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Lee SH, Bae EJ, Perez-Acuna D, Jung MK, Han JW, Mook-Jung I, Lee SJ. Amyloid-β-activated microglia can induce compound proteinopathies. Brain 2024:awae221. [PMID: 39194073 DOI: 10.1093/brain/awae221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/22/2024] [Accepted: 06/17/2024] [Indexed: 08/29/2024] Open
Abstract
Neuropathological features of Alzheimer's disease include amyloid plaques, neurofibrillary tangles and Lewy bodies, with the former preceding the latter two. However, it is not fully understood how these compound proteinopathies are interconnected. Here, we show that transplantation of amyloid-β oligomer-activated microglia into the striatum of naïve mice was sufficient to generate all the features of Alzheimer's disease, including widespread tauopathy and synucleinopathy, gliosis, neuroinflammation, synapse loss, neuronal death, and cognitive and motor deficits. These pathological features were eliminated by microglia depletion and anti-inflammatory drug administration. Our results suggest the crucial roles of microglia-driven inflammation in development of mixed pathology. This study provides not only mechanistic insights into amyloid-β oligomer-triggered proteinopathies but also a novel animal model recapitulating the salient features of Alzheimer's disease.
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Affiliation(s)
- Sang Hwan Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Eun-Jin Bae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Dayana Perez-Acuna
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Min Kyo Jung
- Neural Circuits Research Group, Korea Brain Research Institute, Daegu 41068, Korea
| | - Jong Won Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biochemistry, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Inhee Mook-Jung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University, Seoul 03080, Korea
- Department of Biochemistry, Seoul National University College of Medicine, Seoul 03080, Korea
- Convergence Research Center for Dementia, Medical Research Center, Seoul National University, Seoul 03080, Korea
| | - Seung-Jae Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University, Seoul 03080, Korea
- Convergence Research Center for Dementia, Medical Research Center, Seoul National University, Seoul 03080, Korea
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Kim DK, Suh K, Park J, Lee SE, Han J, Chang S, Kim Y, Mook-Jung I. FGFR3 drives Aβ-induced tau uptake. Exp Mol Med 2024; 56:1631-1642. [PMID: 38951140 PMCID: PMC11297141 DOI: 10.1038/s12276-024-01274-3] [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: 07/27/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 07/03/2024] Open
Abstract
The amyloid cascade hypothesis suggests that amyloid beta (Aβ) contributes to initiating subsequent tau pathology in Alzheimer's disease (AD). However, the underlying mechanisms through which Aβ contributes to tau uptake and propagation remain poorly understood. Here, we show that preexisting amyloid pathology accelerates the uptake of extracellular tau into neurons. Using quantitative proteomic analysis of endocytic vesicles, we reveal that Aβ induces the internalization of fibroblast growth factor receptor 3 (FGFR3). Extracellular tau binds to the extracellular domain of FGFR3 and is internalized by the FGFR3 ligand, fibroblast growth factor 2 (FGF2). Aβ accelerates FGF2 secretion from neurons, thereby inducing the internalization of tau-attached FGFR3. Knockdown of FGFR3 in the hippocampus reduces tau aggregation by decreasing tau uptake and improving memory function in AD model mice. These data suggest FGFR3 in neurons as a novel tau receptor and a key mediator of Aβ-induced tau uptake in AD.
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Affiliation(s)
- Dong Kyu Kim
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Research Center for Dementia, Medical Research Center, Seoul National University, Seoul, Korea
| | - Kyujin Suh
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Research Center for Dementia, Medical Research Center, Seoul National University, Seoul, Korea
| | - Junho Park
- Department of Medical Science, CHA University School of Medicine, Seongnam, Republic of Korea
- Advanced Omics Center, Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | - Sang-Eun Lee
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jihui Han
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Research Center for Dementia, Medical Research Center, Seoul National University, Seoul, Korea
| | - Sunghoe Chang
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Youngsoo Kim
- Department of Medical Science, CHA University School of Medicine, Seongnam, Republic of Korea
- Advanced Omics Center, Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | - Inhee Mook-Jung
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea.
- Convergence Research Center for Dementia, Medical Research Center, Seoul National University, Seoul, Korea.
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3
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Kim DK, Choi H, Lee W, Choi H, Hong SB, Jeong JH, Han J, Han JW, Ryu H, Kim JI, Mook-Jung I. Brain hypothyroidism silences the immune response of microglia in Alzheimer's disease animal model. SCIENCE ADVANCES 2024; 10:eadi1863. [PMID: 38489366 PMCID: PMC10942107 DOI: 10.1126/sciadv.adi1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Thyroid hormone (TH) imbalance is linked to the pathophysiology of reversible dementia and Alzheimer's disease (AD). It is unclear whether tissue hypothyroidism occurs in the AD brain and how it affects on AD pathology. We find that decreased iodothyronine deiodinase 2 is correlated with hippocampal hypothyroidism in early AD model mice before TH alterations in the blood. TH deficiency leads to spontaneous activation of microglia in wild-type mice under nonstimulated conditions, resulting in lowered innate immune responses of microglia in response to inflammatory stimuli or amyloid-β. In AD model mice, TH deficiency aggravates AD pathology by reducing the disease-associated microglia population and microglial phagocytosis. We find that TH deficiency reduces microglial ecto-5'-nucleotidase (CD73) and inhibition of CD73 leads to impaired innate immune responses in microglia. Our findings reveal that TH shapes microglial responses to inflammatory stimuli including amyloid-β, and brain hypothyroidism in early AD model mice aggravates AD pathology by microglial dysfunction.
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Affiliation(s)
- Dong Kyu Kim
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - Hyunjung Choi
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Woochan Lee
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
| | - Hayoung Choi
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - Seok Beom Hong
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - June-Hyun Jeong
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - Jihui Han
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - Jong Won Han
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - Hoon Ryu
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
| | - Inhee Mook-Jung
- Department of Biomedical Science, College of Medicine, Seoul National University, Seoul, Korea
- Convergence Dementia Research Center, College of Medicine, Seoul National University, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
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Zhao T, Zeng J, Zhang R, Fan W, Guan Q, Wang H, Pu L, Jiang Y, Yang H, Wang X, Han L. Serum Olink Proteomics-Based Identification of Protein Biomarkers Associated with the Immune Response in Ischemic Stroke. J Proteome Res 2024; 23:1118-1128. [PMID: 38319990 DOI: 10.1021/acs.jproteome.3c00885] [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] [Indexed: 02/08/2024]
Abstract
The immune response is considered essential for pathology of ischemic stroke (IS), but it remains unclear which immune response-related proteins exhibit altered expression in IS patients. Here, we used Olink proteomics to examine the expression levels of 92 immune response-related proteins in the sera of IS patients (n = 88) and controls (n = 88), and we found that 59 of these proteins were differentially expressed. Feature variables were screened from the differentially expressed proteins by the least absolute shrinkage and selection operator (LASSO) and the random forest and by determining whether their proteins had an area under the curve (AUC) greater than 0.8. Ultimately, we identified six potential protein biomarkers of IS, namely, MASP1, STC1, HCLS1, CLEC4D, PTH1R, and PIK3AP1, and established a logistic regression model that used these proteins to diagnose IS. The AUCs of the models in the internal validation and the test set were 0.962 (95% confidence interval (CI): 0.895-1.000) and 0.954 (95% CI: 0.884-1.000), respectively, and the same protein detection method was performed in an external independent validation set (AUC: 0.857 (95% CI: 0.801-0.913)). These proteins may play a role in immune regulation via the C-type lectin receptor signaling pathway, the PI3K-AKT signaling pathway, and the B-cell receptor signaling pathway.
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Affiliation(s)
- Tian Zhao
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Jingjing Zeng
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Ruijie Zhang
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Weinv Fan
- Department of Neurology, Ningbo No.2 Hospital, Ningbo 315000, China
| | - Qiongfeng Guan
- Department of Neurology, Ningbo No.2 Hospital, Ningbo 315000, China
| | - Han Wang
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Liyuan Pu
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Yannan Jiang
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Huiqun Yang
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
| | - Xiaokun Wang
- Department of Neurology, the Second Affiliated Hospital, Harbin Medical University, Harbin 150081, China
| | - Liyuan Han
- Department of Clinical Epidemiology, Ningbo No. 2 Hospital, Ningbo 315000, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
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Zhuang H, Cao X, Tang X, Zou Y, Yang H, Liang Z, Yan X, Chen X, Feng X, Shen L. Investigating metabolic dysregulation in serum of triple transgenic Alzheimer's disease male mice: implications for pathogenesis and potential biomarkers. Amino Acids 2024; 56:10. [PMID: 38315232 PMCID: PMC10844422 DOI: 10.1007/s00726-023-03375-1] [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: 05/15/2023] [Accepted: 11/11/2023] [Indexed: 02/07/2024]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease that lacks convenient and accessible peripheral blood diagnostic markers and effective drugs. Metabolic dysfunction is one of AD risk factors, which leaded to alterations of various metabolites in the body. Pathological changes of the brain can be reflected in blood metabolites that are expected to explain the disease mechanisms or be candidate biomarkers. The aim of this study was to investigate the changes of targeted metabolites within peripheral blood of AD mouse model, with the purpose of exploring the disease mechanism and potential biomarkers. Targeted metabolomics was used to quantify 256 metabolites in serum of triple transgenic AD (3 × Tg-AD) male mice. Compared with controls, 49 differential metabolites represented dysregulation in purine, pyrimidine, tryptophan, cysteine and methionine and glycerophospholipid metabolism. Among them, adenosine, serotonin, N-acetyl-5-hydroxytryptamine, and acetylcholine play a key role in regulating neural transmitter network. The alteration of S-adenosine-L-homocysteine, S-adenosine-L-methionine, and trimethylamine-N-oxide in AD mice serum can served as indicator of AD risk. The results revealed the changes of metabolites in serum, suggesting that metabolic dysregulation in periphery in AD mice may be related to the disturbances in neuroinhibition, the serotonergic system, sleep function, the cholinergic system, and the gut microbiota. This study provides novel insights into the dysregulation of several key metabolites and metabolic pathways in AD, presenting potential avenues for future research and the development of peripheral biomarkers.
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Affiliation(s)
- Hongbin Zhuang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Xueshan Cao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Yongdong Zou
- Center for Instrumental Analysis, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Hongbo Yang
- Center for Instrumental Analysis, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Zhiyuan Liang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Xi Yan
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Xiaolu Chen
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025, People's Republic of China
| | - Xingui Feng
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, People's Republic of China.
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Park J, Lee SH, Shin D, Kim Y, Kim YS, Seong MY, Lee JJ, Seo HG, Cho WS, Ro YS, Kim Y, Oh BM. Multiplexed Quantitative Proteomics Reveals Proteomic Alterations in Two Rodent Traumatic Brain Injury Models. J Proteome Res 2024; 23:249-263. [PMID: 38064581 DOI: 10.1021/acs.jproteome.3c00544] [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] [Indexed: 01/06/2024]
Abstract
In many cases of traumatic brain injury (TBI), conspicuous abnormalities, such as scalp wounds and intracranial hemorrhages, abate over time. However, many unnoticeable symptoms, including cognitive, emotional, and behavioral dysfunction, often last from several weeks to years after trauma, even for mild injuries. Moreover, the cause of such persistence of symptoms has not been examined extensively. Recent studies have implicated the dysregulation of the molecular system in the injured brain, necessitating an in-depth analysis of the proteome and signaling pathways that mediate the consequences of TBI. Thus, in this study, the brain proteomes of two TBI models were examined by quantitative proteomics during the recovery period to determine the molecular mechanisms of TBI. Our results show that the proteomes in both TBI models undergo distinct changes. A bioinformatics analysis demonstrated robust activation and inhibition of signaling pathways and core proteins that mediate biological processes after brain injury. These findings can help determine the molecular mechanisms that underlie the persistent effects of TBI and identify novel targets for drug interventions.
