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Paudel KR, Singh M, De Rubis G, Kumbhar P, Mehndiratta S, Kokkinis S, El-Sherkawi T, Gupta G, Singh SK, Malik MZ, Mohammed Y, Oliver BG, Disouza J, Patravale V, Hansbro PM, Dua K. Computational and biological approaches in repurposing ribavirin for lung cancer treatment: Unveiling antitumorigenic strategies. Life Sci 2024; 352:122859. [PMID: 38925223 DOI: 10.1016/j.lfs.2024.122859] [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: 01/07/2024] [Revised: 03/11/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
Lung cancer is among leading causes of death worldwide. The five-year survival rate of this disease is extremely low (17.8 %), mainly due to difficult early diagnosis and to the limited efficacy of currently available chemotherapeutics. This underlines the necessity to develop innovative therapies for lung cancer. In this context, drug repurposing represents a viable approach, as it reduces the turnaround time of drug development removing costs associated to safety testing of new molecular entities. Ribavirin, an antiviral molecule used to treat hepatitis C virus infections, is particularly promising as repurposed drug for cancer treatment, having shown therapeutic activity against glioblastoma, acute myeloid leukemia, and nasopharyngeal carcinoma. In the present study, we thoroughly investigated the in vitro anticancer activity of ribavirin against A549 human lung adenocarcinoma cells. From a functional standpoint, ribavirin significantly inhibits cancer hallmarks such as cell proliferation, migration, and colony formation. Mechanistically, ribavirin downregulates the expression of numerous proteins and genes regulating cell migration, proliferation, apoptosis, and cancer angiogenesis. The anticancer potential of ribavirin was further investigated in silico through gene ontology pathway enrichment and protein-protein interaction networks, identifying five putative molecular interactors of ribavirin (Erb-B2 Receptor Tyrosine Kinase 4 (Erb-B4); KRAS; Intercellular Adhesion Molecule 1 (ICAM-1); amphiregulin (AREG); and neuregulin-1 (NRG1)). These interactions were characterized via molecular docking and molecular dynamic simulations. The results of this study highlight the potential of ribavirin as a repurposed chemotherapy against lung cancer, warranting further studies to ascertain the in vivo anticancer activity of this molecule.
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Affiliation(s)
- Keshav Raj Paudel
- Centre of Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia
| | - Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida, Uttar Pradesh, India; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Gabriele De Rubis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Popat Kumbhar
- Department of Pharmaceutics, Tatyasaheb Kore College of Pharmacy, Warananagar, Tal: Panhala, Dist: Kolhapur, Maharashtra 416113, India
| | - Samir Mehndiratta
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Sofia Kokkinis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tammam El-Sherkawi
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Sachin Kumar Singh
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi GT Road, Phagwara 144411, Punjab, India
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait city 15462, Kuwait
| | - Yousuf Mohammed
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Brian G Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - John Disouza
- Department of Pharmaceutics, Tatyasaheb Kore College of Pharmacy, Warananagar, Tal: Panhala, Dist: Kolhapur, Maharashtra 416113, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Philip Michael Hansbro
- Centre of Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia.
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia.
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2
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Mao R, Hu M, Liu X, Ye L, Xu B, Sun M, Xu S, Shao W, Tan Y, Xu Y, Bai F, Shu S. Impairments of GABAergic transmission in hippocampus mediate increased susceptibility of epilepsy in the early stage of Alzheimer's disease. Cell Commun Signal 2024; 22:147. [PMID: 38388921 PMCID: PMC10885444 DOI: 10.1186/s12964-024-01528-7] [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: 12/18/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Patients with Alzheimer's disease (AD) are often co-morbid with unprovoked seizures, making clinical diagnosis and management difficult. Although it has an important role in both AD and epilepsy, abnormal γ-aminobutyric acid (GABA)ergic transmission is recognized only as a compensative change for glutamatergic damage. Neuregulin 1 (NRG1)-ErbB4 signaling can promote GABA release and suppress epileptogenesis, but its effects on cognition in AD are still controversial. METHODS Four-month-old APPswe/PS1dE9 mice (APP mice) were used as animal models in the early stage of AD in this study. Acute/chronic chemical-kindling epilepsy models were established with pentylenetetrazol. Electroencephalogram and Racine scores were performed to assess seizures. Behavioral tests were used to assess cognition and emotion. Electrophysiology, western blot and immunofluorescence were performed to detect the alterations in synapses, GABAergic system components and NRG1-ErbB4 signaling. Furthermore, NRG1 was administrated intracerebroventricularly into APP mice and then its antiepileptic and cognitive effects were evaluated. RESULTS APP mice had increased susceptibility to epilepsy and resulting hippocampal synaptic damage and cognitive impairment. Electrophysiological analysis revealed decreased GABAergic transmission in the hippocampus. This abnormal GABAergic transmission involved a reduction in the number of parvalbumin interneurons (PV+ Ins) and decreased levels of GABA synthesis and transport. We also found impaired NRG1-ErbB4 signaling which mediated by PV+ Ins loss. And NRG1 administration could effectively reduce seizures and improve cognition in four-month-old APP mice. CONCLUSION Our results indicated that abnormal GABAergic transmission mediated hippocampal hyperexcitability, further excitation/inhibition imbalance, and promoted epileptogenesis in the early stage of AD. Appropriate NRG1 administration could down-regulate seizure susceptibility and rescue cognitive function. Our study provided a potential direction for intervening in the co-morbidity of AD and epilepsy.
