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Lin Y, Liang Y, Wang D, Chang Y, Ma Q, Wang Y, He F, Xu D. A contrastive learning approach to integrate spatial transcriptomics and histological images. Comput Struct Biotechnol J 2024; 23:1786-1795. [PMID: 38707535 PMCID: PMC11068546 DOI: 10.1016/j.csbj.2024.04.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, we present ConGcR, a contrastive learning-based model for integrating gene expression, spatial location, and tissue morphology for data representation and spatial tissue architecture identification. Graph convolution and ResNet were used as encoders for gene expression with spatial location and histological image inputs, respectively. We further enhanced ConGcR with a graph auto-encoder as ConGaR to better model spatially embedded representations. We validated our models using 16 human brains, four chicken hearts, eight breast tumors, and 30 human lung spatial transcriptomics samples. The results showed that our models generated more effective embeddings for obtaining tissue architectures closer to the ground truth than other methods. Overall, our models not only can improve tissue architecture identification's accuracy but also may provide valuable insights and effective data representation for other tasks in spatial transcriptome analyses.
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Affiliation(s)
- Yu Lin
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yanchun Liang
- School of Computer Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yuzhou Chang
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, United States
| | - Qin Ma
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, United States
| | - Yan Wang
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Fei He
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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Sun HJ, Lu QB, Zhu XX, Ni ZR, Su JB, Fu X, Chen G, Zheng GL, Nie XW, Bian JS. Pharmacology of Hydrogen Sulfide and Its Donors in Cardiometabolic Diseases. Pharmacol Rev 2024; 76:846-895. [PMID: 38866561 DOI: 10.1124/pharmrev.123.000928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/13/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
Cardiometabolic diseases (CMDs) are major contributors to global mortality, emphasizing the critical need for novel therapeutic interventions. Hydrogen sulfide (H2S) has garnered enormous attention as a significant gasotransmitter with various physiological, pathophysiological, and pharmacological impacts within mammalian cardiometabolic systems. In addition to its roles in attenuating oxidative stress and inflammatory response, burgeoning research emphasizes the significance of H2S in regulating proteins via persulfidation, a well known modification intricately associated with the pathogenesis of CMDs. This review seeks to investigate recent updates on the physiological actions of endogenous H2S and the pharmacological roles of various H2S donors in addressing diverse aspects of CMDs across cellular, animal, and clinical studies. Of note, advanced methodologies, including multiomics, intestinal microflora analysis, organoid, and single-cell sequencing techniques, are gaining traction due to their ability to offer comprehensive insights into biomedical research. These emerging approaches hold promise in characterizing the pharmacological roles of H2S in health and diseases. We will critically assess the current literature to clarify the roles of H2S in diseases while also delineating the opportunities and challenges they present in H2S-based pharmacotherapy for CMDs. SIGNIFICANCE STATEMENT: This comprehensive review covers recent developments in H2S biology and pharmacology in cardiometabolic diseases CMDs. Endogenous H2S and its donors show great promise for the management of CMDs by regulating numerous proteins and signaling pathways. The emergence of new technologies will considerably advance the pharmacological research and clinical translation of H2S.
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Affiliation(s)
- Hai-Jian Sun
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Qing-Bo Lu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Xue-Xue Zhu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Zhang-Rong Ni
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Jia-Bao Su
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Xiao Fu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Guo Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Guan-Li Zheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Xiao-Wei Nie
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Jin-Song Bian
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
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Lebedeva EA, Gonotkov MA, Furman AA, Velegzhaninov IO. Voltage-gated ion channel's gene expression in the myocardium of embryo and adult chickens. Dev Biol 2024; 516:130-137. [PMID: 39127438 DOI: 10.1016/j.ydbio.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
The functioning of the cardiovascular system is critical for embryo survival. Cardiac contractions depend on the sequential activation of different classes of voltage-gated ion channels. Understanding the fundamental features of these interactions is important for identifying the mechanisms of pathologies development in the myocardium. However, at present there is no consensus on which ion channels are involved in the formation of automaticity in the early embryonic stages. The aim of this study was to elucidate the expression of genes encoding various types of ion channels that are involved in the generation of electrical activity chicken heart at different stages of ontogenesis. We analyzed the expression of 14 genes from different families of ion channels. It was revealed that the expression profiles of ion channel genes change depending on the stages of ontogenesis. The HCN4, CACNA1D, SCN1A, SCN5A, KCNA1 genes have maximum expression at the tubular heart stage. In adult, a switch occurs to the higher expression of CACNA1C, KCNH6, RYR and SLC8A1 genes. This data correlated with the results obtained by the microelectrode method. It can be assumed that the automaticity of the tubular heart is mainly due to the mechanism of the «membrane-clock» (hyperpolarization-activated current (If), Ca2+-current L-type (ICaL), Na+-current (INa) and the slow component of the delayed rectifier K+-current (IKs)). Whereas in adult birds, the mechanism for generating electrical impulses is determined by both « membrane- clock» and «Ca2+-clock».
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Affiliation(s)
- E A Lebedeva
- Institute of Physiology Komi Science Center, Ural Branch Russian Academy of Sciences, GSP-2, 50 st. Pervomayskaya, 167982, Syktyvkar, Komi Republic, Russia.
| | - M A Gonotkov
- Institute of Physiology Komi Science Center, Ural Branch Russian Academy of Sciences, GSP-2, 50 st. Pervomayskaya, 167982, Syktyvkar, Komi Republic, Russia
| | - A A Furman
- Institute of Physiology Komi Science Center, Ural Branch Russian Academy of Sciences, GSP-2, 50 st. Pervomayskaya, 167982, Syktyvkar, Komi Republic, Russia
| | - I O Velegzhaninov
- Institute of Biology, Komi Science Center of Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982, Syktyvkar, Komi Republic, Russia
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Qiao C, Huang Y. Reliable imputation of spatial transcriptomes with uncertainty estimation and spatial regularization. PATTERNS (NEW YORK, N.Y.) 2024; 5:101021. [PMID: 39233691 PMCID: PMC11368697 DOI: 10.1016/j.patter.2024.101021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/14/2024] [Accepted: 06/11/2024] [Indexed: 09/06/2024]
Abstract
Imputation of missing features in spatial transcriptomics is urgently needed due to technological limitations. However, most existing computational methods suffer from moderate accuracy and cannot estimate the reliability of the imputation. To fill this research gap, we introduce a computational model, TransImpute, that imputes the missing feature modality in spatial transcriptomics by mapping it from single-cell reference data. We derive a set of attributes that can accurately predict imputation uncertainty, enabling us to select reliably imputed genes. In addition, we introduce a spatial autocorrelation metric as a regularization to avoid overestimating spatial patterns. Multiple datasets from various platforms demonstrate that our approach significantly improves the reliability of downstream analyses in detecting spatial variable genes and interacting ligand-receptor pairs. Therefore, TransImpute offers a reliable approach to spatial analysis of missing features for both matched and unseen modalities, such as nascent RNAs.
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Affiliation(s)
- Chen Qiao
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yuanhua Huang
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Department of Statistics and Actuarial Science, University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China
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5
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Webb CH, Wang Y. Cardiac regeneration in goldfish (Carassius auratus) associated with increased expression of key extracellular matrix molecules. Anat Rec (Hoboken) 2024. [PMID: 39092661 DOI: 10.1002/ar.25549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
Cardiac regeneration is a natural phenomenon that occurs in many species outside of humans. The goldfish (Carassius auratus) is an understudied model of cardiac wound response, despite its ubiquity as pets as well as its relationship to the better-studied zebrafish. In this study, we examined the response of the goldfish heart to a resection injury. We found that by 70 days post-injury, goldfish scarlessly heal cardiac wounds under a certain size, with local cardiomyocyte proliferation driving the restoration of the myocardial layer. We also found the upregulation of extracellular matrix components related to cardiac regeneration in the injury site. This upregulation correlated with the level of cardiomyocyte proliferation occurring in the injury site, indicating an association between the two that warrants further exploration.
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Affiliation(s)
- Charles H Webb
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Yadong Wang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
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6
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Yan Y, Zhu S, Jia M, Chen X, Qi W, Gu F, Valencak TG, Liu JX, Sun HZ. Advances in single-cell transcriptomics in animal research. J Anim Sci Biotechnol 2024; 15:102. [PMID: 39090689 PMCID: PMC11295521 DOI: 10.1186/s40104-024-01063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/12/2024] [Indexed: 08/04/2024] Open
Abstract
Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand for high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of animal research, offering an effective method to study the gene expression of high-throughput single cells of different tissues/organs in animals. In an unprecedented manner, researchers have identified cell types/subtypes and their marker genes, inferred cellular fate trajectories, and revealed cell‒cell interactions in animals using single-cell transcriptomics. In this paper, we introduce the development of single-cell technology and review the processes, advancements, and applications of single-cell transcriptomics in animal research. We summarize recent efforts using single-cell transcriptomics to obtain a more profound understanding of animal nutrition and health, reproductive performance, genetics, and disease models in different livestock species. Moreover, the practical experience accumulated based on a large number of cases is highlighted to provide a reference for determining key factors (e.g., sample size, cell clustering, and cell type annotation) in single-cell transcriptomics analysis. We also discuss the limitations and outlook of single-cell transcriptomics in the current stage. This paper describes the comprehensive progress of single-cell transcriptomics in animal research, offering novel insights and sustainable advancements in agricultural productivity and animal health.