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Affiliation(s)
- Junho Park
- Department of Pharmacology, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Research Institute for Basic Medical Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Seung Hak Lee
- Department of Rehabilitation Medicine, Asan Medical Center, 88 Olympic-Ro 43-Gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Dongyoon Shin
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Yeongshin Kim
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Young Sik Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Min Yong Seong
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Jin Joo Lee
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Han Gil Seo
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Won-Sang Cho
- Department of Neurosurgery, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Young Sun Ro
- Department of Emergency Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Youngsoo Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Byung-Mo Oh
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Institute of Aging, Seoul National University College of Medicine, 71 Ihwajang-gil, Jongno-gu, Seoul 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- National Traffic Injury Rehabilitation Hospital, 260 Jungang-ro, Yangpyeong-gun 12564, Gyeonggi-do, Republic of Korea
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da Silva Beraldo IJ, Prates Rodrigues M, Polanczyk RS, Verano-Braga T, Lopes-Aguiar C. Proteomic-Based Studies on Memory Formation in Normal and Neurodegenerative Disease-Affected Brains. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:129-158. [PMID: 38409419 DOI: 10.1007/978-3-031-50624-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A critical aspect of cognition is the ability to acquire, consolidate, and evoke memories, which is considerably impaired by neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. These mnemonic processes are dependent on signaling cascades, which involve protein expression and degradation. Recent mass spectrometry (MS)-based proteomics has opened a range of possibilities for the study of memory formation and impairment, making it possible to research protein systems not studied before. However, in the context of synaptic proteome related to learning processes and memory formation, a deeper understanding of the synaptic proteome temporal dynamics after induction of synaptic plasticity and the molecular changes underlying the cognitive deficits seen in neurodegenerative diseases is needed. This review analyzes the applications of proteomics for understanding memory processes in both normal and neurodegenerative conditions. Moreover, the most critical experimental studies have been summarized using the PANTHER overrepresentation test. Finally, limitations associated with investigations of memory studies in physiological and neurodegenerative disorders have also been discussed.
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Affiliation(s)
- Ikaro Jesus da Silva Beraldo
- Universidade Federal de Minas Gerais, Departamento de Fisiologia e Biofísica, Laboratório de Neurociências Comportamental e Molecular (LANEC), Belo Horizonte, Brazil
| | - Mateus Prates Rodrigues
- Universidade Federal de Minas Gerais, Departamento de Fisiologia e Biofísica, Laboratório de Neurociências Comportamental e Molecular (LANEC), Belo Horizonte, Brazil
| | - Rafaela Schuttenberg Polanczyk
- Universidade Federal de Minas Gerais, Departamento de Fisiologia e Biofísica, Laboratório de Neurociências Comportamental e Molecular (LANEC), Belo Horizonte, Brazil
| | - Thiago Verano-Braga
- Universidade Federal de Minas Gerais, Departamento de Fisiologia e Biofísica, Núcleo de Proteômica Funcional (NPF), Belo Horizonte, Brazil
- Instituto Nacional de Ciência e Tecnologia em Nano-Biofarmacêutica (INCT-Nanobiofar), Belo Horizonte, Brazil
| | - Cleiton Lopes-Aguiar
- Universidade Federal de Minas Gerais, Departamento de Fisiologia e Biofísica, Laboratório de Neurociências Comportamental e Molecular (LANEC), Belo Horizonte, Brazil.
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Singh A. Brain-derived neurotrophic factor - a key player in the gastrointestinal system. PRZEGLAD GASTROENTEROLOGICZNY 2023; 18:380-392. [PMID: 38572454 PMCID: PMC10985741 DOI: 10.5114/pg.2023.132957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/24/2023] [Indexed: 04/05/2024]
Abstract
Brain-derived neurotrophic factor (BDNF) is highly expressed throughout the gastrointestinal (GI) tract and plays a critical role in the regulation of intestinal motility, secretion, sensation, immunity, and mucosal integrity. Dysregulation of BDNF signalling has been implicated in the pathophysiology of various GI disorders including inflammatory bowel disease, irritable bowel syndrome, functional dyspepsia, and diabetic gastroenteropathy. This review provides a comprehensive overview of BDNF localization, synthesis, receptors, and signalling mechanisms in the gut. In addition, current evidence on the diverse physiologic and pathophysiologic roles of BDNF in the control of intestinal peristalsis, mucosal transport processes, visceral sensation, neuroimmune interactions, gastrointestinal mucosal healing, and enteric nervous system homeostasis are discussed. Finally, the therapeutic potential of targeting BDNF for the treatment of functional GI diseases is explored. Advancing knowledge of BDNF biology and mechanisms of action may lead to new therapies based on harnessing the gut trophic effects of this neurotrophin.
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Affiliation(s)
- Arjun Singh
- Department of Medicine, Division of Gastroenterology and Hepatology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
- Molecular Pharmacology Program and Chemistry, Memorial Sloan Kettering Cancer Center, New York, United States
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9
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Wu D, Yu N, Gao Y, Xiong R, Liu L, Lei H, Jin S, Liu J, Liu Y, Xie J, Liu E, Zhou Q, Liu Y, Li S, Wei L, Lv J, Yu H, Zeng W, Zhou Q, Xu F, Luo MH, Zhang Y, Yang Y, Wang JZ. Targeting a vulnerable septum-hippocampus cholinergic circuit in a critical time window ameliorates tau-impaired memory consolidation. Mol Neurodegener 2023; 18:23. [PMID: 37060096 PMCID: PMC10103508 DOI: 10.1186/s13024-023-00614-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/12/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Abnormal tau accumulation and cholinergic degeneration are hallmark pathologies in the brains of patients with Alzheimer's disease (AD). However, the sensitivity of cholinergic neurons to AD-like tau accumulation and strategies to ameliorate tau-disrupted spatial memory in terms of neural circuits still remain elusive. METHODS To investigate the effect and mechanism of the cholinergic circuit in Alzheimer's disease-related hippocampal memory, overexpression of human wild-type Tau (hTau) in medial septum (MS)-hippocampus (HP) cholinergic was achieved by specifically injecting pAAV-EF1α-DIO-hTau-eGFP virus into the MS of ChAT-Cre mice. Immunostaining, behavioral analysis and optogenetic activation experiments were used to detect the effect of hTau accumulation on cholinergic neurons and the MS-CA1 cholinergic circuit. Patch-clamp recordings and in vivo local field potential recordings were used to analyze the influence of hTau on the electrical signals of cholinergic neurons and the activity of cholinergic neural circuit networks. Optogenetic activation combined with cholinergic receptor blocker was used to detect the role of cholinergic receptors in spatial memory. RESULTS In the present study, we found that cholinergic neurons with an asymmetric discharge characteristic in the MS-hippocampal CA1 pathway are vulnerable to tau accumulation. In addition to an inhibitory effect on neuronal excitability, theta synchronization between the MS and CA1 subsets was significantly disrupted during memory consolidation after overexpressing hTau in the MS. Photoactivating MS-CA1 cholinergic inputs within a critical 3 h time window during memory consolidation efficiently improved tau-induced spatial memory deficits in a theta rhythm-dependent manner. CONCLUSIONS Our study not only reveals the vulnerability of a novel MS-CA1 cholinergic circuit to AD-like tau accumulation but also provides a rhythm- and time window-dependent strategy to target the MS-CA1 cholinergic circuit, thereby rescuing tau-induced spatial cognitive functions.
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Affiliation(s)
- Dongqin Wu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Nana Yu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yang Gao
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Xiong
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Luping Liu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, 999077, China
| | - Huiyang Lei
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Sen Jin
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China
| | - Jiale Liu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yingzhou Liu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiazhao Xie
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Enjie Liu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qiuzhi Zhou
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanchao Liu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shihong Li
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Linyu Wei
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingru Lv
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huilin Yu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenbo Zeng
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qiang Zhou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fuqiang Xu
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min-Hua Luo
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yao Zhang
- Endocrine Department of Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430077, China.
| | - Ying Yang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226000, China.
| | - Jian-Zhi Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226000, China.
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10
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Wang G, Shen X, Song X, Wang N, Wo X, Gao Y. Protective mechanism of gold nanoparticles on human neural stem cells injured by β-amyloid protein through miR-21-5p/SOCS6 pathway. Neurotoxicology 2023; 95:12-22. [PMID: 36623431 DOI: 10.1016/j.neuro.2022.12.011] [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: 07/23/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with progressive memory loss in dementia. Gold nanoparticles (AuNPs) were reported beneficial for human neural stem cells (hNSCs) treated with Amyloid-beta (Aβ), but the neuroprotective mechanisms still are unknown. First, the hNSCs induced by Aβ to construct AD cell model in vitro and AuNPs was performed to assess the therapeutic effect of Aβ-targeted AD treatment. Then, we investigated the effects of AuNPs on hNSCs viability and proinflammatory factors (interleukin 6 and tumor necrosis factor-alpha) by Cell Counting Kit-8 (CCK-8) and enzyme-linked immunosorbent (ELISA). FACS was carried out to determinate Tuj-1 and glial fibrillary acidic protein (GFAP). Reactive oxygen species (ROS) generation and mitochondrial membrane potential was evaluated by ROS and JC-1 assay kit. In addition, miRNA array was used to systematically detect the differential miRNAs. Dual-luciferase reporter assay was applied to verify the targeting relationship between miR-21-5p and the suppressor of cytokine signalling 6(SOCS6). Quantitative PCR (qPCR) and Western blot assessments were also used to detect related gene expression intracellularly or in the supernatant. The results demonstrate that AuNPs co-treatment repressed the high expression of total tau (T-tau), phosphorylated tau (P-tau), and Aβ protein, and reduced apoptosis rate of hNSCs. Aβ-induced decreased mitochondrial membrane potential and mitochondria in the hNSCs were damaged, while AuNPs co-treatment showed a protective effect on mitochondrial membrane potential. Co-treatment with AuNPs significantly increased dynamin-related protein 1 (DRP1), nuclear respiratory factor 1 (NRF1), and mitochondrial transcription factor A (TFAM) mRNA levels. AuNPs may improve mitochondrial function impairment due to Aβ by elevating mitochondrial membrane potential, upregulating regulators of mitochondrial biogenesis, and inhibiting ROS production. hNSCs transfected with miR-21-5p inhibitor reversed AuNPs mediated cytoprotection induced by Aβ. AuNPs upregulation of miR-21-5p expression and exert a mitochondrial protective function. Overexpression of miR-21-5p contributes to enhancing the effect of cytoprotection of AuNPs. MiR-21-5p direct targeting SOCS6 and overexpression SOCS6 exerted opposite effects on hNSCs compared with miR-21-5p mimic group. In conclusion, AuNPs can protect hNSCs from Aβ injury and decrease mitochondrial damage by regulating the miR-21-5p/SOCS6 pathway.
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Affiliation(s)
- Guoqing Wang
- Department of Internal Neurology, Bin Zhou People's Hospital, No.515, Huanghe Seven Road, Binzhou, Shandong Province 256610, PR China.
| | - Xiangpeng Shen
- Department of Internal Neurology, Bin Zhou People's Hospital, No.515, Huanghe Seven Road, Binzhou, Shandong Province 256610, PR China
| | - Xiangkong Song
- Department of Internal Neurology, Bin Zhou People's Hospital, No.515, Huanghe Seven Road, Binzhou, Shandong Province 256610, PR China
| | - Ningfen Wang
- Department of Internal Neurology, Bin Zhou People's Hospital, No.515, Huanghe Seven Road, Binzhou, Shandong Province 256610, PR China
| | - Xuewen Wo
- Department of Internal Neurology, Bin Zhou People's Hospital, No.515, Huanghe Seven Road, Binzhou, Shandong Province 256610, PR China
| | - Yonglei Gao
- Department of Internal Neurology, Bin Zhou People's Hospital, No.515, Huanghe Seven Road, Binzhou, Shandong Province 256610, PR China
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11
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OMICS Analyses Unraveling Related Gene and Protein-Driven Molecular Mechanisms Underlying PACAP 38-Induced Neurite Outgrowth in PC12 Cells. Int J Mol Sci 2023; 24:ijms24044169. [PMID: 36835581 PMCID: PMC9964364 DOI: 10.3390/ijms24044169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The study aimed to understand mechanism/s of neuronal outgrowth in the rat adrenal-derived pheochromocytoma cell line (PC12) under pituitary adenylate cyclase-activating polypeptide (PACAP) treatment. Neurite projection elongation was suggested to be mediated via Pac1 receptor-mediated dephosphorylation of CRMP2, where GSK-3β, CDK5, and Rho/ROCK dephosphorylated CRMP2 within 3 h after addition of PACAP, but the dephosphorylation of CRMP2 by PACAP remained unclear. Thus, we attempted to identify the early factors in PACAP-induced neurite projection elongation via omics-based transcriptomic (whole genome DNA microarray) and proteomic (TMT-labeled liquid chromatography-tandem mass spectrometry) analyses of gene and protein expression profiles from 5-120 min after PACAP addition. The results revealed a number of key regulators involved in neurite outgrowth, including known ones, called 'Initial Early Factors', e.g., genes Inhba, Fst, Nr4a1,2,3, FAT4, Axin2, and proteins Mis12, Cdk13, Bcl91, CDC42, including categories of 'serotonergic synapse, neuropeptide and neurogenesis, and axon guidance'. cAMP signaling and PI3K-Akt signaling pathways and a calcium signaling pathway might be involved in CRMP2 dephosphorylation. Cross-referencing previous research, we tried to map these molecular components onto potential pathways, and we may provide important new information on molecular mechanisms of neuronal differentiation induced by PACAP. Gene and protein expression data are publicly available at NCBI GSE223333 and ProteomeXchange, identifier PXD039992.
