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Gao M, Dong Q, Yang Z, Zou D, Han Y, Chen Z, Xu R. Long non-coding RNA H19 regulates neurogenesis of induced neural stem cells in a mouse model of closed head injury. Neural Regen Res 2024; 19:872-880. [PMID: 37843223 PMCID: PMC10664125 DOI: 10.4103/1673-5374.382255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 10/17/2023] Open
Abstract
Stem cell-based therapies have been proposed as a potential treatment for neural regeneration following closed head injury. We previously reported that induced neural stem cells exert beneficial effects on neural regeneration via cell replacement. However, the neural regeneration efficiency of induced neural stem cells remains limited. In this study, we explored differentially expressed genes and long non-coding RNAs to clarify the mechanism underlying the neurogenesis of induced neural stem cells. We found that H19 was the most downregulated neurogenesis-associated lncRNA in induced neural stem cells compared with induced pluripotent stem cells. Additionally, we demonstrated that H19 levels in induced neural stem cells were markedly lower than those in induced pluripotent stem cells and were substantially higher than those in induced neural stem cell-derived neurons. We predicted the target genes of H19 and discovered that H19 directly interacts with miR-325-3p, which directly interacts with Ctbp2 in induced pluripotent stem cells and induced neural stem cells. Silencing H19 or Ctbp2 impaired induced neural stem cell proliferation, and miR-325-3p suppression restored the effect of H19 inhibition but not the effect of Ctbp2 inhibition. Furthermore, H19 silencing substantially promoted the neural differentiation of induced neural stem cells and did not induce apoptosis of induced neural stem cells. Notably, silencing H19 in induced neural stem cell grafts markedly accelerated the neurological recovery of closed head injury mice. Our results reveal that H19 regulates the neurogenesis of induced neural stem cells. H19 inhibition may promote the neural differentiation of induced neural stem cells, which is closely associated with neurological recovery following closed head injury.
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Affiliation(s)
- Mou Gao
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
- Zhongsai Stem Cell Genetic Engineering Co., Ltd., Sanmenxia, Henan Province, China
| | - Qin Dong
- Department of Neurology, Fu Xing Hospital, Capital Medical University, Beijing, China
| | - Zhijun Yang
- Zhongsai Stem Cell Genetic Engineering Co., Ltd., Sanmenxia, Henan Province, China
| | - Dan Zou
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Yajuan Han
- Zhongsai Stem Cell Genetic Engineering Co., Ltd., Sanmenxia, Henan Province, China
| | - Zhanfeng Chen
- Zhongsai Stem Cell Genetic Engineering Co., Ltd., Sanmenxia, Henan Province, China
| | - Ruxiang Xu
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
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2
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Pyenson BC, Rehan SM. Gene regulation supporting sociality shared across lineages and variation in complexity. Genome 2024; 67:99-108. [PMID: 38096504 DOI: 10.1139/gen-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Across evolutionary lineages, insects vary in social complexity, from those that exhibit extended parental care to those with elaborate divisions of labor. Here, we synthesize the sociogenomic resources from hundreds of species to describe common gene regulatory mechanisms in insects that regulate social organization across phylogeny and levels of social complexity. Different social phenotypes expressed by insects can be linked to the organization of co-expressing gene networks and features of the epigenetic landscape. Insect sociality also stems from processes like the emergence of parental care and the decoupling of ancestral genetic programs. One underexplored avenue is how variation in a group's social environment affects the gene expression of individuals. Additionally, an experimental reduction of gene expression would demonstrate how the activity of specific genes contributes to insect social phenotypes. While tissue specificity provides greater localization of the gene expression underlying social complexity, emerging transcriptomic analysis of insect brains at the cellular level provides even greater resolution to understand the molecular basis of social insect evolution.
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Affiliation(s)
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
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3
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Shen Z, Zhang R, Huang Y, Chen J, Yu M, Li C, Zhang Y, Chen L, Huang X, Yang J, Lin Z, Wang S, Cheng B. The spatial transcriptomic landscape of human gingiva in health and periodontitis. Sci China Life Sci 2024; 67:720-732. [PMID: 38172357 DOI: 10.1007/s11427-023-2467-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/16/2023] [Indexed: 01/05/2024]
Abstract
The gingiva is a key oral barrier that protects oral tissues from various stimuli. A loss of gingival tissue homeostasis causes periodontitis, one of the most prevalent inflammatory diseases in humans. The human gingiva exists as a complex cell network comprising specialized structures. To understand the tissue-specific pathophysiology of the gingiva, we applied a recently developed spatial enhanced resolution omics-sequencing (Stereo-seq) technique to obtain a spatial transcriptome (ST) atlas of the gingiva in healthy individuals and periodontitis patients. By utilizing Stereo-seq, we identified the major cell types present in the gingiva, which included epithelial cells, fibroblasts, endothelial cells, and immune cells, as well as subgroups of epithelial cells and immune cells. We further observed that inflammation-related signalling pathways, such as the JAK-STAT and NF-κB signalling pathways, were significantly upregulated in the endothelial cells of the gingiva of periodontitis patients compared with those of healthy individuals. Additionally, we characterized the spatial distribution of periodontitis risk genes in the gingiva and found that the expression of IFI16 was significantly increased in endothelial cells of inflamed gingiva. In conclusion, our Stereo-seq findings may facilitate the development of innovative therapeutic strategies for periodontitis by mapping periodontitis-relevant genes and pathways and effector cells.
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Affiliation(s)
- Zongshan Shen
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Ran Zhang
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, 100050, China
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, 100050, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Yunjia Huang
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Jiayao Chen
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Mengjun Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Chunhua Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yong Zhang
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Lingling Chen
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xin Huang
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Jichen Yang
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Zhengmei Lin
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Songlin Wang
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, 100050, China.
| | - Bin Cheng
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China.
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4
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Halmos P, Liu X, Gold J, Chen F, Ding L, Raphael BJ. DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. bioRxiv 2024:2024.03.05.583575. [PMID: 38496660 PMCID: PMC10942402 DOI: 10.1101/2024.03.05.583575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and distribution of cell types. In recent studies, SRT has been applied to tissue slices from multiple timepoints during the development of an organism. Alignment of this spatiotemporal transcriptomics data can provide insights into the gene expression programs governing the growth and differentiation of cells over space and time. We introduce DeST-OT (Developmental SpatioTemporal Optimal Transport), a method to align SRT slices from pairs of developmental timepoints using the framework of optimal transport (OT). DeST-OT uses semi-relaxed optimal transport to precisely model cellular growth, death, and differentiation processes that are not well-modeled by existing alignment methods. We demonstrate the advantage of DeST-OT on simulated slices. We further introduce two metrics to quantify the plausibility of a spatiotemporal alignment: a growth distortion metric which quantifies the discrepancy between the inferred and the true cell type growth rates, and a migration metric which quantifies the distance traveled between ancestor and descendant cells. DeST-OT outperforms existing methods on these metrics in the alignment of spatiotemporal transcriptomics data from the development of axolotl brain.
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Affiliation(s)
- Peter Halmos
- Department of Computer Science, Princeton University, 35 Olden St, Princeton, NJ 08544
| | - Xinhao Liu
- Department of Computer Science, Princeton University, 35 Olden St, Princeton, NJ 08544
| | - Julian Gold
- Center for Statistics and Machine Learning, Princeton University, 26 Prospect Ave, Princeton, NJ 08544
| | - Feng Chen
- Departments of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110
| | - Li Ding
- Departments of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108
| | - Benjamin J. Raphael
- Department of Computer Science, Princeton University, 35 Olden St, Princeton, NJ 08544
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5
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Jing Z, Zhu Q, Li L, Xie Y, Wu X, Fang Q, Yang B, Dai B, Xu X, Pan H, Bai Y. Spaco: A comprehensive tool for coloring spatial data at single-cell resolution. Patterns (N Y) 2024; 5:100915. [PMID: 38487801 PMCID: PMC10935509 DOI: 10.1016/j.patter.2023.100915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 03/17/2024]
Abstract
Understanding tissue architecture and niche-specific microenvironments in spatially resolved transcriptomics (SRT) requires in situ annotation and labeling of cells. Effective spatial visualization of these data demands appropriate colorization of numerous cell types. However, current colorization frameworks often inadequately account for the spatial relationships between cell types. This results in perceptual ambiguity in neighboring cells of biological distinct types, particularly in complex environments such as brain or tumor. To address this, we introduce Spaco, a potent tool for spatially aware colorization. Spaco utilizes the Degree of Interlacement metric to construct a weighted graph that evaluates the spatial relationships among different cell types, refining color assignments. Furthermore, Spaco incorporates an adaptive palette selection approach to amplify chromatic distinctions. When benchmarked on four diverse datasets, Spaco outperforms existing solutions, capturing complex spatial relationships and boosting visual clarity. Spaco ensures broad accessibility by accommodating color vision deficiency and offering open-accessible code in both Python and R.
