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Sun Z, Chen Z, Yin M, Wu X, Guo B, Cheng X, Quan R, Sun Y, Zhang Q, Fan Y, Jin C, Yin Y, Hou X, Liu W, Shu M, Xue X, Shi Y, Chen B, Xiao Z, Dai J, Zhao Y. Harnessing developmental dynamics of spinal cord extracellular matrix improves regenerative potential of spinal cord organoids. Cell Stem Cell 2024; 31:772-787.e11. [PMID: 38565140 DOI: 10.1016/j.stem.2024.03.007] [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: 10/17/2023] [Revised: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Neonatal spinal cord tissues exhibit remarkable regenerative capabilities as compared to adult spinal cord tissues after injury, but the role of extracellular matrix (ECM) in this process has remained elusive. Here, we found that early developmental spinal cord had higher levels of ECM proteins associated with neural development and axon growth, but fewer inhibitory proteoglycans, compared to those of adult spinal cord. Decellularized spinal cord ECM from neonatal (DNSCM) and adult (DASCM) rabbits preserved these differences. DNSCM promoted proliferation, migration, and neuronal differentiation of neural progenitor cells (NPCs) and facilitated axonal outgrowth and regeneration of spinal cord organoids more effectively than DASCM. Pleiotrophin (PTN) and Tenascin (TNC) in DNSCM were identified as contributors to these abilities. Furthermore, DNSCM demonstrated superior performance as a delivery vehicle for NPCs and organoids in spinal cord injury (SCI) models. This suggests that ECM cues from early development stages might significantly contribute to the prominent regeneration ability in spinal cord.
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Affiliation(s)
- Zheng Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenni Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Man Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianming Wu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Guo
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaokang Cheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Quan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongheng Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Jin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyun Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianglin Hou
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiyuan Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muya Shu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyu Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhifeng Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, China.
| | - Yannan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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O’Connor SA, Garcia L, Patel AP, Hugnot JP, Paddison PJ, Plaisier CL. Breaking out of the cycle: Including quiescence in cell cycle classification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589816. [PMID: 38659838 PMCID: PMC11042294 DOI: 10.1101/2024.04.16.589816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Single-cell transcriptomics has unveiled a vast landscape of cellular heterogeneity in which the cell cycle is a significant component. We trained a high-resolution cell cycle classifier (ccAFv2) using single cell RNA-seq (scRNA-seq) characterized human neural stem cells. The ccAFv2 classifies six cell cycle states (G1, Late G1, S, S/G2, G2/M, and M/Early G1) and a quiescent-like G0 state, and it incorporates a tunable parameter to filter out less certain classifications. The ccAFv2 classifier performed better than or equivalent to other state-of-the-art methods even while classifying more cell cycle states, including G0. We showcased the versatility of ccAFv2 by successfully applying it to classify cells, nuclei, and spatial transcriptomics data in humans and mice, using various normalization methods and gene identifiers. We provide methods to regress the cell cycle expression patterns out of single cell or nuclei data to uncover underlying biological signals. The classifier can be used either as an R package integrated with Seurat (https://github.com/plaisier-lab/ccafv2_R) or a PyPI package integrated with scanpy (https://pypi.org/project/ccAFv2/). We proved that ccAFv2 has enhanced accuracy, flexibility, and adaptability across various experimental conditions, establishing ccAFv2 as a powerful tool for dissecting complex biological systems, unraveling cellular heterogeneity, and deciphering the molecular mechanisms by which proliferation and quiescence affect cellular processes.
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Affiliation(s)
- Samantha A. O’Connor
- School of Biological and Health Systems Engineering, Arizona State University, Tempe AZ, USA
| | - Leonor Garcia
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Anoop P. Patel
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Jean-Philippe Hugnot
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Patrick J. Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | - Christopher L. Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe AZ, USA
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Cao L, Liu Q, Ma Y, Wang S. Identification of immune-related signature with prognosis in children with stage 4 and 4S neuroblastoma. Clin Transl Oncol 2024; 26:905-916. [PMID: 37709978 DOI: 10.1007/s12094-023-03320-4] [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: 04/29/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023]
Abstract
OBJECTIVE Spontaneous regression of tumors is an attractive phenomenon that most commonly occurs in stage 4S neuroblastoma (NB). However, the mechanism underlying this phenomenon remains unclear. METHODS Datasets correlated with NB were downloaded from online public databases, the differentially expressed genes (DEGs) between stage 4 and 4S associated with immunity were identified, and functional enrichment analysis was utilized to explore the potential functions and signaling pathways of these DEGs. In addition, based on these DEGs, a prognostic signature was constructed and validated, and differences in immune cell infiltration were analyzed. RESULTS A total of 13 DEGs were finally identified, and functional enrichment analysis revealed that these DEGs were primarily enriched in the positive regulation of neuron differentiation and TGF-β signaling pathway. The signature successfully stratifies patients into two risk score groups and performs well in judging prognosis and predicting overall survival time. In addition, the prognostic value of the risk score calculated by the signature was independent of clinical factors. The results of immune cell infiltration showed that patients with a high infiltration of resting CD4 + memory T cells had a better prognosis, while plasma cells had a worse prognosis. CONCLUSION The results of the functional enrichment analysis of these identified DEGs suggested that these DEGs may be related to spontaneous regression of NB. In addition, the prognostic signature has the potential to create new risk stratification in patients with NB.
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Affiliation(s)
- Lijian Cao
- Department of Pediatric Surgical Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University and the National Clinical Research Center for Child Health and Disorders, Chongqing, 400014, People's Republic of China
| | - Qingqing Liu
- Department of Pediatric Surgical Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University and the National Clinical Research Center for Child Health and Disorders, Chongqing, 400014, People's Republic of China
| | - Yue Ma
- Department of Pediatric Surgical Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University and the National Clinical Research Center for Child Health and Disorders, Chongqing, 400014, People's Republic of China
| | - Shan Wang
- Department of Pediatric Surgical Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University and the National Clinical Research Center for Child Health and Disorders, Chongqing, 400014, People's Republic of China.