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12
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Shibato J, Takenoya F, Kimura A, Min CW, Yamashita M, Gupta R, Kim ST, Rakwal R, Shioda S. Examining the Effect of Notocactus ottonis Cold Vacuum Isolated Plant Cell Extract on Hair Growth in C57BL/6 Mice Using a Combination of Physiological and OMICS Analyses. Molecules 2023; 28:molecules28041565. [PMID: 36838553 PMCID: PMC9967486 DOI: 10.3390/molecules28041565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The biological and psychological importance of hair is recognized worldwide. Molecules that can promote the activation of hair follicle stem cells and the initiation of the growth phase have been subjects of research. Clarifying how hair regeneration is regulated may help to provide hair loss treatments, including cosmetic and even psychological interventions. We examined the hair-growing effects of a cell extract (CE) obtained from cactus Notocactus ottonis by the cold vacuum extraction protocol, by investigating its hair-growing effects, relevant mechanisms, and potential factors therein. Using male C57BL/6 mice, vehicle control (VC: propylene glycol: ethanol: water), MXD (minoxidil, positive control), and N. ottonis CE (N-CE, experimental) were applied topically to the backs of mice. The results showed that MXD and N-CE were more effective in promoting hair growth than VC. An increase in number of hair follicles was observed with N-CE in hematoxylin-eosin-stained skin tissue. The metabolite composition of N-CE revealed the presence of growth-promoting factors. Using mouse back whole-skin tissue samples, whole-genome DNA microarray (4 × 44 K, Agilent) and proteomics (TMT-based liquid chromatography-tandem mass spectrometry) analyses were carried out, suggesting the molecular factors underlying hair-promoting effects of N-CE. This study raises the possibility of using the newly described N. ottonis CE as a hair-growth-promoting agent.
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Affiliation(s)
- Junko Shibato
- Department of Functional Morphology, Shonan University of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
| | - Fumiko Takenoya
- Department of Sport Sciences, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ai Kimura
- Department of Sport Sciences, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Michio Yamashita
- Department of Sport Sciences, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Randeep Rakwal
- Institute of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8574, Japan
- Correspondence: (R.R.); (S.S.)
| | - Seiji Shioda
- Department of Functional Morphology, Shonan University of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- Correspondence: (R.R.); (S.S.)
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13
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Bartolo ND, Mortimer N, Manter MA, Sanchez N, Riley M, O'Malley TT, Hooker JM. Identification and Prioritization of PET Neuroimaging Targets for Microglial Phenotypes Associated with Microglial Activity in Alzheimer's Disease. ACS Chem Neurosci 2022; 13:3641-3660. [PMID: 36473177 DOI: 10.1021/acschemneuro.2c00607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Activation of microglial cells accompanies the progression of many neurodegenerative disorders, including Alzheimer's disease (AD). Development of molecular imaging tools specific to microglia can help elucidate the mechanism through which microglia contribute to the pathogenesis and progression of neurodegenerative disorders. Through analysis of published genetic, transcriptomic, and proteomic data sets, we identified 19 genes with microglia-specific expression that we then ranked based on association with the AD characteristics, change in expression, and potential druggability of the target. We believe that the process we used to identify and rank microglia-specific genes is broadly applicable to the identification and evaluation of targets in other disease areas and for applications beyond molecular imaging.
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Affiliation(s)
- Nicole D Bartolo
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
| | - Niall Mortimer
- Human Biology and Data Science, Eisai Center for Genetics Guided Dementia Discovery, 35 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Mariah A Manter
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
| | - Nicholas Sanchez
- Human Biology and Data Science, Eisai Center for Genetics Guided Dementia Discovery, 35 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Misha Riley
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
| | - Tiernan T O'Malley
- Human Biology and Data Science, Eisai Center for Genetics Guided Dementia Discovery, 35 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jacob M Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, Massachusetts 02129, United States
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14
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Xu J, Mao C, Hou Y, Luo Y, Binder JL, Zhou Y, Bekris LM, Shin J, Hu M, Wang F, Eng C, Oprea TI, Flanagan ME, Pieper AA, Cummings J, Leverenz JB, Cheng F. Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer's disease. Cell Rep 2022; 41:111717. [PMID: 36450252 PMCID: PMC9837836 DOI: 10.1016/j.celrep.2022.111717] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/01/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Translating human genetic findings (genome-wide association studies [GWAS]) to pathobiology and therapeutic discovery remains a major challenge for Alzheimer's disease (AD). We present a network topology-based deep learning framework to identify disease-associated genes (NETTAG). We leverage non-coding GWAS loci effects on quantitative trait loci, enhancers and CpG islands, promoter regions, open chromatin, and promoter flanking regions under the protein-protein interactome. Via NETTAG, we identified 156 AD-risk genes enriched in druggable targets. Combining network-based prediction and retrospective case-control observations with 10 million individuals, we identified that usage of four drugs (ibuprofen, gemfibrozil, cholecalciferol, and ceftriaxone) is associated with reduced likelihood of AD incidence. Gemfibrozil (an approved lipid regulator) is significantly associated with 43% reduced risk of AD compared with simvastatin using an active-comparator design (95% confidence interval 0.51-0.63, p < 0.0001). In summary, NETTAG offers a deep learning methodology that utilizes GWAS and multi-genomic findings to identify pathobiology and drug repurposing in AD.
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Affiliation(s)
- Jielin Xu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Chengsheng Mao
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jessica L Binder
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lynn M Bekris
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Jiyoung Shin
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Fei Wang
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Tudor I Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Margaret E Flanagan
- Department of Pathology and Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew A Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106, USA; Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA; Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland 44106, OH, USA; Department of Neuroscience, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, School of Integrated Health Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - James B Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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15
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Min CW, Jang JW, Lee GH, Gupta R, Yoon J, Park HJ, Cho HS, Park SR, Kwon SW, Cho LH, Jung KH, Kim YJ, Wang Y, Kim ST. TMT-based quantitative membrane proteomics identified PRRs potentially involved in the perception of MSP1 in rice leaves. J Proteomics 2022; 267:104687. [PMID: 35914717 DOI: 10.1016/j.jprot.2022.104687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 11/26/2022]
Abstract
Pathogen-associated molecular patterns (PAMPs) play a key role in triggering PAMPs triggered immunity (PTI) in plants. In the case of the rice-Magnaporthe oryzae pathosystem, fewer PAMPs and their pattern recognition receptors (PRRs) have been characterized. Recently, a M. oryzae snodprot1 homolog protein (MSP1) has been identified that functions as PAMP and triggering the PTI responses in rice. However, the molecular mechanism underlying MSP1-induced PTI is currently elusive. Therefore, we generated MSP1 overexpressed transgenic lines of rice, and a tandem mass tag (TMT)-based quantitative membrane proteomic analysis was employed to decipher the potential MSP1-induced signaling in rice using total cytosolic as well as membrane protein fractions. This approach led to the identification of 8033 proteins of which 1826 were differentially modulated in response to overexpression of MSP1 and/or exogenous jasmonic acid treatment. Of these, 20 plasma membrane-localized receptor-like kinases (RLKs) showed increased abundance in MSP1 overexpression lines. Moreover, activation of proteins related to the protein degradation and modification, calcium signaling, redox, and MAPK signaling was observed in transgenic lines expressing MSP1 in the apoplast. Taken together, our results identified potential PRR candidates involved in MSP1 recognition and suggested the overview mechanism of the MSP1-induced PTI signaling in rice leaves. SIGNIFICANCE: In plants, recognition of pathogen pathogen-derived molecules, such as PAMPs, by plant plant-derived PRRs has an essential role for in the activation of PTI against pathogen invasion. Typically, PAMPs are recognized by plasma membrane (PM) localized PRRs, however, identifying the PM-localized PRR proteins is challenging due to their low abundance. In this study, we performed an integrated membrane protein enrichment by microsomal membrane extraction (MME) method and subsequent TMT-labeling-based quantitative proteomic analysis using MSP1 overexpressed rice. Based on these results, we successfully identified various intracellular and membrane membrane-localized proteins that participated in the MSP1-induced immune response and characterized the potential PM-localized PRR candidates in rice.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Gi Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Hyun Ji Park
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hye Sun Cho
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Yiming Wang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea.
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16
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Ferrer I, Andrés-Benito P, Ausín K, Cartas-Cejudo P, Lachén-Montes M, Del Rio JA, Fernández-Irigoyen J, Santamaría E. Dysregulated Protein Phosphorylation in a Mouse Model of FTLD-Tau. J Neuropathol Exp Neurol 2022; 81:696-706. [PMID: 35848963 DOI: 10.1093/jnen/nlac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The neocortex of P301S mice, used as a model of fronto-temporal lobar degeneration linked to tau mutation (FTLD-tau), and wild-type mice, both aged 9 months, were analyzed with conventional label-free phosphoproteomics and SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) to assess the (phospho)proteomes. The total number of identified dysregulated phosphoproteins was 328 corresponding to 524 phosphorylation sites. The majority of dysregulated phosphoproteins, most of them hyperphosphorylated, were proteins of the membranes, synapses, membrane trafficking, membrane vesicles linked to endo- and exocytosis, cytoplasmic vesicles, and cytoskeleton. Another group was composed of kinases. In contrast, proteins linked to DNA, RNA metabolism, RNA splicing, and protein synthesis were hypophosphorylated. Other pathways modulating energy metabolism, cell signaling, Golgi apparatus, carbohydrates, and lipids are also targets of dysregulated protein phosphorylation in P301S mice. The present results, together with accompanying immunohistochemical and Western-blotting studies, show widespread abnormal phosphorylation of proteins, in addition to protein tau, in P301S mice. These observations point to dysregulated protein phosphorylation as a relevant contributory pathogenic component of tauopathies.
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Affiliation(s)
- Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Barcelona, Spain.,Bellvitge University Hospital/Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Barcelona, Spain.,Bellvitge University Hospital/Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain (PC-C, ML-M, ES)
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain (PC-C, ML-M, ES)
| | - José Antonio Del Rio
- Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain (PC-C, ML-M, ES)
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17
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Thu Thuy Nguyen V, Endres K. Targeting gut microbiota to alleviate neuroinflammation in Alzheimer's disease. Adv Drug Deliv Rev 2022; 188:114418. [PMID: 35787390 DOI: 10.1016/j.addr.2022.114418] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 02/08/2023]
Abstract
The gut microbiota came into focus within the last years regarding being associated with or even underlying neuropsychiatric diseases. The existence of the gut-brain-axis makes it highly plausible that bacterial metabolites or toxins that escape the intestinal environment or approach the vagal connections towards the brain, exert devastating effects on the central nervous system. In Alzheimer's disease (AD), growing evidence for dysbiotic changes in the gut microbiota is obtained, even though the question for cause or consequence remains open. Nevertheless, using modulation of microbiota to address inflammatory processes seems an attractive therapeutic approach as certain microbial products such as short chain fatty acids have been proven to exert beneficial cognitive effects. In this review, we summarize, contemporary knowledge on neuroinflammation and inflammatory processes within the brain and even more detailed in the gut in AD, try to conclude whom to target regarding human microbial commensals and report on current interventional trials.
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Affiliation(s)
- Vu Thu Thuy Nguyen
- Department of Psychiatry and Psychotherapy, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany
| | - Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center Mainz, Johannes Gutenberg-University Mainz, Germany.