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Affiliation(s)
- Yunan Yan
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Senlin Zhu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minghui Jia
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xinyi Chen
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenlingli Qi
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fengfei Gu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Teresa G Valencak
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Agency for Health and Food Safety Austria, 1220, Vienna, Austria
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
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Whitman MA, Mantri M, Spanos E, Estroff LA, De Vlaminck I, Fischbach C. Bone mineral density affects tumor growth by shaping microenvironmental heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604333. [PMID: 39091735 PMCID: PMC11291034 DOI: 10.1101/2024.07.19.604333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Breast cancer bone metastasis is the leading cause of mortality in patients with advanced breast cancer. Although decreased mineral density is a known risk factor for bone metastasis, the underlying mechanisms remain poorly understood because studying the isolated effect of bone mineral density on tumor heterogeneity is challenging with conventional approaches. Here, we investigate how bone mineral content affects tumor growth and microenvironmental complexity in vivo by combining single-cell RNA-sequencing with mineral-containing or mineral-free decellularized bone matrices. We discover that the absence of bone mineral significantly influences fibroblast and immune cell heterogeneity, promoting phenotypes that increase tumor growth and alter the response to injury or disease. Importantly, we observe that the stromal response to matrix mineral content depends on host immunocompetence and the murine tumor model used. Collectively, our findings suggest that bone mineral density affects tumor growth by altering microenvironmental complexity in an organism-dependent manner.
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Affiliation(s)
- Matthew A. Whitman
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14850
| | - Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14850
| | - Emmanuel Spanos
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14850
| | - Lara A. Estroff
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY 14850
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14850
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14850
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14850
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14850
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Foglio E, D'Avorio E, Nieri R, Russo MA, Limana F. Epicardial EMT and cardiac repair: an update. Stem Cell Res Ther 2024; 15:219. [PMID: 39026298 PMCID: PMC11264588 DOI: 10.1186/s13287-024-03823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/30/2024] [Indexed: 07/20/2024] Open
Abstract
Epicardial epithelial-to-mesenchymal transition (EMT) plays a pivotal role in both heart development and injury response and involves dynamic cellular changes that are essential for cardiogenesis and myocardial repair. Specifically, epicardial EMT is a crucial process in which epicardial cells lose polarity, migrate into the myocardium, and differentiate into various cardiac cell types during development and repair. Importantly, following EMT, the epicardium becomes a source of paracrine factors that support cardiac growth at the last stages of cardiogenesis and contribute to cardiac remodeling after injury. As such, EMT seems to represent a fundamental step in cardiac repair. Nevertheless, endogenous EMT alone is insufficient to stimulate adequate repair. Redirecting and amplifying epicardial EMT pathways offers promising avenues for the development of innovative therapeutic strategies and treatment approaches for heart disease. In this review, we present a synthesis of recent literature highlighting the significance of epicardial EMT reactivation in adult heart disease patients.
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Affiliation(s)
- Eleonora Foglio
- Technoscience, Parco Scientifico e Tecnologico Pontino, Latina, Italy
| | - Erica D'Avorio
- Dipartimento di Promozione delle Scienze Umane e della Qualità della Vita, San Raffaele University of Rome, Rome, Italy
| | - Riccardo Nieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Federica Limana
- Dipartimento di Promozione delle Scienze Umane e della Qualità della Vita, San Raffaele University of Rome, Rome, Italy.
- Laboratorio di Patologia Cellulare e Molecolare, IRCCS San Raffaele Roma, Rome, Italy.
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9
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Wong D, Martinez J, Quijada P. Exploring the Function of Epicardial Cells Beyond the Surface. Circ Res 2024; 135:353-371. [PMID: 38963865 PMCID: PMC11225799 DOI: 10.1161/circresaha.124.321567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The epicardium, previously viewed as a passive outer layer around the heart, is now recognized as an essential component in development, regeneration, and repair. In this review, we explore the cellular and molecular makeup of the epicardium, highlighting its roles in heart regeneration and repair in zebrafish and salamanders, as well as its activation in young and adult postnatal mammals. We also examine the latest technologies used to study the function of epicardial cells for therapeutic interventions. Analysis of highly regenerative animal models shows that the epicardium is essential in regulating cardiomyocyte proliferation, transient fibrosis, and neovascularization. However, despite the epicardium's unique cellular programs to resolve cardiac damage, it remains unclear how to replicate these processes in nonregenerative mammalian organisms. During myocardial infarction, epicardial cells secrete signaling factors that modulate fibrotic, vascular, and inflammatory remodeling, which differentially enhance or inhibit cardiac repair. Recent transcriptomic studies have validated the cellular and molecular heterogeneity of the epicardium across various species and developmental stages, shedding further light on its function under pathological conditions. These studies have also provided insights into the function of regulatory epicardial-derived signaling molecules in various diseases, which could lead to new therapies and advances in reparative cardiovascular medicine. Moreover, insights gained from investigating epicardial cell function have initiated the development of novel techniques, including using human pluripotent stem cells and cardiac organoids to model reparative processes within the cardiovascular system. This growing understanding of epicardial function holds the potential for developing innovative therapeutic strategies aimed at addressing developmental heart disorders, enhancing regenerative therapies, and mitigating cardiovascular disease progression.
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Affiliation(s)
- David Wong
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90029
- Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, CA 90029
| | - Julie Martinez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90029
- Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, CA 90029
| | - Pearl Quijada
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90029
- Eli and Edythe Broad Stem Research Center, University of California, Los Angeles, CA 90029
- Molecular Biology Institute, University of California, Los Angeles, CA 90029
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10
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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Miranda-Negrón Y, García-Arrarás JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601561. [PMID: 39005414 PMCID: PMC11244903 DOI: 10.1101/2024.07.01.601561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In holothurians, the regenerative process following evisceration involves the development of a "rudiment" or "anlage" at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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11
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Chen S, Xing L, Xie Z, Zhao M, Yu H, Gan J, Zhao H, Ma Z, Li H. Single-cell transcriptomic reveals a cell atlas and diversity of chicken amygdala responded to social hierarchy. iScience 2024; 27:109880. [PMID: 38952686 PMCID: PMC11215297 DOI: 10.1016/j.isci.2024.109880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/29/2024] [Accepted: 04/29/2024] [Indexed: 07/03/2024] Open
Abstract
Amygdala serves as a highly cellular, heterogeneous brain region containing excitatory and inhibitory neurons and is involved in the dopamine and serotoninergic neuron systems. An increasing number of studies have revealed the underpinned mechanism mediating social hierarchy in mammal and vertebrate, however, there are rare studies conducted on how amygdala on social hierarchy in poultry. In this study, we conducted food competition tests and determined the social hierarchy of the rooster. We performed cross-species analysis with mammalian amygdala, and found that cell types of human and rhesus monkeys were more closely related and that of chickens were more distant. We identified 26 clusters and divided them into 10 main clusters, of which GABAergic and glutamatergic neurons were associated with social behaviors. In conclusion, our results provide to serve the developmental studies of the amygdala neuron system and new insights into the underpinned mechanism of social hierarchy in roosters.
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Affiliation(s)
- Siyu Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Limin Xing
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Zhijiang Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Mengqiao Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Hui Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Jiankang Gan
- Guangdong Tinoo’s FOODS Group Co., Ltd, Qingyuan 511500, China
| | - Haiquan Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528250, China
- Guangdong Tinoo’s FOODS Group Co., Ltd, Qingyuan 511500, China
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12
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Jones A, Cai D, Li D, Engelhardt BE. Optimizing the design of spatial genomic studies. Nat Commun 2024; 15:4987. [PMID: 38862492 PMCID: PMC11166654 DOI: 10.1038/s41467-024-49174-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Spatial genomic technologies characterize the relationship between the structural organization of cells and their cellular state. Despite the availability of various spatial transcriptomic and proteomic profiling platforms, these experiments remain costly and labor-intensive. Traditionally, tissue slicing for spatial sequencing involves parallel axis-aligned sections, often yielding redundant or correlated information. We propose structured batch experimental design, a method that improves the cost efficiency of spatial genomics experiments by profiling tissue slices that are maximally informative, while recognizing the destructive nature of the process. Applied to two spatial genomics studies-one to construct a spatially-resolved genomic atlas of a tissue and another to localize a region of interest in a tissue, such as a tumor-our approach collects more informative samples using fewer slices compared to traditional slicing strategies. This methodology offers a foundation for developing robust and cost-efficient design strategies, allowing spatial genomics studies to be deployed by smaller, resource-constrained labs.
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Affiliation(s)
- Andrew Jones
- Department of Computer Science, Princeton University, Princeton, USA
| | - Diana Cai
- Center for Computational Mathematics, Flatiron Institute, New York, USA
| | - Didong Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Barbara E Engelhardt
- Gladstone Institutes, San Francisco, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, USA.
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13
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Zhao SH, Ji XY, Yuan GZ, Cheng T, Liang HY, Liu SQ, Yang FY, Tang Y, Shi S. A Bibliometric Analysis of the Spatial Transcriptomics Literature from 2006 to 2023. Cell Mol Neurobiol 2024; 44:50. [PMID: 38856921 PMCID: PMC11164738 DOI: 10.1007/s10571-024-01484-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
In recent years, spatial transcriptomics (ST) research has become a popular field of study and has shown great potential in medicine. However, there are few bibliometric analyses in this field. Thus, in this study, we aimed to find and analyze the frontiers and trends of this medical research field based on the available literature. A computerized search was applied to the WoSCC (Web of Science Core Collection) Database for literature published from 2006 to 2023. Complete records of all literature and cited references were extracted and screened. The bibliometric analysis and visualization were performed using CiteSpace, VOSviewer, Bibliometrix R Package software, and Scimago Graphica. A total of 1467 papers and reviews were included. The analysis revealed that the ST publication and citation results have shown a rapid upward trend over the last 3 years. Nature Communications and Nature were the most productive and most co-cited journals, respectively. In the comprehensive global collaborative network, the United States is the country with the most organizations and publications, followed closely by China and the United Kingdom. The author Joakim Lundeberg published the most cited paper, while Patrik L. Ståhl ranked first among co-cited authors. The hot topics in ST are tissue recognition, cancer, heterogeneity, immunotherapy, differentiation, and models. ST technologies have greatly contributed to in-depth research in medical fields such as oncology and neuroscience, opening up new possibilities for the diagnosis and treatment of diseases. Moreover, artificial intelligence and big data drive additional development in ST fields.