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Fan C, Cai H, Zhang L, Wu X, Yan J, Jin L, Hu B, He J, Chen Y, Zhao Y, Dai J. Constructing Linear-Oriented Pre-Vascularized Human Spinal Cord Tissues for Spinal Cord Injury Repair. Adv Healthc Mater 2024:e2303388. [PMID: 38537119 DOI: 10.1002/adhm.202303388] [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: 10/05/2023] [Revised: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Repairing spinal cord injury (SCI) is a global medical challenge lacking effective clinical treatment. Developing human-engineered spinal cord tissues that can replenish lost cells and restore a regenerative microenvironment offers promising potential for SCI therapy. However, creating vascularized human spinal cord-like tissues (VSCT) that mimic the diverse cell types and longitudinal parallel structural features of spinal cord tissues remains a significant hurdle. In the present study, VSCTs are engineered using embryonic human spinal cord-derived neural and endothelial cells on linear-ordered collagen scaffolds (LOCS). Studies have shown that astrocytes and endothelial cells align along the scaffolds in VSCT, supporting axon extension from various human neurons myelinated by oligodendrocytes. After transplantation into SCI rats, VSCT survives at the injury sites and promotes endogenous neural regeneration and vascularization, ultimately reducing scarring and enhancing behavioral functional recovery. It suggests that pre-vascularization of engineered spinal cord tissues is beneficial for SCI treatment and highlights the important role of exogenous endothelial cells in tissue engineering.
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Affiliation(s)
- Caixia Fan
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, China
| | - Hui Cai
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences, Suzhou, 215123, China
| | - Lulu Zhang
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences, Suzhou, 215123, China
| | - Xianming Wu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100080, China
| | - Junyan Yan
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, China
| | - Lifang Jin
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, China
| | - Baowei Hu
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, China
| | - Jiaxiong He
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, China
| | - Yanyan Chen
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yannan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100080, China
| | - Jianwu Dai
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences, Suzhou, 215123, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100080, China
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5
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Wang W, Ji Y, Dong Z, Liu Z, Chen S, Dai L, Su X, Jiang Q, Deng H. Characterizing neuroinflammation and identifying prenatal diagnostic markers for neural tube defects through integrated multi-omics analysis. J Transl Med 2024; 22:257. [PMID: 38461288 PMCID: PMC10924416 DOI: 10.1186/s12967-024-05051-8] [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: 12/06/2023] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Neural Tube Defects (NTDs) are congenital malformations of the central nervous system resulting from the incomplete closure of the neural tube during early embryonic development. Neuroinflammation refers to the inflammatory response in the nervous system, typically resulting from damage to neural tissue. Immune-related processes have been identified in NTDs, however, the detailed relationship and underlying mechanisms between neuroinflammation and NTDs remain largely unclear. In this study, we utilized integrated multi-omics analysis to explore the role of neuroinflammation in NTDs and identify potential prenatal diagnostic markers using a murine model. METHODS Nine public datasets from Gene Expression Omnibus (GEO) and ArrayExpress were mined using integrated multi-omics analysis to characterize the molecular landscape associated with neuroinflammation in NTDs. Special attention was given to the involvement of macrophages in neuroinflammation within amniotic fluid, as well as the dynamics of macrophage polarization and their interactions with neural cells at single-cell resolution. We also used qPCR assay to validate the key TFs and candidate prenatal diagnostic genes identified through the integrated analysis in a retinoic acid-induced NTDs mouse model. RESULTS Our analysis indicated that neuroinflammation is a critical pathological feature of NTDs, regulated both transcriptionally and epigenetically within central nervous system tissues. Key alterations in gene expression and pathways highlighted the crucial role of STATs molecules in the JAK-STAT signaling pathway in regulating NTDs-associated neuroinflammation. Furthermore, single-cell resolution analysis revealed significant polarization of macrophages and their interaction with neural cells in amniotic fluid, underscoring their central role in mediating neuroinflammation associated with NTDs. Finally, we identified a set of six potential prenatal diagnostic genes, including FABP7, CRMP1, SCG3, SLC16A10, RNASE6 and RNASE1, which were subsequently validated in a murine NTDs model, indicating their promise as prospective markers for prenatal diagnosis of NTDs. CONCLUSIONS Our study emphasizes the pivotal role of neuroinflammation in the progression of NTDs and underlines the potential of specific inflammatory and neural markers as novel prenatal diagnostic tools. These findings provide important clues for further understanding the underlying mechanisms between neuroinflammation and NTDs, and offer valuable insights for the future development of prenatal diagnostics.
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Affiliation(s)
- Wenshuang Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Ji
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhexu Dong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zheran Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shuang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaolan Su
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qingyuan Jiang
- Department of Obstetrics, Sichuan Provincial Hospital for Women and Children, Chengdu, China.
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
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6
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Zheng C, Tu C, Wang J, Yu Y, Guo X, Sun J, Sun J, Cai W, Yang Q, Sun T. Deciphering Oligodendrocyte Lineages in the Human Fetal Central Nervous System Using Single-Cell RNA Sequencing. Mol Neurobiol 2024; 61:1737-1752. [PMID: 37775719 DOI: 10.1007/s12035-023-03661-9] [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: 11/09/2022] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
Oligodendrocytes form myelin sheaths and wrap axons of neurons to facilitate various crucial neurological functions. Oligodendrocyte progenitor cells (OPCs) persist in the embryonic, postnatal, and adult central nervous system (CNS). OPCs and mature oligodendrocytes are involved in a variety of biological processes such as memory, learning, and diseases. How oligodendrocytes are specified in different regions in the CNS, in particular in humans, remains obscure. We here explored oligodendrocyte development in three CNS regions, subpallium, brainstem, and spinal cord, in human fetuses from gestational week 8 (GW8) to GW12 using single-cell RNA sequencing. We detected multiple lineages of OPCs and illustrated distinct developmental trajectories of oligodendrocyte differentiation in three CNS regions. We also identified major genes, particularly transcription factors, which maintain status of OPC proliferation and promote generation of mature oligodendrocytes. Moreover, we discovered new marker genes that might be crucial for oligodendrocyte specification in humans, and detected common and distinct genes expressed in oligodendrocyte lineages in three CNS regions. Our study has demonstrated molecular heterogeneity of oligodendrocyte lineages in different CNS regions and provided references for further investigation of roles of important genes in oligodendrocyte development in humans.