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18
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Ferrer I, Andrés-Benito P, Ausín K, Cartas-Cejudo P, Lachén-Montes M, del Rio JA, Fernández-Irigoyen J, Santamaría E. Dysregulated Brain Protein Phosphorylation Linked to Increased Human Tau Expression in the hTau Transgenic Mouse Model. Int J Mol Sci 2022; 23:6427. [PMID: 35742871 PMCID: PMC9223516 DOI: 10.3390/ijms23126427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Altered protein phosphorylation is a major pathologic modification in tauopathies and Alzheimer's disease (AD) linked to abnormal tau fibrillar deposits in neurofibrillary tangles (NFTs) and pre-tangles and β-amyloid deposits in AD. hTau transgenic mice, which express 3R and less 4R human tau with no mutations in a murine knock-out background, show increased tau deposition in neurons but not NFTs and pre-tangles at the age of nine months. Label-free (phospho)proteomics and SWATH-MS identified 2065 proteins in hTau and wild-type (WT) mice. Only six proteins showed increased levels in hTau; no proteins were down-regulated. Increased tau phosphorylation in hTau was detected at Ser199, Ser202, Ser214, Ser396, Ser400, Thr403, Ser404, Ser413, Ser416, Ser422, Ser491, and Ser494, in addition to Thr181, Thr231, Ser396/Ser404, but not at Ser202/Thr205. In addition, 4578 phosphopeptides (corresponding to 1622 phosphoproteins) were identified in hTau and WT mice; 64 proteins were differentially phosphorylated in hTau. Sixty proteins were grouped into components of membranes, membrane signaling, synapses, vesicles, cytoskeleton, DNA/RNA/protein metabolism, ubiquitin/proteasome system, cholesterol and lipid metabolism, and cell signaling. These results showed that over-expression of human tau without pre-tangle and NFT formation preferentially triggers an imbalance in the phosphorylation profile of specific proteins involved in the cytoskeletal-membrane-signaling axis.
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Affiliation(s)
- Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, Network Centre of Biomedical Research of Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, University of Barcelona, 08907 Barcelona, Spain;
- Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Calle Feixa Llarga sn, 08907 Barcelona, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, Network Centre of Biomedical Research of Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, University of Barcelona, 08907 Barcelona, Spain;
- Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Calle Feixa Llarga sn, 08907 Barcelona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31192 Pamplona, Spain; (K.A.); (J.F.-I.)
| | - Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea Street, 31192 Pamplona, Spain; (P.C.-C.); (M.L.-M.); (E.S.)
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea Street, 31192 Pamplona, Spain; (P.C.-C.); (M.L.-M.); (E.S.)
| | - José Antonio del Rio
- Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), 08028 Barcelona, Spain;
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Carrer Baldiri Reixac, 08028 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31192 Pamplona, Spain; (K.A.); (J.F.-I.)
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea Street, 31192 Pamplona, Spain; (P.C.-C.); (M.L.-M.); (E.S.)
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19
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Xia P, Chen J, Bai X, Li M, Wang L, Lu Z. Key gene network related to primary ciliary dyskinesia in hippocampus of patients with Alzheimer’s disease revealed by weighted gene co-expression network analysis. BMC Neurol 2022; 22:198. [PMID: 35637434 PMCID: PMC9150314 DOI: 10.1186/s12883-022-02724-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Alzheimer’s disease (AD) is closely related to aging, showing an increasing incidence rate for years. As one of the main brain regions involved in AD, hippocampus has been extensively studied due to its association with many human diseases. However, little is known about its association with primary ciliary dyskinesia (PCD).
Material and Methods
The microarray data of hippocampus on AD were retrieved from the Gene Expression Omnibus (GEO) database to construct the co-expression network by weighted gene co-expression network analysis (WGCNA). The gene network modules associated with AD screened with the common genes were further annotated based on Gene Ontology (GO) database and enriched based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The protein-protein interaction (PPI) network was constructed based on STRING database to identify the hub genes in the network.
Results
Genes involved in PCD were identified in the hippocampus of AD patients. Functional analysis revealed that these genes were mainly enriched in ciliary tissue, ciliary assembly, axoneme assembly, ciliary movement, microtubule based process, microtubule based movement, organelle assembly, axoneme dynamin complex, cell projection tissue, and microtubule cytoskeleton tissue. A total of 20 central genes, e.g., DYNLRB2, ZMYND10, DRC1, DNAH5, WDR16, TTC25, and ARMC4 were identified as hub genes related to PCD in hippocampus of AD patients.
Conclusion
Our study demonstrated that AD and PCD have common metabolic pathways. These common pathways provide novel evidence for further investigation of the pathophysiological mechanism and the hub genes suggest new therapeutic targets for the diagnosis and treatment of AD and PCD.
Subjects
Bioinformatics, Cell Biology, Molecular Biology, Neurology.
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20
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Sanchez-Varo R, Mejias-Ortega M, Fernandez-Valenzuela JJ, Nuñez-Diaz C, Caceres-Palomo L, Vegas-Gomez L, Sanchez-Mejias E, Trujillo-Estrada L, Garcia-Leon JA, Moreno-Gonzalez I, Vizuete M, Vitorica J, Baglietto-Vargas D, Gutierrez A. Transgenic Mouse Models of Alzheimer's Disease: An Integrative Analysis. Int J Mol Sci 2022; 23:5404. [PMID: 35628216 PMCID: PMC9142061 DOI: 10.3390/ijms23105404] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022] Open
Abstract
Alzheimer's disease (AD) constitutes the most prominent form of dementia among elderly individuals worldwide. Disease modeling using murine transgenic mice was first initiated thanks to the discovery of heritable mutations in amyloid precursor protein (APP) and presenilins (PS) genes. However, due to the repeated failure of translational applications from animal models to human patients, along with the recent advances in genetic susceptibility and our current understanding on disease biology, these models have evolved over time in an attempt to better reproduce the complexity of this devastating disease and improve their applicability. In this review, we provide a comprehensive overview about the major pathological elements of human AD (plaques, tauopathy, synaptic damage, neuronal death, neuroinflammation and glial dysfunction), discussing the knowledge that available mouse models have provided about the mechanisms underlying human disease. Moreover, we highlight the pros and cons of current models, and the revolution offered by the concomitant use of transgenic mice and omics technologies that may lead to a more rapid improvement of the present modeling battery.
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Affiliation(s)
- Raquel Sanchez-Varo
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Fisiologia Humana, Histologia Humana, Anatomia Patologica y Educacion Fisica y Deportiva, Facultad de Medicina, Universidad de Malaga, 29071 Malaga, Spain
| | - Marina Mejias-Ortega
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Juan Jose Fernandez-Valenzuela
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Cristina Nuñez-Diaz
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Caceres-Palomo
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Vegas-Gomez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Elisabeth Sanchez-Mejias
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Trujillo-Estrada
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Juan Antonio Garcia-Leon
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Ines Moreno-Gonzalez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Marisa Vizuete
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBIS)-Hospital Universitario Virgen del Rocio/CSIC, 41012 Seville, Spain
| | - Javier Vitorica
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBIS)-Hospital Universitario Virgen del Rocio/CSIC, 41012 Seville, Spain
| | - David Baglietto-Vargas
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Antonia Gutierrez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
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21
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Jung ES, Suh K, Han J, Kim H, Kang H, Choi W, Mook‐Jung I. Amyloid-β activates NLRP3 inflammasomes by affecting microglial immunometabolism through the Syk-AMPK pathway. Aging Cell 2022; 21:e13623. [PMID: 35474599 PMCID: PMC9124305 DOI: 10.1111/acel.13623] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/03/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022] Open
Abstract
Neuroinflammation is considered one of major factors in the pathogenesis of Alzheimer's disease (AD). In particular, inflammasome activation, including NLRP3 inflammasome in microglia, is regarded as fundamental for the pro-inflammatory response of immune cells. However, the precise molecular mechanism through which the NLRP3 inflammasome is associated with AD pathologies remains unclear. Here, we show that amyloid-β activates the NLRP3 inflammasome in microglia by activating Syk and inhibiting AMPK. Deactivated AMPK induces metabolic dysregulation, mitochondrial fragmentation, and reactive oxygen species formation, leading to the activation of the NLRP3 inflammasome. In addition, flufenamic acid (FA), a member of non-steroidal anti-inflammatory drugs, was found to effectively inhibit activation of the microglial NLRP3 inflammasome by regulating Syk and AMPK. Importantly, FA has marked therapeutic effects on major AD pathologies and memory function in vivo in microglia-dependent way. All together, these findings demonstrate the molecular mechanism of microglial NLRP3 inflammasome activation by amyloid-β, which acts as an important mediator of neuroinflammation. Also, we suggest that repurposing of FA for inhibiting microglial activation of the NLRP3 inflammasome is a potential treatment for AD.
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Affiliation(s)
- Eun Sun Jung
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
- Neuroscience Research Institute College of Medicine Seoul National University Seoul Korea
| | - Kyujin Suh
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Jihui Han
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Heyyoung Kim
- School of Biological Sciences and Technology College of Natural Sciences Chonnam National University Gwangju Korea
| | - Hyung‐Sik Kang
- School of Biological Sciences and Technology College of Natural Sciences Chonnam National University Gwangju Korea
| | - Won‐Seok Choi
- School of Biological Sciences and Technology College of Natural Sciences Chonnam National University Gwangju Korea
| | - Inhee Mook‐Jung
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
- Neuroscience Research Institute College of Medicine Seoul National University Seoul Korea
- SNU Dementia Research Center College of Medicine Seoul National University Seoul Korea
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22
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Oh HS, Min U, Jang H, Kim N, Lim J, Chalita M, Chun J. Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:533-549. [PMID: 35362897 DOI: 10.1007/s12275-022-1526-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 02/08/2023]
Abstract
The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and di-sease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.
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Affiliation(s)
- Hyun-Seok Oh
- ChunLab Inc., Seoul, 06194, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Uigi Min
- ChunLab Inc., Seoul, 06194, Republic of Korea
| | - Hyejin Jang
- ChunLab Inc., Seoul, 06194, Republic of Korea
| | - Namil Kim
- ChunLab Inc., Seoul, 06194, Republic of Korea
| | | | | | - Jongsik Chun
- ChunLab Inc., Seoul, 06194, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea. .,School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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23
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Choi H, Lee D, Mook-Jung I. Gut Microbiota as a Hidden Player in the Pathogenesis of Alzheimer's Disease. J Alzheimers Dis 2022; 86:1501-1526. [PMID: 35213369 DOI: 10.3233/jad-215235] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD), the most common neurodegenerative disorder, is accompanied by cognitive impairment and shows representative pathological features, including senile plaques and neurofibrillary tangles in the brain. Recent evidence suggests that several systemic changes outside the brain are associated with AD and may contribute to its pathogenesis. Among the factors that induce systemic changes in AD, the gut microbiota is increasingly drawing attention. Modulation of gut microbiome, along with continuous attempts to remove pathogenic proteins directly from the brain, is a viable strategy to cure AD. Seeking a holistic understanding of the pathways throughout the body that can affect the pathogenesis, rather than regarding AD solely as a brain disease, may be key to successful therapy. In this review, we focus on the role of the gut microbiota in causing systemic manifestations of AD. The review integrates recently emerging concepts and provides potential mechanisms about the involvement of the gut-brain axis in AD, ranging from gut permeability and inflammation to bacterial translocation and cross-seeding.
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Affiliation(s)
- Hyunjung Choi
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.,SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dongjoon Lee
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea.,SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Inhee Mook-Jung
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.,Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea.,SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
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24
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Fang J, Zhang P, Wang Q, Chiang CW, Zhou Y, Hou Y, Xu J, Chen R, Zhang B, Lewis SJ, Leverenz JB, Pieper AA, Li B, Li L, Cummings J, Cheng F. Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer's disease. Alzheimers Res Ther 2022; 14:7. [PMID: 35012639 PMCID: PMC8751379 DOI: 10.1186/s13195-021-00951-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified numerous susceptibility loci for Alzheimer's disease (AD). However, utilizing GWAS and multi-omics data to identify high-confidence AD risk genes (ARGs) and druggable targets that can guide development of new therapeutics for patients suffering from AD has heretofore not been successful. METHODS To address this critical problem in the field, we have developed a network-based artificial intelligence framework that is capable of integrating multi-omics data along with human protein-protein interactome networks to accurately infer accurate drug targets impacted by GWAS-identified variants to identify new therapeutics. When applied to AD, this approach integrates GWAS findings, multi-omics data from brain samples of AD patients and AD transgenic animal models, drug-target networks, and the human protein-protein interactome, along with large-scale patient database validation and in vitro mechanistic observations in human microglia cells. RESULTS Through this approach, we identified 103 ARGs validated by various levels of pathobiological evidence in AD. Via network-based prediction and population-based validation, we then showed that three drugs (pioglitazone, febuxostat, and atenolol) are significantly associated with decreased risk of AD compared with matched control populations. Pioglitazone usage is significantly associated with decreased risk of AD (hazard ratio (HR) = 0.916, 95% confidence interval [CI] 0.861-0.974, P = 0.005) in a retrospective case-control validation. Pioglitazone is a peroxisome proliferator-activated receptor (PPAR) agonist used to treat type 2 diabetes, and propensity score matching cohort studies confirmed its association with reduced risk of AD in comparison to glipizide (HR = 0.921, 95% CI 0.862-0.984, P = 0.0159), an insulin secretagogue that is also used to treat type 2 diabetes. In vitro experiments showed that pioglitazone downregulated glycogen synthase kinase 3 beta (GSK3β) and cyclin-dependent kinase (CDK5) in human microglia cells, supporting a possible mechanism-of-action for its beneficial effect in AD. CONCLUSIONS In summary, we present an integrated, network-based artificial intelligence methodology to rapidly translate GWAS findings and multi-omics data to genotype-informed therapeutic discovery in AD.
