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Huang Y, Chen Q, Wang Z, Wang Y, Lian A, Zhou Q, Zhao G, Xia K, Tang B, Li B, Li J. Risk factors associated with age at onset of Parkinson's disease in the UK Biobank. NPJ Parkinsons Dis 2024; 10:3. [PMID: 38167894 PMCID: PMC10762149 DOI: 10.1038/s41531-023-00623-9] [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: 07/31/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Substantial evidence shown that the age at onset (AAO) of Parkinson's disease (PD) is a major determinant of clinical heterogeneity. However, the mechanisms underlying heterogeneity in the AAO remain unclear. To investigate the risk factors with the AAO of PD, a total of 3156 patients with PD from the UK Biobank were included in this study. We evaluated the effects of polygenic risk scores (PRS), nongenetic risk factors, and their interaction on the AAO using Mann-Whitney U tests and regression analyses. We further identified the genes interacting with nongenetic risk factors for the AAO using genome-wide environment interaction studies. We newly found physical activity (P < 0.0001) was positively associated with AAO and excessive daytime sleepiness (P < 0.0001) was negatively associated with AAO, and reproduced the positive associations of smoking and non-steroidal anti-inflammatory drug intake and the negative association of family history with AAO. In the dose-dependent analyses, smoking duration (P = 1.95 × 10-6), coffee consumption (P = 0.0150), and tea consumption (P = 0.0008) were positively associated with AAO. Individuals with higher PRS had younger AAO (P = 3.91 × 10-5). In addition, we observed a significant interaction between the PRS and smoking for AAO (P = 0.0316). Specifically, several genes, including ANGPT1 (P = 7.17 × 10-7) and PLEKHA6 (P = 4.87 × 10-6), may influence the positive relationship between smoking and AAO. Our data suggests that genetic and nongenetic risk factors are associated with the AAO of PD and that there is an interaction between the two.
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Affiliation(s)
- Yuanfeng Huang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China
| | - Qian Chen
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zheng Wang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yijing Wang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China
| | - Aojie Lian
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, Hunan, China
| | - Qiao Zhou
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China
| | - Guihu Zhao
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, Hunan, China
| | - Beisha Tang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, Hunan, China
| | - Bin Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China.
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
- Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University, Changsha 410008, Hunan, China.
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, Hunan, China.
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Guo Y, Ma J, Li Z, Dang K, Ge Q, Huang Y, Wang GZ, Zhao X. Transcriptomic profiling of nuclei from paraformaldehyde-fixed and formalin-fixed paraffin-embedded brain tissues. Anal Chim Acta 2023; 1281:341861. [PMID: 38783731 DOI: 10.1016/j.aca.2023.341861] [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: 07/27/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 05/25/2024]
Abstract
BACKGROUND Paraformaldehyde (PFA) fixation is necessary for histochemical staining, and formalin-fixed and paraffin-embedded (FFPE) tissue archives are the largest repository of clinically annotated specimens. Single-cell gene expression workflows have recently been developed for PFA-fixed and FFPE tissue specimens. However, for tissues where intact cells are hard to recover, including tissues containing highly interconnected neurons, single-nuclear transcriptomics is beneficial. Moreover, since RNA is very unstable, the effects of standard pathological practice on the transcriptome of samples obtained from such archived specimens like FFPE samples are largely anecdotal. RESULTS We evaluated the effects of polyformaldehyde (PFA) fixation and paraffin-embedding on transcriptional profiles of the mouse hippocampus obtained by RNA sequencing (RNA-seq). The transcriptomic signatures of nuclei isolated from fresh PFA-fixed and fresh FFPE tissues were comparable to those of cryopreserved samples. However, more differentially expressed genes were obtained for brains after PFA fixation for more than 3 days than in fresh PFA-fixed samples, especially genes involved in spliceosome and synaptic-related pathways. Importantly, the real cell states were destroyed, with oligodendrocyte precursor cells depleted in the 1day fixed hippocampus. After fixation for 3 days, the proportions of neuronal cells and oligodendrocytes decreased and microglia increased; however, relative frequencies remained constant for longer fixation durations. The storage time of FFPE samples had a negligible effect on the cell composition. SIGNIFICANCE This represents the first work to investigate the effects of fixation and storage time of brains on its nuclear transcriptome signatures in detail. The fixation time had more influences on the nuclear transcriptomic profiles than FFPE retention time, and the cliff-like effects appeared to occur over a fixed period of 1-3 days. These findings are expected to guide sample preparation for single-nucleus RNA-seq of FFPE samples, particularly in transcriptomic studies focused on brain diseases.
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Affiliation(s)
- Yunxia Guo
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengyue Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Kaitong Dang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yan Huang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Xiangwei Zhao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.
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Verma A, Kommaddi RP, Gnanabharathi B, Hirsch EC, Ravindranath V. Genes critical for development and differentiation of dopaminergic neurons are downregulated in Parkinson's disease. J Neural Transm (Vienna) 2023; 130:495-512. [PMID: 36820885 DOI: 10.1007/s00702-023-02604-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
We performed transcriptome analysis using RNA sequencing on substantia nigra pars compacta (SNpc) from mice after acute and chronic 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) treatment and from Parkinson's disease (PD) patients. Acute and chronic exposure to MPTP resulted in decreased expression of genes involved in sodium channel regulation. However, upregulation of pro-inflammatory pathways was seen after single dose but not after chronic MPTP treatment. Dopamine biosynthesis and synaptic vesicle recycling pathways were downregulated in PD patients and after chronic MPTP treatment in mice. Genes essential for midbrain development and determination of dopaminergic phenotype such as, LMX1B, FOXA1, RSPO2, KLHL1, EBF3, PITX3, RGS4, ALDH1A1, RET, FOXA2, EN1, DLK1, GFRA1, LMX1A, NR4A2, GAP43, SNCA, PBX1, and GRB10 were downregulated in human PD and overexpression of GFP tagged LMX1B rescued MPP+ induced death in SH-SY5Y neurons. Downregulation of gene ensemble involved in development and differentiation of dopaminergic neurons indicate their potential involvement in pathogenesis and progression of human PD.
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Affiliation(s)
- Aditi Verma
- Centre for Neuroscience, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Reddy Peera Kommaddi
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | | | - Etienne C Hirsch
- Sorbonne Université, Institut du Cerveau - ICM, Inserm U 1127, CNRS UMR 7225, 75013, Paris, France
| | - Vijayalakshmi Ravindranath
- Centre for Neuroscience, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India. .,Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India.
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