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Affiliation(s)
- Chenlin Zheng
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Chao Tu
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Yuan Yu
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Xueyu Guo
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Jason Sun
- Maple Glory United School, Xiamen, Fujian, China
- Xiamen Institute of Technology Attached School, Xiamen, Fujian, China
| | - Julianne Sun
- Maple Glory United School, Xiamen, Fujian, China
- Xiamen Institute of Technology Attached School, Xiamen, Fujian, China
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Qingwei Yang
- Department of Neurology, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.
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7
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Gautier O, Gitler AD. It's me, hi, I solved the problem, it's TF-seqFISH. Cell Res 2024; 34:181-182. [PMID: 38177241 PMCID: PMC10907587 DOI: 10.1038/s41422-023-00901-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Affiliation(s)
- Olivia Gautier
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Neurosciences Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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Shi Y, Huang L, Dong H, Yang M, Ding W, Zhou X, Lu T, Liu Z, Zhou X, Wang M, Zeng B, Sun Y, Zhong S, Wang B, Wang W, Yin C, Wang X, Wu Q. Decoding the spatiotemporal regulation of transcription factors during human spinal cord development. Cell Res 2024; 34:193-213. [PMID: 38177242 PMCID: PMC10907391 DOI: 10.1038/s41422-023-00897-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/02/2023] [Indexed: 01/06/2024] Open
Abstract
The spinal cord is a crucial component of the central nervous system that facilitates sensory processing and motor performance. Despite its importance, the spatiotemporal codes underlying human spinal cord development have remained elusive. In this study, we have introduced an image-based single-cell transcription factor (TF) expression decoding spatial transcriptome method (TF-seqFISH) to investigate the spatial expression and regulation of TFs during human spinal cord development. By combining spatial transcriptomic data from TF-seqFISH and single-cell RNA-sequencing data, we uncovered the spatial distribution of neural progenitor cells characterized by combinatorial TFs along the dorsoventral axis, as well as the molecular and spatial features governing neuronal generation, migration, and differentiation along the mediolateral axis. Notably, we observed a sandwich-like organization of excitatory and inhibitory interneurons transiently appearing in the dorsal horns of the developing human spinal cord. In addition, we integrated data from 10× Visium to identify early and late waves of neurogenesis in the dorsal horn, revealing the formation of laminas in the dorsal horns. Our study also illuminated the spatial differences and molecular cues underlying motor neuron (MN) diversification, and the enrichment of Amyotrophic Lateral Sclerosis (ALS) risk genes in MNs and microglia. Interestingly, we detected disease-associated microglia (DAM)-like microglia groups in the developing human spinal cord, which are predicted to be vulnerable to ALS and engaged in the TYROBP causal network and response to unfolded proteins. These findings provide spatiotemporal transcriptomic resources on the developing human spinal cord and potential strategies for spinal cord injury repair and ALS treatment.
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Affiliation(s)
- Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, China.
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Yang
- Changping Laboratory, Beijing, China
| | - Wenyu Ding
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Xiang Zhou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xin Zhou
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Changping Laboratory, Beijing, China
| | - Yinuo Sun
- Changping Laboratory, Beijing, China
| | - Suijuan Zhong
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
| | - Qian Wu
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [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: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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10
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Zhang D, Chen Y, Wei Y, Chen H, Wu Y, Wu L, Li J, Ren Q, Miao C, Zhu T, Liu J, Ke B, Zhou C. Spatial transcriptomics and single-nucleus RNA sequencing reveal a transcriptomic atlas of adult human spinal cord. eLife 2024; 12:RP92046. [PMID: 38289829 PMCID: PMC10945563 DOI: 10.7554/elife.92046] [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] [Indexed: 02/01/2024] Open
Abstract
Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and neural diseases, the underlying organization of neuronal clusters and their spatial location remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell or single-nucleus RNA sequencing in animal models or developing humans. However, molecular evidence of cellular heterogeneity in the adult human spinal cord is limited. Here, we classified spinal cord neurons into 21 subclusters and determined their distribution from nine human donors using single-nucleus RNA sequencing and spatial transcriptomics. Moreover, we compared the human findings with previously published single-nucleus data of the adult mouse spinal cord, which revealed an overall similarity in the neuronal composition of the spinal cord between the two species while simultaneously highlighting some degree of heterogeneity. Additionally, we examined the sex differences in the spinal neuronal subclusters. Several genes, such as SCN10A and HCN1, showed sex differences in motor neurons. Finally, we classified human dorsal root ganglia (DRG) neurons using spatial transcriptomics and explored the putative interactions between DRG and spinal cord neuronal subclusters. In summary, these results illustrate the complexity and diversity of spinal neurons in humans and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.
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Affiliation(s)
- Donghang Zhang
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Yali Chen
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Yiyong Wei
- Department of Anesthesiology, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenhenChina
| | - Hongjun Chen
- Department of Intensive Care Unit, Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Yujie Wu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Lin Wu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Jin Li
- Department of Orthopedic Surgery, Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Qiyang Ren
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Changhong Miao
- Department of Anesthesiology, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Tao Zhu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Jin Liu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Bowen Ke
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Cheng Zhou
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
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11
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Neyazi S, Yamazawa E, Hack K, Tanaka S, Nagae G, Kresbach C, Umeda T, Eckhardt A, Tatsuno K, Pohl L, Hana T, Bockmayr M, Kim P, Dorostkar MM, Takami T, Obrecht D, Takai K, Suwala AK, Komori T, Godbole S, Wefers AK, Otani R, Neumann JE, Higuchi F, Schweizer L, Nakanishi Y, Monoranu CM, Takami H, Engertsberger L, Yamada K, Ruf V, Nomura M, Mohme T, Mukasa A, Herms J, Takayanagi S, Mynarek M, Matsuura R, Lamszus K, Ishii K, Kluwe L, Imai H, von Deimling A, Koike T, Benesch M, Kushihara Y, Snuderl M, Nambu S, Frank S, Omura T, Hagel C, Kugasawa K, Mautner VF, Ichimura K, Rutkowski S, Aburatani H, Saito N, Schüller U. Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation. Acta Neuropathol 2024; 147:22. [PMID: 38265489 PMCID: PMC10808175 DOI: 10.1007/s00401-023-02668-9] [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: 10/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.
