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Qiu Y, Hou Y, Gohel D, Zhou Y, Xu J, Bykova M, Yang Y, Leverenz JB, Pieper AA, Nussinov R, Caldwell JZK, Brown JM, Cheng F. Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer's disease. Cell Rep 2024; 43:114128. [PMID: 38652661 DOI: 10.1016/j.celrep.2024.114128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Shifts in the magnitude and nature of gut microbial metabolites have been implicated in Alzheimer's disease (AD), but the host receptors that sense and respond to these metabolites are largely unknown. Here, we develop a systems biology framework that integrates machine learning and multi-omics to identify molecular relationships of gut microbial metabolites with non-olfactory G-protein-coupled receptors (termed the "GPCRome"). We evaluate 1.09 million metabolite-protein pairs connecting 408 human GPCRs and 335 gut microbial metabolites. Using genetics-derived Mendelian randomization and integrative analyses of human brain transcriptomic and proteomic profiles, we identify orphan GPCRs (i.e., GPR84) as potential drug targets in AD and that triacanthine experimentally activates GPR84. We demonstrate that phenethylamine and agmatine significantly reduce tau hyperphosphorylation (p-tau181 and p-tau205) in AD patient induced pluripotent stem cell-derived neurons. This study demonstrates a systems biology framework to uncover the GPCR targets of human gut microbiota in AD and other complex diseases if broadly applied.
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Affiliation(s)
- Yunguang Qiu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Hou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dhruv Gohel
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yadi Zhou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jielin Xu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Marina Bykova
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuxin Yang
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Neurological 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
| | - Andrew A Pieper
- Brain Health Medicines Center, 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 Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jessica Z K Caldwell
- 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, Las Vegas, NV 89106, USA
| | - J Mark Brown
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Department of Cancer Biology, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; 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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Qin Y, Yang P, He W, Li D, Zeng L, Li J, Zhou T, Peng J, Cao L, Huang W. Novel histone post-translational modifications in Alzheimer's disease: current advances and implications. Clin Epigenetics 2024; 16:39. [PMID: 38461320 PMCID: PMC10924326 DOI: 10.1186/s13148-024-01650-w] [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: 11/04/2023] [Accepted: 02/21/2024] [Indexed: 03/11/2024] Open
Abstract
Alzheimer's disease (AD) has a complex pathogenesis, and multiple studies have indicated that histone post-translational modifications, especially acetylation, play a significant role in it. With the development of mass spectrometry and proteomics, an increasing number of novel HPTMs, including lactoylation, crotonylation, β-hydroxybutyrylation, 2-hydroxyisobutyrylation, succinylation, and malonylation, have been identified. These novel HPTMs closely link substance metabolism to gene regulation, and an increasing number of relevant studies on the relationship between novel HPTMs and AD have become available. This review summarizes the current advances and implications of novel HPTMs in AD, providing insight into the deeper pathogenesis of AD and the development of novel drugs.
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Affiliation(s)
- Yuanyuan Qin
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Ping Yang
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Wanhong He
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Dongze Li
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
| | - Lisha Zeng
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
| | - Junle Li
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Tingting Zhou
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Juan Peng
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Ling Cao
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China.
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China.
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China.
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China.
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China.
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Jensen CS, Gleerup HS, Musaeus CS, Hasselbalch SG, Høgh P, Waldemar G, Simonsen AH. Cerebrospinal fluid glucose is not altered in patients with dementia. Clin Biochem 2023; 112:1-5. [PMID: 36502885 DOI: 10.1016/j.clinbiochem.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/25/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Studies have shown that the pathological changes of many dementia disorders begin several years before clinical onset. A connection between some of these pathophysiological changes and brain hypometabolism, seen in dementia disorders, is well established. Glucose is transported from the blood into the interstitial space, and the decreased demand for glucose by the degenerating brain tissue may thereby mirror increased levels of cerebrospinal fluid (CSF) glucose. In this study, the levels of CSF and plasma glucose and the CSF/plasma glucose ratio were investigated in a large cohort from a mixed memory clinic population in order to evaluate its diagnostic potential. METHOD CSF and plasma samples were taken from 446 patients (Alzheimer's Disease (AD) (n = 320), vascular dementia (VaD) (n = 64), frontotemporal dementia (FTD) (n = 27) and dementia with Lewy bodies (DLB) (n = 35)), and 130 healthy controls (HC) (healthy subjects (HS) (n = 34), non-demented HS (n = 96)). RESULTS No significant differences were found for CSF and plasma glucose or the CSF/plasma glucose ratio between patients with dementia disorders and HC. In addition, no significant differences were observed between the different dementia etiologies. CONCLUSION CSF and plasma glucose were not useful to differentiate between HC and patients with various dementia disorders.
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Affiliation(s)
- Camilla Steen Jensen
- Danish Dementia Research Centre (DDRC), Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Helena Sophia Gleerup
- Danish Dementia Research Centre (DDRC), Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christian Sandøe Musaeus
- Danish Dementia Research Centre (DDRC), Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Steen Gregers Hasselbalch
- Danish Dementia Research Centre (DDRC), Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Peter Høgh
- Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Regional Dementia Research Centre, Department of Neurology, Zealand University Hospital, Roskilde, Denmark
| | - Gunhild Waldemar
- Danish Dementia Research Centre (DDRC), Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Anja Hviid Simonsen
- Danish Dementia Research Centre (DDRC), Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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Lacticaseibacillus rhamnosus Probio-M9-Driven Mouse Mammary Tumor-Inhibitory Effect Is Accompanied by Modulation of Host Gut Microbiota, Immunity, and Serum Metabolome. Nutrients 2022; 15:nu15010005. [PMID: 36615662 PMCID: PMC9824041 DOI: 10.3390/nu15010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/10/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Gut microbiome may influence tumor growth and cancer treatment efficacy, so it is a potential target for tumor prevention/treatment. This pilot study investigated the preventive and therapeutic effects of a probiotic strain, Lacticaseibacillus rhamnosus Probio-M9 (Probio-M9), against murine mammary cancer. Thirty-six female mice were randomly divided into three groups (n = 12 per group): control (without tumor transplantation), model (tumor transplantation; no probiotic administration), and probiotic (30-day oral gavage of probiotic, started seven days before tumor transplantation). Changes in tumor size were recorded, and blood, tumor tissue, and stool samples were collected at the end of the trial for analyses. Comparing with the model group, the probiotic group had a significantly smaller tumor volume (p < 0.05), a higher fecal microbiota Shannon diversity index, with significant modifications in the gut microbiota structure (p < 0.05), characterized by more Alistipes sp._2, Porphyromonadaceae bacterium_7, and Bacteroidales bacterium 55_9 (p < 0.05). Additionally, Probio-M9 administration elevated the serum IFN-γ, IL-9, IL-13, and IL-27 levels and several metabolites (e.g., pyridoxal, nicotinic acid, 3-hydroxybutyric acid, glutamine; p < 0.05), while reducing IL-5 (p < 0.05). These changes might be associated with the protective effect of Probio-M9 against mammary tumor growth. Thus, probiotic administration could harness host gut microbiome in anti-cancer responses.
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Tang Y. Editorial: Nutraceuticals. Curr Opin Pharmacol 2022; 66:102265. [PMID: 35830773 DOI: 10.1016/j.coph.2022.102265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yong Tang
- School of Health and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Acupuncture and Chronobiology Key Laboratory of Sichuan Province, 37 Shi-er Qiao Road, Chengdu 610075, China.
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