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Affiliation(s)
- Rui Mao
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Mengsha Hu
- Department of Neurology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Xuan Liu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Lei Ye
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Bingsong Xu
- Department of Neurology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Min Sun
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Siyi Xu
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Wenxuan Shao
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yi Tan
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China.
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China.
- Jiangsu Provincial Key Discipline of Neurology, Nanjing, China.
- Nanjing Neurology Medical Center, Nanjing, China.
| | - Feng Bai
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China.
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China.
- Jiangsu Provincial Key Discipline of Neurology, Nanjing, China.
- Nanjing Neurology Medical Center, Nanjing, China.
| | - Shu Shu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Department of Neurology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing, China.
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China.
- Jiangsu Provincial Key Discipline of Neurology, Nanjing, China.
- Nanjing Neurology Medical Center, Nanjing, China.
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Zhang Q, Liu J, Liu H, Ao L, Xi Y, Chen D. Genome-wide epistasis analysis reveals gene-gene interaction network on an intermediate endophenotype P-tau/Aβ 42 ratio in ADNI cohort. Sci Rep 2024; 14:3984. [PMID: 38368488 PMCID: PMC10874417 DOI: 10.1038/s41598-024-54541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/14/2024] [Indexed: 02/19/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the elderly worldwide. The exact etiology of AD, particularly its genetic mechanisms, remains incompletely understood. Traditional genome-wide association studies (GWAS), which primarily focus on single-nucleotide polymorphisms (SNPs) with main effects, provide limited explanations for the "missing heritability" of AD, while there is growing evidence supporting the important role of epistasis. In this study, we performed a genome-wide SNP-SNP interaction detection using a linear regression model and employed multiple GPUs for parallel computing, significantly enhancing the speed of whole-genome analysis. The cerebrospinal fluid (CSF) phosphorylated tau (P-tau)/amyloid-[Formula: see text] (A[Formula: see text]) ratio was used as a quantitative trait (QT) to enhance statistical power. Age, gender, and clinical diagnosis were included as covariates to control for potential non-genetic factors influencing AD. We identified 961 pairs of statistically significant SNP-SNP interactions, explaining a high-level variance of P-tau/A[Formula: see text] level, all of which exhibited marginal main effects. Additionally, we replicated 432 previously reported AD-related genes and found 11 gene-gene interaction pairs overlapping with the protein-protein interaction (PPI) network. Our findings may contribute to partially explain the "missing heritability" of AD. The identified subnetwork may be associated with synaptic dysfunction, Wnt signaling pathway, oligodendrocytes, inflammation, hippocampus, and neuronal cells.
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Affiliation(s)
- Qiushi Zhang
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Junfeng Liu
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Hongwei Liu
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong Street, Harbin, China
| | - Lang Ao
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Yang Xi
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Dandan Chen
- School of Automation Engineering, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China.
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong Street, Harbin, China.
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Kwon Y, Kang M, Jeon YM, Lee S, Lee HW, Park JS, Kim HJ. Identification and characterization of novel ERBB4 variant associated with sporadic amyotrophic lateral sclerosis (ALS). J Neurol Sci 2024; 457:122885. [PMID: 38278691 DOI: 10.1016/j.jns.2024.122885] [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: 09/26/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is the most common type of motor neuron disease characterized by progressive motor neuron degeneration in brain and spinal cord. Most cases are sporadic in ALS and 5-10% of cases are familiar. >50 genes are known to be associated with ALS and one of them is ERBB4. In this paper, we report the case of a 53-year-old ALS patient with progressive muscle weakness and fasciculation, but he had no cognitive decline. We performed the next generation sequencing (NGS) and in silico analysis, it predicted a highly pathogenic variant, c.2116 A > G, p.Asn706Asp (N706D) in the ERBB4 gene. The amino acid residue is highly conserved among species. ERBB4 is a member of the ERBB family of receptor tyrosine kinases. ERBB4 has multiple tyrosine phosphorylation sites, including an autophosphorylation site at tyrosine 1284 residue. Autophosphorylation of ERBB4 promotes biological activity and it associated with NRG-1/ERBB4 pathway. It is already known that tyrosine 128 phosphorylation of ERBB4 is decreased in patients who have ALS-associated ERBB4 mutations. We generated ERBB4 N706D construct using site-directed mutagenesis and checked the phosphorylation level of ERBB4 N706D in NSC-34 cells. We found that the phosphorylation of ERBB4 N706D was decreased compared to ERBB4 wild-type, indicating a loss of function mutation in ERBB4. We report a novel variant in ERBB4 gene leading to ALS through dysfunction of ERBB4.