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Affiliation(s)
- Zehua Jing
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310012, China
| | | | - Linxuan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
| | - Yue Xie
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
| | - Xinchao Wu
- BGI Research, Hangzhou 310012, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qi Fang
- BGI Research, Shenzhen 518083, China
| | - Bolin Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310012, China
| | - Baojun Dai
- BGI Research, Hangzhou 310012, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
- BGI Research, Shenzhen 518083, China
| | - Hailin Pan
- BGI Research, Hangzhou 310012, China
- BGI Research, Shenzhen 518083, China
| | - Yinqi Bai
- BGI Research, Hangzhou 310012, China
- BGI Research, Shenzhen 518083, China
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6
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Sun ED, Ma R, Navarro Negredo P, Brunet A, Zou J. TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. Nat Methods 2024; 21:444-454. [PMID: 38347138 DOI: 10.1038/s41592-024-02184-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024]
Abstract
Whole-transcriptome spatial profiling of genes at single-cell resolution remains a challenge. To address this limitation, spatial gene expression prediction methods have been developed to infer the spatial expression of unmeasured transcripts, but the quality of these predictions can vary greatly. Here we present Transcript Imputation with Spatial Single-cell Uncertainty Estimation (TISSUE) as a general framework for estimating uncertainty for spatial gene expression predictions and providing uncertainty-aware methods for downstream inference. Leveraging conformal inference, TISSUE provides well-calibrated prediction intervals for predicted expression values across 11 benchmark datasets. Moreover, it consistently reduces the false discovery rate for differential gene expression analysis, improves clustering and visualization of predicted spatial transcriptomics and improves the performance of supervised learning models trained on predicted gene expression profiles. Applying TISSUE to a MERFISH spatial transcriptomics dataset of the adult mouse subventricular zone, we identified subtypes within the neural stem cell lineage and developed subtype-specific regional classifiers.
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Affiliation(s)
- Eric D Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Rong Ma
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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7
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Aung TN, Bates KM, Rimm DL. High-Plex Assessment of Biomarkers in Tumors. Mod Pathol 2024; 37:100425. [PMID: 38219953 DOI: 10.1016/j.modpat.2024.100425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
The assessment of biomarkers plays a critical role in the diagnosis and treatment of many cancers. Biomarkers not only provide diagnostic, prognostic, or predictive information but also can act as effective targets for new pharmaceutical therapies. As the utility of biomarkers increases, it becomes more important to utilize accurate and efficient methods for biomarker discovery and, ultimately, clinical assessment. High-plex imaging studies, defined here as assessment of 8 or more biomarkers on a single slide, have become the method of choice for biomarker discovery and assessment of biomarker spatial context. In this review, we discuss methods of measuring biomarkers in slide-mounted tissue samples, detail the various high-plex methods that allow for the simultaneous assessment of multiple biomarkers in situ, and describe the impact of high-plex biomarker assessment on the future of anatomic pathology.
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Affiliation(s)
- Thazin N Aung
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Katherine M Bates
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut; Department of Internal Medicine (Medical Oncology), Yale University School of Medicine, New Haven, Connecticut.
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8
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Zhang L, Xiong Z, Xiao M. A Review of the Application of Spatial Transcriptomics in Neuroscience. Interdiscip Sci 2024:10.1007/s12539-024-00603-4. [PMID: 38374297 DOI: 10.1007/s12539-024-00603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Since spatial transcriptomics can locate and distinguish the gene expression of functional genes in special regions and tissue, it is important for us to investigate the brain development, the development mechanism of brain diseases, and the relationship between brain structure and function in Neuroscience (or Brain science). While previous studies have introduced the crucial spatial transcriptomic techniques and data analysis methods, there are few studies to comprehensively overview the key methods, data resources, and technological applications of spatial transcriptomics in Neuroscience. For these reasons, we first investigate several common spatial transcriptomic data analysis approaches and data resources. Second, we introduce the applications of the spatial transcriptomic data analysis approaches in Neuroscience. Third, we summarize the integrating spatial transcriptomics with other technologies in Neuroscience. Finally, we discuss the challenges and future research directions of spatial transcriptomics in Neuroscience.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Zhenqi Xiong
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Ming Xiao
- College of Computer Science, Sichuan University, Chengdu, 610065, China.
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9
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. Adv Sci (Weinh) 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] [What about the content of this article? (0)] [Affiliation(s)] [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 C, Gao J, Chen HY, Kong L, Cao G, Guo X, Liu W, Ren B, Wei DQ. STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. PLoS Comput Biol 2024; 20:e1011935. [PMID: 38416785 PMCID: PMC10927115 DOI: 10.1371/journal.pcbi.1011935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/11/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Spatial transcriptomic (ST) clustering employs spatial and transcription information to group spots spatially coherent and transcriptionally similar together into the same spatial domain. Graph convolution network (GCN) and graph attention network (GAT), fed with spatial coordinates derived adjacency and transcription profile derived feature matrix are often used to solve the problem. Our proposed method STGIC (spatial transcriptomic clustering with graph and image convolution) is designed for techniques with regular lattices on chips. It utilizes an adaptive graph convolution (AGC) to get high quality pseudo-labels and then resorts to dilated convolution framework (DCF) for virtual image converted from gene expression information and spatial coordinates of spots. The dilation rates and kernel sizes are set appropriately and updating of weight values in the kernels is made to be subject to the spatial distance from the position of corresponding elements to kernel centers so that feature extraction of each spot is better guided by spatial distance to neighbor spots. Self-supervision realized by Kullback-Leibler (KL) divergence, spatial continuity loss and cross entropy calculated among spots with high confidence pseudo-labels make up the training objective of DCF. STGIC attains state-of-the-art (SOTA) clustering performance on the benchmark dataset of 10x Visium human dorsolateral prefrontal cortex (DLPFC). Besides, it's capable of depicting fine structures of other tissues from other species as well as guiding the identification of marker genes. Also, STGIC is expandable to Stereo-seq data with high spatial resolution.
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Affiliation(s)
- Chen Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Junhui Gao
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Yu Chen
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Lingxin Kong
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guangshuo Cao
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang
| | - Xiangyu Guo
- Smart-Health Initiative, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Wei Liu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Bin Ren
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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11
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Yuan M, Wan H, Wang Z, Guo Q, Deng M. SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data. Brief Bioinform 2024; 25:bbad533. [PMID: 38279647 PMCID: PMC10818138 DOI: 10.1093/bib/bbad533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/13/2023] [Accepted: 12/19/2023] [Indexed: 01/28/2024] Open
Abstract
MOTIVATION The rapid development of spatial transcriptome technologies has enabled researchers to acquire single-cell-level spatial data at an affordable price. However, computational analysis tools, such as annotation tools, tailored for these data are still lacking. Recently, many computational frameworks have emerged to integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics datasets. While some frameworks can utilize well-annotated scRNA-seq data to annotate spatial expression patterns, they overlook critical aspects. First, existing tools do not explicitly consider cell type mapping when aligning the two modalities. Second, current frameworks lack the capability to detect novel cells, which remains a key interest for biologists. RESULTS To address these problems, we propose an annotation method for spatial transcriptome data called SPANN. The main tasks of SPANN are to transfer cell-type labels from well-annotated scRNA-seq data to newly generated single-cell resolution spatial transcriptome data and discover novel cells from spatial data. The major innovations of SPANN come from two aspects: SPANN automatically detects novel cells from unseen cell types while maintaining high annotation accuracy over known cell types. SPANN finds a mapping between spatial transcriptome samples and RNA data prototypes and thus conducts cell-type-level alignment. Comprehensive experiments using datasets from various spatial platforms demonstrate SPANN's capabilities in annotating known cell types and discovering novel cell states within complex tissue contexts. AVAILABILITY The source code of SPANN can be accessed at https://github.com/ddb-qiwang/SPANN-torch. CONTACT dengmh@math.pku.edu.cn.
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Affiliation(s)
- Musu Yuan
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Hui Wan
- School of Mathematical Sciences, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Zihao Wang
- Biomedical Interdisciplinary Research Center, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Qirui Guo
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
- School of Mathematical Sciences, Peking University, Yiheyuan Road, 100871, Beijing, China
- Center for Statistical Science, Peking University, Yiheyuan Road, 100871, Beijing, China
- Biomedical Interdisciplinary Research Center, Peking University, Yiheyuan Road, 100871, Beijing, China
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12
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Hu Y, Xiao K, Yang H, Liu X, Zhang C, Shi Q. Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics. Brief Bioinform 2024; 25:bbae016. [PMID: 38324623 PMCID: PMC10849194 DOI: 10.1093/bib/bbae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/29/2023] [Indexed: 02/09/2024] Open
Abstract
Recent advances in spatially resolved transcriptomics (SRT) have brought ever-increasing opportunities to characterize expression landscape in the context of tissue spatiality. Nevertheless, there still exist multiple challenges to accurately detect spatial functional regions in tissue. Here, we present a novel contrastive learning framework, SPAtially Contrastive variational AutoEncoder (SpaCAE), which contrasts transcriptomic signals of each spot and its spatial neighbors to achieve fine-grained tissue structures detection. By employing a graph embedding variational autoencoder and incorporating a deep contrastive strategy, SpaCAE achieves a balance between spatial local information and global information of expression, enabling effective learning of representations with spatial constraints. Particularly, SpaCAE provides a graph deconvolutional decoder to address the smoothing effect of local spatial structure on expression's self-supervised learning, an aspect often overlooked by current graph neural networks. We demonstrated that SpaCAE could achieve effective performance on SRT data generated from multiple technologies for spatial domains identification and data denoising, making it a remarkable tool to obtain novel insights from SRT studies.
