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Gong Y, Haeri M, Zhang X, Li Y, Liu A, Wu D, Zhang Q, Jazwinski SM, Zhou X, Wang X, Jiang L, Chen YP, Yan X, Swerdlow RH, Shen H, Deng HW. Spatial Dissection of the Distinct Cellular Responses to Normal Aging and Alzheimer's Disease in Human Prefrontal Cortex at Single-Nucleus Resolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24306783. [PMID: 38826275 PMCID: PMC11142279 DOI: 10.1101/2024.05.21.24306783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Aging significantly elevates the risk for Alzheimer's disease (AD), contributing to the accumulation of AD pathologies, such as amyloid-β (Aβ), inflammation, and oxidative stress. The human prefrontal cortex (PFC) is highly vulnerable to the impacts of both aging and AD. Unveiling and understanding the molecular alterations in PFC associated with normal aging (NA) and AD is essential for elucidating the mechanisms of AD progression and developing novel therapeutics for this devastating disease. In this study, for the first time, we employed a cutting-edge spatial transcriptome platform, STOmics® SpaTial Enhanced Resolution Omics-sequencing (Stereo-seq), to generate the first comprehensive, subcellular resolution spatial transcriptome atlas of the human PFC from six AD cases at various neuropathological stages and six age, sex, and ethnicity matched controls. Our analyses revealed distinct transcriptional alterations across six neocortex layers, highlighted the AD-associated disruptions in laminar architecture, and identified changes in layer-to-layer interactions as AD progresses. Further, throughout the progression from NA to various stages of AD, we discovered specific genes that were significantly upregulated in neurons experiencing high stress and in nearby non-neuronal cells, compared to cells distant from the source of stress. Notably, the cell-cell interactions between the neurons under the high stress and adjacent glial cells that promote Aβ clearance and neuroprotection were diminished in AD in response to stressors compared to NA. Through cell-type specific gene co-expression analysis, we identified three modules in excitatory and inhibitory neurons associated with neuronal protection, protein dephosphorylation, and negative regulation of Aβ plaque formation. These modules negatively correlated with AD progression, indicating a reduced capacity for toxic substance clearance in AD subject samples. Moreover, we have discovered a novel transcription factor, ZNF460, that regulates all three modules, establishing it as a potential new therapeutic target for AD. Overall, utilizing the latest spatial transcriptome platform, our study developed the first transcriptome-wide atlas with subcellular resolution for assessing the molecular alterations in the human PFC due to AD. This atlas sheds light on the potential mechanisms underlying the progression from NA to AD.
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Affiliation(s)
- Yun Gong
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Mohammad Haeri
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Xiao Zhang
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Yisu Li
- Department of Cell and Molecular Biology, School of Science of Engineering, Tulane University, New Orleans, LA, 70118, USA
| | - Anqi Liu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Di Wu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Qilei Zhang
- School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410008, China
| | - S. Michal Jazwinski
- Tulane Center for Aging, Deming Department of Medicine, Tulane University School of Medicne, New Orleans, LA 70112, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiaoying Wang
- Clinical Neuroscience Research Center, Departments of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Lindong Jiang
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Yi-Ping Chen
- Department of Cell and Molecular Biology, School of Science of Engineering, Tulane University, New Orleans, LA, 70118, USA
| | - Xiaoxin Yan
- School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Russell H. Swerdlow
- Department of Neurology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
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Chen Y, Zhang L, Shi X, Han J, Chen J, Zhang X, Xie D, Li Z, Niu X, Chen L, Yang C, Sun X, Zhou T, Su P, Li N, Greenblatt MB, Ke R, Huang J, Chen Z, Xu R. Characterization of the Nucleus Pulposus Progenitor Cells via Spatial Transcriptomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303752. [PMID: 38311573 PMCID: PMC11095158 DOI: 10.1002/advs.202303752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/11/2024] [Indexed: 02/06/2024]
Abstract
Loss of refreshment in nucleus pulposus (NP) cellularity leads to intervertebral disc (IVD) degeneration. Nevertheless, the cellular sequence of NP cell differentiation remains unclear, although an increasing body of literature has identified markers of NP progenitor cells (NPPCs). Notably, due to their fragility, the physical enrichment of NP-derived cells has limited conventional transcriptomic approaches in multiple studies. To overcome this limitation, a spatially resolved transcriptional atlas of the mouse IVD is generated via the 10x Genomics Visium platform dividing NP spots into two clusters. Based on this, most reported NPPC-markers, including Cathepsin K (Ctsk), are rare and predominantly located within the NP-outer subset. Cell lineage tracing further evidence that a small number of Ctsk-expressing cells generate the entire adult NP tissue. In contrast, Tie2, which has long suggested labeling NPPCs, is actually neither expressed in NP subsets nor labels NPPCs and their descendants in mouse models; consistent with this, an in situ sequencing (ISS) analysis validated the absence of Tie2 in NP tissue. Similarly, no Tie2-cre-mediated labeling of NPPCs is observed in an IVD degenerative mouse model. Altogether, in this study, the first spatial transcriptomic map of the IVD is established, thereby providing a public resource for bone biology.