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Affiliation(s)
- Younghwi Kwon
- Dementia Research Group, Korea Brain Research Institute (KBRI), Daegu, South Korea
| | - Minsung Kang
- Department of Neurology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Yu-Mi Jeon
- Dementia Research Group, Korea Brain Research Institute (KBRI), Daegu, South Korea
| | - Shinrye Lee
- Dementia Research Group, Korea Brain Research Institute (KBRI), Daegu, South Korea
| | - Ho-Won Lee
- Department of Neurology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea; Department of Neurology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea; Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Jin-Sung Park
- Department of Neurology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea; Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea.
| | - Hyung-Jun Kim
- Dementia Research Group, Korea Brain Research Institute (KBRI), Daegu, South Korea; Department of Brain Sciences, DGIST, Daegu, South Korea.
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Lacar B, Ferdosi S, Alavi A, Stukalov A, Venkataraman GR, de Geus M, Dodge H, Wu CY, Kivisakk P, Das S, Guturu H, Hyman B, Batzoglou S, Arnold SE, Siddiqui A. Identification of Novel Biomarkers for Alzheimer's Disease and Related Dementias Using Unbiased Plasma Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574446. [PMID: 38260620 PMCID: PMC10802486 DOI: 10.1101/2024.01.05.574446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) and related dementias (ADRD) is a complex disease with multiple pathophysiological drivers that determine clinical symptomology and disease progression. These diseases develop insidiously over time, through many pathways and disease mechanisms and continue to have a huge societal impact for affected individuals and their families. While emerging blood-based biomarkers, such as plasma p-tau181 and p-tau217, accurately detect Alzheimer neuropthology and are associated with faster cognitive decline, the full extension of plasma proteomic changes in ADRD remains unknown. Earlier detection and better classification of the different subtypes may provide opportunities for earlier, more targeted interventions, and perhaps a higher likelihood of successful therapeutic development. In this study, we aim to leverage unbiased mass spectrometry proteomics to identify novel, blood-based biomarkers associated with cognitive decline. 1,786 plasma samples from 1,005 patients were collected over 12 years from partcipants in the Massachusetts Alzheimer's Disease Research Center Longitudinal Cohort Study. Patient metadata includes demographics, final diagnoses, and clinical dementia rating (CDR) scores taken concurrently. The Proteograph™ Product Suite (Seer, Inc.) and liquid-chromatography mass-spectrometry (LC-MS) analysis were used to process the plasma samples in this cohort and generate unbiased proteomics data. Data-independent acquisition (DIA) mass spectrometry results yielded 36,259 peptides and 4,007 protein groups. Linear mixed effects models revealed 138 differentially abundant proteins between AD and healthy controls. Machine learning classification models for AD diagnosis identified potential candidate biomarkers including MBP, BGLAP, and APoD. Cox regression models were created to determine the association of proteins with disease progression and suggest CLNS1A, CRISPLD2, and GOLPH3 as targets of further investigation as potential biomarkers. The Proteograph workflow provided deep, unbiased coverage of the plasma proteome at a speed that enabled a cohort study of almost 1,800 samples, which is the largest, deep, unbiased proteomics study of ADRD conducted to date.