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Affiliation(s)
- Yaofeng Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024; University of Chinese Academy of Sciences, China
| | - Kai Xiao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hengyu Yang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024; University of Chinese Academy of Sciences, China
| | - Xiaoping Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024; University of Chinese Academy of Sciences, China
| | - Chuanchao Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024; University of Chinese Academy of Sciences, China
| | - Qianqian Shi
- Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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13
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Kiessling P, Kuppe C. Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases. Genome Med 2024; 16:14. [PMID: 38238823 PMCID: PMC10795303 DOI: 10.1186/s13073-024-01282-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches. We discuss the advancements in low-resolution and high-resolution spatial multi-omics methods which can resolve up to 10,000 of individual molecules at subcellular level. By applying and integrating these techniques, researchers have recently gained valuable insights into the molecular circuits and mechanisms which govern cell biology along the cardiovascular disease spectrum. We provide an overview of current data analysis approaches, with a focus on data integration of multi-omic datasets, highlighting strengths and weaknesses of various computational pipelines. These tools play a crucial role in analyzing and interpreting spatial multi-omics datasets, facilitating the discovery of new findings, and enhancing translational cardiovascular research. Despite nontrivial challenges, such as the need for standardization of experimental setups, data analysis, and improved computational tools, the application of spatial multi-omics holds tremendous potential in revolutionizing our understanding of human disease processes and the identification of novel biomarkers and therapeutic targets. Exciting opportunities lie ahead for the spatial multi-omics field and will likely contribute to the advancement of personalized medicine for cardiovascular diseases.
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Affiliation(s)
- Paul Kiessling
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Kuppe
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany.
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14
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Deng Y, Lu Y, Li M, Shen J, Qin S, Zhang W, Zhang Q, Shen Z, Li C, Jia T, Chen P, Peng L, Chen Y, Zhang W, Liu H, Zhang L, Rong L, Wang X, Chen D. SCAN: Spatiotemporal Cloud Atlas for Neural cells. Nucleic Acids Res 2024; 52:D998-D1009. [PMID: 37930842 PMCID: PMC10767991 DOI: 10.1093/nar/gkad895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
The nervous system is one of the most complicated and enigmatic systems within the animal kingdom. Recently, the emergence and development of spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq) technologies have provided an unprecedented ability to systematically decipher the cellular heterogeneity and spatial locations of the nervous system from multiple unbiased aspects. However, efficiently integrating, presenting and analyzing massive multiomic data remains a huge challenge. Here, we manually collected and comprehensively analyzed high-quality scRNA-seq and ST data from the nervous system, covering 10 679 684 cells. In addition, multi-omic datasets from more than 900 species were included for extensive data mining from an evolutionary perspective. Furthermore, over 100 neurological diseases (e.g. Alzheimer's disease, Parkinson's disease, Down syndrome) were systematically analyzed for high-throughput screening of putative biomarkers. Differential expression patterns across developmental time points, cell types and ST spots were discerned and subsequently subjected to extensive interpretation. To provide researchers with efficient data exploration, we created a new database with interactive interfaces and integrated functions called the Spatiotemporal Cloud Atlas for Neural cells (SCAN), freely accessible at http://47.98.139.124:8799 or http://scanatlas.net. SCAN will benefit the neuroscience research community to better exploit the spatiotemporal atlas of the neural system and promote the development of diagnostic strategies for various neurological disorders.
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Affiliation(s)
- Yushan Deng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yubao Lu
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Mengrou Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Jiayi Shen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Siying Qin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wei Zhang
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Qiang Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Zhaoyang Shen
- Life Sciences and Technology College, China Pharmaceutical University, Nanjing 211198, China
| | - Changxiao Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Tengfei Jia
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Peixin Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Lingmin Peng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yangfeng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wensheng Zhang
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Liangming Zhang
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai 200000, China
| | - Dongsheng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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15
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Xu Z, Wang W, Yang T, Li L, Ma X, Chen J, Wang J, Huang Y, Gould J, Lu H, Du W, Sahu SK, Yang F, Li Z, Hu Q, Hua C, Hu S, Liu Y, Cai J, You L, Zhang Y, Li Y, Zeng W, Chen A, Wang B, Liu L, Chen F, Ma K, Xu X, Wei X. STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization. Nucleic Acids Res 2024; 52:D1053-D1061. [PMID: 37953328 PMCID: PMC10767841 DOI: 10.1093/nar/gkad933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023] Open
Abstract
Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.
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Affiliation(s)
- Zhicheng Xu
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Weiwen Wang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Ling Li
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Xizheng Ma
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Jing Chen
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Jieyu Wang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Yan Huang
- BGI Research, Shenzhen 518083, China
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | | | - Fan Yang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | | | - Qingjiang Hu
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Cong Hua
- BGI Research, Wuhan 430074, China
| | - Shoujie Hu
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Yiqun Liu
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Jia Cai
- BGI Research, Wuhan 430074, China
| | - Lijin You
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | | | | | - Wenjun Zeng
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Ao Chen
- BGI Research, Shenzhen 518083, China
| | - Bo Wang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | | | | | - Kailong Ma
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Xun Xu
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI research, Shenzhen 518120, China
| | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen 518120, China
- Guangdong Provincial Genomics Data Center, BGI research, Shenzhen 518120, China
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16
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Yamashita N, Kramann R. Mechanisms of kidney fibrosis and routes towards therapy. Trends Endocrinol Metab 2024; 35:31-48. [PMID: 37775469 DOI: 10.1016/j.tem.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]
Abstract
Kidney fibrosis is the final common pathway of virtually all chronic kidney diseases (CKDs) and is therefore considered to be a promising therapeutic target for these conditions. However, despite great progress in recent years, no targeted antifibrotic therapies for the kidney have been approved, likely because the complex mechanisms that initiate and drive fibrosis are not yet completely understood. Recent single-cell genomic approaches have allowed novel insights into kidney fibrosis mechanisms in mouse and human, particularly the heterogeneity and differentiation processes of myofibroblasts, the role of injured epithelial cells and immune cells, and their crosstalk mechanisms. In this review we summarize the key mechanisms that drive kidney fibrosis, including recent advances in understanding the mechanisms, as well as potential routes for developing novel targeted antifibrotic therapeutics.
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Affiliation(s)
- Noriyuki Yamashita
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology, and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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17
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Su J, Reynier JB, Fu X, Zhong G, Jiang J, Escalante RS, Wang Y, Aparicio L, Izar B, Knowles DA, Rabadan R. Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data. Genome Biol 2023; 24:291. [PMID: 38110959 PMCID: PMC10726548 DOI: 10.1186/s13059-023-03138-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution reveals plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allows for spatial mapping of reference populations with significantly reduced ambiguity.
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Affiliation(s)
- Jiayu Su
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Jean-Baptiste Reynier
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Xi Fu
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Guojie Zhong
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Jiahao Jiang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Yiping Wang
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Luis Aparicio
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Benjamin Izar
- Program for Mathematical Genomics, Columbia University, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Knowles
- Department of Systems Biology, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
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18
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Yin R, Xia K, Xu X. Spatial transcriptomics drives a new era in plant research. Plant J 2023; 116:1571-1581. [PMID: 37651723 DOI: 10.1111/tpj.16437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
SUMMARYThe plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.
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Affiliation(s)
- Ruilian Yin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
| | - Keke Xia
- BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518120, China
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19
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Li Q, Wang Y, Ji L, He J, Liu H, Xue W, Yue H, Dong R, Liu X, Wang D, Zhang H. Cellular and molecular mechanisms of fibrosis and resolution in bleomycin-induced pulmonary fibrosis mouse model revealed by spatial transcriptome analysis. Heliyon 2023; 9:e22461. [PMID: 38125541 PMCID: PMC10730595 DOI: 10.1016/j.heliyon.2023.e22461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
The bleomycin-induced pulmonary fibrosis mouse model is commonly used in idiopathic pulmonary fibrosis research, but its cellular and molecular changes and efficiency as a model at the molecular level are not fully understood. In this study, we used spatial transcriptome technology to investigate the cellular and molecular changes in the lungs of bleomycin-induced pulmonary fibrosis mouse models. Our analyses revealed cell dynamics during fibrosis in epithelial cells, mesenchymal cells, immunocytes, and erythrocytes with their spatial distribution available. We confirmed the differentiation of the alveolar type II (AT2) cell type expressing Krt8, and we inferred their trajectories from both the AT2 cells and club cells. In addition to the fibrosis process, we also noticed evidence of self-resolving, especially to identify possible self-resolving related genes, including Prkca. Our findings provide insights into the cellular and molecular mechanisms underlying fibrosis resolution and represent the first spatiotemporal transcriptome dataset of the bleomycin-induced fibrosis mouse model.
