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Zhang C, Wang L, Shi Q. Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics. Comput Struct Biotechnol J 2024; 23:2109-2115. [PMID: 38800634 PMCID: PMC11126885 DOI: 10.1016/j.csbj.2024.05.028] [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: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Spatial transcriptomics techniques, while measuring gene expression, retain spatial location information, aiding in situ studies of organismal tissue architecture and the progression of pathological processes. These techniques generate vast amounts of omics data, necessitating the development of computational methods to reveal the underlying tissue microenvironment heterogeneity. The main directions in spatial transcriptomics data analysis are spatial domain detection and spatial deconvolution, which can identify spatial functional regions and parse the distribution of cell types in spatial transcriptomics data by integrating single-cell transcriptomics data. In these two research directions, many computational methods have been successively proposed. This article will categorize them into three types: machine learning-based methods, probabilistic models-based methods, and deep learning-based methods. It will list and discuss the representative algorithms of each type along with their advantages and disadvantages and describe the datasets and evaluation metrics used to assess these computational methods, facilitating researchers in selecting suitable computational methods according to their research needs. Finally, combining the latest technological developments and the advantages and disadvantages of current algorithms, this article will look forward to the future directions of computational method development.
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Affiliation(s)
- Chuanchao Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024; University of Chinese Academy of Sciences, China
| | - Lequn Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianqian Shi
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Sarkar H, Chitra U, Gold J, Raphael BJ. A count-based model for delineating cell-cell interactions in spatial transcriptomics data. Bioinformatics 2024; 40:i481-i489. [PMID: 38940134 DOI: 10.1093/bioinformatics/btae219] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role in cellular development, tissue homeostasis, and other critical biological functions. Since direct measurement of CCIs is challenging, multiple methods have been developed to infer CCIs by quantifying correlations between the gene expression of the ligands and receptors that mediate CCIs, originally from bulk RNA-sequencing data and more recently from single-cell or spatially resolved transcriptomics (SRT) data. SRT has a particular advantage over single-cell approaches, since ligand-receptor correlations can be computed between cells or spots that are physically close in the tissue. However, the transcript counts of individual ligands and receptors in SRT data are generally low, complicating the inference of CCIs from expression correlations. RESULTS We introduce Copulacci, a count-based model for inferring CCIs from SRT data. Copulacci uses a Gaussian copula to model dependencies between the expression of ligands and receptors from nearby spatial locations even when the transcript counts are low. On simulated data, Copulacci outperforms existing CCI inference methods based on the standard Spearman and Pearson correlation coefficients. Using several real SRT datasets, we show that Copulacci discovers biologically meaningful ligand-receptor interactions that are lowly expressed and undiscoverable by existing CCI inference methods. AVAILABILITY AND IMPLEMENTATION Copulacci is implemented in Python and available at https://github.com/raphael-group/copulacci.
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Affiliation(s)
- Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ, 08540, United States
| | - Uthsav Chitra
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
| | - Julian Gold
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, 08540, United States
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
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Michaud ME, Mota L, Bakhtiari M, Thomas BE, Tomeo J, Pilcher W, Contreras M, Ferran C, Bhasin SS, Pradhan-Nabzdyk L, LoGerfo FW, Liang P, Bhasin MK. Early Injury Landscape in Vein Harvest by Single-Cell and Spatial Transcriptomics. Circ Res 2024; 135:110-134. [PMID: 38808504 PMCID: PMC11189745 DOI: 10.1161/circresaha.123.323939] [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: 11/02/2023] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Vein graft failure following cardiovascular bypass surgery results in significant patient morbidity and cost to the healthcare system. Vein graft injury can occur during autogenous vein harvest and preparation, as well as after implantation into the arterial system, leading to the development of intimal hyperplasia, vein graft stenosis, and, ultimately, bypass graft failure. Although previous studies have identified maladaptive pathways that occur shortly after implantation, the specific signaling pathways that occur during vein graft preparation are not well defined and may result in a cumulative impact on vein graft failure. We, therefore, aimed to elucidate the response of the vein conduit wall during