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Affiliation(s)
| | | | | | | | | | - Matthijs de Geus
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Hiroko Dodge
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Chao-Yi Wu
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Pia Kivisakk
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Sudeshna Das
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | | | - Brad Hyman
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | | | - Steven E. Arnold
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
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Carello-Collar G, Bellaver B, Ferreira PCL, Ferrari-Souza JP, Ramos VG, Therriault J, Tissot C, De Bastiani MA, Soares C, Pascoal TA, Rosa-Neto P, Souza DO, Zimmer ER. The GABAergic system in Alzheimer's disease: a systematic review with meta-analysis. Mol Psychiatry 2023; 28:5025-5036. [PMID: 37419974 DOI: 10.1038/s41380-023-02140-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/17/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The γ-aminobutyric acid (GABA)ergic system is the primary inhibitory neurotransmission system in the mammalian brain. Its dysregulation has been shown in multiple brain conditions, but in Alzheimer's disease (AD) studies have provided contradictory results. Here, we conducted a systematic review with meta-analysis to investigate whether the GABAergic system is altered in AD patients compared to healthy controls (HC), following the PRISMA 2020 Statement. We searched PubMed and Web of Science from database inception to March 18th, 2023 for studies reporting GABA, glutamate decarboxylase (GAD) 65/67, GABAA, GABAB, and GABAC receptors, GABA transporters (GAT) 1-3 and vesicular GAT in the brain, and GABA levels in the cerebrospinal fluid (CSF) and blood. Heterogeneity was estimated using the I2 index, and the risk of bias was assessed with an adapted questionnaire from the Joanna Briggs Institute Critical Appraisal Tools. The search identified 3631 articles, and 48 met the final inclusion criteria (518 HC, mean age 72.2, and 603 AD patients, mean age 75.6). Random-effects meta-analysis [standardized mean difference (SMD)] revealed that AD patients presented lower GABA levels in the brain (SMD = -0.48 [95% CI = -0.7, -0.27], adjusted p value (adj. p) < 0.001) and in the CSF (-0.41 [-0.72, -0.09], adj. p = 0.042), but not in the blood (-0.63 [-1.35, 0.1], adj. p = 0.176). In addition, GAD65/67 (-0.67 [-1.15, -0.2], adj. p = 0.006), GABAA receptor (-0.51 [-0.7, -0.33], adj. p < 0.001), and GABA transporters (-0.51 [-0.92, -0.09], adj. p = 0.016) were lower in the AD brain. Here, we showed a global reduction of GABAergic system components in the brain and lower GABA levels in the CSF of AD patients. Our findings suggest the GABAergic system is vulnerable to AD pathology and should be considered a potential target for developing pharmacological strategies and novel AD biomarkers.
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Affiliation(s)
- Giovanna Carello-Collar
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
| | - Bruna Bellaver
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Pamela C L Ferreira
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - João Pedro Ferrari-Souza
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Vanessa G Ramos
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
| | - Joseph Therriault
- McGill Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada
- Translational Neuroimaging Laboratory, McGill University Research Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada
- Departments of Neurology and Neurosurgery, McGill University, Montreal, QC, H3A 1A1, Canada
| | - Cécile Tissot
- McGill Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada
- Translational Neuroimaging Laboratory, McGill University Research Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada
- Departments of Neurology and Neurosurgery, McGill University, Montreal, QC, H3A 1A1, Canada
| | - Marco A De Bastiani
- Department of Pharmacology, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
| | - Carolina Soares
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Tharick A Pascoal
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Pedro Rosa-Neto
- McGill Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada
- Translational Neuroimaging Laboratory, McGill University Research Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada
- Departments of Neurology and Neurosurgery, McGill University, Montreal, QC, H3A 1A1, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Diogo O Souza
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
- Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil
| | - Eduardo R Zimmer
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil.
- McGill Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada.
- Translational Neuroimaging Laboratory, McGill University Research Centre for Studies in Aging, McGill University, Montreal, QC, H4H 1R3, Canada.
- Department of Pharmacology, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil.
- Graduate Program in Biological Sciences: Pharmacology and Therapeutics, Department of Pharmacology, Institute of Health Basic Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil.
- Brain Institute of Rio Grande Do Sul, Pontifical Catholic University of Rio Grande Do Sul, Porto Alegre, RS, 90610-000, Brazil.
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7
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Deng A, Wang S, Qin J, Yang P, Shen S, Zhou H, Chen X. ErbB4 processing is involved in OGD/R induced neuron injury. J Stroke Cerebrovasc Dis 2023; 32:107373. [PMID: 37734179 DOI: 10.1016/j.jstrokecerebrovasdis.2023.107373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
OBJECTIVE Our previous study found that ErbB4 gene expression was changed after oxygen-glucose deprivation/reperfusion (OGD/R). However, the exact role and mechanism of ErbB4 in brain ischemia are largely unknown. In this study, we explored the protective effects of ErbB4 and its possible mechanism after OGD/R. METHODS Cerebral ischemia/reperfusion (I/R) injury model was established in vitro and in vivo. Cell viability, apoptosis, and ROS production were measured by MTT, TUNEL, and fluorescent probe 2', 7'-dichlorofluorescein diacetate (DCFH-DA). Infarct size was evaluated by TTC. We performed bioinformatics analyses to screen for novel key genes involved in ErbB4 changes. RNA-Seq was used to transcriptome analysis. RNA and protein expression were detected by quantitative RT‒PCR and western bloting. RESULTS The expression of 80-kDa ErbB4 decreased after cerebral I/R injury in vitro and in vivo. Co-expression network analysis revealed that ErbB4 expression was correlated with the changes in Adrb1, Adrb2, Ldlr, and Dab2. Quantitative RT‒PCR revealed that the mRNA expression levels of Adrb1, Adrb2, and Dab2 were upregulated, and that of Ldlr was decreased after OGD/R. Activation of ErbB4 expression by neuregulin 1 (NRG1) significantly promoted cell survival, attenuated hippocampal apoptosis, and decreased ROS production after OGD/R. Furthermore, the elimination of ErbB4 using a specific siRNA reversed these beneficial effects. CONCLUSION Our data revealed the neuroprotective effects of ErbB4 against OGD/R injury, and the action could be related to changes in the ErbB4 membrane-associated fragment and the expression of Adrb1, Adrb2, Ldlr, and Dab2.