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Affiliation(s)
| | - Yue Wang
- BGI-Beijing, Beijing 102601, China
| | - Liu Ji
- Dalian Maternal and Child Health Hospital of Liaoning Province, Dalian 116033, China
| | - Jianhan He
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | | | | | - Huihui Yue
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Ruihan Dong
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Xin Liu
- BGI-Beijing, Beijing 102601, China
| | - Daqing Wang
- Dalian Maternal and Child Health Hospital of Liaoning Province, Dalian 116033, China
| | - Huilan Zhang
- Department of Clinical Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
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20
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Sun T, Grassam-Rowe A, Pu Z, Li Y, Ren H, An Y, Guo X, Hu W, Liu Y, Zheng Y, Liu Z, Kou K, Ou X, Chen T, Fan X, Liu Y, Tu S, He Y, Ren Y, Chen A, Shang Z, Xia Z, Miquerol L, Smart N, Zhang H, Tan X, Shou W, Lei M. Dbh + catecholaminergic cardiomyocytes contribute to the structure and function of the cardiac conduction system in murine heart. Nat Commun 2023; 14:7801. [PMID: 38016975 PMCID: PMC10684617 DOI: 10.1038/s41467-023-42658-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
The heterogeneity of functional cardiomyocytes arises during heart development, which is essential to the complex and highly coordinated cardiac physiological function. Yet the biological and physiological identities and the origin of the specialized cardiomyocyte populations have not been fully comprehended. Here we report a previously unrecognised population of cardiomyocytes expressing Dbhgene encoding dopamine beta-hydroxylase in murine heart. We determined how these myocytes are distributed across the heart by utilising advanced single-cell and spatial transcriptomic analyses, genetic fate mapping and molecular imaging with computational reconstruction. We demonstrated that they form the key functional components of the cardiac conduction system by using optogenetic electrophysiology and conditional cardiomyocyte Dbh gene deletion models. We revealed their close relationship with sympathetic innervation during cardiac conduction system formation. Our study thus provides new insights into the development and heterogeneity of the mammalian cardiac conduction system by revealing a new cardiomyocyte population with potential catecholaminergic endocrine function.
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Affiliation(s)
- Tianyi Sun
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | | | - Zhaoli Pu
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Yangpeng Li
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Huiying Ren
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Yanru An
- BGI Research, Shenzhen, 518103, China
| | - Xinyu Guo
- BGI Research, Qingdao, 266555, China
| | - Wei Hu
- Department of Physics & Astronomy, The University of Manchester, Brunswick Street, Manchester, M13 9PL, UK
| | - Ying Liu
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, USA
| | - Yuqing Zheng
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Zhu Liu
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Kun Kou
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xianhong Ou
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Tangting Chen
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xuehui Fan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Yangyang Liu
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, USA
| | - Shu Tu
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Yu He
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Yue Ren
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Ao Chen
- BGI Research, Shenzhen, 518103, China
| | | | - Zhidao Xia
- Centre for Nanohealth, Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Lucile Miquerol
- Aix Marseille University, CNRS Institut de Biologie du Développement de Marseille UMR 7288, 13288, Marseille, France
| | - Nicola Smart
- Department of Physiology, Anatomy & Genetics, Sherrington Building, Oxford, University of, Oxford, OX1 3PT, UK
| | - Henggui Zhang
- Department of Physics & Astronomy, The University of Manchester, Brunswick Street, Manchester, M13 9PL, UK
- Beijing Academy of Artificial Intelligence, 100084, Beijing, China
| | - Xiaoqiu Tan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China.
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China.
| | - Weinian Shou
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, USA.
| | - Ming Lei
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China.
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21
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Fang Z, Liu T, Zheng R, A J, Yin M, Li M. stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics. Brief Bioinform 2023; 25:bbad500. [PMID: 38189544 PMCID: PMC10772985 DOI: 10.1093/bib/bbad500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
With the development of spatially resolved transcriptomics technologies, it is now possible to explore the gene expression profiles of single cells while preserving their spatial context. Spatial clustering plays a key role in spatial transcriptome data analysis. In the past 2 years, several graph neural network-based methods have emerged, which significantly improved the accuracy of spatial clustering. However, accurately identifying the boundaries of spatial domains remains a challenging task. In this article, we propose stAA, an adversarial variational graph autoencoder, to identify spatial domain. stAA generates cell embedding by leveraging gene expression and spatial information using graph neural networks and enforces the distribution of cell embeddings to a prior distribution through Wasserstein distance. The adversarial training process can make cell embeddings better capture spatial domain information and more robust. Moreover, stAA incorporates global graph information into cell embeddings using labels generated by pre-clustering. Our experimental results show that stAA outperforms the state-of-the-art methods and achieves better clustering results across different profiling platforms and various resolutions. We also conducted numerous biological analyses and found that stAA can identify fine-grained structures in tissues, recognize different functional subtypes within tumors and accurately identify developmental trajectories.
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Affiliation(s)
- Zhaoyu Fang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Teng Liu
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404031, China
- Translational Medicine Research Center (TMRC), School of Medicine, Chongqing University, Chongqing 401331, China
| | - Ruiqing Zheng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Jin A
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Mingzhu Yin
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404031, China
- Translational Medicine Research Center (TMRC), School of Medicine, Chongqing University, Chongqing 401331, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
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22
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Benotmane JK, Kueckelhaus J, Will P, Zhang J, Ravi VM, Joseph K, Sankowski R, Beck J, Lee-Chang C, Schnell O, Heiland DH. High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq. Nat Commun 2023; 14:7432. [PMID: 37973846 PMCID: PMC10654577 DOI: 10.1038/s41467-023-43201-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Spatial resolution of the T cell repertoire is essential for deciphering cancer-associated immune dysfunction. Current spatially resolved transcriptomic technologies are unable to directly annotate T cell receptors (TCR). We present spatially resolved T cell receptor sequencing (SPTCR-seq), which integrates optimized target enrichment and long-read sequencing for highly sensitive TCR sequencing. The SPTCR computational pipeline achieves yield and coverage per TCR comparable to alternative single-cell TCR technologies. Our comparison of PCR-based and SPTCR-seq methods underscores SPTCR-seq's superior ability to reconstruct the entire TCR architecture, including V, D, J regions and the complementarity-determining region 3 (CDR3). Employing SPTCR-seq, we assess local T cell diversity and clonal expansion across spatially discrete niches. Exploration of the reciprocal interaction of the tumor microenvironmental and T cells discloses the critical involvement of NK and B cells in T cell exhaustion. Integrating spatially resolved omics and TCR sequencing provides as a robust tool for exploring T cell dysfunction in cancers and beyond.
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Affiliation(s)
- Jasim Kada Benotmane
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
| | - Jan Kueckelhaus
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
| | - Paulina Will
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
| | - Junyi Zhang
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
| | - Vidhya M Ravi
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
- Translational NeuroOncology Research Group, Medical Center-University of Freiburg, Freiburg, Germany
| | - Kevin Joseph
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany
- Translational NeuroOncology Research Group, Medical Center-University of Freiburg, Freiburg, Germany
- Center for NeuroModulation (NeuroModul), University of Freiburg, Freiburg, Germany
| | - Roman Sankowski
- Institute of Neuropathology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Catalina Lee-Chang
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Translational NeuroOncology Research Group, Medical Center-University of Freiburg, Freiburg, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, Freiburg University, Freiburg, Germany.
- Microenvironment and Immunology Research Laboratory, Medical Center-University of Freiburg, Freiburg, Germany.
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany.
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23
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Tibi M, Biton Hayun S, Hochgerner H, Lin Z, Givon S, Ophir O, Shay T, Mueller T, Segev R, Zeisel A. A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types. Sci Adv 2023; 9:eadh7693. [PMID: 37910612 PMCID: PMC10619943 DOI: 10.1126/sciadv.adh7693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Teleost fish form the largest group of vertebrates and show a tremendous variety of adaptive behaviors, making them critically important for the study of brain evolution and cognition. The neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon. We mapped cell types using single-cell RNA sequencing and spatial transcriptomics, resulting in de novo molecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly conserved goldfish homologs. We suggest elements of a hippocampal formation across the goldfish pallium. Last, aiding study of the teleostan everted telencephalon, we describe substantial molecular similarities between goldfish and zebrafish neuronal taxonomies.
