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Wang YM, Wang WC, Pan Y, Zeng L, Wu J, Wang ZB, Zhuang XL, Li ML, Cooper DN, Wang S, Shao Y, Wang LM, Fan YY, He Y, Hu XT, Wu DD. Regional and aging-specific cellular architecture of non-human primate brains. Genome Med 2025; 17:41. [PMID: 40296047 PMCID: PMC12038948 DOI: 10.1186/s13073-025-01469-x] [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: 01/19/2024] [Accepted: 04/08/2025] [Indexed: 04/30/2025] Open
Abstract
BACKGROUND Deciphering the functionality and dynamics of brain networks across different regions and age groups in non-human primates (NHPs) is crucial for understanding the evolution of human cognition as well as the processes underlying brain pathogenesis. However, systemic delineation of the cellular composition and molecular connections among multiple brain regions and their alterations induced by aging in NHPs remain largely unresolved. METHODS In this study, we performed single-nucleus RNA sequencing on 39 samples collected from 10 brain regions of two young and two aged rhesus macaques using the DNBelab C4 system. Validation of protein expression of signatures specific to particular cell types, brain regions, and aging was conducted through a series of immunofluorescence and immunohistochemistry staining experiments. Loss-of-function experiments mediated by short hairpin RNA (shRNA) targeting two age-related genes (i.e., VSNL1 and HPCAL4) were performed in U251 glioma cells to verify their aging effects. Senescence-associated beta-galactosidase (SA-β-gal) staining and quantitative PCR (qPCR) of senescence marker genes were employed to assess cellular senescence in U251 cells. RESULTS We have established a large-scale cell atlas encompassing over 330,000 cells for the rhesus macaque brain. Our analysis identified numerous gene expression signatures that were specific to particular cell types, subtypes, brain regions, and aging. These datasets greatly expand our knowledge of primate brain organization and highlight the potential involvement of specific molecular and cellular components in both the regionalization and functional integrity of the brain. Our analysis also disclosed extensive transcriptional alterations and cell-cell connections across brain regions in the aging macaques. Finally, by examining the heritability enrichment of human complex traits and diseases, we determined that neurological traits were significantly enriched in neuronal cells and multiple regions with aging-relevant gene expression signatures, while immune-related traits exhibited pronounced enrichment in microglia. CONCLUSIONS Taken together, our study presents a valuable resource for investigating the cellular and molecular architecture of the primate nervous system, thereby expanding our understanding of the mechanisms underlying brain function, aging, and disease.
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Affiliation(s)
- Yun-Mei Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen-Chao Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yongzhang Pan
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Zeng
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jing Wu
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zheng-Bo Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Yunnan Key Laboratory of Primate Biomedical Research, Kunming, 650107, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sheng Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong Shao
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Li-Min Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ying-Yin Fan
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yonghan He
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xin-Tian Hu
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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Wang E, Zou N, Zhang J, Bao Y, Ya Y, Shen J, Jia Y, Mao C, Fan G. Altered functional activity and connectivity in Parkinson's disease with chronic pain: a resting-state fMRI study. Front Aging Neurosci 2025; 17:1499262. [PMID: 40099248 PMCID: PMC11911387 DOI: 10.3389/fnagi.2025.1499262] [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: 09/23/2024] [Accepted: 02/18/2025] [Indexed: 03/19/2025] Open
Abstract
Background Chronic pain is a common non-motor symptom of Parkinson's disease (PD) that significantly impacts patients' quality of life, but its neural mechanisms remain poorly understood. This study investigated changes in spontaneous neuronal activity and functional connectivity (FC) associated with chronic pain in PD patients. Methods The study included 41 PD patients with chronic pain (PDP), 41 PD patients without pain (nPDP), and 29 healthy controls. Pain severity was assessed using the visual analog scale (VAS). Resting-state fMRI images were used to measure the amplitude of low-frequency fluctuations (ALFF) as an indicator of regional brain activity. Subsequently, FC analysis was performed to evaluate synchronization between ALFF-identified regions and the entire brain. Results Compared to nPDP patients, PDP patients exhibited decreased ALFF in the right putamen, and increased ALFF in motor regions, including the right superior frontal gyrus/supplementary motor area and the left paracentral lobule/primary motor cortex. Additionally, PDP patients exhibited diminished right putamen-based FC in the midbrain, anterior cingulate cortex, orbitofrontal cortex, middle frontal gyrus, middle temporal gyrus, and posterior cerebellar lobe. The correlation analysis revealed that ALFF values in the right putamen were negatively associated with VAS scores in PDP patients. Conclusion This study demonstrates that chronic pain in PD is associated with reduced ALFF in the putamen and disrupted FC with brain regions involved in pain perception and modulation, highlighting the critical role of dopaminergic degeneration in the development and maintenance of pain in PD.
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Affiliation(s)
- Erlei Wang
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Nan Zou
- Department of Radiology, Nanjing TCM Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Jinru Zhang
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yiqing Bao
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Ya
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Junkang Shen
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yujing Jia
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chengjie Mao
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Guohua Fan
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Sun R, Wang X, Sun X, Zhao B, Zhang X, Gong X, Wong SH, Chan MTV, Wu WKK. Emerging Roles of Long Non-Coding RNAs in Ankylosing Spondylitis. Front Immunol 2022; 13:790924. [PMID: 35222376 PMCID: PMC8866863 DOI: 10.3389/fimmu.2022.790924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
Ankylosing spondylitis (AS) is a chronic systemic autoimmune disease characterized by inflammation, bone erosion, spur formation of the spine and the sacroiliac joints. However, the etiology and molecular pathogenesis of AS remain largely unclear. Recently, a growing number of studies showed that long non-coding RNAs (lncRNAs) played critical roles in the development and progression of autoimmune and orthopedic conditions, including AS. Studies demonstrated that a myriad of lncRNAs (e.g. H19, MEG3, LOC645166) pertinent to regulation of inflammatory signals were deregulated in AS. A number of lncRNAs might also serve as new biomarkers for the diagnosis and predicting the outcomes of AS. In this review, we summarize lncRNA profiling studies on AS and the functional roles and mechanism of key lncRNAs relevant to AS pathogenesis. We also discuss their potential values as biomarkers and druggable targets for this potentially disabling condition.
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Affiliation(s)
- Ruifu Sun
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, China
| | - Xuesong Wang
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, China
| | - Xiaohong Sun
- Department Obstetrics and Gynecology of Qingdao Hospital Central, Central Qingdao Hospital, Qingdao, China
| | - Bing Zhao
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, China
| | - Xiugong Zhang
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, China
| | - Xiaojin Gong
- Department Spinal of Qingdao Hospital Central, Qingdao Hospital Central, Qingdao, China
| | - Sunny Hei Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- State Key Laboratory of Digestive Disease and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Matthew Tak Vai Chan
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - William Ka Kei Wu
- State Key Laboratory of Digestive Disease and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
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