harvest and following implantation, probing the key maladaptive pathways driving graft failure with the overarching goal of identifying therapeutic targets for biologic intervention to minimize these natural responses to surgical vein graft injury. METHODS Employing a novel approach to investigating vascular pathologies, we harnessed both single-nuclei RNA-sequencing and spatial transcriptomics analyses to profile the genomic effects of vein grafts after harvest and distension, then compared these findings to vein grafts obtained 24 hours after carotid-carotid vein bypass implantation in a canine model (n=4). RESULTS Spatial transcriptomic analysis of canine cephalic vein after initial conduit harvest and distention revealed significant enrichment of pathways (P<0.05) involved in the activation of endothelial cells (ECs), fibroblasts, and vascular smooth muscle cells, namely pathways responsible for cellular proliferation and migration and platelet activation across the intimal and medial layers, cytokine signaling within the adventitial layer, and ECM (extracellular matrix) remodeling throughout the vein wall. Subsequent single-nuclei RNA-sequencing analysis supported these findings and further unveiled distinct EC and fibroblast subpopulations with significant upregulation (P<0.05) of markers related to endothelial injury response and cellular activation of ECs, fibroblasts, and vascular smooth muscle cells. Similarly, in vein grafts obtained 24 hours after arterial bypass, there was an increase in myeloid cell, protomyofibroblast, injury response EC, and mesenchymal-transitioning EC subpopulations with a concomitant decrease in homeostatic ECs and fibroblasts. Among these markers were genes previously implicated in vein graft injury, including VCAN, FBN1, and VEGFC, in addition to novel genes of interest, such as GLIS3 and EPHA3. These genes were further noted to be driving the expression of genes implicated in vascular remodeling and graft failure, such as IL-6, TGFBR1, SMAD4, and ADAMTS9. By integrating the spatial transcriptomics and single-nuclei RNA-sequencing data sets, we highlighted the spatial architecture of the vein graft following distension, wherein activated and mesenchymal-transitioning ECs, myeloid cells, and fibroblasts were notably enriched in the intima and media of distended veins. Finally, intercellular communication network analysis unveiled the critical roles of activated ECs, mesenchymal-transitioning ECs, protomyofibroblasts, and vascular smooth muscle cells in upregulating signaling pathways associated with cellular proliferation (MDK [midkine], PDGF [platelet-derived growth factor], VEGF [vascular endothelial growth factor]), transdifferentiation (Notch), migration (ephrin, semaphorin), ECM remodeling (collagen, laminin, fibronectin), and inflammation (thrombospondin), following distension. CONCLUSIONS Vein conduit harvest and distension elicit a prompt genomic response facilitated by distinct cellular subpopulations heterogeneously distributed throughout the vein wall. This response was found to be further exacerbated following vein graft implantation, resulting in a cascade of maladaptive gene regulatory networks. Together, these results suggest that distension initiates the upregulation of pathological pathways that may ultimately contribute to bypass graft failure and presents potential early targets warranting investigation for targeted therapies. This work highlights the first applications of single-nuclei and spatial transcriptomic analyses to investigate venous pathologies, underscoring the utility of these methodologies and providing a foundation for future investigations.
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Affiliation(s)
- Marina E. Michaud
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA (M.E.M., M.B., B.E.T., S.S.B., M.K.B.)
| | - Lucas Mota
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
| | - Mojtaba Bakhtiari
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA (M.E.M., M.B., B.E.T., S.S.B., M.K.B.)
| | - Beena E. Thomas
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA (M.E.M., M.B., B.E.T., S.S.B., M.K.B.)
| | - John Tomeo
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
| | - William Pilcher
- Department of Biomedical Engineering, Emory University, Atlanta, GA (W.P., M.K.B.)
| | - Mauricio Contreras
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
| | - Christiane Ferran
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
- Department of Medicine, Beth Israel Deaconess Medical Center, Center for Vascular Biology Research and the Division of Nephrology (C.F.), Harvard Medical School, Boston, MA
| | - Swati S. Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA (M.E.M., M.B., B.E.T., S.S.B., M.K.B.)
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, GA (S.S.B., M.K.B.)
| | - Leena Pradhan-Nabzdyk
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
| | - Frank W. LoGerfo
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
| | - Patric Liang
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center (L.M., J.T., M.C., C.F., L.P.-N., F.W.L., P.L.), Harvard Medical School, Boston, MA
| | - Manoj K. Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA (M.E.M., M.B., B.E.T., S.S.B., M.K.B.)
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, GA (S.S.B., M.K.B.)
- Department of Biomedical Engineering, Emory University, Atlanta, GA (W.P., M.K.B.)
