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Yilmaz A, Liraz-Zaltsman S, Shohami E, Gordevičius J, Kerševičiūtė I, Sherman E, Bahado-Singh RO, Graham SF. The longitudinal biochemical profiling of TBI in a drop weight model of TBI. Sci Rep 2023; 13:22260. [PMID: 38097614 PMCID: PMC10721861 DOI: 10.1038/s41598-023-48539-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Traumatic brain injury (TBI) is a major cause of mortality and disability worldwide, particularly among individuals under the age of 45. It is a complex, and heterogeneous disease with a multifaceted pathophysiology that remains to be elucidated. Metabolomics has the potential to identify metabolic pathways and unique biochemical profiles associated with TBI. Herein, we employed a longitudinal metabolomics approach to study TBI in a weight drop mouse model to reveal metabolic changes associated with TBI pathogenesis, severity, and secondary injury. Using proton nuclear magnetic resonance (1H NMR) spectroscopy, we biochemically profiled post-mortem brain from mice that suffered mild TBI (N = 25; 13 male and 12 female), severe TBI (N = 24; 11 male and 13 female) and sham controls (N = 16; 11 male and 5 female) at baseline, day 1 and day 7 following the injury. 1H NMR-based metabolomics, in combination with bioinformatic analyses, highlights a few significant metabolites associated with TBI severity and perturbed metabolism related to the injury. We report that the concentrations of taurine, creatinine, adenine, dimethylamine, histidine, N-Acetyl aspartate, and glucose 1-phosphate are all associated with TBI severity. Longitudinal metabolic observation of brain tissue revealed that mild TBI and severe TBI lead distinct metabolic profile changes. A multi-class model was able to classify the severity of injury as well as time after TBI with estimated 86% accuracy. Further, we identified a high degree of correlation between respective hemisphere metabolic profiles (r > 0.84, p < 0.05, Pearson correlation). This study highlights the metabolic changes associated with underlying TBI severity and secondary injury. While comprehensive, future studies should investigate whether: (a) the biochemical pathways highlighted here are recapitulated in the brain of TBI sufferers and (b) if the panel of biomarkers are also as effective in less invasively harvested biomatrices, for objective and rapid identification of TBI severity and prognosis.
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Affiliation(s)
- Ali Yilmaz
- Metabolomics Department, Beaumont Research Institute, Beaumont Health, Royal Oak, MI, 48073, USA
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA
| | - Sigal Liraz-Zaltsman
- Department of Pharmacology, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Ramat-Gan, Israel
- Department of Sports Therapy, Institute for Health and Medical Professions, Ono Academic College, Qiryat Ono, Israel
| | - Esther Shohami
- Department of Pharmacology, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Juozas Gordevičius
- VUGENE LLC, 625 EKenmoor Avenue Southeast, Suite 301, PMB 96578, Grand Rapids, MI, 49546, USA
| | - Ieva Kerševičiūtė
- VUGENE LLC, 625 EKenmoor Avenue Southeast, Suite 301, PMB 96578, Grand Rapids, MI, 49546, USA
| | - Eric Sherman
- Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Ray O Bahado-Singh
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA
| | - Stewart F Graham
- Metabolomics Department, Beaumont Research Institute, Beaumont Health, Royal Oak, MI, 48073, USA.
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA.
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Petkova-Kirova P, Baas S, Wagenpfeil G, Hartz P, Unger MM, Bernhardt R. SNPs in cytochrome P450 genes decide on the fate of individuals with genetic predisposition to Parkinson's disease. Front Pharmacol 2023; 14:1244516. [PMID: 37601072 PMCID: PMC10436510 DOI: 10.3389/fphar.2023.1244516] [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: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Parkinson's disease (PD) is one of the most frequent neurological diseases affecting millions of people worldwide. While the majority of PD cases are of unknown origin (idiopathic), about 5%-10% are familial and linked to mutations in different known genes. However, there are also people with a genetic predisposition to PD who do not develop the disease. To elucidate factors leading to the manifestation of PD we compared the occurrence of single nucleotide polymorphisms (SNPs) in various cytochrome P450 (P450) genes in people with a genetic predisposition and suffering from PD (GPD) to that of people, who are genetically predisposed, but show no symptoms of the disease (GUN). We used the PPMI (Parkinson's Progression Markers Initiative) database and the gene sequences of all 57 P450s as well as their three redox partners. Corresponding odds ratios (OR) and confidence intervals (CI) were calculated to assess the incidence of the various SNPs in the two groups of individuals and consequently their relation to PD. We identified for the first time SNPs that are significantly (up to 10fold!) over- or under-represented in GPD patients compared to GUN. SNPs with OR > 5 were found in 10 P450s being involved in eicosanoid, vitamin A and D metabolism as well as cholesterol degradation pointing to an important role of endogenous factors for the manifestation of PD clinical symptoms. Moreover, 12 P450s belonging to all P450 substrate classes as well as POR have SNPs that are significantly under-represented (OR < 0.2) in GPD compared to GUN, indicating a protective role of those SNPs and the corresponding P450s regarding disease advancement. To the best of our knowledge our data for the first time demonstrate an association between known PD predisposition genes and SNPs in other genes, shown here for different P450 genes and for their redox partner POR, which promote the manifestation of the disease in familial PD. Our results thus shed light onto the pathogenesis of PD, especially the switch from GUN to GPD and might further help to advance novel strategies for preventing the development or progression of the disease.