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Affiliation(s)
- Yu Chen
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
| | - Long Zhang
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
| | - Xueqing Shi
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
| | - Jie Han
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
| | - Jingyu Chen
- Gene Denovo Biotechnology CoGuangzhou510006China
| | - Xinya Zhang
- School of Medicine and School of Biomedical SciencesHuaqiao UniversityQuanzhou362000China
| | - Danlin Xie
- School of Medicine and School of Biomedical SciencesHuaqiao UniversityQuanzhou362000China
- School of Life SciencesWestlake UniversityHangzhou310030China
| | - Zan Li
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
| | - Xing Niu
- China Medical UniversityShenyangLiaoning110122China
| | - Lijie Chen
- China Medical UniversityShenyangLiaoning110122China
| | - Chaoyong Yang
- Department of Chemical BiologyCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamen361005China
| | - Xiujie Sun
- Department of Obstetrics and GynecologySchool of MedicineXiang'an Hospital of Xiamen UniversityXiamen UniversityXiamen361102China
| | - Taifeng Zhou
- Department of Spine SurgeryGuangdong Provincial Key Laboratory of Orthopedics and TraumatologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510080China
| | - Peiqiang Su
- Department of Spine SurgeryGuangdong Provincial Key Laboratory of Orthopedics and TraumatologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510080China
| | - Na Li
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
| | - Matthew B. Greenblatt
- Department of Pathology and Laboratory MedicineWeill Cornell Medical CollegeNew YorkNY10065USA
- Research DivisionHospital for Special SurgeryNew YorkNY10065USA
| | - Rongqin Ke
- School of Medicine and School of Biomedical SciencesHuaqiao UniversityQuanzhou362000China
| | - Jianming Huang
- Department of OrthopedicsChengong Hospital (the 73th Group Military Hospital of People's Liberation Army) affiliated to Xiamen UniversityXiamen361000China
| | - Zhe‐Sheng Chen
- College of Pharmacy and Health SciencesSt. John's UniversityNew YorkNY11439USA
| | - Ren Xu
- The First Affiliated Hospital of Xiamen University‐ICMRS Collaborating Center for Skeletal Stem CellsState Key Laboratory of Cellular Stress BiologyFaculty of Medicine and Life SciencesSchool of MedicineXiamen UniversityXiamen361102China
- Xiamen Key Laboratory of Regeneration MedicineFujian Provincial Key Laboratory of Organ and Tissue RegenerationSchool of MedicineXiamen UniversityXiamen361102China
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Okabe M, Sato T, Takahashi M, Honjo A, Okawa M, Ishida M, Kukimoto-Niino M, Shirouzu M, Miyamoto Y, Yamauchi J. Autism Spectrum Disorder- and/or Intellectual Disability-Associated Semaphorin-5A Exploits the Mechanism by Which Dock5 Signalosome Molecules Control Cell Shape. Curr Issues Mol Biol 2024; 46:3092-3107. [PMID: 38666924 PMCID: PMC11049140 DOI: 10.3390/cimb46040194] [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: 02/12/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that includes autism, Asperger's syndrome, and pervasive developmental disorder. Individuals with ASD may exhibit difficulties in social interactions, communication challenges, repetitive behaviors, and restricted interests. While genetic mutations in individuals with ASD can either activate or inactivate the activities of the gene product, impacting neuronal morphogenesis and causing symptoms, the underlying mechanism remains to be fully established. Herein, for the first time, we report that genetically conserved Rac1 guanine-nucleotide exchange factor (GEF) Dock5 signalosome molecules control process elongation in the N1E-115 cell line, a model line capable of achieving neuronal morphological changes. The increased elongation phenotypes observed in ASD and intellectual disability (ID)-associated Semaphorin-5A (Sema5A) Arg676-to-Cys [p.R676C] were also mediated by Dock5 signalosome molecules. Indeed, knockdown of Dock5 using clustered regularly interspaced short palindromic repeat (CRISPR)/CasRx-based guide(g)RNA specifically recovered the mutated Sema5A-induced increase in process elongation in cells. Knockdown of Elmo2, an adaptor molecule of Dock5, also exhibited similar recovery. Comparable results were obtained when transfecting the interaction region of Dock5 with Elmo2. The activation of c-Jun N-terminal kinase (JNK), one of the primary signal transduction molecules underlying process elongation, was ameliorated by either their knockdown or transfection. These results suggest that the Dock5 signalosome comprises abnormal signaling involved in the process elongation induced by ASD- and ID-associated Sema5A. These molecules could be added to the list of potential therapeutic target molecules for abnormal neuronal morphogenesis in ASD at the molecular and cellular levels.
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Affiliation(s)
- Miyu Okabe
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
| | - Takanari Sato
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
| | - Mikito Takahashi
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
| | - Asahi Honjo
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
| | - Maho Okawa
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
| | - Miki Ishida
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
| | - Mutsuko Kukimoto-Niino
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, Yokohama 230-0045, Japan; (M.K.-N.); (M.S.)
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, Yokohama 230-0045, Japan; (M.K.-N.); (M.S.)
| | - Yuki Miyamoto
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
- Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Junji Yamauchi
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (M.O.); (Y.M.)
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, Yokohama 230-0045, Japan; (M.K.-N.); (M.S.)
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
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