by serving as useful models, they can significantly contribute to better annotation and follow-up physiological studies of human ASAP1.
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Affiliation(s)
- Jia Cui
- Department of Microbiology, Changzhi Medical College, Changzhi, 046000, PR China; Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China
| | - Da Wen
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China
| | - Liqing Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, 030012, PR China
| | - Chaoqun Meng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China
| | - Yuhuan Wang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China
| | - Zhonghua Zhao
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China.
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China.
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2
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Nguyen QA, Chou WH, Hsieh MC, Chang CM, Luo WT, Tai YT, Chang WC. Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy. Front Oncol 2023; 13:1054406. [PMID: 37182141 PMCID: PMC10170308 DOI: 10.3389/fonc.2023.1054406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/27/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. Methods In this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. Results In total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). Conclusions We identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.
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Affiliation(s)
- Quynh-Anh Nguyen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Mao-Chih Hsieh
- Department of General Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Che-Mai Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wei-Tzu Luo
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ting Tai
- Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
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Qin X, Zhang Y, He Y, Chen K, Zhang Y, Li P, Jiang Y, Li S, Li T, Yang H, Wu C, Zheng C, Zhu J, You F, Liu Y. Shear stress triggered circular dorsal ruffles formation to facilitate cancer cell migration. Arch Biochem Biophys 2021; 709:108967. [PMID: 34157295 DOI: 10.1016/j.abb.2021.108967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022]
Abstract
Circular dorsal ruffles (CDRs) are a kind of special ring-shaped membrane structure rich in F-actin, it is highly involved in the invasion-metastasis of tumor. Shear stress is one of the biophysical elements that affects the fate of tumor cells. However, how shear stress contributes to the CDRs formation is still unclear. In this study, we found that shear stress stimulated the formation of CDRs and promoted the migration of human breast MDA-MB-231 carcinoma cells. Integrin-linked kinase (ILK) mediated the recruiting of ADP-ribosylation factors (ARAP1/Arf1) to CDRs. Meanwhile, the transfection of ARAP1 or Arf1 mutant decreased the number of cells with CDRs, the CDRs areas and perimeters, thus blocked the cancer cell migration. This indicated that the ARAP1/Arf1 were necessary for the CDRs formation and cancer cell migration. Further study revealed that shear stress could stimulate the formation of intracellular macropinocytosis (MPS) thus promoted the ARAP1/Arf1 transportation to early endosome to regulate cancer cell migration after the depolymerization of CDRs. Our study elucidates that the CDRs formation is essential in shear stress-induced breast cancer cell migration, which provides a new research target for exploring the cytoskeletal mechanisms of breast cancer malignance.
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Affiliation(s)
- Xiang Qin
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Yuehui Zhang
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Yuchen He
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Kang Chen
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Yixi Zhang
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Ping Li
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Ying Jiang
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Shun Li
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Tingting Li
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Hong Yang
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Chunhui Wu
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China
| | - Chuan Zheng
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan, PR China
| | - Jie Zhu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan, PR China
| | - Fengming You
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan, PR China
| | - Yiyao Liu
- Department of Biophysics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, PR China; TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu, 610072, Sichuan, PR China.
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Stratifying Cumulus Cell Samples Based on Molecular Profiling to Help Resolve Biomarker Discrepancies and to Predict Oocyte Developmental Competence. Int J Mol Sci 2021; 22:ijms22126377. [PMID: 34203623 PMCID: PMC8232172 DOI: 10.3390/ijms22126377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
To increase the efficiency of assisted reproductive techniques (ART), molecular studies have been performed to identify the best predictive biomarkers for selecting the most suitable germ cells for fertilization and the best embryo for intra-uterine transfer. However, across different studies, no universal markers have been found. In this study, we addressed this issue by generating gene expression and CpG methylation profiles of outer cumulus cells obtained during intra-cytoplasmic sperm injection (ICSI). We also studied the association of the generated genomic data with the clinical parameters (spindle presence, zona pellucida birefringence, pronuclear pattern, estrogen level, endometrium size and lead follicle size) and the pregnancy result. Our data highlighted the presence of several parameters that affect analysis, such as inter-individual differences, inter-treatment differences, and, above all, specific treatment protocol differences. When comparing the pregnancy outcome following the long protocol (GnRH agonist) of ovarian stimulation, we identified the single gene markers (NME6 and ASAP1, FDR < 5%) which were also correlated with endometrium size, upstream regulators (e.g., EIF2AK3, FSH, ATF4, MKNK1, and TP53) and several bio-functions related to cell death (apoptosis) and cellular growth and proliferation. In conclusion, our study highlighted the need to stratify samples that are very heterogeneous and to use pathway analysis as a more reliable and universal method for identifying markers that can predict oocyte development potential.
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ASAP1 regulates the uptake of Mycobacterium tuberculosis H37Ra in THP1-derived macrophages by remodeling actin cytoskeleton. Tuberculosis (Edinb) 2021; 129:102090. [PMID: 34058694 DOI: 10.1016/j.tube.2021.102090] [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: 09/07/2020] [Revised: 04/02/2021] [Accepted: 05/16/2021] [Indexed: 11/23/2022]
Abstract
Tuberculosis is initiated by the entry of Mycobacterium tuberculosis (Mtb) into macrophages in the lungs. A study of the cellular factors responsible for the entry of Mtb into host cells will potentially benefit the development of therapeutic treatments or preventive agents against Mtb infection. Using human THP1-derived macrophages as a model, we found that infection of Mtb H37Ra transiently reduced the level of ASAP1, an ADP ribosylation factor (Arf)-GTPase activating protein. Furthermore, knockdown of ASAP1 increased the efficiency of H37Ra entry into the cell and altered the status of actin remodeling as indicated by the enhanced aggregation of F-actin and the increased numbers of vinculin- and paxillin-rich puncta. Collectively, the results in this report identified ASAP1 as a regulator controlling the entry of Mtb H37Ra into macrophage by remodeling actin cytoskeleton.