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Affiliation(s)
- Polina Petkova-Kirova
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Gudrun Wagenpfeil
- Institut für Medizinische Biometrie, Epidemiologie und Medizinische Informatik, Universität des Saarlandes, Homburg, Germany
| | - Philip Hartz
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Rita Bernhardt
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
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Han K, Ji L, Wang C, Shao Y, Chen C, Liu L, Feng M, Yang F, Wu X, Li X, Xie Q, He L, Shi Y, He G, Dong Z, Yu T. The host genetics affects gut microbiome diversity in Chinese depressed patients. Front Genet 2023; 13:976814. [PMID: 36699448 PMCID: PMC9868868 DOI: 10.3389/fgene.2022.976814] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
The gut microbiome and host genetics are both associated with major depressive disorder (MDD); however, the molecular mechanisms among the associations are poorly understood, especially in the Asian, Chinese group. Our study applied linear discriminant analysis (LDA) effect size (LEfSe) and genome-wide association analysis in the cohort with both gut sequencing data and genomics data. We reported the different gut microbiota characteristics between MDD and control groups in the Chinese group and further constructed the association between host genetics and the gut microbiome. Actinobacteria and Pseudomonades were found more in the MDD group. We found significant differences in the ACE and Chao indexes of alpha diversity while no discrepancy in beta diversity. We found three associations between host genetics with microbiome features: beta diversity and rs6108 (p = 8.65 × 10-9), Actinobacteria and rs77379751 (p = 8.56 × 10-9), and PWY-5913 and rs1775633082 (p = 4.54 × 10-8). A species of the Romboutsia genus was co-associated with the species of Ruminococcus gnavus in an internetwork through four genes: METTL8, ITGB2, OTULIN, and PROSER3, with a strict threshold (p < 5 × 10-4). Furthermore, our findings suggested that the gut microbiome diversity might affect microRNA expression in the brain and influenced SERPINA5 and other spatially close genes afterward. These findings suggest new linkages between depression and gut microbiome in Asian, Chinese people, which might be mediated by genes and microRNA regulation in space distance.
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Affiliation(s)
- Ke Han
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Ji
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Chenliu Wang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Shao
- Asbios (Tianjin) Biotechnology Co., Ltd., Tianjin, China
| | - Changfeng Chen
- School of Mental Health, Jining Medical University, Jining, China
| | - Liangjie Liu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mofan Feng
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Yang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Qinglian Xie
- Out-patient Department of West China Hospital, Sichuan University, Chengdu, China
| | - Lin He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Guang He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Guang He, ; Zaiquan Dong, ; Tao Yu,
| | - Zaiquan Dong
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Guang He, ; Zaiquan Dong, ; Tao Yu,
| | - Tao Yu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Center for Women and Children’s Health, Shanghai, China,*Correspondence: Guang He, ; Zaiquan Dong, ; Tao Yu,
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Molecular and Cellular Interactions in Pathogenesis of Sporadic Parkinson Disease. Int J Mol Sci 2022; 23:ijms232113043. [PMID: 36361826 PMCID: PMC9657547 DOI: 10.3390/ijms232113043] [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: 08/20/2022] [Revised: 10/16/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
Abstract
An increasing number of the population all around the world suffer from age-associated neurodegenerative diseases including Parkinson’s disease (PD). This disorder presents different signs of genetic, epigenetic and environmental origin, and molecular, cellular and intracellular dysfunction. At the molecular level, α-synuclein (αSyn) was identified as the principal molecule constituting the Lewy bodies (LB). The gut microbiota participates in the pathogenesis of PD and may contribute to the loss of dopaminergic neurons through mitochondrial dysfunction. The most important pathogenetic link is an imbalance of Ca2+ ions, which is associated with redox imbalance in the cells and increased generation of reactive oxygen species (ROS). In this review, genetic, epigenetic and environmental factors that cause these disorders and their cause-and-effect relationships are considered. As a constituent of environmental factors, the example of organophosphates (OPs) is also reviewed. The role of endothelial damage in the pathogenesis of PD is discussed, and a ‘triple hit hypothesis’ is proposed as a modification of Braak’s dual hit one. In the absence of effective therapies for neurodegenerative diseases, more and more evidence is emerging about the positive impact of nutritional structure and healthy lifestyle on the state of blood vessels and the risk of developing these diseases.
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