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Affiliation(s)
- Shu-Han Zhao
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Xin-Yu Ji
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave, Beijing, 100700, People's Republic of China
| | - Guo-Zhen Yuan
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Tao Cheng
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Hai-Yi Liang
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Si-Qi Liu
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Fu-Yi Yang
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yang Tang
- School of Chinese Medicine, Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Shuai Shi
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China.
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14
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Duan Z, Riffle D, Li R, Liu J, Min MR, Zhang J. Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. Bioinformatics 2024; 40:btae339. [PMID: 38806165 PMCID: PMC11256934 DOI: 10.1093/bioinformatics/btae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/18/2024] [Accepted: 05/26/2024] [Indexed: 05/30/2024] Open
Abstract
MOTIVATION Recent advances in spatial transcriptomics allow spatially resolved gene expression measurements with cellular or even sub-cellular resolution, directly characterizing the complex spatiotemporal gene expression landscape and cell-to-cell interactions in their native microenvironments. Due to technology limitations, most spatial transcriptomic technologies still yield incomplete expression measurements with excessive missing values. Therefore, gene imputation is critical to filling in missing data, enhancing resolution, and improving overall interpretability. However, existing methods either require additional matched single-cell RNA-seq data, which is rarely available, or ignore spatial proximity or expression similarity information. RESULTS To address these issues, we introduce Impeller, a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. Impeller has two unique characteristics distinct from existing approaches. First, it builds a heterogeneous graph with two types of edges representing spatial proximity and expression similarity. Therefore, Impeller can simultaneously model smooth gene expression changes across spatial dimensions and capture similar gene expression signatures of faraway cells from the same type. Moreover, Impeller incorporates both short- and long-range cell-to-cell interactions (e.g. via paracrine and endocrine) by stacking multiple GNN layers. We use a learnable path operator in Impeller to avoid the over-smoothing issue of the traditional Laplacian matrices. Extensive experiments on diverse datasets from three popular platforms and two species demonstrate the superiority of Impeller over various state-of-the-art imputation methods. AVAILABILITY AND IMPLEMENTATION The code and preprocessed data used in this study are available at https://github.com/aicb-ZhangLabs/Impeller and https://zenodo.org/records/11212604.
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Affiliation(s)
- Ziheng Duan
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, United States
| | - Dylan Riffle
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, United States
| | - Ren Li
- Mathematical, Computational, and Systems Biology, University of California, Irvine, Irvine, CA 92697, United States
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, United States
| | - Martin Renqiang Min
- Department of Machine Learning, NEC Labs America, Princeton, NJ 08540, United States
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, United States
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15
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Zhou P, Bocci F, Li T, Nie Q. Spatial transition tensor of single cells. Nat Methods 2024; 21:1053-1062. [PMID: 38755322 PMCID: PMC11166574 DOI: 10.1038/s41592-024-02266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/02/2024] [Indexed: 05/18/2024]
Abstract
Spatial transcriptomics and messenger RNA splicing encode extensive spatiotemporal information for cell states and transitions. The current lineage-inference methods either lack spatial dynamics for state transition or cannot capture different dynamics associated with multiple cell states and transition paths. Here we present spatial transition tensor (STT), a method that uses messenger RNA splicing and spatial transcriptomes through a multiscale dynamical model to characterize multistability in space. By learning a four-dimensional transition tensor and spatial-constrained random walk, STT reconstructs cell-state-specific dynamics and spatial state transitions via both short-time local tensor streamlines between cells and long-time transition paths among attractors. Benchmarking and applications of STT on several transcriptome datasets via multiple technologies on epithelial-mesenchymal transitions, blood development, spatially resolved mouse brain and chicken heart development, indicate STT's capability in recovering cell-state-specific dynamics and their associated genes not seen using existing methods. Overall, STT provides a consistent multiscale description of single-cell transcriptome data across multiple spatiotemporal scales.
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Affiliation(s)
- Peijie Zhou
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- Center for Machine Learning Research, Peking University, Beijing, China
- AI for Science Institute, Beijing, China
- National Engineering Laboratory for Big Data Analysis and Applications, Beijing, China
| | - Federico Bocci
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - Tiejun Li
- LMAM and School of Mathematical Sciences, Peking University, Beijing, China
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- Department of Cell and Developmental Biology, University of California, Irvine, Irvine, CA, USA.
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16
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Zhang T, Ai D, Wei P, Xu Y, Bi Z, Ma F, Li F, Chen XJ, Zhang Z, Zou X, Guo Z, Zhao Y, Li JL, Ye M, Feng Z, Zhang X, Zheng L, Yu J, Li C, Tu T, Zeng H, Lei J, Zhang H, Hong T, Zhang L, Luo B, Li Z, Xing C, Jia C, Li L, Sun W, Ge WP. The subcommissural organ regulates brain development via secreted peptides. Nat Neurosci 2024; 27:1103-1115. [PMID: 38741020 DOI: 10.1038/s41593-024-01639-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/03/2024] [Indexed: 05/16/2024]
Abstract
The subcommissural organ (SCO) is a gland located at the entrance of the aqueduct of Sylvius in the brain. It exists in species as distantly related as amphioxus and humans, but its function is largely unknown. Here, to explore its function, we compared transcriptomes of SCO and non-SCO brain regions and found three genes, Sspo, Car3 and Spdef, that are highly expressed in the SCO. Mouse strains expressing Cre recombinase from endogenous promoter/enhancer elements of these genes were used to genetically ablate SCO cells during embryonic development, resulting in severe hydrocephalus and defects in neuronal migration and development of neuronal axons and dendrites. Unbiased peptidomic analysis revealed enrichment of three SCO-derived peptides, namely, thymosin beta 4, thymosin beta 10 and NP24, and their reintroduction into SCO-ablated brain ventricles substantially rescued developmental defects. Together, these data identify a critical role for the SCO in brain development.
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Affiliation(s)
- Tingting Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
| | - Daosheng Ai
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
| | - Pingli Wei
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Xu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Zhanying Bi
- Chinese Institute for Brain Research, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Fengfei Ma
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengzhi Li
- Chinese Institute for Brain Research, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning and IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Xing-Jun Chen
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
| | - Zhaohuan Zhang
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiaoxiao Zou
- Chinese Institute for Brain Research, Beijing, China
- Changping Laboratory, Beijing, China
| | - Zongpei Guo
- Chinese Institute for Brain Research, Beijing, China
| | - Yue Zhao
- Chinese Institute for Brain Research, Beijing, China
| | - Jun-Liszt Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
| | - Meng Ye
- Chinese Institute for Brain Research, Beijing, China
- Changping Laboratory, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Ziyan Feng
- Chinese Institute for Brain Research, Beijing, China
| | | | - Lijun Zheng
- Chinese Institute for Brain Research, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jie Yu
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Chunli Li
- National Institute of Biological Sciences, Beijing, China
| | - Tianqi Tu
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, China
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jianfeng Lei
- Medical Imaging laboratory of Core Facility Center, Capital Medical University, Beijing, China
| | - Hongqi Zhang
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, China
| | - Tao Hong
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Benyan Luo
- Department of Neurology, First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Zhen Li
- Chinese Institute for Brain Research, Beijing, China
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, Department of Bioinformatics, School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chenxi Jia
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Lingjun Li
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
| | - Wenzhi Sun
- Chinese Institute for Brain Research, Beijing, China.
- School of Basic Medical Sciences, Capital Medical University, Beijing, China.
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, China.
- Changping Laboratory, Beijing, China.
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing, China.
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17
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Quek YJ, Tay A. Nanoscale Methods for Longitudinal Extraction of Intracellular Contents. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314184. [PMID: 38459829 DOI: 10.1002/adma.202314184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Longitudinal analysis of intracellular contents including gene and protein expression is crucial for deciphering the fundamentally dynamic nature of cells. This offers invaluable insights into complex tissue composition and behavior, and drives progress in disease diagnosis, biomarker discovery, and drug development. Traditional longitudinal analysis workflows, involving the destruction of cells at various timepoints, limit insights to singular moments and fail to account for cellular heterogeneity. Current non-destructive approaches, like temporal modeling with single-cell ribonucleic acid sequencing (RNA-seq) and live-cell fluorescence imaging, either rely on biological assumptions or possess the risk of cellular perturbation. Recent advances in nanoscale technologies for non-destructive intracellular content extraction offer a promising solution to these challenges. These novel methods work at the nanoscale to non-destructively access cellular membranes and can be broadly classified into three mechanisms: tip-facilitated aspiration, membrane-based, and probe-based methods. This perspective focuses on these emerging nanotechnologies for repeated intracellular content extraction. Their potential in longitudinal analysis is discussed, the critical requirements for effective repeated sampling are addressed, and the suitability of each technique for various applications is explored. Furthermore, unresolved challenges in repeated sampling are highlighted to encourage further research in this growing field.
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Affiliation(s)
- Ying Jie Quek
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Andy Tay
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, 117599, Singapore
- Tissue Engineering Programme, National University of Singapore, Singapore, 117510, Singapore
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18
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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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19
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Niyakan S, Sheng J, Cao Y, Zhang X, Xu Z, Wu L, Wong ST, Qian X. MUSTANG: Multi-sample spatial transcriptomics data analysis with cross-sample transcriptional similarity guidance. PATTERNS (NEW YORK, N.Y.) 2024; 5:100986. [PMID: 38800365 PMCID: PMC11117058 DOI: 10.1016/j.patter.2024.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/25/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Spatially resolved transcriptomics has revolutionized genome-scale transcriptomic profiling by providing high-resolution characterization of transcriptional patterns. Here, we present our spatial transcriptomics analysis framework, MUSTANG (MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance), which is capable of performing multi-sample spatial transcriptomics spot cellular deconvolution by allowing both cross-sample expression-based similarity information sharing as well as spatial correlation in gene expression patterns within samples. Experiments on a semi-synthetic spatial transcriptomics dataset and three real-world spatial transcriptomics datasets demonstrate the effectiveness of MUSTANG in revealing biological insights inherent in the cellular characterization of tissue samples under study.