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Affiliation(s)
- Aiqing Deng
- Department of Pharmacy, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Shouyan Wang
- Department of Histology and Embryology, Medical School, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Jianxin Qin
- Department of Histology and Embryology, Medical School, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Panpan Yang
- Department of Histology and Embryology, Medical School, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Shaoze Shen
- Department of Histology and Embryology, Medical School, Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Hongzhi Zhou
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, People's Republic of China
| | - Xia Chen
- Department of Histology and Embryology, Medical School, Nantong University, Nantong, Jiangsu 226001, People's Republic of China.
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8
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Ma S, Wang D, Xie D. Identification of disulfidptosis-related genes and subgroups in Alzheimer's disease. Front Aging Neurosci 2023; 15:1236490. [PMID: 37600517 PMCID: PMC10436325 DOI: 10.3389/fnagi.2023.1236490] [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: 06/07/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Background Alzheimer's disease (AD), a common neurological disorder, has no effective treatment due to its complex pathogenesis. Disulfidptosis, a newly discovered type of cell death, seems to be closely related to the occurrence of various diseases. In this study, through bioinformatics analysis, the expression and function of disulfidptosis-related genes (DRGs) in Alzheimer's disease were explored. Methods Differential analysis was performed on the gene expression matrix of AD, and the intersection of differentially expressed genes and disulfidptosis-related genes in AD was obtained. Hub genes were further screened using multiple machine learning methods, and a predictive model was constructed. Finally, 97 AD samples were divided into two subgroups based on hub genes. Results In this study, a total of 22 overlapping genes were identified, and 7 hub genes were further obtained through machine learning, including MYH9, IQGAP1, ACTN4, DSTN, ACTB, MYL6, and GYS1. Furthermore, the diagnostic capability was validated using external datasets and clinical samples. Based on these genes, a predictive model was constructed, with a large area under the curve (AUC = 0.8847), and the AUCs of the two external validation datasets were also higher than 0.7, indicating the high accuracy of the predictive model. Using unsupervised clustering based on hub genes, 97 AD samples were divided into Cluster1 (n = 24) and Cluster2 (n = 73), with most hub genes expressed at higher levels in Cluster2. Immune infiltration analysis revealed that Cluster2 had a higher level of immune infiltration and immune scores. Conclusion A close association between disulfidptosis and Alzheimer's disease was discovered in this study, and a predictive model was established to assess the risk of disulfidptosis subtype in AD patients. This study provides new perspectives for exploring biomarkers and potential therapeutic targets for Alzheimer's disease.
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Affiliation(s)
- Shijia Ma
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Dan Wang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Daojun Xie
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
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9
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Deshpande P, Chimata AV, Snider E, Singh A, Kango-Singh M, Singh A. N-Acetyltransferase 9 ameliorates Aβ42-mediated neurodegeneration in the Drosophila eye. Cell Death Dis 2023; 14:478. [PMID: 37507384 PMCID: PMC10382493 DOI: 10.1038/s41419-023-05973-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Alzheimer's disease (AD), a progressive neurodegenerative disorder, manifests as accumulation of amyloid-beta-42 (Aβ42) plaques and intracellular accumulation of neurofibrillary tangles (NFTs) that results in microtubule destabilization. Targeted expression of human Aβ42 (GMR > Aβ42) in developing Drosophila eye retinal neurons results in Aβ42 plaque(s) and mimics AD-like extensive neurodegeneration. However, there remains a gap in our understanding of the underlying mechanism(s) for Aβ42-mediated neurodegeneration. To address this gap in information, we conducted a forward genetic screen, and identified N-acetyltransferase 9 (Mnat9) as a genetic modifier of GMR > Aβ42 neurodegenerative phenotype. Mnat9 is known to stabilize microtubules by inhibiting c-Jun-N- terminal kinase (JNK) signaling. We found that gain-of-function of Mnat9 rescues GMR > Aβ42 mediated neurodegenerative phenotype whereas loss-of-function of Mnat9 exhibits the converse phenotype of enhanced neurodegeneration. Here, we propose a new neuroprotective function of Mnat9 in downregulating the JNK signaling pathway to ameliorate Aβ42-mediated neurodegeneration, which is independent of its acetylation activity. Transgenic flies expressing human NAT9 (hNAT9), also suppresses Aβ42-mediated neurodegeneration thereby suggesting functional conservation in the interaction of fly Mnat9 or hNAT9 with JNK-mediated neurodegeneration. These studies add to the repertoire of molecular mechanisms that mediate cell death response following accumulation of Aβ42 and may provide new avenues for targeting neurodegeneration.