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Zhang J, Zhang Q, Zhang J, Wang Q. Expression of ACAP1 Is Associated with Tumor Immune Infiltration and Clinical Outcome of Ovarian Cancer. DNA Cell Biol 2020; 39:1545-1557. [PMID: 32456571 DOI: 10.1089/dna.2020.5596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
ADP-ribosylation factor (Arf) GTPase-activating protein (GAP) with coiled-coil, ankyrin repeat and PH domains 1 (ACAP1) is an Arf6 GAP that regulates membrane trafficking and is critical for the migratory potential of cells. However, the roles of ACAP1 have not been fully explored and its association with clinicopathological features in ovarian cancer is still unknown. In this study, we systematically analyzed multiple databases, including TISIDB, Tumor Immune Estimation Resource (TIMER2.0), Gene Expression Omnibus (GEO), CORTECON, Kaplan-Meier Plotter and LinkedOmics platforms to reveal the clinical significance and function of ACAP1 in ovarian cancer. We found that the expression of ACAP1 was upregulated in ovarian cancer and high ACAP1 expression predicted poor prognosis. Our data demonstrated that the expression and methylation status of ACAP1 were strongly correlated with immune infiltration levels, immunomodulators, and chemokines. Gene set enrichment analysis (GSEA) analysis also showed that the mechanism of ACAP1 in regulating ovarian cancer was related to a variety of immune-related pathways. In addition, we also revealed that the expression of ACAP1 was altered during cell differentiation and associated with cancer cell stemness markers. Our study highlights the clinical significance of ACAP1 in ovarian cancer and provides insight into the novel function of ACAP1 in regulation of tumor immune microenvironment and cancer cell stemness.
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Affiliation(s)
- Jiawen Zhang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qinyi Zhang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jing Zhang
- Department of Integrated Therapy, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qingying Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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Expression of ArfGAP3 in Vaginal Anterior Wall of Patients With Pelvic Floor Organ Prolapse in Pelvic Organ Prolapse and Non-Pelvic Organ Prolapse Patients. Female Pelvic Med Reconstr Surg 2020; 27:e64-e69. [PMID: 31868832 PMCID: PMC7774809 DOI: 10.1097/spv.0000000000000808] [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] [Indexed: 11/26/2022]
Abstract
The purpose of this study was to study the expression of adenosine diphosphate ribosylation factor GTPase-activating protein 3 (ArfGAP3) in the anterior vaginal wall of patients with pelvic organ prolapse (POP).
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8
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Tanna CE, Goss LB, Ludwig CG, Chen PW. Arf GAPs as Regulators of the Actin Cytoskeleton-An Update. Int J Mol Sci 2019; 20:ijms20020442. [PMID: 30669557 PMCID: PMC6358971 DOI: 10.3390/ijms20020442] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
Arf GTPase-activating proteins (Arf GAPs) control the activity of ADP-ribosylation factors (Arfs) by inducing GTP hydrolysis and participate in a diverse array of cellular functions both through mechanisms that are dependent on and independent of their Arf GAP activity. A number of these functions hinge on the remodeling of actin filaments. Accordingly, some of the effects exerted by Arf GAPs involve proteins known to engage in regulation of the actin dynamics and architecture, such as Rho family proteins and nonmuscle myosin 2. Circular dorsal ruffles (CDRs), podosomes, invadopodia, lamellipodia, stress fibers and focal adhesions are among the actin-based structures regulated by Arf GAPs. Arf GAPs are thus important actors in broad functions like adhesion and motility, as well as the specialized functions of bone resorption, neurite outgrowth, and pathogen internalization by immune cells. Arf GAPs, with their multiple protein-protein interactions, membrane-binding domains and sites for post-translational modification, are good candidates for linking the changes in actin to the membrane. The findings discussed depict a family of proteins with a critical role in regulating actin dynamics to enable proper cell function.
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Affiliation(s)
- Christine E Tanna
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
| | - Louisa B Goss
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
| | - Calvin G Ludwig
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
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Donato L, Scimone C, Nicocia G, D'Angelo R, Sidoti A. Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. Cell Cycle 2018; 18:84-104. [PMID: 30569795 DOI: 10.1080/15384101.2018.1558873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is a very heterogeneous inherited ocular disorder group characterized by progressive retinal disruption. Retinal pigment epithelium (RPE) degeneration, due to oxidative stress which arrests the metabolic support to photoreceptors, represents one of the principal causes of RP. Here, the role of oxidative stress in RP onset and progression was analyzed by a comparative whole transcriptome analysis of human RPE cells, treated with 100 µg/ml of oxLDL and untreated, at different time points. Experiment was thrice repeated and performed on Ion ProtonTM sequencing system. Data analysis, including low quality reads trimming and gene expression quantification, was realized by CLC Genomics Workbench software. The whole analysis highlighted 14 clustered "macro-pathways" and many sub-pathways, classified by selection of 5271 genes showing the highest alteration of expression. Among them, 23 genes were already known to be RP causative ones (15 over-expressed and 8 down-expressed), and their enrichment and intersection analyses highlighted new 77 candidate related genes (49 over-expressed and 28 down-expressed). A final filtering analysis then highlighted 29 proposed candidate genes. This data suggests that many new genes, not yet associated with RP, could influence its etiopathogenesis.
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Affiliation(s)
- Luigi Donato
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Concetta Scimone
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Giacomo Nicocia
- c Department of Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Rosalia D'Angelo
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Antonina Sidoti
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
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