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Affiliation(s)
- Jiansong Fang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Pengyue Zhang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Quan Wang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37212, USA
| | - Chien-Wei Chiang
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH, 43210, USA
| | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jielin Xu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37212, USA
| | - Bin Zhang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Stephen J Lewis
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - James B Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Andrew A Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH, 44106, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Neuroscience, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37212, USA.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37212, USA.
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH, 43210, USA.
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, School of Integrated Health Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, 44106, USA.
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Fang J, Zhang P, Zhou Y, Chiang CW, Tan J, Hou Y, Stauffer S, Li L, Pieper AA, Cummings J, Cheng F. Endophenotype-based in silico network medicine discovery combined with insurance record data mining identifies sildenafil as a candidate drug for Alzheimer's disease. NATURE AGING 2021; 1:1175-1188. [PMID: 35572351 PMCID: PMC9097949 DOI: 10.1038/s43587-021-00138-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We developed an endophenotype disease module-based methodology for Alzheimer's disease (AD) drug repurposing and identified sildenafil as a potential disease risk modifier. Based on retrospective case-control pharmacoepidemiologic analyses of insurance claims data for 7.23 million individuals, we found that sildenafil usage was significantly associated with a 69% reduced risk of AD (hazard ratio = 0.31, 95% confidence interval 0.25-0.39, P<1.0×10-8). Propensity score stratified analyses confirmed that sildenafil is significantly associated with a decreased risk of AD across all four drug cohorts we tested (diltiazem, glimepiride, losartan and metformin) after adjusting age, sex, race, and disease comorbidities. We also found that sildenafil increases neurite growth and decreases phospho-tau expression in AD patient-induced pluripotent stem cells-derived neuron models, supporting mechanistically its potential beneficial effect in Alzheimer's disease. The association between sildenafil use and decreased incidence of AD does not establish causality or its direction, which requires a randomized clinical trial approach.
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Affiliation(s)
- Jiansong Fang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Pengyue Zhang
- Department of Biostatistics, School of Medicine, Indiana University
| | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Chien-Wei Chiang
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Juan Tan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shaun Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Andrew A. Pieper
- Harrington Discovery Institute, University Hospital Case Medical Center; Department of Psychiatry, Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes Cleveland VAMC, Cleveland, OH 44106, USA
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, School of Integrated Health Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.,Correspondence to: Feixiong Cheng, Ph.D., Lerner Research Institute, Cleveland Clinic, , Tel: +1-216-4447654; Fax: +1-216-6361609
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Pauls E, Bayod S, Mateo L, Alcalde V, Juan-Blanco T, Sánchez-Soto M, Saido TC, Saito T, Berrenguer-Llergo A, Attolini CSO, Gay M, de Oliveira E, Duran-Frigola M, Aloy P. Identification and drug-induced reversion of molecular signatures of Alzheimer's disease onset and progression in App NL-G-F, App NL-F, and 3xTg-AD mouse models. Genome Med 2021; 13:168. [PMID: 34702310 PMCID: PMC8547095 DOI: 10.1186/s13073-021-00983-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/29/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In spite of many years of research, our understanding of the molecular bases of Alzheimer's disease (AD) is still incomplete, and the medical treatments available mainly target the disease symptoms and are hardly effective. Indeed, the modulation of a single target (e.g., β-secretase) has proven to be insufficient to significantly alter the physiopathology of the disease, and we should therefore move from gene-centric to systemic therapeutic strategies, where AD-related changes are modulated globally. METHODS Here we present the complete characterization of three murine models of AD at different stages of the disease (i.e., onset, progression and advanced). We combined the cognitive assessment of these mice with histological analyses and full transcriptional and protein quantification profiling of the hippocampus. Additionally, we derived specific Aβ-related molecular AD signatures and looked for drugs able to globally revert them. RESULTS We found that AD models show accelerated aging and that factors specifically associated with Aβ pathology are involved. We discovered a few proteins whose abundance increases with AD progression, while the corresponding transcript levels remain stable, and showed that at least two of them (i.e., lfit3 and Syt11) co-localize with Aβ plaques in the brain. Finally, we found two NSAIDs (dexketoprofen and etodolac) and two anti-hypertensives (penbutolol and bendroflumethiazide) that overturn the cognitive impairment in AD mice while reducing Aβ plaques in the hippocampus and partially restoring the physiological levels of AD signature genes to wild-type levels. CONCLUSIONS The characterization of three AD mouse models at different disease stages provides an unprecedented view of AD pathology and how this differs from physiological aging. Moreover, our computational strategy to chemically revert AD signatures has shown that NSAID and anti-hypertensive drugs may still have an opportunity as anti-AD agents, challenging previous reports.
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Affiliation(s)
- Eduardo Pauls
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Sergi Bayod
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Lídia Mateo
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Víctor Alcalde
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Teresa Juan-Blanco
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Marta Sánchez-Soto
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Antoni Berrenguer-Llergo
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Camille Stephan-Otto Attolini
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Marina Gay
- Proteomics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | | | - Miquel Duran-Frigola
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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27
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Nguyen TV, Gupta R, Annas D, Yoon J, Kim YJ, Lee GH, Jang JW, Park KH, Rakwal R, Jung KH, Min CW, Kim ST. An Integrated Approach for the Efficient Extraction and Solubilization of Rice Microsomal Membrane Proteins for High-Throughput Proteomics. FRONTIERS IN PLANT SCIENCE 2021; 12:723369. [PMID: 34567038 PMCID: PMC8460067 DOI: 10.3389/fpls.2021.723369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
The preparation of microsomal membrane proteins (MPs) is critically important to microsomal proteomics. To date most research studies have utilized an ultracentrifugation-based approach for the isolation and solubilization of plant MPs. However, these approaches are labor-intensive, time-consuming, and unaffordable in certain cases. Furthermore, the use of sodium dodecyl sulfate (SDS) and its removal prior to a mass spectrometry (MS) analysis through multiple washing steps result in the loss of proteins. To address these limitations, this study introduced a simple micro-centrifugation-based MP extraction (MME) method from rice leaves, with the efficacy of this approach being compared with a commercially available plasma membrane extraction kit (PME). Moreover, this study assessed the subsequent solubilization of isolated MPs in an MS-compatible surfactant, namely, 4-hexylphenylazosulfonate (Azo) and SDS using a label-free proteomic approach. The results validated the effectiveness of the MME method, specifically in the enrichment of plasma membrane proteins as compared with the PME method. Furthermore, the findings showed that Azo demonstrated several advantages over SDS in solubilizing the MPs, which was reflected through a label-free quantitative proteome analysis. Altogether, this study provided a relatively simple and rapid workflow for the efficient extraction of MPs with an Azo-integrated MME approach for bottom-up proteomics.
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Affiliation(s)
- Truong Van Nguyen
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of General Education, College of General Education, Kookmin University, Seoul, South Korea
| | - Dicky Annas
- Department of Chemistry, Pusan National University, Busan, South Korea
| | - Jinmi Yoon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Yu-Jin Kim
- Department of Life Science & Environmental Biochemistry, Pusan National University, Miryang, South Korea
| | - Gi Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Kang Hyun Park
- Department of Chemistry, Pusan National University, Busan, South Korea
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
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28
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Bisogno T, Lauritano A, Piscitelli F. The Endocannabinoid System: A Bridge between Alzheimer's Disease and Gut Microbiota. Life (Basel) 2021; 11:934. [PMID: 34575083 PMCID: PMC8470731 DOI: 10.3390/life11090934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that progresses from mild cognitive impairment to severe dementia over time. The main clinical hallmarks of the disease (e.g., beta-amyloid plaques and neurofibrillary tangles) begin during preclinical AD when cognitive deficits are not yet apparent. Hence, a more profound understanding of AD pathogenesis is needed to develop new therapeutic strategies. In this context, the endocannabinoid (eCB) system and the gut microbiome are increasingly emerging as important players in maintaining the general homeostasis and the health status of the host. However, their interaction has come to light just recently with gut microbiota regulating the eCB tone at both receptor and enzyme levels in intestinal and adipose tissues. Importantly, eCB system and gut microbiome, have been suggested to play a role in AD in both animal and human studies. Therefore, the microbiome gut-brain axis and the eCB system are potential common denominators in the AD physiopathology. Hence, the aim of this review is to provide a general overview on the role of both the eCB system and the microbiome gut-brain axis in AD and to suggest possible mechanisms that underlie the potential interplay of these two systems.
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Affiliation(s)
- Tiziana Bisogno
- Endocannabinoid Research Group, Istituto di Farmacologia Traslazionale, Consiglio Nazionale Delle Ricerche, Area Della Ricerca di Roma 2 Via Fosso del Cavaliere 100, 00133 Roma, Italy
| | - Anna Lauritano
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
| | - Fabiana Piscitelli
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
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29
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Schächtle MA, Rosshart SP. The Microbiota-Gut-Brain Axis in Health and Disease and Its Implications for Translational Research. Front Cell Neurosci 2021; 15:698172. [PMID: 34335190 PMCID: PMC8321234 DOI: 10.3389/fncel.2021.698172] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/16/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past decades, microbiome research has evolved rapidly and became a hot topic in basic, preclinical and clinical research, for the pharmaceutical industry and for the general public. With the help of new high-throughput sequencing technologies tremendous progress has been made in the characterization of host-microbiota interactions identifying the microbiome as a major factor shaping mammalian physiology. This development also led to the discovery of the gut-brain axis as the crucial connection between gut microbiota and the nervous system. Consequently, a rapidly growing body of evidence emerged suggesting that the commensal gut microbiota plays a vital role in brain physiology. Moreover, it became evident that the communication along this microbiota-gut-brain axis is bidirectional and primarily mediated by biologically active microbial molecules and metabolites. Further, intestinal dysbiosis leading to changes in the bidirectional relationship between gut microbiota and the nervous system was linked to the pathogenesis of several psychiatric and neurological disorders. Here, we discuss the impact of the gut microbiota on the brain in health and disease, specifically as regards to neuronal homeostasis, development and normal aging as well as their role in neurological diseases of the highest socioeconomic burden such as Alzheimer's disease and stroke. Subsequently, we utilize Alzheimer's disease and stroke to examine the translational research value of current mouse models in the spotlight of microbiome research. Finally, we propose future strategies on how we could conduct translational microbiome research in the field of neuroscience that may lead to the identification of novel treatments for human diseases.
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Affiliation(s)
- Melanie Anna Schächtle
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Patrick Rosshart
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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30
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Chung S, Yang J, Kim HJ, Hwang EM, Lee W, Suh K, Choi H, Mook-Jung I. Plexin-A4 mediates amyloid-β-induced tau pathology in Alzheimer's disease animal model. Prog Neurobiol 2021; 203:102075. [PMID: 34004220 DOI: 10.1016/j.pneurobio.2021.102075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
Amyloid-β (Aβ) and tau are major pathological hallmarks of Alzheimer's disease (AD). Several studies have revealed that Aβ accelerates pathological tau transition and spreading during the disease progression, and that reducing tau can mitigate pathological features of AD. However, molecular links between Aβ and tau pathologies remain elusive. Here, we suggest a novel role for the plexin-A4 as an Aβ receptor that induces aggregated tau pathology. Plexin-A4, previously known as proteins involved in regulating axon guidance and synaptic plasticity, can bound to Aβ with co-receptor, neuropilin-2. Genetic downregulation of plexin-A4 in neurons was sufficient to prevent Aβ-induced activation of CDK5 and reduce tau hyperphosphorylation and aggregation, even in the presence of Aβ. In an AD mouse model that manifests both Aβ and tau pathologies, genetic downregulation of plexin-A4 in the hippocampus reduced tau pathology and ameliorated spatial memory impairment. Collectively, these results indicate that the plexin-A4 is capable of mediating Aβ-induced tau pathology in AD pathogenesis.