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Affiliation(s)
- Seyednami Niyakan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Jianting Sheng
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX 77030, USA
| | - Yuliang Cao
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX 77030, USA
| | - Xiang Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Zhan Xu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ling Wu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Stephen T.C. Wong
- Department of System Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX 77030, USA
| | - Xiaoning Qian
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
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20
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Xiao J, Yu X, Meng F, Zhang Y, Zhou W, Ren Y, Li J, Sun Y, Sun H, Chen G, He K, Lu L. Integrating spatial and single-cell transcriptomics reveals tumor heterogeneity and intercellular networks in colorectal cancer. Cell Death Dis 2024; 15:326. [PMID: 38729966 PMCID: PMC11087651 DOI: 10.1038/s41419-024-06598-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/20/2024] [Accepted: 03/07/2024] [Indexed: 05/12/2024]
Abstract
Single cell RNA sequencing (scRNA-seq), a powerful tool for studying the tumor microenvironment (TME), does not preserve/provide spatial information on tissue morphology and cellular interactions. To understand the crosstalk between diverse cellular components in proximity in the TME, we performed scRNA-seq coupled with spatial transcriptomic (ST) assay to profile 41,700 cells from three colorectal cancer (CRC) tumor-normal-blood pairs. Standalone scRNA-seq analyses revealed eight major cell populations, including B cells, T cells, Monocytes, NK cells, Epithelial cells, Fibroblasts, Mast cells, Endothelial cells. After the identification of malignant cells from epithelial cells, we observed seven subtypes of malignant cells that reflect heterogeneous status in tumor, including tumor_CAV1, tumor_ATF3_JUN | FOS, tumor_ZEB2, tumor_VIM, tumor_WSB1, tumor_LXN, and tumor_PGM1. By transferring the cellular annotations obtained by scRNA-seq to ST spots, we annotated four regions in a cryosection from CRC patients, including tumor, stroma, immune infiltration, and colon epithelium regions. Furthermore, we observed intensive intercellular interactions between stroma and tumor regions which were extremely proximal in the cryosection. In particular, one pair of ligands and receptors (C5AR1 and RPS19) was inferred to play key roles in the crosstalk of stroma and tumor regions. For the tumor region, a typical feature of TMSB4X-high expression was identified, which could be a potential marker of CRC. The stroma region was found to be characterized by VIM-high expression, suggesting it fostered a stromal niche in the TME. Collectively, single cell and spatial analysis in our study reveal the tumor heterogeneity and molecular interactions in CRC TME, which provides insights into the mechanisms underlying CRC progression and may contribute to the development of anticancer therapies targeting on non-tumor components, such as the extracellular matrix (ECM) in CRC. The typical genes we identified may facilitate to new molecular subtypes of CRC.
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Affiliation(s)
- Jing Xiao
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Xinyang Yu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Fanlin Meng
- CapitalBio Technology Corporation, Beijing, China
| | - Yuncong Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Wenbin Zhou
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Yonghong Ren
- CapitalBio Technology Corporation, Beijing, China
| | - Jingxia Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Yimin Sun
- CapitalBio Technology Corporation, Beijing, China
| | - Hongwei Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau SAR, China.
- Zhuhai UM Science & Technology Research Institute, Zhuhai, Guangdong, China.
| | - Ke He
- Minimally Invasive Tumor Therapies Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China.
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China.
- Guangzhou First People's Hospital, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China.
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21
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Abedini-Nassab R, Taheri F, Emamgholizadeh A, Naderi-Manesh H. Single-Cell RNA Sequencing in Organ and Cell Transplantation. BIOSENSORS 2024; 14:189. [PMID: 38667182 PMCID: PMC11048310 DOI: 10.3390/bios14040189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Single-cell RNA sequencing is a high-throughput novel method that provides transcriptional profiling of individual cells within biological samples. This method typically uses microfluidics systems to uncover the complex intercellular communication networks and biological pathways buried within highly heterogeneous cell populations in tissues. One important application of this technology sits in the fields of organ and stem cell transplantation, where complications such as graft rejection and other post-transplantation life-threatening issues may occur. In this review, we first focus on research in which single-cell RNA sequencing is used to study the transcriptional profile of transplanted tissues. This technology enables the analysis of the donor and recipient cells and identifies cell types and states associated with transplant complications and pathologies. We also review the use of single-cell RNA sequencing in stem cell implantation. This method enables studying the heterogeneity of normal and pathological stem cells and the heterogeneity in cell populations. With their remarkably rapid pace, the single-cell RNA sequencing methodologies will potentially result in breakthroughs in clinical transplantation in the coming years.
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Affiliation(s)
- Roozbeh Abedini-Nassab
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
| | - Fatemeh Taheri
- Biomedical Engineering Department, University of Neyshabur, Neyshabur P.O. Box 9319774446, Iran
| | - Ali Emamgholizadeh
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran;
- Department of Biophysics, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
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22
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Zhang T, Ai D, Wei P, Xu Y, Bi Z, Ma F, Li F, Chen XJ, Zhang Z, Zou X, Guo Z, Zhao Y, Li JL, Ye M, Feng Z, Zhang X, Zheng L, Yu J, Li C, Tu T, Zeng H, Lei J, Zhang H, Hong T, Zhang L, Luo B, Li Z, Xing C, Jia C, Li L, Sun W, Ge WP. The subcommissural organ regulates brain development via secreted peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.30.587415. [PMID: 38585720 PMCID: PMC10996762 DOI: 10.1101/2024.03.30.587415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The subcommissural organ (SCO) is a gland located at the entrance of the aqueduct of Sylvius in the brain. It exists in species as distantly related as amphioxus and humans, but its function is largely unknown. To explore its function, we compared transcriptomes of SCO and non-SCO brain regions and found three genes, Sspo, Car3, and Spdef, that are highly expressed in the SCO. Mouse strains expressing Cre recombinase from endogenous promoter/enhancer elements of these genes were used to genetically ablate SCO cells during embryonic development, resulting in severe hydrocephalus and defects in neuronal migration and development of neuronal axons and dendrites. Unbiased peptidomic analysis revealed enrichment of three SCO-derived peptides, namely thymosin beta 4, thymosin beta 10, and NP24, and their reintroduction into SCO-ablated brain ventricles substantially rescued developmental defects. Together, these data identify a critical role for the SCO in brain development.
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Affiliation(s)
- Tingting Zhang
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Daosheng Ai
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Pingli Wei
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison, Wisconsin 53705, USA
| | - Ying Xu
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhanying Bi
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Fengfei Ma
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison, Wisconsin 53705, USA
| | - Fengzhi Li
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- Beijing Normal University, State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing 100875, China
| | - Xing-jun Chen
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Zhaohuan Zhang
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Xiaoxiao Zou
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- Changping Laboratory, Beijing 102206, China
| | - Zongpei Guo
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Yue Zhao
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Jun-Liszt Li
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Meng Ye
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Changping Laboratory, Beijing 102206, China
| | - Ziyan Feng
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Xinshuang Zhang
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Lijun Zheng
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jie Yu
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- Department of Neurology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Chunli Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Tianqi Tu
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing 100053, China
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jianfeng Lei
- Medical Imaging laboratory of Core Facility Center, Capital Medical University, Beijing 100054, China
| | - Hongqi Zhang
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing 100053, China
| | - Tao Hong
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing 100053, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Benyan Luo
- Department of Neurology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Zhen Li
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, Department of Bioinformatics, School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Chenxi Jia
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lingjun Li
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison, Wisconsin 53705, USA
| | - Wenzhi Sun
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Woo-ping Ge
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
- Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing 100053, China
- Changping Laboratory, Beijing 102206, China
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23
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Guo X, Ning J, Chen Y, Liu G, Zhao L, Fan Y, Sun S. Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies. Brief Funct Genomics 2024; 23:95-109. [PMID: 37022699 DOI: 10.1093/bfgp/elad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
Differential expression (DE) analysis is a necessary step in the analysis of single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data. Unlike traditional bulk RNA-seq, DE analysis for scRNA-seq or SRT data has unique characteristics that may contribute to the difficulty of detecting DE genes. However, the plethora of DE tools that work with various assumptions makes it difficult to choose an appropriate one. Furthermore, a comprehensive review on detecting DE genes for scRNA-seq data or SRT data from multi-condition, multi-sample experimental designs is lacking. To bridge such a gap, here, we first focus on the challenges of DE detection, then highlight potential opportunities that facilitate further progress in scRNA-seq or SRT analysis, and finally provide insights and guidance in selecting appropriate DE tools or developing new computational DE methods.
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Affiliation(s)
- Xiya Guo
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Jin Ning
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yuanze Chen
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Guoliang Liu
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Liyan Zhao
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yue Fan
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Shiquan Sun
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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24
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Duan B, Chen S, Cheng X, Liu Q. Multi-slice spatial transcriptome domain analysis with SpaDo. Genome Biol 2024; 25:73. [PMID: 38504325 PMCID: PMC10949687 DOI: 10.1186/s13059-024-03213-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo, a tool for multi-slice spatial domain analysis, including modules for multi-slice spatial domain detection, reference-based annotation, and multiple slice clustering at both single-cell and spot resolutions. We demonstrate SpaDo's effectiveness with over 40 multi-slice spatial transcriptome datasets from 7 sequencing platforms. Our findings highlight SpaDo's potential to reveal novel biological insights in multi-slice spatial transcriptomes.