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Affiliation(s)
| | | | - Emily Snider
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Aditi Singh
- Interdisciplinary Graduate Studies, College of Arts and Sciences, University of Dayton, Dayton, OH, 45469, USA
| | - Madhuri Kango-Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
- Premedical Program, University of Dayton, Dayton, OH, 45469, USA
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA.
- Premedical Program, University of Dayton, Dayton, OH, 45469, USA.
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA.
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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10
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Wang X, Mei D, Lu Z, Zhang Y, Sun Y, Lu T, Yan H, Yue W. Genome-wide association study identified six loci associated with adverse drug reactions to aripiprazole in schizophrenia patients. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2023; 9:44. [PMID: 37491364 PMCID: PMC10368716 DOI: 10.1038/s41537-023-00369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023]
Abstract
Aripiprazole is recommended for routine use in schizophrenia patients. However, the biological mechanism for the adverse drug reactions (ADRs) among schizophrenia patients with the antipsychotic drug aripiprazole is far from clear. To explore the potential genetic factors that may cause movement-related adverse antipsychotic effects in patients, we conducted an association analysis between movement-related ADRs and SNPs in schizophrenia patients receiving aripiprazole monotherapy. In this study, multiple ADRs of 384 patients were quantified within 6-week treatment, and the scores of movement-related ADRs at baseline and follow-up time points during treatment were obtained. The highest score record was used as the quantitative index in analysis, and genetic analysis at the genome-wide level was conducted. The SNP rs4149181 in SLC22A8 [P = 2.28 × 10-8] showed genome-wide significance, and rs2284223 in ADCYAP1R1 [P = 9.76 × 10-8], rs73258503 in KCNIP4 [P = 1.39 × 10-7], rs678428 in SMAD9 [P = 4.70 × 10-7], rs6421034 in NAP1L4 [P = 6.80 × 10-7], and rs1394796 in ERBB4 [P = 8.60 × 10-7] were found to be significantly associated with movement-related ADRs. The combined prediction model of these six loci showed acceptable performance in predicting adverse events [area under the curve (AUC): 0.84]. Combined with the function and network of the above genes and other candidate loci (KCNA1, CACNG1, etc.), we hypothesize that SLC22A8 and KCNIP4-Kv channel perform their respective functions as transporter or channel and participate in the in vivo metabolism or effects of aripiprazole. The above results imply the important function of ion transporters and channels in movement-related adverse antipsychotic effects in aripiprazole monotherapy schizophrenia patients.
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Affiliation(s)
- Xueping Wang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China
| | - Dongli Mei
- School of Nursing, Peking University, 10019, Beijing, China
| | - Zhe Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China
| | - Yuyanan Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China
| | - Yaoyao Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China
| | - Tianlan Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China
| | - Hao Yan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China.
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China.
| | - Weihua Yue
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.
- National Clinical Research Center for Mental Disorders & NHC Key Laboratory of Mental Health (Peking University), 100191, Beijing, China.
- Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences (No. 2018RU006), Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China.
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11
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Neuregulin-1/PI3K signaling effects on oligodendrocyte proliferation, remyelination and behaviors deficit in a male mouse model of ischemic stroke. Exp Neurol 2023; 362:114323. [PMID: 36690057 DOI: 10.1016/j.expneurol.2023.114323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
In this study, we investigated the effect of neuregulin-1 (NRG1) on demyelination and neurological function in an ischemic stroke model, and further explored its neuroprotective mechanisms. Adult male ICR mice underwent photothrombotic ischemia surgery and were injected with NRG1 beginning 30 min after ischemia. Cylinder and grid walking tests were performed to evaluate the forepaw function. In addition, the effect of NRG1 on neuronal damage/death (Cresyl violet, CV), neuronal nuclei (NeuN), nestin, doublecortin (DCX), myelin basic protein (MBP), non-phosphorylated neurofilaments (SMI-32), adenomatous polyposis coli (APC), erythroblastic leukemia viral oncogene homolog (ErbB) 2, 4 and serine-threonine protein kinase (Akt) in cortex were evaluated using immunohistochemistry, immunofluorescence and western blot. The cylinder and grid walking tests exposed that treatment of NRG1 observably regained the forepaw function. NRG1 treatment reduced cerebral infarction, restored forepaw function, promoted proliferation and differentiation of neuron and increased oligodendrogliogenesis. The neuroprotective effect of NRG1 is involved in its activation of PI3K/Akt signaling pathway via ErbB2, as shown by the suppression of the effect of NRG1 by the PI3K inhibitor LY294002. Our results demonstrate that NRG1 is effective in ameliorating the both acute phase neuroprotection and long-term neurological functions via resumption of neuronal proliferation and differentiation and oligodendrogliogenesis in a male mouse model of ischemic stroke.