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Affiliation(s)
- Sunwoo Chung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Jinhee Yang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; Biorchestra Co., Ltd., Techno 4-ro 17, Daejeon 34013, South Korea.
| | - Haeng Jun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Eun Mi Hwang
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea.
| | - Wonik Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Kyujin Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Hayoung Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
| | - Inhee Mook-Jung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; SNU Dementia Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea.
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31
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Pieters VM, Co IL, Wu NC, McGuigan AP. Applications of Omics Technologies for Three-Dimensional In Vitro Disease Models. Tissue Eng Part C Methods 2021; 27:183-199. [PMID: 33406987 DOI: 10.1089/ten.tec.2020.0300] [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] [Indexed: 12/23/2022] Open
Abstract
Omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, multiomics, and integrated modalities, have greatly contributed to our understanding of various diseases by enabling researchers to probe the molecular wiring of cellular systems in a high-throughput and precise manner. With the development of tissue-engineered three-dimensional (3D) in vitro disease models, such as organoids and spheroids, there is potential of integrating omics technologies with 3D disease models to elucidate the complex links between genotype and phenotype. These 3D disease models have been used to model cancer, infectious disease, toxicity, neurological disorders, and others. In this review, we provide an overview of omics technologies, highlight current and emerging studies, discuss the associated experimental design considerations, barriers and challenges of omics technologies, and provide an outlook on the future applications of omics technologies with 3D models. Overall, this review aims to provide a valuable resource for tissue engineers seeking to leverage omics technologies for diving deeper into biological discovery. Impact statement With the emergence of three-dimensional (3D) in vitro disease models, tissue engineers are increasingly interested to investigate these systems to address biological questions related to disease mechanism, drug target discovery, therapy resistance, and more. Omics technologies are a powerful and high-throughput approach, but their application for 3D disease models is not maximally utilized. This review illustrates the achievements and potential of using omics technologies to leverage the full potential of 3D in vitro disease models. This will improve the quality of such models, advance our understanding of disease, and contribute to therapy development.
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Affiliation(s)
- Vera M Pieters
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Ileana L Co
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Nila C Wu
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Alison P McGuigan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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32
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Zheng Q, Li G, Wang S, Zhou Y, Liu K, Gao Y, Zhou Y, Zheng L, Zhu L, Deng Q, Wu M, Di A, Zhang L, Zhao Y, Zhang H, Sun H, Dong C, Xu H, Wang X. Trisomy 21-induced dysregulation of microglial homeostasis in Alzheimer's brains is mediated by USP25. SCIENCE ADVANCES 2021; 7:7/1/eabe1340. [PMID: 33523861 PMCID: PMC7775784 DOI: 10.1126/sciadv.abe1340] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/05/2020] [Indexed: 05/11/2023]
Abstract
Down syndrome (DS), caused by trisomy of chromosome 21, is the most significant risk factor for early-onset Alzheimer's disease (AD); however, underlying mechanisms linking DS and AD remain unclear. Here, we show that triplication of homologous chromosome 21 genes aggravates neuroinflammation in combined murine DS-AD models. Overexpression of USP25, a deubiquitinating enzyme encoded by chromosome 21, results in microglial activation and induces synaptic and cognitive deficits, whereas genetic ablation of Usp25 reduces neuroinflammation and rescues synaptic and cognitive function in 5×FAD mice. Mechanistically, USP25 deficiency attenuates microglia-mediated proinflammatory cytokine overproduction and synapse elimination. Inhibition of USP25 reestablishes homeostatic microglial signatures and restores synaptic and cognitive function in 5×FAD mice. In summary, we demonstrate an unprecedented role for trisomy 21 and pathogenic effects associated with microgliosis as a result of the increased USP25 dosage, implicating USP25 as a therapeutic target for neuroinflammation in DS and AD.
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Affiliation(s)
- Qiuyang Zheng
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Guilin Li
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Shihua Wang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Ying Zhou
- Department of Translational Medicine, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Ke Liu
- Department of Translational Medicine, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Yue Gao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Yulin Zhou
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, China
| | - Liangkai Zheng
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, China
| | - Lin Zhu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Qingfang Deng
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Meiling Wu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Anjie Di
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Lishan Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Yingjun Zhao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Hongfeng Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Hao Sun
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Chen Dong
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Huaxi Xu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
- Center for Brain Sciences, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361003, China
| | - Xin Wang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China.
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Rutsch A, Kantsjö JB, Ronchi F. The Gut-Brain Axis: How Microbiota and Host Inflammasome Influence Brain Physiology and Pathology. Front Immunol 2020; 11:604179. [PMID: 33362788 PMCID: PMC7758428 DOI: 10.3389/fimmu.2020.604179] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022] Open
Abstract
The human microbiota has a fundamental role in host physiology and pathology. Gut microbial alteration, also known as dysbiosis, is a condition associated not only with gastrointestinal disorders but also with diseases affecting other distal organs. Recently it became evident that the intestinal bacteria can affect the central nervous system (CNS) physiology and inflammation. The nervous system and the gastrointestinal tract are communicating through a bidirectional network of signaling pathways called the gut-brain axis, which consists of multiple connections, including the vagus nerve, the immune system, and bacterial metabolites and products. During dysbiosis, these pathways are dysregulated and associated with altered permeability of the blood-brain barrier (BBB) and neuroinflammation. However, numerous mechanisms behind the impact of the gut microbiota in neuro-development and -pathogenesis remain poorly understood. There are several immune pathways involved in CNS homeostasis and inflammation. Among those, the inflammasome pathway has been linked to neuroinflammatory conditions such as multiple sclerosis, Alzheimer's and Parkinson's diseases, but also anxiety and depressive-like disorders. The inflammasome complex assembles upon cell activation due to exposure to microbes, danger signals, or stress and lead to the production of pro-inflammatory cytokines (interleukin-1β and interleukin-18) and to pyroptosis. Evidences suggest that there is a reciprocal influence of microbiota and inflammasome activation in the brain. However, how this influence is precisely working is yet to be discovered. Herein, we discuss the status of the knowledge and the open questions in the field focusing on the function of intestinal microbial metabolites or products on CNS cells during healthy and inflammatory conditions, such as multiple sclerosis, Alzheimer's and Parkinson's diseases, and also neuropsychiatric disorders. In particular, we focus on the innate inflammasome pathway as immune mechanism that can be involved in several of these conditions, upon exposure to certain microbes.
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Affiliation(s)
| | | | - Francesca Ronchi
- Maurice Müller Laboratories, Department of Biomedical Research, Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Berne, Berne, Switzerland
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Fang J, Pieper AA, Nussinov R, Lee G, Bekris L, Leverenz JB, Cummings J, Cheng F. Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. Med Res Rev 2020; 40:2386-2426. [PMID: 32656864 PMCID: PMC7561446 DOI: 10.1002/med.21709] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 12/16/2022]
Abstract
Following two decades of more than 400 clinical trials centered on the "one drug, one target, one disease" paradigm, there is still no effective disease-modifying therapy for Alzheimer's disease (AD). The inherent complexity of AD may challenge this reductionist strategy. Recent observations and advances in network medicine further indicate that AD likely shares common underlying mechanisms and intermediate pathophenotypes, or endophenotypes, with other diseases. In this review, we consider AD pathobiology, disease comorbidity, pleiotropy, and therapeutic development, and construct relevant endophenotype networks to guide future therapeutic development. Specifically, we discuss six main endophenotype hypotheses in AD: amyloidosis, tauopathy, neuroinflammation, mitochondrial dysfunction, vascular dysfunction, and lysosomal dysfunction. We further consider how this endophenotype network framework can provide advances in computational and experimental strategies for drug-repurposing and identification of new candidate therapeutic strategies for patients suffering from or at risk for AD. We highlight new opportunities for endophenotype-informed, drug discovery in AD, by exploiting multi-omics data. Integration of genomics, transcriptomics, radiomics, pharmacogenomics, and interactomics (protein-protein interactions) are essential for successful drug discovery. We describe experimental technologies for AD drug discovery including human induced pluripotent stem cells, transgenic mouse/rat models, and population-based retrospective case-control studies that may be integrated with multi-omics in a network medicine methodology. In summary, endophenotype-based network medicine methodologies will promote AD therapeutic development that will optimize the usefulness of available data and support deep phenotyping of the patient heterogeneity for personalized medicine in AD.
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Affiliation(s)
- Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Andrew A Pieper
- Harrington Discovery Institute, University Hospital Case Medical Center; Department of Psychiatry, Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes Cleveland VAMC, Cleveland, OH 44106, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Garam Lee
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV 89106, USA
| | - Lynn Bekris
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - James B. Leverenz
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jeffrey Cummings
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV 89106, USA
- Department of Brain Health, School of Integrated Health Sciences, UNLV, Las Vegas, NV 89154, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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You L, Yang C, Du Y, Wang W, Sun M, Liu J, Ma B, Pang L, Zeng Y, Zhang Z, Dong X, Yin X, Ni J. A Systematic Review of the Pharmacology, Toxicology and Pharmacokinetics of Matrine. Front Pharmacol 2020; 11:01067. [PMID: 33041782 PMCID: PMC7526649 DOI: 10.3389/fphar.2020.01067] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
Matrine (MT) is a naturally occurring alkaloid and an bioactive component of Chinese herbs, such as Sophora flavescens and Radix Sophorae tonkinensis. Emerging evidence suggests that MT possesses anti-cancer, anti-inflammatory, anti-oxidant, antiviral, antimicrobial, anti-fibrotic, anti-allergic, antinociceptive, hepatoprotective, cardioprotective, and neuroprotective properties. These pharmacological properties form the foundation for its application in the treatment of various diseases, such as multiple types of cancers, hepatitis, skin diseases, allergic asthma, diabetic cardiomyopathy, pain, Alzheimer's disease (AD), Parkinson's disease (PD), and central nervous system (CNS) inflammation. However, an increasing number of published studies indicate that MT has serious adverse effects, the most obvious being liver toxicity and neurotoxicity, which are major factors limiting its clinical use. Pharmacokinetic studies have shown that MT has low oral bioavailability and short half-life in vivo. This review summarizes the latest advances in research on the pharmacology, toxicology, and pharmacokinetics of MT, with a focus on its biological properties and mechanism of action. The review provides insight into the future of research on traditional Chinese medicine.