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Affiliation(s)
- Sina Neyazi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Karoline Hack
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Nagae
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Takayoshi Umeda
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Alicia Eckhardt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Radiotherapy and Radiation Oncology, Hubertus Wald Tumor Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kenji Tatsuno
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Lara Pohl
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Taijun Hana
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Phyo Kim
- Utsunomiya Neurospine Center, Symphony Clinic, Utsunomiya, Japan
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Toshihiro Takami
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Keisuke Takai
- Department of Neurosurgery, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Shweta Godbole
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ryohei Otani
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fumi Higuchi
- Department of Neurosurgery, University of Teikyo Hospital, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt Am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Yuta Nakanishi
- Department of Neurosurgery, Osaka Metropolitan City University Graduate School of Medicine, Osaka, Japan
| | - Camelia-Maria Monoranu
- Department of Neuropathology, Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lara Engertsberger
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Keisuke Yamada
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Viktoria Ruf
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Theresa Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiko Matsuura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuhiko Ishii
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lan Kluwe
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hideaki Imai
- Department of Neurosurgery, Japan Community Health Care Organization Tokyo Shinjuku Medical Center, Tokyo, Japan
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Martin Benesch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York City, USA
| | - Shohei Nambu
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Stephan Frank
- Division of Neuropathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Takaki Omura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuha Kugasawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Viktor F Mautner
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo, Japan
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hiroyuki Aburatani
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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12
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Chae S, Park TJ, Kwon T. Convergent differentiation of multiciliated cells. Sci Rep 2023; 13:23028. [PMID: 38155158 PMCID: PMC10754865 DOI: 10.1038/s41598-023-50077-5] [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: 09/22/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Multiciliated cells (MCCs) are epithelial cells that control body fluid flow and contribute to the clearance of pathogenic microbes and other particles from the airways, egg transport in oviducts, and circulation of cerebrospinal fluid in the central nervous system. Although MCCs have shared functions to control fluid flow via coordinated motility of multiple ciliary structures, they are found in multiple mammalian tissues originating from distinct germ layers and differentiate via distinct developmental pathways. To understand the similarities and differences of MCCs in multiple tissues, we investigated single-cell transcriptome data of nasal epithelial cells, bronchial tubes, fallopian tubes, and ependymal cells in the subventricular zone from humans and mice by cross-species data integration. Expression of cilia-associated genes was indistinguishable between these MCCs, although cell populations had unique properties by the species and tissue, demonstrating that they share the same final differentiation status for ciliary functions. We further analyzed the final differentiation step of MCCs from their distinctive progenitors and confirmed their convergent gene set expression for ciliogenesis at the final step. These results may provide new insight into understanding ciliogenesis during the developmental process.
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Affiliation(s)
- Shinhyeok Chae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tae Joo Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
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13
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Wyart C, Carbo-Tano M. Design of mechanosensory feedback during undulatory locomotion to enhance speed and stability. Curr Opin Neurobiol 2023; 83:102777. [PMID: 37666012 DOI: 10.1016/j.conb.2023.102777] [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: 06/06/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 09/06/2023]
Abstract
Undulatory locomotion relies on the propagation of a wave of excitation in the spinal cord leading to consequential activation of segmental skeletal muscles along the body. Although this process relies on self-generated oscillations of motor circuits in the spinal cord, mechanosensory feedback is crucial to entrain the underlying oscillatory activity and thereby, to enhance movement power and speed. This effect is achieved through directional projections of mechanosensory neurons either sensing stretching or compression of the trunk along the rostrocaudal axis. Different mechanosensory feedback pathways act in concert to shorten and fasten the excitatory wave propagating along the body. While inhibitory mechanosensory cells feedback inhibition on excitatory premotor interneurons and motor neurons, excitatory mechanosensory cells feedforward excitation to premotor excitatory interneurons. Together, diverse mechanosensory cells coordinate the activity of skeletal muscles controlling the head and tail to optimize speed and stabilize balance during fast locomotion.
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Affiliation(s)
- Claire Wyart
- Sorbonne Université, INSERM U1127, UMR CNRS 7225, Institut du Cerveau (ICM), 47 bld de l'hôpital, Paris 75013, France.
| | - Martin Carbo-Tano
- Sorbonne Université, INSERM U1127, UMR CNRS 7225, Institut du Cerveau (ICM), 47 bld de l'hôpital, Paris 75013, France. https://twitter.com/martincarbotano
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14
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Zheng X, Liu Z, He Z, Xu J, Wang Y, Gong C, Zhang R, Zhang SC, Chen H, Wang W. Preclinical long-term safety of intraspinal transplantation of human dorsal spinal GABA neural progenitor cells. iScience 2023; 26:108306. [PMID: 38026209 PMCID: PMC10661464 DOI: 10.1016/j.isci.2023.108306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Human pluripotent stem cell (hPSC)-derived neurons have shown promise in treating spinal cord injury (SCI). We previously showed that hPSC-derived dorsal spinal γ-aminobutyric acid (GABA) neurons can alleviate spasticity and promote locomotion in rats with SCI, but their long-term safety remains elusive. Here, we characterized the long-term fate and safety of human dorsal spinal GABA neural progenitor cells (NPCs) in naive rats over one year. All grafted NPCs had undergone differentiation, yielding mainly neurons and astrocytes. Fully mature human neurons grew many axons and formed numerous synapses with rat neural circuits, together with mature human astrocytes that structurally integrated into the rat spinal cord. The sensorimotor function of rats was not impaired by intraspinal transplantation, even when human neurons were activated or inhibited by designer receptors exclusively activated by designer drugs (DREADDs). These findings represent a significant step toward the clinical translation of human spinal neuron transplantation for treating SCI.