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Affiliation(s)
- Muhammad Tibi
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Stav Biton Hayun
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Zhige Lin
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Shachar Givon
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Osnat Ophir
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Thomas Mueller
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
| | - Ronen Segev
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
- The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
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24
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Demircan T, Süzek BE. The Dynamic Landscapes of Circular RNAs in Axolotl, a Regenerative Medicine Model, with Implications for Early Phase of Limb Regeneration. OMICS 2023; 27:526-535. [PMID: 37943672 DOI: 10.1089/omi.2023.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Circular RNAs (circRNAs) are of relevance to regenerative medicine and play crucial roles in post-transcriptional and translational regulation of biological processes. circRNAs are a class of RNA molecules that are formed through a unique splicing process, resulting in a covalently closed-loop structure. Recent advancements in RNA sequencing technologies and specialized computational tools have facilitated the identification and functional characterization of circRNAs. These molecules are known to exhibit stability, developmental regulation, and specific expression patterns in different tissues and cell types across various organisms. However, our understanding of circRNA expression and putative function in model organisms for regeneration is limited. In this context, this study reports, for the first time, on the repertoire of circRNAs in axolotl, a widely used model organism for regeneration. We generated RNA-seq data from intact limb, wound, and blastema tissues of axolotl during limb regeneration. The analysis revealed the presence of 35,956 putative axolotl circRNAs, among which 5331 unique circRNAs exhibited orthology with human circRNAs. In silico data analysis underlined the potential roles of axolotl circRNAs in cell cycle, cell death, and cell senescence-related pathways during limb regeneration, suggesting the participation of circRNAs in regulation of diverse functions pertinent to regenerative medicine. These new observations help advance our understanding of the dynamic landscape of axolotl circRNAs, and by extension, inform future regenerative medicine research and innovation that harness this model organism.
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Affiliation(s)
- Turan Demircan
- Medical Biology Department, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
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25
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Lu A, Li K, Su G, Yang P. Revealing Academic Evolution and Frontier Pattern in the Field of Uveitis Using Bibliometric Analysis, Natural Language Processing, and Machine Learning. Ocul Immunol Inflamm 2023:1-16. [PMID: 38427350 DOI: 10.1080/09273948.2023.2262028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 03/02/2024]
Abstract
PURPOSE Numerous uveitis articles were published in this century, underneath which hides valuable intelligence. We aimed to characterize the evolution and patterns in this field. METHODS We divided the 15,994 uveitis papers into four consecutive time periods for bibliometric analysis, and applied latent Dirichlet allocation topic modeling and machine learning techniques to the latest period. . RESULTS The yearly publication pattern fitted the curve: 1.21335x2 - 4,848.95282x + 4,844,935.58876 (R2 = 0.98311). The USA, the most productive country/region, focused on topics like ankylosing spondylitis and biologic therapy, whereas China (mainland) focused on topics like OCT and Behcet disease. The logistic regression showed the highest accuracy (71.6%) in the test set. CONCLUSION In this century, a growing number of countries/regions/authors/journals are involved in the uveitis study, promoting the scientific output and thematic evolution. Our pioneering study uncovers the evolving academic trends and frontier patterns in this field using bibliometric analysis and AI algorithms.
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Affiliation(s)
- Ao Lu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Keyan Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
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26
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Rahman MN, Noman AA, Turza AM, Abrar MA, Samee MAH, Rahman MS. ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data. Bioinformatics 2023; 39:btad594. [PMID: 37756699 PMCID: PMC10564617 DOI: 10.1093/bioinformatics/btad594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 09/03/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
MOTIVATION Spatial domain identification is a very important problem in the field of spatial transcriptomics. The state-of-the-art solutions to this problem focus on unsupervised methods, as there is lack of data for a supervised learning formulation. The results obtained from these methods highlight significant opportunities for improvement. RESULTS In this article, we propose a potential avenue for enhancement through the development of a semi-supervised convolutional neural network based approach. Named "ScribbleDom", our method leverages human expert's input as a form of semi-supervision, thereby seamlessly combines the cognitive abilities of human experts with the computational power of machines. ScribbleDom incorporates a loss function that integrates two crucial components: similarity in gene expression profiles and adherence to the valuable input of a human annotator through scribbles on histology images, providing prior knowledge about spot labels. The spatial continuity of the tissue domains is taken into account by extracting information on the spot microenvironment through convolution filters of varying sizes, in the form of "Inception" blocks. By leveraging this semi-supervised approach, ScribbleDom significantly improves the quality of spatial domains, yielding superior results both quantitatively and qualitatively. Our experiments on several benchmark datasets demonstrate the clear edge of ScribbleDom over state-of-the-art methods-between 1.82% to 169.38% improvements in adjusted Rand index for 9 of the 12 human dorsolateral prefrontal cortex samples, and 15.54% improvement in the melanoma cancer dataset. Notably, when the expert input is absent, ScribbleDom can still operate, in a fully unsupervised manner like the state-of-the-art methods, and produces results that remain competitive. AVAILABILITY AND IMPLEMENTATION Source code is available at Github (https://github.com/1alnoman/ScribbleDom) and Zenodo (https://zenodo.org/badge/latestdoi/681572669).
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Affiliation(s)
- Mohammad Nuwaisir Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Abdullah Al Noman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Abir Mohammad Turza
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Mohammed Abid Abrar
- Department of Computer Science and Engineering, Brac University, Dhaka 1212, Bangladesh
| | - Md Abul Hassan Samee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - M Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
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27
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Li Z, Chen X, Zhang X, Jiang R, Chen S. Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics. Genome Res 2023; 33:1757-1773. [PMID: 37903634 PMCID: PMC10691543 DOI: 10.1101/gr.277891.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/19/2023] [Indexed: 11/01/2023]
Abstract
Rapid advances in spatial transcriptomics (ST) have revolutionized the interrogation of spatial heterogeneity and increase the demand for comprehensive methods to effectively characterize spatial domains. As a prerequisite for ST data analysis, spatial domain characterization is a crucial step for downstream analyses and biological implications. Here we propose a prior-based self-attention framework for spatial transcriptomics (PAST), a variational graph convolutional autoencoder for ST, which effectively integrates prior information via a Bayesian neural network, captures spatial patterns via a self-attention mechanism, and enables scalable application via a ripple walk sampler strategy. Through comprehensive experiments on data sets generated by different technologies, we show that PAST can effectively characterize spatial domains and facilitate various downstream analyses, including ST visualization, spatial trajectory inference and pseudotime analysis. Also, we highlight the advantages of PAST for multislice joint embedding and automatic annotation of spatial domains in newly sequenced ST data. Compared with existing methods, PAST is the first ST method that integrates reference data to analyze ST data. We anticipate that PAST will open up new avenues for researchers to decipher ST data with customized reference data, which expands the applicability of ST technology.
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Affiliation(s)
- Zhen Li
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaoyang Chen
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China
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28
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Jung N, Kim TK. Spatial transcriptomics in neuroscience. Exp Mol Med 2023; 55:2105-2115. [PMID: 37779145 PMCID: PMC10618223 DOI: 10.1038/s12276-023-01093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 10/03/2023] Open
Abstract
The brain is one of the most complex living tissue types and is composed of an exceptional diversity of cell types displaying unique functional connectivity. Single-cell RNA sequencing (scRNA-seq) can be used to efficiently map the molecular identities of the various cell types in the brain by providing the transcriptomic profiles of individual cells isolated from the tissue. However, the lack of spatial context in scRNA-seq prevents a comprehensive understanding of how different configurations of cell types give rise to specific functions in individual brain regions and how each distinct cell is connected to form a functional unit. To understand how the various cell types contribute to specific brain functions, it is crucial to correlate the identities of individual cells obtained through scRNA-seq with their spatial information in intact tissue. Spatial transcriptomics (ST) can resolve the complex spatial organization of cell types in the brain and their connectivity. Various ST tools developed during the past decade based on imaging and sequencing technology have permitted the creation of functional atlases of the brain and have pulled the properties of neural circuits into ever-sharper focus. In this review, we present a summary of several ST tools and their applications in neuroscience and discuss the unprecedented insights these tools have made possible.
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Affiliation(s)
- Namyoung Jung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, 03722, Republic of Korea.
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29
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Lamanna F, Hervas-Sotomayor F, Oel AP, Jandzik D, Sobrido-Cameán D, Santos-Durán GN, Martik ML, Stundl J, Green SA, Brüning T, Mößinger K, Schmidt J, Schneider C, Sepp M, Murat F, Smith JJ, Bronner ME, Rodicio MC, Barreiro-Iglesias A, Medeiros DM, Arendt D, Kaessmann H. A lamprey neural cell type atlas illuminates the origins of the vertebrate brain. Nat Ecol Evol 2023; 7:1714-1728. [PMID: 37710042 PMCID: PMC10555824 DOI: 10.1038/s41559-023-02170-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The vertebrate brain emerged more than ~500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey-a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits-based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of cell types, tissue structures and gene expression programs of the ancestral vertebrate brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral brain was probably devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors in the jawed vertebrate lineage. Altogether, our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.