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Affiliation(s)
- Longtai You
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chunjing Yang
- Department of Pharmacy, Beijing Shijitan Hospital Affiliated to Capital University of Medical Sciences, Beijing, China
| | - Yuanyuan Du
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wenping Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Mingyi Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Baorui Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Linnuo Pang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yawen Zeng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhiqin Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoxv Dong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xingbin Yin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jian Ni
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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Min CW, Hyeon H, Gupta R, Park J, Cheon YE, Lee GH, Jang JW, Ryu HW, Lee BW, Park SU, Kim Y, Kim JK, Kim ST. Integrated Proteomics and Metabolomics Analysis Highlights Correlative Metabolite-Protein Networks in Soybean Seeds Subjected to Warm-Water Soaking. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8057-8067. [PMID: 32609497 DOI: 10.1021/acs.jafc.0c00986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Soaking of soybean seeds is a prerequisite for the production of soy foods, and it has been shown that the extent of water absorbed during different imbibition conditions directly affects the quality of the subsequent soybean seed products by yet unknown mechanisms. In order to elucidate the molecular changes in soybean seeds during different soaking temperatures, we performed an integrated proteomics and metabolomics analysis of seeds soaked at 4, 25, and 55 °C. Proteomics analysis revealed that various enzymes related to carbohydrate and protein hydrolysis were activated in soybean seeds during water soaking at 55 °C. Interestingly, results obtained from this integrated proteomics and metabolomics study showed changes in various metabolites, including isoflavones, amino acids, and sugars, that were positively correlated with proteome changes occurring upon soaking at 55 °C. Furthermore, soaking of soybean seeds at 55 °C resulted in degradation of indigestible anti-nutrients such as raffinose oligosaccharides. Taken together, our results suggest that the seed soaking at a high temperature (55 °C) increases the nutritional value of soybean seeds by decreasing the contents of some of the common anti-nutrients.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Hyejin Hyeon
- Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Republic of Korea
| | - Ye Eun Cheon
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Gi Hyun Lee
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Hyung Won Ryu
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Byong Won Lee
- Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
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Min CW, Park J, Bae JW, Agrawal GK, Rakwal R, Kim Y, Yang P, Kim ST, Gupta R. In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis. Cells 2020; 9:E1517. [PMID: 32580392 PMCID: PMC7349688 DOI: 10.3390/cells9061517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Jin Woo Bae
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1Tennodai, Tsukuba 3058574, Japan
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
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Zhang X, Liu W, Cao Y, Tan W. Hippocampus Proteomics and Brain Lipidomics Reveal Network Dysfunction and Lipid Molecular Abnormalities in APP/PS1 Mouse Model of Alzheimer’s Disease. J Proteome Res 2020; 19:3427-3437. [DOI: 10.1021/acs.jproteome.0c00255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xueju Zhang
- College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
- Postdoctoral Innovation Base, Zhuhai Yuanzhi Health Technology Co. Ltd., Hengqin New Area, Zhuhai, Guangdong 519000, China
| | - Weiwei Liu
- College of Biomedicine, Guangdong University of Technology, Higher Education Mega Center, Guangzhou, Guangdong 510006, China
| | - Yan Cao
- College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
- Postdoctoral Innovation Base, Zhuhai Yuanzhi Health Technology Co. Ltd., Hengqin New Area, Zhuhai, Guangdong 519000, China
| | - Wen Tan
- Postdoctoral Innovation Base, Zhuhai Yuanzhi Health Technology Co. Ltd., Hengqin New Area, Zhuhai, Guangdong 519000, China
- College of Biomedicine, Guangdong University of Technology, Higher Education Mega Center, Guangzhou, Guangdong 510006, China
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Shin D, Park J, Han D, Moon JH, Ryu HS, Kim Y. Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer. Clin Proteomics 2020; 17:16. [PMID: 32489334 PMCID: PMC7247212 DOI: 10.1186/s12014-020-09280-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background Metastasis of breast cancer to distal organs is fatal. However, few studies have identified biomarkers that are associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers, such as HER2, ER, and PR, to differentiate between distant and nondistant metastatic breast cancers accurately has necessitated the development of novel biomarker candidates. Methods An integrated proteomics approach that combined filter-aided sample preparation, tandem mass tag labeling (TMT), high pH fractionation, and high-resolution MS was applied to acquire in-depth proteomic data from FFPE distant metastatic breast cancer tissues. A bioinformatics analysis was performed with regard to gene ontology and signaling pathways using differentially expressed proteins (DEPs) to examine the molecular characteristics of distant metastatic breast cancer. In addition, real-time polymerase chain reaction (RT-PCR) and invasion/migration assays were performed to validate the differential regulation and function of our protein targets. Results A total of 9441 and 8746 proteins were identified from the pooled and individual sample sets, respectively. Based on our criteria, TUBB2A was selected as a novel biomarker candidate. The metastatic activities of TUBB2A were subsequently validated. In our bioinformatics analysis using DEPs, we characterized the overall molecular features of distant metastasis and measured differences in the molecular functions of distant metastatic breast cancer between breast cancer subtypes. Conclusions Our report is the first study to examine the distant metastatic breast cancer proteome using FFPE tissues. The depth of our dataset allowed us to discover a novel biomarker candidate and a proteomic characteristics of distant metastatic breast cancer. Distinct molecular features of various breast cancer subtypes were also established. Our proteomic data constitute a valuable resource for research on distant metastatic breast cancer.
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Affiliation(s)
- Dongyoon Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehakro, Seoul, 30380 Korea
| | - Joonho Park
- Interdisciplinary Program for Bioengineering, Seoul National University College of Engineering, Seoul, Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehakro, Seoul, Korea
| | - Ji Hye Moon
- Department of Pathology, Seoul National University Hospital, 101 Daehakro, Seoul, 03080 Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, 101 Daehakro, Seoul, 03080 Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehakro, Seoul, 30380 Korea.,Interdisciplinary Program for Bioengineering, Seoul National University College of Engineering, Seoul, Korea
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Rayaprolu S, Gao T, Xiao H, Ramesha S, Weinstock LD, Shah J, Duong DM, Dammer EB, Webster JA, Lah JJ, Wood LB, Betarbet R, Levey AI, Seyfried NT, Rangaraju S. Flow-cytometric microglial sorting coupled with quantitative proteomics identifies moesin as a highly-abundant microglial protein with relevance to Alzheimer's disease. Mol Neurodegener 2020; 15:28. [PMID: 32381088 PMCID: PMC7206797 DOI: 10.1186/s13024-020-00377-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Proteomic characterization of microglia provides the most proximate assessment of functionally relevant molecular mechanisms of neuroinflammation. However, microglial proteomics studies have been limited by low cellular yield and contamination by non-microglial proteins using existing enrichment strategies. METHODS We coupled magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) of microglia with tandem mass tag-mass spectrometry (TMT-MS) to obtain a highly-pure microglial proteome and identified a core set of highly-abundant microglial proteins in adult mouse brain. We interrogated existing human proteomic data for Alzheimer's disease (AD) relevance of highly-abundant microglial proteins and performed immuno-histochemical and in-vitro validation studies. RESULTS Quantitative multiplexed proteomics by TMT-MS of CD11b + MACS-enriched (N = 5 mice) and FACS-isolated (N = 5 mice), from adult wild-type mice, identified 1791 proteins. A total of 203 proteins were highly abundant in both datasets, representing a core-set of highly abundant microglial proteins. In addition, we found 953 differentially enriched proteins comparing MACS and FACS-based approaches, indicating significant differences between both strategies. The FACS-isolated microglia proteome was enriched with cytosolic, endoplasmic reticulum, and ribosomal proteins involved in protein metabolism and immune system functions, as well as an abundance of canonical microglial proteins. Conversely, the MACS-enriched microglia proteome was enriched with mitochondrial and synaptic proteins and higher abundance of neuronal, oligodendrocytic and astrocytic proteins. From the 203 consensus microglial proteins with high abundance in both datasets, we confirmed microglial expression of moesin (Msn) in wild-type and 5xFAD mouse brains as well as in human AD brains. Msn expression is nearly exclusively found in microglia that surround Aβ plaques in 5xFAD brains. In in-vitro primary microglial studies, Msn silencing by siRNA decreased Aβ phagocytosis and increased lipopolysaccharide-induced production of the pro-inflammatory cytokine, tumor necrosis factor (TNF). In network analysis of human brain proteomic data, Msn was a hub protein of an inflammatory co-expression module positively associated with AD neuropathological features and cognitive dysfunction. CONCLUSIONS Using FACS coupled with TMT-MS as the method of choice for microglial proteomics, we define a core set of highly-abundant adult microglial proteins. Among these, we validate Msn as highly-abundant in plaque-associated microglia with relevance to human AD.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Tianwen Gao
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
- Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Hailian Xiao
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Supriya Ramesha
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Laura D. Weinstock
- Parker H. Petit Institute for Bioengineering and Bioscience, Wallace H. Coulter Department of Biomedical Engineering, and Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Jheel Shah
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Duc M. Duong
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University, Atlanta, GA 30322 USA
| | - Eric B. Dammer
- School of Medicine, Emory University, Atlanta, GA 30322 USA
| | - James A. Webster
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Levi B. Wood
- Parker H. Petit Institute for Bioengineering and Bioscience, Wallace H. Coulter Department of Biomedical Engineering, and Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Ranjita Betarbet
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University, Atlanta, GA 30322 USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA 30322 USA
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41
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Hippocampal complement C3 might contribute to cognitive impairment induced by anesthesia and surgery. Neuroreport 2020; 31:507-514. [PMID: 32168099 DOI: 10.1097/wnr.0000000000001422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Postoperative cognitive dysfunction is a well-recognized complication after major surgery in the elderly, but its pathophysiological mechanism is not fully understood. In the present study, we used liquid chromatography-tandem mass spectrometry combined with tandem mass tags to identify differentially expressed proteins and perform further functional studies on protein of interest. Here, we showed that hippocampal complement C3 was significantly upregulated after surgery, which was accompanied by marked decreases in synaptic related proteins and density. In aged patients undergoing gastrointestinal surgery, we also found significantly increased plasma level of C3b postoperatively and were negatively associated with cognitive performance. Notably, selective inhibition of complement C3 by compstatin was able to rescue synaptic and cognitive impairments induced by surgery in aged mice. Collectively, our study confirms that surgery can induce cognitive impairments, and the possible mechanisms might be related to abnormal complement signaling and synaptic disruption.
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Qin T, Prins S, Groeneveld GJ, Van Westen G, de Vries HE, Wong YC, Bischoff LJ, de Lange EC. Utility of Animal Models to Understand Human Alzheimer's Disease, Using the Mastermind Research Approach to Avoid Unnecessary Further Sacrifices of Animals. Int J Mol Sci 2020; 21:ijms21093158. [PMID: 32365768 PMCID: PMC7247586 DOI: 10.3390/ijms21093158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/18/2022] Open
Abstract
To diagnose and treat early-stage (preclinical) Alzheimer’s disease (AD) patients, we need body-fluid-based biomarkers that reflect the processes that occur in this stage, but current knowledge on associated processes is lacking. As human studies on (possible) onset and early-stage AD would be extremely expensive and time-consuming, we investigate the potential value of animal AD models to help to fill this knowledge gap. We provide a comprehensive overview of processes associated with AD pathogenesis and biomarkers, current knowledge on AD-related biomarkers derived from on human and animal brains and body fluids, comparisons of biomarkers obtained in human AD and frequently used animal AD models, and emerging body-fluid-based biomarkers. In human studies, amyloid beta (Aβ), hyperphosphorylated tau (P-tau), total tau (T-tau), neurogranin, SNAP-25, glial fibrillary acidic protein (GFAP), YKL-40, and especially neurofilament light (NfL) are frequently measured. In animal studies, the emphasis has been mostly on Aβ. Although a direct comparison between human (familial and sporadic) AD and (mostly genetic) animal AD models cannot be made, still, in brain, cerebrospinal fluid (CSF), and blood, a majority of similar trends are observed for human AD stage and animal AD model life stage. This indicates the potential value of animal AD models in understanding of the onset and early stage of AD. Moreover, animal studies can be smartly designed to provide mechanistic information on the interrelationships between the different AD processes in a longitudinal fashion and may also include the combinations of different conditions that may reflect comorbidities in human AD, according to the Mastermind Research approach.
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Affiliation(s)
- Tian Qin
- Predictive Pharmacology, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC Leiden, The Netherlands; (T.Q.); (L.J.M.B.)
| | - Samantha Prins
- Centre for Human Drug Research (CHDR), 2333 CL Leiden, The Netherlands; (S.P.); (G.J.G.)
| | - Geert Jan Groeneveld
- Centre for Human Drug Research (CHDR), 2333 CL Leiden, The Netherlands; (S.P.); (G.J.G.)
| | - Gerard Van Westen
- Computational Drug Discovery, Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC Leiden, The Netherlands;
| | - Helga E. de Vries
- Neuro-immunology research group, Department of Molecular Cell Biology and Immunology, Amsterdam Neuroscience, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands;
| | - Yin Cheong Wong
- Advanced Modelling and Simulation, UCB Celltech, Slough SL1 3WE, UK;
| | - Luc J.M. Bischoff
- Predictive Pharmacology, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC Leiden, The Netherlands; (T.Q.); (L.J.M.B.)
| | - Elizabeth C.M. de Lange
- Predictive Pharmacology, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC Leiden, The Netherlands; (T.Q.); (L.J.M.B.)
- Correspondence: ; Tel.: +31-71-527-6330
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András IE, Sewell BB, Toborek M. HIV-1 and Amyloid Beta Remodel Proteome of Brain Endothelial Extracellular Vesicles. Int J Mol Sci 2020; 21:ijms21082741. [PMID: 32326569 PMCID: PMC7215366 DOI: 10.3390/ijms21082741] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 01/01/2023] Open
Abstract
Amyloid beta (Aβ) depositions are more abundant in HIV-infected brains. The blood-brain barrier, with its backbone created by endothelial cells, is assumed to be a core player in Aβ homeostasis and may contribute to Aβ accumulation in the brain. Exposure to HIV increases shedding of extracellular vesicles (EVs) from human brain endothelial cells and alters EV-Aβ levels. EVs carrying various cargo molecules, including a complex set of proteins, can profoundly affect the biology of surrounding neurovascular unit cells. In the current study, we sought to examine how exposure to HIV, alone or together with Aβ, affects the surface and total proteomic landscape of brain endothelial EVs. By using this unbiased approach, we gained an unprecedented, high-resolution insight into these changes. Our data suggest that HIV and Aβ profoundly remodel the proteome of brain endothelial EVs, altering the pathway networks and functional interactions among proteins. These events may contribute to the EV-mediated amyloid pathology in the HIV-infected brain and may be relevant to HIV-1-associated neurocognitive disorders.