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Affiliation(s)
- Xiaolong Zheng
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhixian Liu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ziyu He
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jia Xu
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Stem Cell Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - YaNan Wang
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - ChenZi Gong
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ruoying Zhang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Su-Chun Zhang
- Waisman Center, Department of Neuroscience and Department of Neurology, University of Wisconsin, Madison, WI, USA
- Program in Neuroscience & Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Hong Chen
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Stem Cell Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
- Key Laboratory of Neurological Diseases of Chinese Ministry of Education, the School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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15
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Santi MD, Zhang M, Liu N, Viet CT, Xie T, Jensen DD, Amit M, Pan H, Ye Y. Repurposing EGFR Inhibitors for Oral Cancer Pain and Opioid Tolerance. Pharmaceuticals (Basel) 2023; 16:1558. [PMID: 38004424 PMCID: PMC10674507 DOI: 10.3390/ph16111558] [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: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Oral cancer pain remains a significant public health concern. Despite the development of improved treatments, pain continues to be a debilitating clinical feature of the disease, leading to reduced oral mobility and diminished quality of life. Opioids are the gold standard treatment for moderate-to-severe oral cancer pain; however, chronic opioid administration leads to hyperalgesia, tolerance, and dependence. The aim of this review is to present accumulating evidence that epidermal growth factor receptor (EGFR) signaling, often dysregulated in cancer, is also an emerging signaling pathway critically involved in pain and opioid tolerance. We presented preclinical and clinical data to demonstrate how repurposing EGFR inhibitors typically used for cancer treatment could be an effective pharmacological strategy to treat oral cancer pain and to prevent or delay the development of opioid tolerance. We also propose that EGFR interaction with the µ-opioid receptor and glutamate N-methyl-D-aspartate receptor could be two novel downstream mechanisms contributing to pain and morphine tolerance. Most data presented here support that repurposing EGFR inhibitors as non-opioid analgesics in oral cancer pain is promising and warrants further research.
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Affiliation(s)
- Maria Daniela Santi
- Translational Research Center, College of Dentistry, New York University, New York, NY 10010, USA; (M.D.S.); (M.Z.); (N.L.); (D.D.J.)
- Pain Research Center, Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USA
| | - Morgan Zhang
- Translational Research Center, College of Dentistry, New York University, New York, NY 10010, USA; (M.D.S.); (M.Z.); (N.L.); (D.D.J.)
- Pain Research Center, Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USA
| | - Naijiang Liu
- Translational Research Center, College of Dentistry, New York University, New York, NY 10010, USA; (M.D.S.); (M.Z.); (N.L.); (D.D.J.)
- Pain Research Center, Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USA
| | - Chi T. Viet
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Loma Linda University, Loma Linda, CA 92350, USA;
| | - Tongxin Xie
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (T.X.); (M.A.)
| | - Dane D. Jensen
- Translational Research Center, College of Dentistry, New York University, New York, NY 10010, USA; (M.D.S.); (M.Z.); (N.L.); (D.D.J.)
- Pain Research Center, Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USA
| | - Moran Amit
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (T.X.); (M.A.)
| | - Huilin Pan
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Yi Ye
- Translational Research Center, College of Dentistry, New York University, New York, NY 10010, USA; (M.D.S.); (M.Z.); (N.L.); (D.D.J.)
- Pain Research Center, Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USA
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16
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Bukatova S, Bacova Z, Osacka J, Bakos J. Mini review of molecules involved in altered postnatal neurogenesis in autism. Int J Neurosci 2023:1-15. [PMID: 37815399 DOI: 10.1080/00207454.2023.2269304] [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: 12/15/2022] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
The neurobiology of autism is complex, but emerging research points to potential abnormalities and alterations in neurogenesis. The aim of the present review is to describe the advances in the understanding of the role of selected neurotrophins, neuropeptides, and other compounds secreted by neuronal cells in the processes of postnatal neurogenesis in conjunction with autism. We characterize the fundamental mechanisms of neuronal cell proliferation, generation of major neuronal cell types with special emphasis on neurogenic niches - the subventricular zone and hippocampal areas. We also discuss changes in intracellular calcium levels and calcium-dependent transcription factors in the context of the regulation of neurogenesis and cell fate determination. To sum up, this review provides specific insight into the known association between alterations in the function of the entire spectrum of molecules involved in neurogenesis and the etiology of autism pathogenesis.
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Affiliation(s)
- Stanislava Bukatova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Bacova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Osacka
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jan Bakos
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- Faculty of Medicine, Comenius University, Bratislava, Slovakia
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17
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Roome RB, Levine AJ. The organization of spinal neurons: Insights from single cell sequencing. Curr Opin Neurobiol 2023; 82:102762. [PMID: 37657185 PMCID: PMC10727478 DOI: 10.1016/j.conb.2023.102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/16/2023] [Accepted: 07/22/2023] [Indexed: 09/03/2023]
Abstract
To understand how the spinal cord enacts complex sensorimotor functions, researchers have studied, classified, and functionally probed it's many neuronal populations for over a century. Recent developments in single-cell RNA-sequencing can characterize the gene expression signatures of the entire set of spinal neuron types and can simultaneously provide an unbiased view of their relationships to each other. This approach has revealed that the location of neurons predicts transcriptomic variability, as dorsal spinal neurons become highly distinct over development as ventral spinal neurons become less so. Temporal specification is also a major source of gene expression variation, subdividing many of the canonical embryonic lineage domains. Together, birthdate and cell body location are fundamental organizing features of spinal neuron diversity.
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Affiliation(s)
- R Brian Roome
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA. https://twitter.com/BrianRoome
| | - Ariel J Levine
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA.