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Affiliation(s)
- Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | | | - A Phillip Oel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Department of Zoology, Comenius University, Bratislava, Slovakia
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gabriel N Santos-Durán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Megan L Martik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - María Celina Rodicio
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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30
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Feng W, Liu S, Deng Q, Fu S, Yang Y, Dai X, Wang S, Wang Y, Liu Y, Lin X, Pan X, Hao S, Yuan Y, Gu Y, Zhang X, Li H, Liu L, Liu C, Fei JF, Wei X. A scATAC-seq atlas of chromatin accessibility in axolotl brain regions. Sci Data 2023; 10:627. [PMID: 37709774 PMCID: PMC10502032 DOI: 10.1038/s41597-023-02533-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is an excellent model for investigating regeneration, the interaction between regenerative and developmental processes, comparative genomics, and evolution. The brain, which serves as the material basis of consciousness, learning, memory, and behavior, is the most complex and advanced organ in axolotl. The modulation of transcription factors is a crucial aspect in determining the function of diverse regions within the brain. There is, however, no comprehensive understanding of the gene regulatory network of axolotl brain regions. Here, we utilized single-cell ATAC sequencing to generate the chromatin accessibility landscapes of 81,199 cells from the olfactory bulb, telencephalon, diencephalon and mesencephalon, hypothalamus and pituitary, and the rhombencephalon. Based on these data, we identified key transcription factors specific to distinct cell types and compared cell type functions across brain regions. Our results provide a foundation for comprehensive analysis of gene regulatory programs, which are valuable for future studies of axolotl brain development, regeneration, and evolution, as well as on the mechanisms underlying cell-type diversity in vertebrate brains.
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Affiliation(s)
- Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Sulei Fu
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Yunzhi Yang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Dai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yijin Wang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yang Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiangyu Pan
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- Guangdong Cardiovsacular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yue Yuan
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Hanbo Li
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI-Qingdao, Qingdao, 266555, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
| | - Longqi Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Xiaoyu Wei
- BGI-Hangzhou, Hangzhou, 310012, China.
- BGI-Shenzhen, Shenzhen, 518103, China.
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31
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Cheng M, Jiang Y, Xu J, Mentis AFA, Wang S, Zheng H, Sahu SK, Liu L, Xu X. Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges. J Genet Genomics 2023; 50:625-640. [PMID: 36990426 DOI: 10.1016/j.jgg.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology, from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing, by which the scientific community has been able to visualize life at an unprecedented resolution. Most recently, the Spatially Resolved Transcriptomics (SRT) technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life, including the origin of different cellular populations developed from totipotent cells and human diseases. In this review, we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools, as well as the representative SRT applications. With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects, we can foresee the bright future of such new tools in understanding life at the most profound analytical level.
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Affiliation(s)
| | - Yujia Jiang
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China
| | | | | | - Shuai Wang
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, Guangdong 518103, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Longqi Liu
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xun Xu
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China; BGI-Shenzhen, Shenzhen, Guangdong 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, Guangdong 518120, China.
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Chen L, Li J, Ou Y, Kang M, Deng J, Wang Y, Liang S, Hong X, Gong S, Fei JF, Hou FF, Zhang F. The axolotl kidney: a novel model to study kidney regeneration. Kidney Int 2023; 104:599-604. [PMID: 37290601 DOI: 10.1016/j.kint.2023.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/06/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Liting Chen
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Jing Li
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Yanping Ou
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Meixia Kang
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Juan Deng
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Youliang Wang
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Shiting Liang
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Xizhen Hong
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Siqiao Gong
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China
| | - Ji-Feng Fei
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Fan Fan Hou
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China.
| | - Fujian Zhang
- Division of Nephrology, Nanfang Hospital, Southern Medical University; National Clinical Research Center for Kidney Disease; State Key Laboratory of Organ Failure Research; Guangdong Provincial Institute of Nephrology; Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou, China.
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Dong M, Kluger H, Fan R, Kluger Y. SIMVI reveals intrinsic and spatial-induced states in spatial omics data. bioRxiv 2023:2023.08.28.554970. [PMID: 37693629 PMCID: PMC10491129 DOI: 10.1101/2023.08.28.554970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Spatial omics analyze gene expression and interaction dynamics in relation to tissue structure and function. However, existing methods cannot model the intrinsic and spatial-induced variation in spatial omics data, thus failing to identify true spatial interaction effects. Here, we present Spatial Interaction Modeling using Variational Inference (SIMVI), an annotation-free framework that disentangles cell intrinsic and spatial-induced latent variables for modeling gene expression in spatial omics data. SIMVI enables novel downstream analyses, such as clustering and differential expression analysis based on disentangled representations, spatial effect (SE) identification, SE interpretation, and transfer learning on new measurements / modalities. We benchmarked SIMVI on both simulated and real datasets and show that SIMVI uniquely generates highly accurate SE inferences in synthetic datasets and unveils intrinsic variation in complex real datasets. We applied SIMVI to spatial omics data from diverse platforms and tissues (MERFISH human cortex / mouse liver, Slide-seqv2 mouse hippocampus, Spatial-ATAC-RNA-seq) and revealed various region-specific and cell-type-specific spatial interactions. In addition, our experiments on MERFISH human cortex and spatial-ATAC-RNA-seq showcased SIMVI's power in identifying SEs for new samples / modalities. Finally, we applied SIMVI on a newly collected CosMx melanoma dataset. Using SIMVI, we identified immune cells associated with spatial-dependent interactions and revealed the underlying spatial variations associated with patient outcomes.
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Affiliation(s)
- Mingze Dong
- Interdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Harriet Kluger
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Rong Fan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Yuval Kluger
- Interdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
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34
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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Abstract
Spatial transcriptomic technologies enable measurement of expression levels of genes systematically throughout tissue space, deepening our understanding of cellular organizations and interactions within tissues as well as illuminating biological insights in neuroscience, developmental biology and a range of diseases, including cancer. A variety of spatial technologies have been developed and/or commercialized, differing in spatial resolution, sensitivity, multiplexing capability, throughput and coverage. In this paper, we review key enabling spatial transcriptomic technologies and their applications as well as the perspective of the techniques and new emerging technologies that are developed to address current limitations of spatial methodologies. In addition, we describe how spatial transcriptomics data can be integrated with other omics modalities, complementing other methods in deciphering cellar interactions and phenotypes within tissues as well as providing novel insight into tissue organization.
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Affiliation(s)
- Tsai-Ying Chen
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (T.-Y.C.); (L.Y.)
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Li You
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (T.-Y.C.); (L.Y.)
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Jose Angelito U. Hardillo
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Department of Otorhinolaryngology, Head and Neck Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (T.-Y.C.); (L.Y.)
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Department of Otorhinolaryngology, Head and Neck Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
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38
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Hanafusa Y, Shiraishi A, Hattori F. Machine learning discriminates P2X7-mediated intracellular calcium sparks in human-induced pluripotent stem cell-derived neural stem cells. Sci Rep 2023; 13:12673. [PMID: 37542080 PMCID: PMC10403609 DOI: 10.1038/s41598-023-39846-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Adenosine triphosphate (ATP) is an extracellular signaling molecule that mainly affects the pathophysiological situation in the body and can be sensed by purinergic receptors, including ionotropic P2X7. Neuronal stem cells (NSCs) remain in adult neuronal tissues and can contribute to physiological processes via activation by evoked pathophysiological situations. In this study, we revealed that human-induced pluripotent stem cell-derived NSCs (iNSCs) have ATP-sensing ability primarily via the purinergic and ionotropic receptor P2X7. Next, to develop a machine learning (ML)-based screening system for food-derived neuronal effective substances and their effective doses, we collected ATP-triggered calcium responses of iNSCs pretreated with several substances and doses. Finally, we discovered that ML was performed using composite images, each containing nine waveform images, to achieve a better ML model (MLM) with higher precision. Our MLM can correctly sort subtle unidentified changes in waveforms produced by pretreated iNSCs with each substance and/or dose into the positive group, with common mRNA expression changes belonging to the gene ontology signatures.
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Affiliation(s)
- Yuki Hanafusa
- Innovative Regenerative Medicine, Graduate School of Medicine, Kansai Medical University, Osaka, Japan
- Group Quality Assurance Division, Safety Science Institute, Suntory Holdings Ltd., Tokyo, Japan
| | - Akira Shiraishi
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Fumiyuki Hattori
- Innovative Regenerative Medicine, Graduate School of Medicine, Kansai Medical University, Osaka, Japan.
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Fangma Y, Liu M, Liao J, Chen Z, Zheng Y. Dissecting the brain with spatially resolved multi-omics. J Pharm Anal 2023; 13:694-710. [PMID: 37577383 PMCID: PMC10422112 DOI: 10.1016/j.jpha.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
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Affiliation(s)
- Yijia Fangma
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Mengting Liu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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Krieger KL, Mann EK, Lee KJ, Bolterstein E, Jebakumar D, Ittmann MM, Dal Zotto VL, Shaban M, Sreekumar A, Gassman NR. Spatial mapping of the DNA adducts in cancer. DNA Repair (Amst) 2023; 128:103529. [PMID: 37390674 PMCID: PMC10330576 DOI: 10.1016/j.dnarep.2023.103529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
DNA adducts and strand breaks are induced by various exogenous and endogenous agents. Accumulation of DNA damage is implicated in many disease processes, including cancer, aging, and neurodegeneration. The continuous acquisition of DNA damage from exogenous and endogenous stressors coupled with defects in DNA repair pathways contribute to the accumulation of DNA damage within the genome and genomic instability. While mutational burden offers some insight into the level of DNA damage a cell may have experienced and subsequently repaired, it does not quantify DNA adducts and strand breaks. Mutational burden also infers the identity of the DNA damage. With advances in DNA adduct detection and quantification methods, there is an opportunity to identify DNA adducts driving mutagenesis and correlate with a known exposome. However, most DNA adduct detection methods require isolation or separation of the DNA and its adducts from the context of the nuclei. Mass spectrometry, comet assays, and other techniques precisely quantify lesion types but lose the nuclear context and even tissue context of the DNA damage. The growth in spatial analysis technologies offers a novel opportunity to leverage DNA damage detection with nuclear and tissue context. However, we lack a wealth of techniques capable of detecting DNA damage in situ. Here, we review the limited existing in situ DNA damage detection methods and examine their potential to offer spatial analysis of DNA adducts in tumors or other tissues. We also offer a perspective on the need for spatial analysis of DNA damage in situ and highlight Repair Assisted Damage Detection (RADD) as an in situ DNA adduct technique with the potential to integrate with spatial analysis and the challenges to be addressed.