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12
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Jonnakuti VS, Wagner EJ, Maletić-Savatić M, Liu Z, Yalamanchili HK. PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.523471. [PMID: 36747700 PMCID: PMC9900750 DOI: 10.1101/2023.01.23.523471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
More than half of human genes exercise alternative polyadenylation (APA) and generate mRNA transcripts with varying 3' untranslated regions (UTR). However, current computational approaches for identifying cleavage and polyadenylation sites (C/PASs) and quantifying 3'UTR length changes from bulk RNA-seq data fail to unravel tissue- and disease-specific APA dynamics. Here, we developed a next-generation bioinformatics algorithm and application, PolyAMiner-Bulk, that utilizes an attention-based machine learning architecture and an improved vector projection-based engine to infer differential APA dynamics accurately. When applied to earlier studies, PolyAMiner-Bulk accurately identified more than twice the number of APA changes in an RBM17 knockdown bulk RNA-seq dataset compared to current generation tools. Moreover, on a separate dataset, PolyAMiner-Bulk revealed novel APA dynamics and pathways in scleroderma pathology and identified differential APA in a gene that was identified as being involved in scleroderma pathogenesis in an independent study. Lastly, we used PolyAMiner-Bulk to analyze the RNA-seq data of post-mortem prefrontal cortexes from the ROSMAP data consortium and unraveled novel APA dynamics in Alzheimer's Disease. Our method, PolyAMiner-Bulk, creates a paradigm for future alternative polyadenylation analysis from bulk RNA-seq data.
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Affiliation(s)
- Venkata Soumith Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Mirjana Maletić-Savatić
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
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13
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Zhang X, Yang S, Han S, Sun Y, Han M, Zheng X, Li F, Wei Y, Wang Y, Bi J. Differential methylation of circRNA m6A in an APP/PS1 Alzheimer's disease mouse model. Mol Med Rep 2023; 27:55. [PMID: 36660942 PMCID: PMC9879070 DOI: 10.3892/mmr.2023.12942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/25/2022] [Indexed: 01/19/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic neurological disease characterized by memory loss and progressive cognitive impairment. The characteristic AD pathologies include extracellular senile plaques formed by β‑amyloid protein deposition, neurofibrillary tangles formed by hyper‑phosphorylation of τ protein and neuronal loss caused by glial cell proliferation. However, the pathogenesis of AD is still unclear. Dysregulation of RNA methylation is associated with biological processes, including neurodevelopment and neurodegenerative disease. N6‑methyladenosine (m6A) is the main modification in eukaryotic RNA and may be associated with the pathophysiology of AD. Circular RNA (circRNA) is a new type of evolutionarily conserved non‑coding RNA without 5'‑cap and 3'‑polyadenylic acid tail. circRNA undergoes m6A RNA methylation and may be involved in the pathogenesis of AD. In the present study, high‑throughput sequencing was performed to assess the degree of circRNA m6A methylation in APP/PS1 AD and C57BL/6 mice. These results suggested that circRNA m6A methylation in AD mice was markedly altered compared to the control group. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to predict associated pathways; genes with different circRNA m6A methylation in AD mice were associated with 'axon guidance', 'long‑term potentiation', 'glutamatergic synapse', 'cholinergic synapse', 'GABAergic synapse' and 'long‑term depression'. Methylated RNA immunoprecipitation reverse transcription‑quantitative PCR demonstrated that among the eight selected circRNA m6A genes, there were five genes that demonstrated significantly increased methylation and three demonstrated significantly decreased methylation. In summary, the present study indicated that circRNA m6A methylation may be associated with pathogenesis of AD.