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18
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Xu B, Liu D, Liu W, Long G, Liu W, Wu Y, He X, Shen Y, Jiang P, Yin M, Fan Y, Shen H, Shi L, Zhang Q, Xue W, Jin C, Chen Z, Chen B, Li J, Hu Y, Li X, Xiao Z, Zhao Y, Dai J. Engineered human spinal cord-like tissues with dorsal and ventral neuronal progenitors for spinal cord injury repair in rats and monkeys. Bioact Mater 2023; 27:125-137. [PMID: 37064803 PMCID: PMC10090126 DOI: 10.1016/j.bioactmat.2023.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/05/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Transplanting human neural progenitor cells is a promising method of replenishing the lost neurons after spinal cord injury (SCI), but differentiating neural progenitor cells into the diverse types of mature functional spinal cord neurons in vivo is challenging. In this study, engineered human embryonic spinal cord-like tissues with dorsal and ventral neuronal characters (DV-SC) were generated by inducing human neural progenitor cells (hscNPCs) to differentiate into various types of dorsal and ventral neuronal cells on collagen scaffold in vitro. Transplantation of DV-SC into complete SCI models in rats and monkeys showed better therapeutic effects than undifferentiated hscNPCs, including pronounced cell survival and maturation. DV-SC formed a targeted connection with the host's ascending and descending axons, partially restored interrupted neural circuits, and improved motor evoked potentials and the hindlimb function of animals with SCI. This suggests that the transplantation of pre-differentiated hscNPCs with spinal cord dorsal and ventral neuronal characteristics could be a promising strategy for SCI repair.
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19
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Zhu Y, Luan C, Gong L, Gu Y, Wang X, Sun H, Chen Z, Zhou Q, Liu C, Shan Q, Gu X, Zhou S. SnRNA-seq reveals the heterogeneity of spinal ventral horn and mechanism of motor neuron axon regeneration. iScience 2023; 26:107264. [PMID: 37502257 PMCID: PMC10368823 DOI: 10.1016/j.isci.2023.107264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/02/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Spinal motor neurons, the distinctive neurons of the central nervous system, extend into the peripheral nervous system and have outstanding ability of axon regeneration after injury. Here, we explored the heterogeneity of spinal ventral horn cells after rat sciatic nerve crush via single-nuclei RNA sequencing. Interestingly, regeneration mainly occurred in a Sncg+ and Anxa2+ motor neuron subtype (MN2) surrounded by a newly emerged microglia subtype (Mg6) after injury. Subsequently, microglia depletion slowed down the regeneration of sciatic nerve. OPCs were also involved into the regeneration process. Knockdown of Cacna2d2 in vitro and systemic blocking of Cacna2d2 in vivo improved the axon growth ability, hinting us the importance of Ca2+. Ultimately, we proposed three possible phases of motor neuron axon regeneration: preparation stage, early regeneration stage, and regeneration stage. Taken together, our study provided a resource for deciphering the underlying mechanism of motor neuron axon regeneration in a single cell dimension.
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Affiliation(s)
- Ye Zhu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300000, China
| | - Chengcheng Luan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300000, China
| | - Leilei Gong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Yun Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Xinghui Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Zhifeng Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Qiang Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Chang Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Qi Shan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300000, China
| | - Xiaosong Gu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300000, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Songlin Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
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20
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Fan Y, Wu X, Han S, Zhang Q, Sun Z, Chen B, Xue X, Zhang H, Chen Z, Yin M, Xiao Z, Zhao Y, Dai J. Single-cell analysis reveals region-heterogeneous responses in rhesus monkey spinal cord with complete injury. Nat Commun 2023; 14:4796. [PMID: 37558705 PMCID: PMC10412553 DOI: 10.1038/s41467-023-40513-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Spinal cord injury (SCI) leads to severe sensory and motor dysfunction below the lesion. However, the cellular dynamic responses and heterogeneity across different regions below the lesion remain to be elusive. Here, we used single-cell transcriptomics to investigate the region-related cellular responses in female rhesus monkeys with complete thoracic SCI from acute to chronic phases. We found that distal lumbar tissue cells were severely impacted, leading to degenerative microenvironments characterized by disease-associated microglia and oligodendrocytes activation alongside increased inhibitory interneurons proportion following SCI. By implanting scaffold into the injury sites, we could improve the injury microenvironment through glial cells and fibroblast regulation while remodeling spared lumbar tissues via reduced inhibitory neurons proportion and improved phagocytosis and myelination. Our findings offer crucial pathological insights into the spared distal tissues and proximal tissues after SCI, emphasizing the importance of scaffold-based treatment approaches targeting heterogeneous microenvironments.
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Affiliation(s)
- Yongheng Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xianming Wu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Sufang Han
- College of Animal Science, South China Agricultural University, 510642, Guangzhou, China
| | - Qi Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zheng Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Bing Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoyu Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Haipeng Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhenni Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Man Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhifeng Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Yannan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.
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21
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Xu B, Yin M, Yang Y, Zou Y, Liu W, Qiao L, Zhang J, Wang Z, Wu Y, Shen H, Sun M, Liu W, Xue W, Fan Y, Zhang Q, Chen B, Wu X, Shi Y, Lu F, Zhao Y, Xiao Z, Dai J. Transplantation of neural stem progenitor cells from different sources for severe spinal cord injury repair in rat. Bioact Mater 2023; 23:300-313. [DOI: 10.1016/j.bioactmat.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/28/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
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22
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Andersen J, Thom N, Shadrach JL, Chen X, Onesto MM, Amin ND, Yoon SJ, Li L, Greenleaf WJ, Müller F, Pașca AM, Kaltschmidt JA, Pașca SP. Single-cell transcriptomic landscape of the developing human spinal cord. Nat Neurosci 2023; 26:902-914. [PMID: 37095394 DOI: 10.1038/s41593-023-01311-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/20/2023] [Indexed: 04/26/2023]
Abstract
Understanding spinal cord assembly is essential to elucidate how motor behavior is controlled and how disorders arise. The human spinal cord is exquisitely organized, and this complex organization contributes to the diversity and intricacy of motor behavior and sensory processing. But how this complexity arises at the cellular level in the human spinal cord remains unknown. Here we transcriptomically profiled the midgestation human spinal cord with single-cell resolution and discovered remarkable heterogeneity across and within cell types. Glia displayed diversity related to positional identity along the dorso-ventral and rostro-caudal axes, while astrocytes with specialized transcriptional programs mapped into white and gray matter subtypes. Motor neurons clustered at this stage into groups suggestive of alpha and gamma neurons. We also integrated our data with multiple existing datasets of the developing human spinal cord spanning 22 weeks of gestation to investigate the cell diversity over time. Together with mapping of disease-related genes, this transcriptomic mapping of the developing human spinal cord opens new avenues for interrogating the cellular basis of motor control in humans and guides human stem cell-based models of disease.