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Affiliation(s)
- Kimiko L Krieger
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
| | - Elise K Mann
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Kevin J Lee
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Elyse Bolterstein
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Deborah Jebakumar
- Department of Anatomic Pathology, Baylor Scott & White Medical Center, Temple, TX 76508, USA; Texas A&M College of Medicine, Temple, TX 76508, USA
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Human Tissue Acquisition & Pathology Shared Resource, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valeria L Dal Zotto
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Mohamed Shaban
- Department of Electrical and Computer Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natalie R Gassman
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Zou Q, Liu M, Liu K, Zhang Y, North BJ, Wang B. E3 ubiquitin ligases in cancer stem cells: key regulators of cancer hallmarks and novel therapeutic opportunities. Cell Oncol (Dordr) 2023; 46:545-570. [PMID: 36745329 PMCID: PMC10910623 DOI: 10.1007/s13402-023-00777-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human malignancies are composed of heterogeneous subpopulations of cancer cells with phenotypic and functional diversity. Among them, a unique subset of cancer stem cells (CSCs) has both the capacity for self-renewal and the potential to differentiate and contribute to multiple tumor properties. As such, CSCs are promising cellular targets for effective cancer therapy. At the molecular level, hyper-activation of multiple stemness regulatory signaling pathways and downstream transcription factors play critical roles in controlling CSCs establishment and maintenance. To regulate CSC properties, these stemness pathways are controlled by post-translational modifications including, but not limited to phosphorylation, acetylation, methylation, and ubiquitination. CONCLUSION In this review, we focus on E3 ubiquitin ligases and their roles and mechanisms in regulating essential hallmarks of CSCs, such as self-renewal, invasion and metastasis, metabolic reprogramming, immune evasion, and therapeutic resistance. Moreover, we discuss emerging therapeutic approaches to eliminate CSCs through targeting E3 ubiquitin ligases by chemical inhibitors and proteolysis-targeting chimera (PROTACs) which are currently under development at the discovery, preclinical, and clinical stages. Several outstanding issues such as roles for E3 ubiquitin ligases in heterogeneity and phenotypical/functional evolution of CSCs remain to be studied under pathologically and clinically relevant conditions. With the rapid application of functional genomic and proteomic approaches at single cell, spatiotemporal, and even single molecule levels, we anticipate that more specific and precise functions of E3 ubiquitin ligases will be delineated in dictating CSC properties. Rational design and proper translation of these mechanistic understandings may lead to novel therapeutic modalities for cancer procession medicine.
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Affiliation(s)
- Qiang Zou
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing University Medical School, Chongqing, 400030, People's Republic of China
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China
| | - Meng Liu
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China
- Department of Gastroenterology, Chongqing University Cancer Hospital, Chongqing University Medical School, Chongqing, 400030, People's Republic of China
| | - Kewei Liu
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China
| | - Yi Zhang
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing University Medical School, Chongqing, 400030, People's Republic of China.
| | - Brian J North
- Biomedical Sciences Department, Creighton University School of Medicine, Omaha, NE, 68178, USA.
| | - Bin Wang
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China.
- Institute of Pathology and Southwest Cancer Center, and Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, People's Republic of China.
- Jinfeng Laboratory, Chongqing, 401329, People's Republic of China.
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Park H, Jo SH, Lee RH, Macks CP, Ku T, Park J, Lee CW, Hur JK, Sohn CH. Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research. Adv Sci (Weinh) 2023; 10:e2206939. [PMID: 37026425 PMCID: PMC10238226 DOI: 10.1002/advs.202206939] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/10/2023] [Indexed: 06/04/2023]
Abstract
Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional biological studies to "in situ" biology, spatial transcriptomics can provide transcriptome-scale spatial information. Currently, the ability to simultaneously characterize gene expression profiles of cells and relevant cellular environment is a paradigm shift for biological studies. In this review, recent progress in spatial transcriptomics and its applications in neuroscience and cancer studies are highlighted. Technical aspects of existing technologies and future directions of new developments (as of March 2023), computational analysis of spatial transcriptome data, application notes in neuroscience and cancer studies, and discussions regarding future directions of spatial multi-omics and their expanding roles in biomedical applications are emphasized.
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Affiliation(s)
- Han‐Eol Park
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
- School of Biological SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Song Hyun Jo
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Rosalind H. Lee
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Christian P. Macks
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jihwan Park
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Chung Whan Lee
- Department of ChemistryGachon UniversitySeongnamGyeonggi‐do13120Republic of Korea
| | - Junho K. Hur
- Department of GeneticsCollege of MedicineHanyang UniversitySeoul04763Republic of Korea
| | - Chang Ho Sohn
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
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Chen M, Jiang J, Hou J. Single-cell technologies in multiple myeloma: new insights into disease pathogenesis and translational implications. Biomark Res 2023; 11:55. [PMID: 37259170 DOI: 10.1186/s40364-023-00502-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy characterized by clonal proliferation of plasma cells. Although therapeutic advances have been made to improve clinical outcomes and to prolong patients' survival in the past two decades, MM remains largely incurable. Single-cell sequencing (SCS) is a powerful method to dissect the cellular and molecular landscape at single-cell resolution, instead of providing averaged results. The application of single-cell technologies promises to address outstanding questions in myeloma biology and has revolutionized our understanding of the inter- and intra-tumor heterogeneity, tumor microenvironment, and mechanisms of therapeutic resistance in MM. In this review, we summarize the recently developed SCS methodologies and latest MM research progress achieved by single-cell profiling, including information regarding the cancer and immune cell landscapes, tumor heterogeneities, underlying mechanisms and biomarkers associated with therapeutic response and resistance. We also discuss future directions of applying transformative SCS approaches with contribution to clinical translation.
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Affiliation(s)
- Mengping Chen
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jinxing Jiang
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jian Hou
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Zhang Y, Mei Y, Cao A, Li S, He C, Song L, Gao J, Zhu Y, Cao X. Transcriptome analyses of betta fish (Betta splendens) provide novel insights into fin regeneration and color-related genes. Gene 2023:147508. [PMID: 37230203 DOI: 10.1016/j.gene.2023.147508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
The betta fish (Betta splendens), an important ornamental fish, haswell-developed and colorful fins.After fin amputation, betta fish can easily regenerate finssimilar to the originalsin terms of structureand color. The powerful fin regeneration ability and a variety of colors in the betta fish are fascinating. However, the underlying molecular mechanisms are still not fully understood. In this study, tail fin amputation and regeneration experiments were performed on two kinds of betta fish: red and white color betta fish. Then, transcriptome analyseswere conducted to screen out fin regeneration and color-relatedgenes in betta fish. Through enrichment analyses of differentially expressed genes (DEGs), we founda series of enrichment pathways and genes related to finregeneration, including cell cycle (i.e. plcg2), TGF-beta signaling pathway (i.e. bmp6), PI3K-Akt signaling pathway (i.e. loxl2aand loxl2b), Wnt signaling pathway(i.e. lef1), gap junctions (i.e. cx43), angiogenesis (i.e. foxp1), and interferon regulatory factor (i.e. irf8). Meanwhile, some fin color-related pathways and genes were identified in betta fish, especially melanogenesis (i.e. tyr, tyrp1a, tyrp1b, and mc1r) and carotenoid color genes (i.e. pax3, pax7, sox10, and ednrba). In conclusion, this studycan not only enrich the research onfish tissue regeneration, but also has a potential significance for the aquaculture and breeding of the betta fish.