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44
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Kim YG, Woo J, Park J, Kim S, Lee YS, Kim Y, Kim SJ. Quantitative Proteomics Reveals Distinct Molecular Signatures of Different Cerebellum-Dependent Learning Paradigms. J Proteome Res 2020; 19:2011-2025. [PMID: 32181667 DOI: 10.1021/acs.jproteome.9b00826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cerebellum improves motor performance by adjusting motor gain appropriately. As de novo protein synthesis is essential for the formation and retention of memories, we hypothesized that motor learning in the opposite direction would induce a distinct pattern of protein expression in the cerebellum. We conducted quantitative proteomic profiling to compare the level of protein expression in the cerebellum at 1 and 24 h after training from mice that underwent different paradigms of cerebellum-dependent oculomotor learning from specific directional changes in motor gain. We quantified a total of 43 proteins that were significantly regulated in each of the three learning paradigms in the cerebellum at 1 and 24 h after learning. In addition, functional enrichment analysis identified protein groups that were differentially enriched or depleted in the cerebellum at 24 h after the three oculomotor learnings, suggesting that distinct biological pathways may be engaged in the formation of three oculomotor memories. Weighted correlation network analysis discovered groups of proteins significantly correlated with oculomotor memory. Finally, four proteins (Snca, Sncb, Cttn, and Stmn1) from the protein group correlated with the learning amount after oculomotor training were validated by Western blot. This study provides a comprehensive and unbiased list of proteins related to three cerebellum-dependent motor learning paradigms, suggesting the distinct nature of protein expression in the cerebellum for each learning paradigm. The proteomics data have been deposited to the ProteomeXchange Consortium with identifiers <PXD008433>.
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Affiliation(s)
- Yong Gyu Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jongmin Woo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Korea
| | - Sooyong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yong-Seok Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Korea
| | - Sang Jeong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
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45
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Neuropathological Mechanisms Associated with Pesticides in Alzheimer's Disease. TOXICS 2020; 8:toxics8020021. [PMID: 32218337 PMCID: PMC7355712 DOI: 10.3390/toxics8020021] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/14/2020] [Accepted: 03/22/2020] [Indexed: 12/12/2022]
Abstract
Environmental toxicants have been implicated in neurodegenerative diseases, and pesticide exposure is a suspected environmental risk factor for Alzheimer’s disease (AD). Several epidemiological analyses have affirmed a link between pesticides and incidence of sporadic AD. Meanwhile, in vitro and animal models of AD have shed light on potential neuropathological mechanisms. In this paper, a perspective on neuropathological mechanisms underlying pesticides’ induction of AD is provided. Proposed mechanisms range from generic oxidative stress induction in neurons to more AD-specific processes involving amyloid-beta (Aβ) and hyperphosphorylated tau (p-tau). Mechanisms that are more speculative or indirect in nature, including somatic mutation, epigenetic modulation, impairment of adult neurogenesis, and microbiota dysbiosis, are also discussed. Chronic toxicity mechanisms of environmental pesticide exposure crosstalks in complex ways and could potentially be mutually enhancing, thus making the deciphering of simplistic causal relationships difficult.
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46
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A TMT-Based Quantitative Proteome Analysis to Elucidate the TSWV Induced Signaling Cascade in Susceptible and Resistant Cultivars of Solanum lycopersicum. PLANTS 2020; 9:plants9030290. [PMID: 32110948 PMCID: PMC7154910 DOI: 10.3390/plants9030290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/22/2020] [Accepted: 02/22/2020] [Indexed: 01/12/2023]
Abstract
Tomato spotted wilt virus (TSWV), transmitted by small insects known as thrips, is one of the major threats to tomato productivity across the globe. In addition to tomato, this virus infects more than 1000 other plants belonging to 85 families and is a cause of serious concern. Very little, however, is known about the molecular mechanism of TSWV induced signaling in plants. Here, we used a tandem mass tags (TMT)-based quantitative proteome approach to investigate the protein profiles of tomato leaves of two cultivars (cv 2621 and 2689; susceptible and resistant to TSWV infection, respectively) following TSWV inoculation. This approach resulted in the identification of 5112 proteins of which 1022 showed significant changes in response to TSWV. While the proteome of resistant cultivar majorly remains unaltered, the proteome of susceptible cultivar showed distinct differences following TSWV inoculation. TSWV modulated proteins in tomato included those with functions previously implicated in plant defense including secondary metabolism, reactive oxygen species (ROS) detoxification, mitogen-activated protein (MAP) kinase signaling, calcium signaling and jasmonate biosynthesis, among others. Taken together, results reported here provide new insights into the TSWV induced signaling in tomato leaves and may be useful in the future to manage this deadly disease of plants.
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47
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Kim MS, Kim Y, Choi H, Kim W, Park S, Lee D, Kim DK, Kim HJ, Choi H, Hyun DW, Lee JY, Choi EY, Lee DS, Bae JW, Mook-Jung I. Transfer of a healthy microbiota reduces amyloid and tau pathology in an Alzheimer's disease animal model. Gut 2020; 69:283-294. [PMID: 31471351 DOI: 10.1136/gutjnl-2018-317431] [Citation(s) in RCA: 317] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 08/16/2019] [Accepted: 08/17/2019] [Indexed: 01/21/2023]
Abstract
OBJECTIVE Cerebral amyloidosis and severe tauopathy in the brain are key pathological features of Alzheimer's disease (AD). Despite a strong influence of the intestinal microbiota on AD, the causal relationship between the gut microbiota and AD pathophysiology is still elusive. DESIGN Using a recently developed AD-like pathology with amyloid and neurofibrillary tangles (ADLPAPT) transgenic mouse model of AD, which shows amyloid plaques, neurofibrillary tangles and reactive gliosis in their brains along with memory deficits, we examined the impact of the gut microbiota on AD pathogenesis. RESULTS Composition of the gut microbiota in ADLPAPT mice differed from that of healthy wild-type (WT) mice. Besides, ADLPAPT mice showed a loss of epithelial barrier integrity and chronic intestinal and systemic inflammation. Both frequent transfer and transplantation of the faecal microbiota from WT mice into ADLPAPT mice ameliorated the formation of amyloid β plaques and neurofibrillary tangles, glial reactivity and cognitive impairment. Additionally, the faecal microbiota transfer reversed abnormalities in the colonic expression of genes related to intestinal macrophage activity and the circulating blood inflammatory monocytes in the ADLPAPT recipient mice. CONCLUSION These results indicate that microbiota-mediated intestinal and systemic immune aberrations contribute to the pathogenesis of AD in ADLPAPT mice, providing new insights into the relationship between the gut (colonic gene expression, gut permeability), blood (blood immune cell population) and brain (pathology) axis and AD (memory deficits). Thus, restoring gut microbial homeostasis may have beneficial effects on AD treatment.
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Affiliation(s)
- Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Republic of Korea.,Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Yoonhee Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyunjung Choi
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Woojin Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sumyung Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dongjoon Lee
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Kyu Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Haeng Jun Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hayoung Choi
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Republic of Korea
| | - Eun Young Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Republic of Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea .,Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
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48
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Guest PC, Rahmoune H, Martins-de-Souza D. Proteomic Analysis of Rat Hippocampus for Studies of Cognition and Memory Loss with Aging. Methods Mol Biol 2020; 2138:407-417. [PMID: 32219767 DOI: 10.1007/978-1-0716-0471-7_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This chapter describes a protocol for proteomic profiling of the rat hippocampal proteome using a combination of liquid chromatography tandem mass spectrometry (LC-MS/MS) and data analysis to determine the cellular location of the identified proteins. In the example given, many of these proteins were localized in the plasma membrane and nucleus. These could be of interest in further studies of neurological and neurodegenerative disorders linked with hippocampal dysfunction, such as aging, major depression, and Alzheimer's disease.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
| | - Hassan Rahmoune
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), São Paulo, Brazil
- UNICAMP Neurobiology Center, Campinas, Brazil
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49
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Choi H, Kim HJ, Yang J, Chae S, Lee W, Chung S, Kim J, Choi H, Song H, Lee CK, Jun JH, Lee YJ, Lee K, Kim S, Sim H, Choi YI, Ryu KH, Park J, Lee D, Han S, Hwang D, Kyung J, Mook‐Jung I. Acetylation changes tau interactome to degrade tau in Alzheimer's disease animal and organoid models. Aging Cell 2020; 19:e13081. [PMID: 31763743 PMCID: PMC6974726 DOI: 10.1111/acel.13081] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/26/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is an age‐related neurodegenerative disease. The most common pathological hallmarks are amyloid plaques and neurofibrillary tangles in the brain. In the brains of patients with AD, pathological tau is abnormally accumulated causing neuronal loss, synaptic dysfunction, and cognitive decline. We found a histone deacetylase 6 (HDAC6) inhibitor, CKD‐504, changed the tau interactome dramatically to degrade pathological tau not only in AD animal model (ADLPAPT) brains containing both amyloid plaques and neurofibrillary tangles but also in AD patient‐derived brain organoids. Acetylated tau recruited chaperone proteins such as Hsp40, Hsp70, and Hsp110, and this complex bound to novel tau E3 ligases including UBE2O and RNF14. This complex degraded pathological tau through proteasomal pathway. We also identified the responsible acetylation sites on tau. These dramatic tau‐interactome changes may result in tau degradation, leading to the recovery of synaptic pathology and cognitive decline in the ADLPAPT mice.
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Affiliation(s)
- Heesun Choi
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Haeng Jun Kim
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Jinhee Yang
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
- Department of Pharmacology CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Sehyun Chae
- Center for Plant Aging Research Institute for Basic Science DGIST Daegu Korea
- Korea Brain Bank Korea Brain Research Institute Daegu Korea
| | - Wonik Lee
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Sunwoo Chung
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Jisoo Kim
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
- Department of Pharmacology CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Hyunjung Choi
- Interdisciplinary Graduate Program in Genetic Engineering Seoul National University Seoul Korea
| | - Hyeseung Song
- Department of Medicinal Chemistry CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Chang Kon Lee
- Department of Medicinal Chemistry CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Jae Hyun Jun
- Department of Pharmacology CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Yong Jae Lee
- Department of Pharmacology CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Kyunghyeon Lee
- Department of Nonclinical Development CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Semi Kim
- Department of Nonclinical Development CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Hye‐ri Sim
- Department of Nonclinical Development CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Young Il Choi
- Department of Pharmacology CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Keun Ho Ryu
- Department of Nonclinical Development CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Jong‐Chan Park
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Dongjoon Lee
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Sun‐Ho Han
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
| | - Daehee Hwang
- Center for Plant Aging Research Institute for Basic Science DGIST Daegu Korea
- Department of New Biology DGIST Daegu Korea
| | - Jangbeen Kyung
- Department of Pharmacology CKD Research Institute CKD Pharmaceutical Company Seoul Korea
| | - Inhee Mook‐Jung
- Department of Biochemistry and Biomedical Sciences College of Medicine Seoul National University Seoul Korea
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50
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Frost GR, Jonas LA, Li YM. Friend, Foe or Both? Immune Activity in Alzheimer's Disease. Front Aging Neurosci 2019; 11:337. [PMID: 31920620 PMCID: PMC6916654 DOI: 10.3389/fnagi.2019.00337] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/21/2019] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is marked by the presence of amyloid beta (Aβ) plaques, neurofibrillary tangles (NFT), neuronal death and synaptic loss, and inflammation in the brain. AD research has, in large part, been dedicated to the understanding of Aβ and NFT deposition as well as to the pharmacological reduction of these hallmarks. However, recent GWAS data indicates neuroinflammation plays a critical role in AD development, thereby redirecting research efforts toward unveiling the complexities of AD-associated neuroinflammation. It is clear that the innate immune system is intimately associated with AD progression, however, the specific roles of glia and neuroinflammation in AD pathology remain to be described. Moreover, inflammatory processes have largely been painted as detrimental to AD pathology, when in fact, many immune mechanisms such as phagocytosis aid in the reduction of AD pathologies. In this review, we aim to outline the delicate balance between the beneficial and detrimental aspects of immune activation in AD as a more thorough understanding of these processes is critical to development of effective therapeutics for AD.
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Affiliation(s)
- Georgia R. Frost
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, Manhattan, NY, United States
| | - Lauren A. Jonas
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, Manhattan, NY, United States
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, Ithaca, NY, United States
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, Manhattan, NY, United States
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, Ithaca, NY, United States
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