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Affiliation(s)
- Jimena Andersen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Nicholas Thom
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | | | - Xiaoyu Chen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | - Massimo Mario Onesto
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Neal D Amin
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | - Se-Jin Yoon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | - Li Li
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Fabian Müller
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Anca M Pașca
- Department of Pediatrics, Division of Neonatology, Stanford University, Stanford, CA, USA
| | | | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA.
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23
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Li X, Andrusivova Z, Czarnewski P, Langseth CM, Andersson A, Liu Y, Gyllborg D, Braun E, Larsson L, Hu L, Alekseenko Z, Lee H, Avenel C, Kallner HK, Åkesson E, Adameyko I, Nilsson M, Linnarsson S, Lundeberg J, Sundström E. Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nat Neurosci 2023; 26:891-901. [PMID: 37095395 PMCID: PMC10166856 DOI: 10.1038/s41593-023-01312-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/20/2023] [Indexed: 04/26/2023]
Abstract
The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.
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Affiliation(s)
- Xiaofei Li
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Paulo Czarnewski
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Stockholm, Sweden
| | | | - Alma Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Artificial Intelligence and Machine Learning, Research and Early Development, Genentech. Inc., South San Francisco, CA, USA
| | - Yang Liu
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Daniel Gyllborg
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Emelie Braun
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lijuan Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Zhanna Alekseenko
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hower Lee
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christophe Avenel
- Department of Information Technology, Uppsala University, Uppsala, Sweden
- BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Helena Kopp Kallner
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
- Department of Obstetrics and Gynecology, Danderyd Hospital, Danderyd, Sweden
| | - Elisabet Åkesson
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Sundström
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
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24
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Jin C, Wu Y, Zhang H, Xu B, Liu W, Ji C, Li P, Chen Z, Chen B, Li J, Wu X, Jiang P, Hu Y, Xiao Z, Zhao Y, Dai J. Spinal cord tissue engineering using human primary neural progenitor cells and astrocytes. Bioeng Transl Med 2023; 8:e10448. [PMID: 36925694 PMCID: PMC10013752 DOI: 10.1002/btm2.10448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/24/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022] Open
Abstract
Neural progenitor cell (NPC) transplantation is a promising approach for repairing spinal cord injury (SCI). However, cell survival, maturation and integration after transplantation are still major challenges. Here, we produced a novel centimeter-scale human spinal cord neural tissue (hscNT) construct with human spinal cord neural progenitor cells (hscNPCs) and human spinal cord astrocytes (hscAS) on a linearly ordered collagen scaffold (LOCS). The hscAS promoted hscNPC adhesion, survival and neurite outgrowth on the LOCS, to form a linearly ordered spinal cord-like structure consisting of mature neurons and glia cells. When transplanted into rats with SCI, the hscNT created a favorable microenvironment by inhibiting inflammation and glial scar formation, and promoted neural and vascular regeneration. Notably, the hscNT promoted neural circuit reconstruction and motor functional recovery. Engineered human spinal cord implants containing astrocytes and neurons assembled on axon guidance scaffolds may therefore have potential in the treatment of SCI.
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Affiliation(s)
- Chen Jin
- University of the Chinese Academy of Sciences Beijing China.,State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Yayu Wu
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Haipeng Zhang
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Bai Xu
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Wenbin Liu
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Chunnan Ji
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Panpan Li
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Zhenni Chen
- University of the Chinese Academy of Sciences Beijing China.,State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Bing Chen
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Jiayin Li
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Xianming Wu
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Peipei Jiang
- Department of Obstetrics and Gynecology The Affiliated Drum Tower Hospital of Nanjing University Medical School Nanjing China
| | - Yali Hu
- Department of Obstetrics and Gynecology The Affiliated Drum Tower Hospital of Nanjing University Medical School Nanjing China
| | - Zhifeng Xiao
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Yannan Zhao
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
| | - Jianwu Dai
- University of the Chinese Academy of Sciences Beijing China.,State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing China
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25
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Yadav A, Matson KJE, Li L, Hua I, Petrescu J, Kang K, Alkaslasi MR, Lee DI, Hasan S, Galuta A, Dedek A, Ameri S, Parnell J, Alshardan MM, Qumqumji FA, Alhamad SM, Wang AP, Poulen G, Lonjon N, Vachiery-Lahaye F, Gaur P, Nalls MA, Qi YA, Maric D, Ward ME, Hildebrand ME, Mery PF, Bourinet E, Bauchet L, Tsai EC, Phatnani H, Le Pichon CE, Menon V, Levine AJ. A cellular taxonomy of the adult human spinal cord. Neuron 2023; 111:328-344.e7. [PMID: 36731429 PMCID: PMC10044516 DOI: 10.1016/j.neuron.2023.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/30/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023]
Abstract
The mammalian spinal cord functions as a community of cell types for sensory processing, autonomic control, and movement. While animal models have advanced our understanding of spinal cellular diversity, characterizing human biology directly is important to uncover specialized features of basic function and human pathology. Here, we present a cellular taxonomy of the adult human spinal cord using single-nucleus RNA sequencing with spatial transcriptomics and antibody validation. We identified 29 glial clusters and 35 neuronal clusters, organized principally by anatomical location. To demonstrate the relevance of this resource to human disease, we analyzed spinal motoneurons, which degenerate in amyotrophic lateral sclerosis (ALS) and other diseases. We found that compared with other spinal neurons, human motoneurons are defined by genes related to cell size, cytoskeletal structure, and ALS, suggesting a specialized molecular repertoire underlying their selective vulnerability. We include a web resource to facilitate further investigations into human spinal cord biology.