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Affiliation(s)
- Bin Duan
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
| | - Shaoqi Chen
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Xiaojie Cheng
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
| | - Qi Liu
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
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25
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Yan K, Liu Q, Huang R, Jiang Y, Bian Z, Li S, Li L, Shen F, Tsuneyama K, Zhang Q, Lian Z, Guan H, Xu B. Spatial transcriptomics reveals prognosis-associated cellular heterogeneity in the papillary thyroid carcinoma microenvironment. Clin Transl Med 2024; 14:e1594. [PMID: 38426403 PMCID: PMC10905537 DOI: 10.1002/ctm2.1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common malignant endocrine tumour, and its incidence and prevalence are increasing considerably. Cellular heterogeneity in the tumour microenvironment is important for PTC prognosis. Spatial transcriptomics is a powerful technique for cellular heterogeneity study. METHODS In conjunction with a clinical pathologist identification method, spatial transcriptomics was employed to characterise the spatial location and RNA profiles of PTC-associated cells within the tissue sections. The spatial RNA-clinical signature genes for each cell type were extracted and applied to outlining the distribution regions of specific cells on the entire section. The cellular heterogeneity of each cell type was further revealed by ContourPlot analysis, monocle analysis, trajectory analysis, ligand-receptor analysis and Gene Ontology enrichment analysis. RESULTS The spatial distribution region of tumour cells, typical and atypical follicular cells (FCs and AFCs) and immune cells were accurately and comprehensively identified in all five PTC tissue sections. AFCs were identified as a transitional state between FCs and tumour cells, exhibiting a higher resemblance to the latter. Three tumour foci were shared among all patients out of the 13 observed. Notably, tumour foci No. 2 displayed elevated expression levels of genes associated with lower relapse-free survival in PTC patients. We discovered key ligand-receptor interactions, including LAMB3-ITGA2, FN1-ITGA3 and FN1-SDC4, involved in the transition of PTC cells from FCs to AFCs and eventually to tumour cells. High expression of these patterns correlated with reduced relapse-free survival. In the tumour immune microenvironment, reduced interaction between myeloid-derived TGFB1 and TGFBR1 in tumour focus No. 2 contributed to tumourigenesis and increased heterogeneity. The spatial RNA-clinical analysis method developed here revealed prognosis-associated cellular heterogeneity in the PTC microenvironment. CONCLUSIONS The occurrence of tumour foci No. 2 and three enhanced ligand-receptor interactions in the AFC area/tumour foci reduced the relapse-free survival of PTC patients, potentially leading to improved prognostic strategies and targeted therapies for PTC patients.
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Affiliation(s)
- Kai Yan
- Guangdong Cardiovascular InstituteGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Qing‐Zhi Liu
- Chronic Disease LaboratoryInstitutes for Life SciencesSouth China University of TechnologyGuangzhouChina
| | - Rong‐Rong Huang
- Guangdong Cardiovascular InstituteGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yi‐Hua Jiang
- Guangdong Cardiovascular InstituteGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and ApplicationGuangzhouChina
| | - Zhen‐Hua Bian
- School of Biomedical Sciences and EngineeringSouth China University of TechnologyGuangzhou International CampusGuangzhouChina
| | - Si‐Jin Li
- Department of Thyroid SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Liang Li
- Medical Research InstituteGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Fei Shen
- Department of Thyroid SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory MedicineInstitute of Biomedical SciencesTokushima University Graduate SchoolTokushimaJapan
| | - Qing‐Ling Zhang
- Department of PathologyGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Zhe‐Xiong Lian
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Haixia Guan
- Department of EndocrinologyGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Bo Xu
- Department of Thyroid SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
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26
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Xu N, Gonzalez BA, Yutzey KE. Macrophage lineages in heart development and regeneration. Curr Top Dev Biol 2024; 156:1-17. [PMID: 38556420 DOI: 10.1016/bs.ctdb.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
During development, macrophage subpopulations derived from hematopoietic progenitors take up residence in the developing heart. Embryonic macrophages are detectable at the early stages of heart formation in the nascent myocardium, valves and coronary vasculature. The specific subtypes of macrophages present in the developing heart reflect the generation of hematopoietic progenitors in the yolk sac, aorta-gonad-mesonephros, fetal liver, and postnatal bone marrow. Ablation studies have demonstrated specific requirements for embryonic macrophages in valve remodeling, coronary and lymphatic vessel development, specialized conduction system maturation, and myocardial regeneration after neonatal injury. The developmental origins of macrophage lineages change over time, with embryonic lineages having more reparative and remodeling functions in comparison to the bone marrow derived myeloid lineages of adults. Here we review the contributions and functions of cardiac macrophages in the developing heart with potential regenerative and reparative implications for cardiovascular disease.
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Affiliation(s)
- Na Xu
- The Heart Institute, Cincinnati Children's Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Brittany A Gonzalez
- The Heart Institute, Cincinnati Children's Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Katherine E Yutzey
- The Heart Institute, Cincinnati Children's Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
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27
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Mantri M, Zhang HH, Spanos E, Ren YA, De Vlaminck I. A spatiotemporal molecular atlas of the ovulating mouse ovary. Proc Natl Acad Sci U S A 2024; 121:e2317418121. [PMID: 38252830 PMCID: PMC10835069 DOI: 10.1073/pnas.2317418121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Ovulation is essential for reproductive success, yet the underlying cellular and molecular mechanisms are far from clear. Here, we applied high-resolution spatiotemporal transcriptomics to map out cell type- and ovulation stage-specific molecular programs as function of time during follicle maturation and ovulation in mice. Our analysis revealed dynamic molecular transitions within granulosa cell types that occur in tight coordination with mesenchymal cell proliferation. We identified molecular markers for the emerging cumulus cell fate during the preantral-to-antral transition. We describe transcriptional programs that respond rapidly to ovulation stimulation and those associated with follicle rupture, highlighting the prominent roles of apoptotic and metabolic pathways during the final stages of follicle maturation. We further report stage-specific oocyte-cumulus cell interactions and diverging molecular differentiation in follicles approaching ovulation. Collectively, this study provides insights into the cellular and molecular processes that regulate mouse ovarian follicle maturation and ovulation with important implications for advancing therapeutic strategies in reproductive medicine.
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Affiliation(s)
- Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14850
| | | | - Emmanuel Spanos
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14850
| | - Yi A. Ren
- Department of Animal Science, Cornell University, Ithaca, NY14850
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14850
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28
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Ter Mors B, Spieler V, Merino Asumendi E, Gantert B, Lühmann T, Meinel L. Bioresponsive Cytokine Delivery Responding to Matrix Metalloproteinases. ACS Biomater Sci Eng 2024; 10:29-37. [PMID: 37102329 DOI: 10.1021/acsbiomaterials.2c01320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Cytokines are regulated in acute and chronic inflammation, including rheumatoid arthritis (RA) and myocardial infarction (MI). However, the dynamic windows within which cytokine activity/inhibition is desirable in RA and MI change timely and locally during the disease. Therefore, traditional, static delivery regimens are unlikely to meet the idiosyncrasy of these highly dynamic pathophysiological and individual processes. Responsive delivery systems and biomaterials, sensing surrogate markers of inflammation (i.e., matrix metalloproteinases - MMPs) and answering with drug release, may present drug activity at the right time, manner, and place. This article discusses MMPs as surrogate markers for disease activity in RA and MI to clock drug discharge to MMP concentration profiles from MMP-responsive drug delivery systems and biomaterials.
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Affiliation(s)
- Björn Ter Mors
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Valerie Spieler
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eduardo Merino Asumendi
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Benedikt Gantert
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tessa Lühmann
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), 97080 Würzburg, Germany
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29
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Tung LW, Groppa E, Soliman H, Lin B, Chang C, Cheung CW, Ritso M, Guo D, Rempel L, Sinha S, Eisner C, Brassard J, McNagny K, Biernaskie J, Rossi F. Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction. Nat Commun 2023; 14:8498. [PMID: 38129410 PMCID: PMC10739910 DOI: 10.1038/s41467-023-44227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Therapeutic angiogenesis represents a promising avenue to revascularize the ischemic heart. Its limited success is partly due to our poor understanding of the cardiac stroma, specifically mural cells, and their response to ischemic injury. Here, we combine single-cell and positional transcriptomics to assess the behavior of mural cells within the healing heart. In response to myocardial infarction, mural cells adopt an altered state closely associated with the infarct and retain a distinct lineage from fibroblasts. This response is concurrent with vascular rarefaction and reduced vascular coverage by mural cells. Positional transcriptomics reveals that the infarcted heart is governed by regional-dependent and temporally regulated programs. While the remote zone acts as an important source of pro-angiogenic signals, the infarct zone is accentuated by chronic activation of anti-angiogenic, pro-fibrotic, and inflammatory cues. Together, our work unveils the spatiotemporal programs underlying cardiac repair and establishes an association between vascular deterioration and mural cell dysfunction.