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Affiliation(s)
- Yunbang Zhang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China
| | - Yihui Mei
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Aiying Cao
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Sen Li
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Chuan He
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Liyuan Song
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Gao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China
| | - Yurong Zhu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
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Cai X, Tacke F, Guillot A, Liu H. Cholangiokines: undervalued modulators in the hepatic microenvironment. Front Immunol 2023; 14:1192840. [PMID: 37261338 PMCID: PMC10229055 DOI: 10.3389/fimmu.2023.1192840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
Abstract
The biliary epithelial cells, also known as cholangiocytes, line the intra- and extrahepatic bile ducts, forming a barrier between intra- and extra-ductal environments. Cholangiocytes are mostly known to modulate bile composition and transportation. In hepatobiliary diseases, bile duct injury leads to drastic alterations in cholangiocyte phenotypes and their release of soluble mediators, which can vary depending on the original insult and cellular states (quiescence, senescence, or proliferation). The cholangiocyte-secreted cytokines (also termed cholangiokines) drive ductular cell proliferation, portal inflammation and fibrosis, and carcinogenesis. Hence, despite the previous consensus that cholangiocytes are bystanders in liver diseases, their diverse secretome plays critical roles in modulating the intrahepatic microenvironment. This review summarizes recent insights into the cholangiokines under both physiological and pathological conditions, especially as they occur during liver injury-regeneration, inflammation, fibrosis and malignant transformation processes.
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Affiliation(s)
- Xiurong Cai
- Department of Hematology, Oncology and Tumor Immunology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Adrien Guillot
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Hanyang Liu
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
- Center of Gastrointestinal Diseases, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, China
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Liu L, Qiu L, Zhu Y, Luo L, Han X, Man M, Li F, Ren M, Xing Y. Comparisons between Plant and Animal Stem Cells Regarding Regeneration Potential and Application. Int J Mol Sci 2023; 24. [PMID: 36901821 DOI: 10.3390/ijms24054392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Regeneration refers to the process by which organisms repair and replace lost tissues and organs. Regeneration is widespread in plants and animals; however, the regeneration capabilities of different species vary greatly. Stem cells form the basis for animal and plant regeneration. The essential developmental processes of animals and plants involve totipotent stem cells (fertilized eggs), which develop into pluripotent stem cells and unipotent stem cells. Stem cells and their metabolites are widely used in agriculture, animal husbandry, environmental protection, and regenerative medicine. In this review, we discuss the similarities and differences in animal and plant tissue regeneration, as well as the signaling pathways and key genes involved in the regulation of regeneration, to provide ideas for practical applications in agriculture and human organ regeneration and to expand the application of regeneration technology in the future.
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Wang S, Shibata Y, Fu L, Tanizaki Y, Luu N, Bao L, Peng Z, Shi YB. Thyroid hormone receptor knockout prevents the loss of Xenopus tail regeneration capacity at metamorphic climax. Cell Biosci 2023; 13:40. [PMID: 36823612 PMCID: PMC9948486 DOI: 10.1186/s13578-023-00989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Animal regeneration is the natural process of replacing or restoring damaged or missing cells, tissues, organs, and even entire body to full function. Studies in mammals have revealed that many organs lose regenerative ability soon after birth when thyroid hormone (T3) level is high. This suggests that T3 play an important role in organ regeneration. Intriguingly, plasma T3 level peaks during amphibian metamorphosis, which is very similar to postembryonic development in humans. In addition, many organs, such as heart and tail, also lose their regenerative ability during metamorphosis. These make frogs as a good model to address how the organs gradually lose their regenerative ability during development and what roles T3 may play in this. Early tail regeneration studies have been done mainly in the tetraploid Xenopus laevis (X. laevis), which is difficult for gene knockout studies. Here we use the highly related but diploid anuran X. tropicalis to investigate the role of T3 signaling in tail regeneration with gene knockout approaches. RESULTS We discovered that X. tropicalis tadpoles could regenerate their tail from premetamorphic stages up to the climax stage 59 then lose regenerative capacity as tail resorption begins, just like what observed for X. laevis. To test the hypothesis that T3-induced metamorphic program inhibits tail regeneration, we used TR double knockout (TRDKO) tadpoles lacking both TRα and TRβ, the only two receptor genes in vertebrates, for tail regeneration studies. Our results showed that TRs were not necessary for tail regeneration at all stages. However, unlike wild type tadpoles, TRDKO tadpoles retained regenerative capacity at the climax stages 60/61, likely in part by increasing apoptosis at the early regenerative period and enhancing subsequent cell proliferation. In addition, TRDKO animals had higher levels of amputation-induced expression of many genes implicated to be important for tail regeneration, compared to the non-regenerative wild type tadpoles at stage 61. Finally, the high level of apoptosis in the remaining uncut portion of the tail as wild type tadpoles undergo tail resorption after stage 61 appeared to also contribute to the loss of regenerative ability. CONCLUSIONS Our findings for the first time revealed an evolutionary conservation in the loss of tail regeneration capacity at metamorphic climax between X. laevis and X. tropicalis. Our studies with molecular and genetic approaches demonstrated that TR-mediated, T3-induced gene regulation program is responsible not only for tail resorption but also for the loss of tail regeneration capacity. Further studies by using the model should uncover how T3 modulates the regenerative outcome and offer potential new avenues for regenerative medicines toward human patients.
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Affiliation(s)
- Shouhong Wang
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yuki Shibata
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Biology, Nippon Medical School, Musashino, Tokyo, Japan
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nga Luu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Zhaoyi Peng
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an, People's Republic of China
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA.
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Schumacher D, Kramann R. Multiomic Spatial Mapping of Myocardial Infarction and Implications for Personalized Therapy. Arterioscler Thromb Vasc Biol 2023; 43:192-202. [PMID: 36579644 DOI: 10.1161/atvbaha.122.318333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ischemic heart disease including myocardial infarction is still the leading cause of death worldwide. Although the survival early after myocardial infarction has been significantly improved by the introduction of percutaneous coronary intervention, long-term morbidity and mortality remain high. The elevated long-term mortality is mainly driven by cardiac remodeling processes triggering ischemic heart failure and electric instability. Despite the new developments in pharmaco-therapy of heart failure, we still lack targeted therapies for cardiac remodeling and fibrosis. Single-cell and genomic technologies allow us to map the human heart at unprecedented resolution and allow to gain insights into cellular and molecular heterogeneity. However, these technologies rely on digested tissue and isolated cells or nuclei and thus lack spatial information. Spatial information is critical to understand tissue homeostasis and disease and can be utilized to identify disease-driving cell populations and mechanisms including cellular cross-talk. Here, we discuss recent advances in single-cell and spatial genomic technologies that give insights into cellular and molecular mechanisms of cardiac remodeling after injury and can be utilized to identify novel therapeutic targets and pave the way toward new therapies in heart failure.
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Affiliation(s)
- David Schumacher
- Institute of Experimental Medicine and Systems Biology (D.S., R.K.), RWTH Aachen University, Germany.,Department of Anesthesiology, University Hospital (D.S.), RWTH Aachen University, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology (D.S., R.K.), RWTH Aachen University, Germany.,Department of Nephrology and Clinical Immunology (R.K.), RWTH Aachen University, Germany.,Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, the Netherlands (R.K.)
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Pan XY, Zeng YY, Liu YM, Fei JF. Resolving vertebrate brain evolution through salamander brain development and regeneration. Zool Res 2023; 44:219-222. [PMID: 36594394 PMCID: PMC9841178 DOI: 10.24272/j.issn.2095-8137.2022.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Xiang-Yu Pan
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China,Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Yan-Yun Zeng
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Yan-Mei Liu
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, China.,Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, Guangdong 510631, China. E-mail:
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China.,School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China.,School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China. E-mail:
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Fu S, Peng C, Zeng YY, Qiu Y, Liu Y, Fei JF. Establishing an Efficient Electroporation-Based Method to Manipulate Target Gene Expression in the Axolotl Brain. Cell Transplant 2023; 32:9636897231200059. [PMID: 37724837 PMCID: PMC10510365 DOI: 10.1177/09636897231200059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The tetrapod salamander species axolotl (Ambystoma mexicanum) is capable of regenerating injured brain. For better understanding the mechanisms of brain regeneration, it is very necessary to establish a rapid and efficient gain-of-function and loss-of-function approaches to study gene function in the axolotl brain. Here, we establish and optimize an electroporation-based method to overexpress or knockout/knockdown target gene in ependymal glial cells (EGCs) in the axolotl telencephalon. By orientating the electrodes, we were able to achieve specific expression of EGFP in EGCs located in dorsal, ventral, medial, or lateral ventricular zones. We then studied the role of Cdc42 in brain regeneration by introducing Cdc42 into EGCs through electroporation, followed by brain injury. Our findings showed that overexpression of Cdc42 in EGCs did not significantly affect EGC proliferation and production of newly born neurons, but it disrupted their apical polarity, as indicated by the loss of the ZO-1 tight junction marker. This disruption led to a ventricular accumulation of newly born neurons, which are failed to migrate into the neuronal layer where they could mature, thus resulted in a delayed brain regeneration phenotype. Furthermore, when electroporating CAS9-gRNA protein complexes against TnC (Tenascin-C) into EGCs of the brain, we achieved an efficient knockdown of TnC. In the electroporation-targeted area, TnC expression is dramatically reduced at both mRNA and protein levels. Overall, this study established a rapid and efficient electroporation-based gene manipulation approach allowing for investigation of gene function in the process of axolotl brain regeneration.
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Affiliation(s)
- Sulei Fu
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Cheng Peng
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yan-Yun Zeng
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuanhui Qiu
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, China
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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