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Affiliation(s)
- Xiao Zhang
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Suge Yang
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Song Han
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yuan Sun
- Department of Outpatients, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Min Han
- Department of Geriatric Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Xiaolei Zheng
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Fan Li
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yan Wei
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yun Wang
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China,Correspondence to: Dr Yun Wang, Department of Neurological Medicine, The Second Hospital of Shandong University, 247 Beiyuan Road, Jinan, Shandong 250033, P.R. China, E-mail:
| | - Jianzhong Bi
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
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14
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Identifying Genes that Affect Differentiation of Human Neural Stem Cells and Myelination of Mature Oligodendrocytes. Cell Mol Neurobiol 2022:10.1007/s10571-022-01313-5. [DOI: 10.1007/s10571-022-01313-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
AbstractHuman neural stem cells (NSCs) are self-renewing, multipotent cells of the central nervous system (CNS). They are characterized by their ability to differentiate into a range of cells, including oligodendrocytes (OLs), neurons, and astrocytes, depending on exogenous stimuli. An efficient and easy directional differentiation method was developed for obtaining large quantities of high-quality of human OL progenitor cells (OPCs) and OLs from NSCs. RNA sequencing, immunofluorescence staining, flow cytometry, western blot, label-free proteomic sequencing, and qPCR were performed in OL lines differentiated from NSC lines. The changes in the positive rate of typical proteins were analyzed expressed by NSCs, neurons, astrocytes, OPCs, and OLs. We assessed Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of differentially expressed (DE) messenger RNAs (mRNAs) related to the differentiation of NSCs and the maturation of OLs. The percentage of NSCs differentiated into neurons, astrocytes, and OLs was 82.13%, 80.19%, and 90.15%, respectively. We found that nestin, PAX6, Musashi, and vimentin were highly expressed in NSCs; PDGFR-α, A2B5, NG2, OLIG2, SOX10, and NKX2-2 were highly expressed in OPCs; and CNP, GALC, PLP1, and MBP were highly expressed in OLs. RNA sequencing, western blot and qPCR revealed that ERBB4 and SORL1 gradually increased during NSC–OL differentiation. In conclusion, NSCs can differentiate into neurons, astrocytes, and OLs efficiently. PDGFR-α, APC, ID4, PLLP, and other markers were related to NSC differentiation and OL maturation. Moreover, we refined a screening method for ERBB4 and SORL1, which may underlie NSC differentiation and OL maturation.
Graphical Abstract
Potential unreported genes and proteins may regulate differentiation of human neural stem cells into oligodendrocyte lineage. Neural stem cells (NSCs) can differentiate into neurons, astrocytes, and oligodendrocyte (OLs) efficiently. By analyzing the DE mRNAs and proteins of NSCs and OLs lineage, we could identify reported markers and unreported markers of ERBB4 and SORL1 that may underlie regulate NSC differentiation and OL maturation.
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15
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Guo Q, Wu G, Huang F, Wei Z, Wang JZ, Zhang B, Liu R, Yang Y, Wang X, Li HL. Novel small molecular compound 2JY-OBZ4 alleviates AD pathology in cell models via regulating multiple targets. Aging (Albany NY) 2022; 14:8077-8094. [PMID: 36227154 PMCID: PMC9596221 DOI: 10.18632/aging.204336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
Alzheimer’s disease (AD) is the most common form of neurodegenerative dementia, characterized by cognitive deficits and memory dysfunction, which is clinically incurable so far. Novel small molecular compound 2JY-OBZ4 is one of structural analogue of Huperzine A (Hup-A), an anti-AD drug in China. In our previous work, 2JY-OBZ4 exhibited potent effects on tau hyperphosphorylation, Aβ production and acetylcholinesterase (AChE) activity. However, 2JY-OBZ4's anti-AD effects and the underlying molecular mechanisms remain unclear. We here reported that 2JY-OBZ4 resisted tau hyperphosphorylation at Thr181 and Ser396 sites in HEK293-hTau cells transfected with GSK-3β, decreased tau phosphorylation via upregulating the activity of PP2A in HEK293-hTau cells and reduced Aβ production through regulating protein levels of APP cleavage enzymes in N2a-hAPP cells. Meanwhile, we found that 2JY-OBZ4 had no adverse effects on cell viability of mice primary neuron even at high concentration, and ameliorated synaptic loss induced by human oligomeric Aβ42. 2JY-OBZ4 had moderate AChE inhibitory activity with the half maximal inhibitory concentration (IC50) to be 39.48 μg/ml in vitro, which is more than two times higher than Hup-A. Together, 2JY-OBZ4 showed promising therapeutic effects in AD cell models through regulating multiple targets. The research provides a new candidate for the therapeutic development of AD.
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Affiliation(s)
- Qian Guo
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong JS 226001, China
| | - Gang Wu
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong JS 226001, China
| | - Fang Huang
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhen Wei
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jian-Zhi Wang
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong JS 226001, China.,Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Bin Zhang
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rong Liu
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yang Yang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaochuan Wang
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong JS 226001, China.,Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430056, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China
| | - Hong-Lian Li
- School of Basic Medicine, Key Laboratory of Education Ministry, Hubei Province of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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16
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Ruan W, Shen S, Xu Y, Ran N, Zhang H. Mechanistic insights into procyanidins as therapies for Alzheimer's disease: A review. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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