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Affiliation(s)
- Lin Wei Tung
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Elena Groppa
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Borea Therapeutics, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Hesham Soliman
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Aspect Biosystems, 1781 W 75th Ave, Vancouver, BC, V6P 6P2, Canada
- Faculty of Pharmaceutical Sciences, Minia University, Minia, Egypt
| | - Bruce Lin
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Chihkai Chang
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Chun Wai Cheung
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Morten Ritso
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - David Guo
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Lucas Rempel
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Sarthak Sinha
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christine Eisner
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Julyanne Brassard
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Kelly McNagny
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Fabio Rossi
- School of Biomedical Engineering & Department of Medical Genetics, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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30
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Odogwu NM, Hagen C, Nelson TJ. Transcriptome studies of congenital heart diseases: identifying current gaps and therapeutic frontiers. Front Genet 2023; 14:1278747. [PMID: 38152655 PMCID: PMC10751320 DOI: 10.3389/fgene.2023.1278747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
Congenital heart disease (CHD) are genetically complex and comprise a wide range of structural defects that often predispose to - early heart failure, a common cause of neonatal morbidity and mortality. Transcriptome studies of CHD in human pediatric patients indicated a broad spectrum of diverse molecular signatures across various types of CHD. In order to advance research on congenital heart diseases (CHDs), we conducted a detailed review of transcriptome studies on this topic. Our analysis identified gaps in the literature, with a particular focus on the cardiac transcriptome signatures found in various biological specimens across different types of CHDs. In addition to translational studies involving human subjects, we also examined transcriptomic analyses of CHDs in a range of model systems, including iPSCs and animal models. We concluded that RNA-seq technology has revolutionized medical research and many of the discoveries from CHD transcriptome studies draw attention to biological pathways that concurrently open the door to a better understanding of cardiac development and related therapeutic avenue. While some crucial impediments to perfectly studying CHDs in this context remain obtaining pediatric cardiac tissue samples, phenotypic variation, and the lack of anatomical/spatial context with model systems. Combining model systems, RNA-seq technology, and integrating algorithms for analyzing transcriptomic data at both single-cell and high throughput spatial resolution is expected to continue uncovering unique biological pathways that are perturbed in CHDs, thus facilitating the development of novel therapy for congenital heart disease.
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Affiliation(s)
- Nkechi Martina Odogwu
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Clinton Hagen
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Timothy J. Nelson
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
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31
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Kuroki Y, Agata K. Isolation of planarian viable cells using fluorescence-activated cell sorting for advancing single-cell transcriptome analysis. Genes Cells 2023; 28:800-810. [PMID: 37723830 DOI: 10.1111/gtc.13068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
Preparing viable single cells is critical for conducting single-cell RNA sequencing (scRNA-seq) because the presence of ambient RNA from dead or damaged cells can interfere with data analysis. Here, we developed a method for isolating viable single cells from adult planarian bodies using fluorescence-activated cell sorting (FACS). This method was then applied to both adult pluripotent stem cells (aPSCs) and differentiating/differentiated cells. Initially, we employed a violet instead of ultraviolet (UV) laser to excite Hoechst 33342 to reduce cellular damage. After optimization of cell staining conditions and FACS compensation, we generated FACS profiles similar to those created using a previous method that employed a UV laser. Despite successfully obtaining high-quality RNA sequencing data for aPSCs, non-aPSCs produced low-quality RNA reads (i.e., <60% of cells possessing barcoding mRNAs). Subsequently, we identified an effective FACS gating condition that excluded low-quality cells and tissue debris without staining. This non-staining isolation strategy not only reduced post-dissociation time but also enabled high-quality scRNA-seq results for all cell types (i.e., >80%). Taken together, these findings imply that the non-staining FACS strategy may be beneficial for isolating viable cells not only from planarians but also from other organisms and tissues for scRNA-seq studies.
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Affiliation(s)
- Yoshihito Kuroki
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
| | - Kiyokazu Agata
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
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32
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Yuan Z, Yao J. Harnessing computational spatial omics to explore the spatial biology intricacies. Semin Cancer Biol 2023; 95:25-41. [PMID: 37400044 DOI: 10.1016/j.semcancer.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
Spatially resolved transcriptomics (SRT) has unlocked new dimensions in our understanding of intricate tissue architectures. However, this rapidly expanding field produces a wealth of diverse and voluminous data, necessitating the evolution of sophisticated computational strategies to unravel inherent patterns. Two distinct methodologies, gene spatial pattern recognition (GSPR) and tissue spatial pattern recognition (TSPR), have emerged as vital tools in this process. GSPR methodologies are designed to identify and classify genes exhibiting noteworthy spatial patterns, while TSPR strategies aim to understand intercellular interactions and recognize tissue domains with molecular and spatial coherence. In this review, we provide a comprehensive exploration of SRT, highlighting crucial data modalities and resources that are instrumental for the development of methods and biological insights. We address the complexities and challenges posed by the use of heterogeneous data in developing GSPR and TSPR methodologies and propose an optimal workflow for both. We delve into the latest advancements in GSPR and TSPR, examining their interrelationships. Lastly, we peer into the future, envisaging the potential directions and perspectives in this dynamic field.
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Affiliation(s)
- Zhiyuan Yuan
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
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33
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Sanchez-Fernandez C, Rodriguez-Outeiriño L, Matias-Valiente L, Ramírez de Acuña F, Franco D, Aránega AE. Understanding Epicardial Cell Heterogeneity during Cardiogenesis and Heart Regeneration. J Cardiovasc Dev Dis 2023; 10:376. [PMID: 37754805 PMCID: PMC10531887 DOI: 10.3390/jcdd10090376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023] Open
Abstract
The outermost layer of the heart, the epicardium, is an essential cell population that contributes, through epithelial-to-mesenchymal transition (EMT), to the formation of different cell types and provides paracrine signals to the developing heart. Despite its quiescent state during adulthood, the adult epicardium reactivates and recapitulates many aspects of embryonic cardiogenesis in response to cardiac injury, thereby supporting cardiac tissue remodeling. Thus, the epicardium has been considered a crucial source of cell progenitors that offers an important contribution to cardiac development and injured hearts. Although several studies have provided evidence regarding cell fate determination in the epicardium, to date, it is unclear whether epicardium-derived cells (EPDCs) come from specific, and predetermined, epicardial cell subpopulations or if they are derived from a common progenitor. In recent years, different approaches have been used to study cell heterogeneity within the epicardial layer using different experimental models. However, the data generated are still insufficient with respect to revealing the complexity of this epithelial layer. In this review, we summarize the previous works documenting the cellular composition, molecular signatures, and diversity within the developing and adult epicardium.
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Affiliation(s)
- Cristina Sanchez-Fernandez
- Cardiovascular Development Group, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (C.S.-F.); (L.R.-O.); (L.M.-V.); (F.R.d.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, 18016 Granada, Spain
| | - Lara Rodriguez-Outeiriño
- Cardiovascular Development Group, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (C.S.-F.); (L.R.-O.); (L.M.-V.); (F.R.d.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, 18016 Granada, Spain
| | - Lidia Matias-Valiente
- Cardiovascular Development Group, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (C.S.-F.); (L.R.-O.); (L.M.-V.); (F.R.d.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, 18016 Granada, Spain
| | - Felicitas Ramírez de Acuña
- Cardiovascular Development Group, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (C.S.-F.); (L.R.-O.); (L.M.-V.); (F.R.d.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, 18016 Granada, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (C.S.-F.); (L.R.-O.); (L.M.-V.); (F.R.d.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, 18016 Granada, Spain
| | - Amelia Eva Aránega
- Cardiovascular Development Group, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (C.S.-F.); (L.R.-O.); (L.M.-V.); (F.R.d.A.); (D.F.)
- Medina Foundation, Technology Park of Health Sciences, 18016 Granada, Spain
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34
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Allen C, Chang Y, Neelon B, Chang W, Kim HJ, Li Z, Ma Q, Chung D. A Bayesian multivariate mixture model for high throughput spatial transcriptomics. Biometrics 2023; 79:1775-1787. [PMID: 35895854 PMCID: PMC10134739 DOI: 10.1111/biom.13727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 07/18/2022] [Indexed: 01/11/2023]
Abstract
High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seek to identify sub-populations of cells within a tissue sample that may inform biological phenomena. Existing computational methods either ignore the spatial heterogeneity in gene expression profiles, fail to account for important statistical features such as skewness, or are heuristic-based network clustering methods that lack the inferential benefits of statistical modeling. To address this gap, we develop SPRUCE: a Bayesian spatial multivariate finite mixture model based on multivariate skew-normal distributions, which is capable of identifying distinct cellular sub-populations in HST data. We further implement a novel combination of Pólya-Gamma data augmentation and spatial random effects to infer spatially correlated mixture component membership probabilities without relying on approximate inference techniques. Via a simulation study, we demonstrate the detrimental inferential effects of ignoring skewness or spatial correlation in HST data. Using publicly available human brain HST data, SPRUCE outperforms existing methods in recovering expertly annotated brain layers. Finally, our application of SPRUCE to human breast cancer HST data indicates that SPRUCE can distinguish distinct cell populations within the tumor microenvironment. An R package spruce for fitting the proposed models is available through The Comprehensive R Archive Network.
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Affiliation(s)
- Carter Allen
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, U.S.A
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, U.S.A
| | - Yuzhou Chang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, U.S.A
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, U.S.A
| | - Brian Neelon
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, U.S.A
| | - Won Chang
- Division of Statistics and Data Science, University of Cincinnati, Cincinnati, OH, U.S.A
| | - Hang J. Kim
- Division of Statistics and Data Science, University of Cincinnati, Cincinnati, OH, U.S.A
| | - Zihai Li
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, U.S.A
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, U.S.A
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, U.S.A
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, U.S.A
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, U.S.A
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35
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Mantri M, Zhang HH, Spanos E, Ren YA, Vlaminck ID. A Spatiotemporal Molecular Atlas of the Ovulating Mouse Ovary. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554210. [PMID: 37662215 PMCID: PMC10473623 DOI: 10.1101/2023.08.21.554210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Ovulation is essential for reproductive success, yet the underlying cellular and molecular mechanisms are far from clear. Here, we applied high-resolution spatiotemporal transcriptomics to map out cell-type- and ovulation-stage-specific molecular programs as function of time during follicle maturation and ovulation in mice. Our analysis revealed dynamic molecular transitions within granulosa cell types that occur in tight coordination with mesenchymal cell proliferation. We identified new molecular markers for the emerging cumulus cell fate during the preantral-to-antral transition. We describe transcriptional programs that respond rapidly to ovulation stimulation and those associated with follicle rupture, highlighting the prominent roles of apoptotic and metabolic pathways during the final stages of follicle maturation. We further report stage-specific oocyte-cumulus cell interactions and diverging molecular differentiation in follicles approaching ovulation. Collectively, this study provides insights into the cellular and molecular processes that regulate mouse ovarian follicle maturation and ovulation with important implications for advancing therapeutic strategies in reproductive medicine.