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Affiliation(s)
- Archana Yadav
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA
| | - Kaya J E Matson
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Johns Hopkins University Department of Biology, Baltimore, MD 21218, USA
| | - Li Li
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Isabelle Hua
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Joana Petrescu
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA; Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Kristy Kang
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA; Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Mor R Alkaslasi
- Unit on the Development of Neurodegeneration, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA; Department of Neuroscience, Brown University, Providence, RI, USA
| | - Dylan I Lee
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA
| | - Saadia Hasan
- Inherited Neurodegenerative Diseases Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ahmad Galuta
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Annemarie Dedek
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Neuroscience, Carleton University, Ottawa, ON, Canada
| | - Sara Ameri
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jessica Parnell
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Neuroscience, Carleton University, Ottawa, ON, Canada
| | | | | | - Saud M Alhamad
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Alick Pingbei Wang
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Gaetan Poulen
- Department of Neurosurgery, Gui de Chauliac Hospital, and Donation and Transplantation Coordination Unit, Montpellier University Medical Center, Montpellier, France
| | - Nicolas Lonjon
- Department of Neurosurgery, Gui de Chauliac Hospital, and Donation and Transplantation Coordination Unit, Montpellier University Medical Center, Montpellier, France
| | - Florence Vachiery-Lahaye
- Department of Neurosurgery, Gui de Chauliac Hospital, and Donation and Transplantation Coordination Unit, Montpellier University Medical Center, Montpellier, France
| | - Pallavi Gaur
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Glen Echo, MD, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke; Bethesda, MD, USA
| | - Michael E Ward
- Inherited Neurodegenerative Diseases Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Michael E Hildebrand
- Inherited Neurodegenerative Diseases Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Pierre-Francois Mery
- Institute of Functional Genomics, Montpellier University, CNRS, INSERM, Montpellier, France
| | - Emmanuel Bourinet
- Institute of Functional Genomics, Montpellier University, CNRS, INSERM, Montpellier, France
| | - Luc Bauchet
- Department of Neurosurgery, Gui de Chauliac Hospital, and Donation and Transplantation Coordination Unit, Montpellier University Medical Center, Montpellier, France; Institute of Functional Genomics, Montpellier University, CNRS, INSERM, Montpellier, France
| | - Eve C Tsai
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Hemali Phatnani
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA; Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Claire E Le Pichon
- Unit on the Development of Neurodegeneration, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Vilas Menon
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA.
| | - Ariel J Levine
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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26
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Cao Y, Zhu S, Yu B, Yao C. Single-cell RNA sequencing for traumatic spinal cord injury. FASEB J 2022; 36:e22656. [PMID: 36374259 DOI: 10.1096/fj.202200943r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/28/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
Traumatic spinal cord injury (tSCI) is a severe injury of the central nervous system (CNS) with complicated pathological microenvironment that results in hemorrhage, inflammation, and scar formation. The microenvironment of the injured spinal cord comprises heterogeneous neurons, glial cells, inflammatory cells, and stroma-related cells. Increasing evidence has indicated that the altered cellular and molecular microenvironment following tSCI is a key factor impeding functional recovery. Single-cell RNA sequencing (scRNA-seq) has provided deep insights into the dynamic cellular and molecular changes in the microenvironment by comprehensively characterizing the diversity of spinal cord cell types. Specifically, scRNA-seq enables the exploration of the molecular mechanisms underlying tSCI by elucidating intercellular communication in spinal cord samples between normal and injury conditions at a single-cell resolution. Here, we first described the pathological and physiological processes after tSCI and gave a brief introduction of the scRNA-seq technology. We then focused on the recent scRNA-seq researches in tSCI, which characterized diverse cell-type populations and specific cell-cell interactions in tSCI. In addition, we also highlighted some potential directions for the research of scRNA-seq in tSCI in the future.
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Affiliation(s)
- Yuqi Cao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Shunxing Zhu
- Laboratory Animals Center, Nantong University, Nantong, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Chun Yao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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27
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Vinsland E, Linnarsson S. Single-cell RNA-sequencing of mammalian brain development: insights and future directions. Development 2022; 149:275457. [DOI: 10.1242/dev.200180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ABSTRACT
Understanding human brain development is of fundamental interest but is also very challenging. Single-cell RNA-sequencing studies in mammals have revealed that brain development is a highly dynamic process with tremendous, previously concealed, cellular heterogeneity. This Spotlight discusses key insights from these studies and their implications for experimental models. We survey published single-cell RNA-sequencing studies of mouse and human brain development, organized by anatomical regions and developmental time points. We highlight remaining gaps in the field, predominantly concerning human brain development. We propose future directions to fill the remaining gaps, and necessary complementary techniques to create an atlas integrated in space and time of human brain development.
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Affiliation(s)
- Elin Vinsland
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden
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28
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Zhang Q, Wu X, Fan Y, Jiang P, Zhao Y, Yang Y, Han S, Xu B, Chen B, Han J, Sun M, Zhao G, Xiao Z, Hu Y, Dai J. Single-cell analysis reveals dynamic changes of neural cells in developing human spinal cord. EMBO Rep 2021; 22:e52728. [PMID: 34605607 PMCID: PMC8567249 DOI: 10.15252/embr.202152728] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/25/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
During central nervous system development, neurogenesis and gliogenesis occur in an orderly manner to create precise neural circuitry. However, no systematic dataset of neural lineage development that covers both neurogenesis and gliogenesis for the human spinal cord is available. We here perform single-cell RNA sequencing of human spinal cord cells during embryonic and fetal stages that cover neuron generation as well as astrocytes and oligodendrocyte differentiation. We also map the timeline of sensory neurogenesis and gliogenesis in the spinal cord. We further identify a group of EGFR-expressing transitional glial cells with radial morphology at the onset of gliogenesis, which progressively acquires differentiated glial cell characteristics. These EGFR-expressing transitional glial cells exhibited a unique position-specific feature during spinal cord development. Cell crosstalk analysis using CellPhoneDB indicated that EGFR glial cells can persistently interact with other neural cells during development through Delta-Notch and EGFR signaling. Together, our results reveal stage-specific profiles and dynamics of neural cells during human spinal cord development.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Xianming Wu
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yongheng Fan
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Peipei Jiang
- Department of Obstetrics and GynecologyThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Yannan Zhao
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yaming Yang
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Sufang Han
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Bai Xu
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Bing Chen
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Jin Han
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Minghan Sun
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Guangfeng Zhao
- Department of Obstetrics and GynecologyThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Zhifeng Xiao
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yali Hu
- Department of Obstetrics and GynecologyThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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