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Affiliation(s)
- Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | | | - Emmanuel Spanos
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Yi A Ren
- Department of Animal Science, Cornell University, Ithaca, New York
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
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36
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Chen TY, You L, Hardillo JAU, Chien MP. Spatial Transcriptomic Technologies. Cells 2023; 12:2042. [PMID: 37626852 PMCID: PMC10453065 DOI: 10.3390/cells12162042] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
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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37
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Cheng C, Chen W, Jin H, Chen X. A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication. Cells 2023; 12:1970. [PMID: 37566049 PMCID: PMC10417635 DOI: 10.3390/cells12151970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of cellular heterogeneity, identification of rare but significant cell types, and exploration of cell-cell communications and interactions. Its broad applications span both basic and clinical research domains. In this comprehensive review, we survey the current landscape of scRNA-seq analysis methods and tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, and the inference of cell-cell communication. We review the challenges encountered in scRNA-seq analysis, including issues of sparsity or low expression, reliability of cell annotation, and assumptions in data integration, and discuss the potential impact of suboptimal clustering and differential expression analysis tools on downstream analyses, particularly in identifying cell subpopulations. Finally, we discuss recent advancements and future directions for enhancing scRNA-seq analysis. Specifically, we highlight the development of novel tools for annotating single-cell data, integrating and interpreting multimodal datasets covering transcriptomics, epigenomics, and proteomics, and inferring cellular communication networks. By elucidating the latest progress and innovation, we provide a comprehensive overview of the rapidly advancing field of scRNA-seq analysis.
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Affiliation(s)
- Changde Cheng
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
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38
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Lother A, Kohl P. The heterocellular heart: identities, interactions, and implications for cardiology. Basic Res Cardiol 2023; 118:30. [PMID: 37495826 PMCID: PMC10371928 DOI: 10.1007/s00395-023-01000-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
The heterocellular nature of the heart has been receiving increasing attention in recent years. In addition to cardiomyocytes as the prototypical cell type of the heart, non-myocytes such as endothelial cells, fibroblasts, or immune cells are coming more into focus. The rise of single-cell sequencing technologies enables identification of ever more subtle differences and has reignited the question of what defines a cell's identity. Here we provide an overview of the major cardiac cell types, describe their roles in homeostasis, and outline recent findings on non-canonical functions that may be of relevance for cardiology. We highlight modes of biochemical and biophysical interactions between different cardiac cell types and discuss the potential implications of the heterocellular nature of the heart for basic research and therapeutic interventions.
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Affiliation(s)
- Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.
- Interdisciplinary Medical Intensive Care, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany.
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, Faculty of Medicine, University Heart Center, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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39
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Weber LM, Saha A, Datta A, Hansen KD, Hicks SC. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes. Nat Commun 2023; 14:4059. [PMID: 37429865 DOI: 10.1038/s41467-023-39748-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Feature selection to identify spatially variable genes or other biologically informative genes is a key step during analyses of spatially-resolved transcriptomics data. Here, we propose nnSVG, a scalable approach to identify spatially variable genes based on nearest-neighbor Gaussian processes. Our method (i) identifies genes that vary in expression continuously across the entire tissue or within a priori defined spatial domains, (ii) uses gene-specific estimates of length scale parameters within the Gaussian process models, and (iii) scales linearly with the number of spatial locations. We demonstrate the performance of our method using experimental data from several technological platforms and simulations. A software implementation is available at https://bioconductor.org/packages/nnSVG .
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Affiliation(s)
- Lukas M Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Arkajyoti Saha
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Abhirup Datta
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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40
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Arts JA, Laberthonnière C, Lima Cunha D, Zhou H. Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease. Cells 2023; 12:1808. [PMID: 37443842 PMCID: PMC10340756 DOI: 10.3390/cells12131808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.
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Affiliation(s)
- Julian A. Arts
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Camille Laberthonnière
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Dulce Lima Cunha
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Huiqing Zhou
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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41
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Yin Z, Herron S, Silveira S, Kleemann K, Gauthier C, Mallah D, Cheng Y, Margeta MA, Pitts KM, Barry JL, Subramanian A, Shorey H, Brandao W, Durao A, Delpech JC, Madore C, Jedrychowski M, Ajay AK, Murugaiyan G, Hersh SW, Ikezu S, Ikezu T, Butovsky O. Identification of a protective microglial state mediated by miR-155 and interferon-γ signaling in a mouse model of Alzheimer's disease. Nat Neurosci 2023; 26:1196-1207. [PMID: 37291336 PMCID: PMC10619638 DOI: 10.1038/s41593-023-01355-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/05/2023] [Indexed: 06/10/2023]
Abstract
Microglia play a critical role in brain homeostasis and disease progression. In neurodegenerative conditions, microglia acquire the neurodegenerative phenotype (MGnD), whose function is poorly understood. MicroRNA-155 (miR-155), enriched in immune cells, critically regulates MGnD. However, its role in Alzheimer's disease (AD) pathogenesis remains unclear. Here, we report that microglial deletion of miR-155 induces a pre-MGnD activation state via interferon-γ (IFN-γ) signaling, and blocking IFN-γ signaling attenuates MGnD induction and microglial phagocytosis. Single-cell RNA-sequencing analysis of microglia from an AD mouse model identifies Stat1 and Clec2d as pre-MGnD markers. This phenotypic transition enhances amyloid plaque compaction, reduces dystrophic neurites, attenuates plaque-associated synaptic degradation and improves cognition. Our study demonstrates a miR-155-mediated regulatory mechanism of MGnD and the beneficial role of IFN-γ-responsive pre-MGnD in restricting neurodegenerative pathology and preserving cognitive function in an AD mouse model, highlighting miR-155 and IFN-γ as potential therapeutic targets for AD.
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Affiliation(s)
- Zhuoran Yin
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shawn Herron
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Sebastian Silveira
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kilian Kleemann
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- School of Computing, University of Portsmouth, Portsmouth, UK
| | - Christian Gauthier
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dania Mallah
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yiran Cheng
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Milica A Margeta
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Kristen M Pitts
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Jen-Li Barry
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- ARCND, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Shorey
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wesley Brandao
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana Durao
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jean-Christophe Delpech
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Laboratoire NutriNeuro, UMR 1286, Bordeaux INP, INRAE, University of Bordeaux, Bordeaux, France
| | - Charlotte Madore
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratoire NutriNeuro, UMR 1286, Bordeaux INP, INRAE, University of Bordeaux, Bordeaux, France
| | - Mark Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Amrendra K Ajay
- Department of Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gopal Murugaiyan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel W Hersh
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Seiko Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tsuneya Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA.
| | - Oleg Butovsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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42
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Liu C, Yang F, Su X, Zhang Z, Xing Y. ScRNA-seq and spatial transcriptomics: exploring the occurrence and treatment of coronary-related diseases starting from development. Front Cardiovasc Med 2023; 10:1064949. [PMID: 37416923 PMCID: PMC10319627 DOI: 10.3389/fcvm.2023.1064949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 05/22/2023] [Indexed: 07/08/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a new technology that can be used to explore molecular changes in complex cell clusters at the single-cell level. Single-cell spatial transcriptomic technology complements the cell-space location information lost during single-cell sequencing. Coronary artery disease is an important cardiovascular disease with high mortality rates. Many studies have explored the physiological development and pathological changes in coronary arteries from the perspective of single cells using single-cell spatial transcriptomic technology. This article reviews the molecular mechanisms underlying coronary artery development and diseases as revealed by scRNA-seq combined with spatial transcriptomic technology. Based on these mechanisms, we discuss the possible new treatments for coronary diseases.
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43
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Streef TJ, Groeneveld EJ, van Herwaarden T, Hjortnaes J, Goumans MJ, Smits AM. Single-cell analysis of human fetal epicardium reveals its cellular composition and identifies CRIP1 as a modulator of EMT. Stem Cell Reports 2023:S2213-6711(23)00229-1. [PMID: 37390825 PMCID: PMC10362506 DOI: 10.1016/j.stemcr.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023] Open
Abstract
The epicardium plays an essential role in cardiogenesis by providing cardiac cell types and paracrine cues to the developing myocardium. The human adult epicardium is quiescent, but recapitulation of developmental features may contribute to adult cardiac repair. The cell fate of epicardial cells is proposed to be determined by the developmental persistence of specific subpopulations. Reports on this epicardial heterogeneity have been inconsistent, and data regarding the human developing epicardium are scarce. Here we specifically isolated human fetal epicardium and used single-cell RNA sequencing to define its composition and to identify regulators of developmental processes. Few specific subpopulations were observed, but a clear distinction between epithelial and mesenchymal cells was present, resulting in novel population-specific markers. Additionally, we identified CRIP1 as a previously unknown regulator involved in epicardial epithelial-to-mesenchymal transition. Overall, our human fetal epicardial cell-enriched dataset provides an excellent platform to study the developing epicardium in great detail.
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Affiliation(s)
- Thomas J Streef
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Esmee J Groeneveld
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tessa van Herwaarden
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jesper Hjortnaes
- Department of Cardiothoracic Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Marie José Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Anke M Smits
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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44
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Su D, Jiao Z, Li S, Yue L, Li C, Deng M, Hu L, Dai L, Gao B, Wang J, Zhang H, Xiao H, Chen F, Yang H, Zhou D. Spatiotemporal single-cell transcriptomic profiling reveals inflammatory cell states in a mouse model of diffuse alveolar damage. EXPLORATION (BEIJING, CHINA) 2023; 3:20220171. [PMID: 37933384 PMCID: PMC10624389 DOI: 10.1002/exp.20220171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/10/2023] [Indexed: 11/08/2023]
Abstract
Diffuse alveolar damage (DAD) triggers neutrophilic inflammation in damaged tissues of the lung, but little is known about the distinct roles of tissue structural cells in modulating the recruitment of neutrophils to damaged areas. Here, by combining single-cell and spatial transcriptomics, and using quantitative assays, we systematically analyze inflammatory cell states in a mouse model of DAD-induced neutrophilic inflammation after aerosolized intratracheal inoculation with ricin toxin. We show that homeostatic resident fibroblasts switch to a hyper-inflammatory state, and the subsequent occurrence of a CXCL1-CXCR2 chemokine axis between activated fibroblasts (AFib) as the signal sender and neutrophils as the signal receiver triggers further neutrophil recruitment. We also identify an anatomically localized inflamed niche (characterized by a close-knit spatial intercellular contact between recruited neutrophils and AFib) in peribronchial regions that facilitate the pulmonary inflammation outbreak. Our findings identify an intricate interplay between hyper-inflammatory fibroblasts and neutrophils and provide an overarching profile of dynamically changing inflammatory microenvironments during DAD progression.
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Affiliation(s)
- Duo Su
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Reproductive Genetics CenterBethune International Peace HospitalShijiazhuangChina
| | - Zhouguang Jiao
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- State Key Laboratory of Biochemical Engineering, Institute of Process EngineeringChinese Academy of SciencesBeijingChina
| | - Sha Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Liya Yue
- Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Cuidan Li
- Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Mengyun Deng
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Lingfei Hu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Lupeng Dai
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Bo Gao
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Jinglin Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physical and ChemistryInstitute of Chemistry, Chinese Academy of ScienceBeijingChina
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physical and ChemistryInstitute of Chemistry, Chinese Academy of ScienceBeijingChina
| | - Fei Chen
- Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Huiying Yang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
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45
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Cho JM, Poon MLS, Zhu E, Wang J, Butcher JT, Hsiai T. Quantitative 4D imaging of biomechanical regulation of ventricular growth and maturation. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 26:100438. [PMID: 37424697 PMCID: PMC10327868 DOI: 10.1016/j.cobme.2022.100438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abnormal cardiac development is intimately associated with congenital heart disease. During development, a sponge-like network of muscle fibers in the endocardium, known as trabeculation, becomes compacted. Biomechanical forces regulate myocardial differentiation and proliferation to form trabeculation, while the molecular mechanism is still enigmatic. Biomechanical forces, including intracardiac hemodynamic flow and myocardial contractile force, activate a host of molecular signaling pathways to mediate cardiac morphogenesis. While mechanotransduction pathways to initiate ventricular trabeculation is well studied, deciphering the relative importance of hemodynamic shear vs. mechanical contractile forces to modulate the transition from trabeculation to compaction requires advanced imaging tools and genetically tractable animal models. For these reasons, the advent of 4-D multi-scale light-sheet imaging and complementary multiplex live imaging via micro-CT in the beating zebrafish heart and live chick embryos respectively. Thus, this review highlights the complementary animal models and advanced imaging needed to elucidate the mechanotransduction underlying cardiac ventricular development.
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Affiliation(s)
- Jae Min Cho
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA
- Department of Medicine, Greater Los Angeles VA Healthcare System
| | - Mong Lung Steve Poon
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University
| | - Enbo Zhu
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA
- Department of Medicine, Greater Los Angeles VA Healthcare System
| | | | - Jonathan T. Butcher
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University
| | - Tzung Hsiai
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA
- Department of Medicine, Greater Los Angeles VA Healthcare System
- Department of Bioengineering, UCLA
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46
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Ogi DA, Jin S. Transcriptome-Powered Pluripotent Stem Cell Differentiation for Regenerative Medicine. Cells 2023; 12:1442. [PMID: 37408278 DOI: 10.3390/cells12101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 07/07/2023] Open
Abstract
Pluripotent stem cells are endless sources for in vitro engineering human tissues for regenerative medicine. Extensive studies have demonstrated that transcription factors are the key to stem cell lineage commitment and differentiation efficacy. As the transcription factor profile varies depending on the cell type, global transcriptome analysis through RNA sequencing (RNAseq) has been a powerful tool for measuring and characterizing the success of stem cell differentiation. RNAseq has been utilized to comprehend how gene expression changes as cells differentiate and provide a guide to inducing cellular differentiation based on promoting the expression of specific genes. It has also been utilized to determine the specific cell type. This review highlights RNAseq techniques, tools for RNAseq data interpretation, RNAseq data analytic methods and their utilities, and transcriptomics-enabled human stem cell differentiation. In addition, the review outlines the potential benefits of the transcriptomics-aided discovery of intrinsic factors influencing stem cell lineage commitment, transcriptomics applied to disease physiology studies using patients' induced pluripotent stem cell (iPSC)-derived cells for regenerative medicine, and the future outlook on the technology and its implementation.
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Affiliation(s)
- Derek A Ogi
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
- Center of Biomanufacturing for Regenerative Medicine, State University of New York at Binghamton, Binghamton, NY 13902, USA
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47
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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48
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Lu Y, Chen Q, An L. SPADE: Spatial Deconvolution for Domain Specific Cell-type Estimation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536924. [PMID: 37131788 PMCID: PMC10153127 DOI: 10.1101/2023.04.14.536924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The advent of spatial transcriptomics technology has allowed for the acquisition of gene expression profiles with multi-cellular resolution in a spatially resolved manner, presenting a new milestone in the field of genomics. However, the aggregate gene expression from heterogeneous cell types obtained by these technologies poses a significant challenge for a comprehensive delineation of cell type-specific spatial patterns. Here, we propose SPADE (SPAtial DEconvolution), an in-silico method designed to address this challenge by incorporating spatial patterns during cell type decomposition. SPADE utilizes a combination of single-cell RNA sequencing data, spatial location information, and histological information to computationally estimate the proportion of cell types present at each spatial location. In our study, we showcased the effectiveness of SPADE by conducting analyses on synthetic data. Our results indicated that SPADE was able to successfully identify cell type-specific spatial patterns that were not previously identified by existing deconvolution methods. Furthermore, we applied SPADE to a real-world dataset analyzing the developmental chicken heart, where we observed that SPADE was able to accurately capture the intricate processes of cellular differentiation and morphogenesis within the heart. Specifically, we were able to reliably estimate changes in cell type compositions over time, which is a critical aspect of understanding the underlying mechanisms of complex biological systems. These findings underscore the potential of SPADE as a valuable tool for analyzing complex biological systems and shedding light on their underlying mechanisms. Taken together, our results suggest that SPADE represents a significant advancement in the field of spatial transcriptomics, providing a powerful tool for characterizing complex spatial gene expression patterns in heterogeneous tissues.
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49
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Wirth J, Huber N, Yin K, Brood S, Chang S, Martinez-Jimenez CP, Meier M. Spatial transcriptomics using multiplexed deterministic barcoding in tissue. Nat Commun 2023; 14:1523. [PMID: 36934108 PMCID: PMC10024691 DOI: 10.1038/s41467-023-37111-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/02/2023] [Indexed: 03/20/2023] Open
Abstract
Spatially resolved transcriptomics of tissue sections enables advances in fundamental and applied biomedical research. Here, we present Multiplexed Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with a 50 µm resolution. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared to previous reports. Furthermore, the introduction of alignment markers allowed seamless registration of images and spatial transcriptomic spots. Together with technological advances, we provide an open-source computational pipeline to prepare raw sequencing data for downstream analysis. The functionality of xDBiT was demonstrated by acquiring 16 spatially resolved transcriptomic datasets from five different murine organs, including the cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of spatial transcriptomes allowed for in-depth characterization of the murine kidney.
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Affiliation(s)
- Johannes Wirth
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Nina Huber
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Kelvin Yin
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Sophie Brood
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Simon Chang
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany.
- TUM School of Medicine, Technical University of Munich, Munich, Germany.
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany.
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany.
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50
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Yuan Z, Pan W, Zhao X, Zhao F, Xu Z, Li X, Zhao Y, Zhang MQ, Yao J. SODB facilitates comprehensive exploration of spatial omics data. Nat Methods 2023; 20:387-399. [PMID: 36797409 DOI: 10.1038/s41592-023-01773-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/06/2023] [Indexed: 02/18/2023]
Abstract
Spatial omics technologies generate wealthy but highly complex datasets. Here we present Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources and a suite of interactive data analytical modules. SODB currently maintains >2,400 experiments from >25 spatial omics technologies, which are freely accessible as a unified data format compatible with various computational packages. SODB also provides multiple interactive data analytical modules, especially a unique module, Spatial Omics View (SOView). We conduct comprehensive statistical analyses and illustrate the utility of both basic and advanced analytical modules using multiple spatial omics datasets. We demonstrate SOView utility with brain spatial transcriptomics data and recover known anatomical structures. We further delineate functional tissue domains with associated marker genes that were obscured when analyzed using previous methods. We finally show how SODB may efficiently facilitate computational method development. The SODB website is https://gene.ai.tencent.com/SpatialOmics/ . The command-line package is available at https://pysodb.readthedocs.io/en/latest/ .
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Affiliation(s)
- Zhiyuan Yuan
- Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
- Tencent AI Lab, Shenzhen, China.
| | - Wentao Pan
- Tencent AI Lab, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzen, China
| | | | - Fangyuan Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiu Li
- Shenzhen International Graduate School, Tsinghua University, Shenzen, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX, USA.
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