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Monasterio G, Morales RA, Bejarano DA, Abalo XM, Fransson J, Larsson L, Schlitzer A, Lundeberg J, Das S, Villablanca EJ. A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract. Nat Protoc 2024:10.1038/s41596-024-01001-2. [PMID: 38906985 DOI: 10.1038/s41596-024-01001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/19/2024] [Indexed: 06/23/2024]
Abstract
Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for proper biological function. To comprehensively characterize and understand the cell circuitry underlying biological processes within tissues, it is crucial to preserve their spatial information. Here we report a simple mounting technique to maximize the area of the tissue to be analyzed, encompassing the whole length of the murine gastrointestinal (GI) tract, from mouth to rectum. Using this method, analysis of the whole murine GI tract can be performed in a single slide not only by means of histological staining, immunohistochemistry and in situ hybridization but also by multiplexed antibody staining and spatial transcriptomic approaches. We demonstrate the utility of our method in generating a comprehensive gene and protein expression profile of the whole GI tract by combining the versatile tissue-rolling technique with a cutting-edge transcriptomics method (Visium) and two cutting-edge proteomics methods (ChipCytometry and CODEX-PhenoCycler) in a systematic and easy-to-follow step-by-step procedure. The entire process, including tissue rolling, processing and sectioning, can be achieved within 2-3 d for all three methods. For Visium spatial transcriptomics, an additional 2 d are needed, whereas for spatial proteomics assays (ChipCytometry and CODEX-PhenoCycler), another 3-4 d might be considered. The whole process can be accomplished by researchers with skills in performing murine surgery, and standard histological and molecular biology methods.
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Affiliation(s)
- Gustavo Monasterio
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - David A Bejarano
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Xesús M Abalo
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer Fransson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
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5
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Jin Y, Zuo Y, Li G, Liu W, Pan Y, Fan T, Fu X, Yao X, Peng Y. Advances in spatial transcriptomics and its applications in cancer research. Mol Cancer 2024; 23:129. [PMID: 38902727 PMCID: PMC11188176 DOI: 10.1186/s12943-024-02040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
Malignant tumors have increasing morbidity and high mortality, and their occurrence and development is a complicate process. The development of sequencing technologies enabled us to gain a better understanding of the underlying genetic and molecular mechanisms in tumors. In recent years, the spatial transcriptomics sequencing technologies have been developed rapidly and allow the quantification and illustration of gene expression in the spatial context of tissues. Compared with the traditional transcriptomics technologies, spatial transcriptomics technologies not only detect gene expression levels in cells, but also inform the spatial location of genes within tissues, cell composition of biological tissues, and interaction between cells. Here we summarize the development of spatial transcriptomics technologies, spatial transcriptomics tools and its application in cancer research. We also discuss the limitations and challenges of current spatial transcriptomics approaches, as well as future development and prospects.
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Affiliation(s)
- Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuanli Zuo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gang Li
- Department of Thoracic Surgery, The Public Health Clinical Center of Chengdu, Chengdu, 610061, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yitong Pan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ting Fan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Fu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaojun Yao
- Department of Thoracic Surgery, The Public Health Clinical Center of Chengdu, Chengdu, 610061, China.
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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Qian J, Bao H, Shao X, Fang Y, Liao J, Chen Z, Li C, Guo W, Hu Y, Li A, Yao Y, Fan X, Cheng Y. Simulating multiple variability in spatially resolved transcriptomics with scCube. Nat Commun 2024; 15:5021. [PMID: 38866768 PMCID: PMC11169532 DOI: 10.1038/s41467-024-49445-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
A pressing challenge in spatially resolved transcriptomics (SRT) is to benchmark the computational methods. A widely-used approach involves utilizing simulated data. However, biases exist in terms of the currently available simulated SRT data, which seriously affects the accuracy of method evaluation and validation. Herein, we present scCube ( https://github.com/ZJUFanLab/scCube ), a Python package for independent, reproducible, and technology-diverse simulation of SRT data. scCube not only enables the preservation of spatial expression patterns of genes in reference-based simulations, but also generates simulated data with different spatial variability (covering the spatial pattern type, the resolution, the spot arrangement, the targeted gene type, and the tissue slice dimension, etc.) in reference-free simulations. We comprehensively benchmark scCube with existing single-cell or SRT simulators, and demonstrate the utility of scCube in benchmarking spot deconvolution, gene imputation, and resolution enhancement methods in detail through three applications.
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Affiliation(s)
- Jingyang Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Hudong Bao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yin Fang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310013, China
| | - Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Zhuo Chen
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310013, China
| | - Chengyu Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Wenbo Guo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yining Hu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Anyao Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yue Yao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Yiyu Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China.
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Shoaran M, Sabaie H, Mostafavi M, Rezazadeh M. A comprehensive review of the applications of RNA sequencing in celiac disease research. Gene 2024; 927:148681. [PMID: 38871036 DOI: 10.1016/j.gene.2024.148681] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
RNA sequencing (RNA-seq) has undergone substantial advancements in recent decades and has emerged as a vital technique for profiling the transcriptome. The transition from bulk sequencing to single-cell and spatial approaches has facilitated the achievement of higher precision at cell resolution. It provides valuable biological knowledge about individual immune cells and aids in the discovery of the molecular mechanisms that contribute to the development of autoimmune diseases. Celiac disease (CeD) is an autoimmune disorder characterized by a strong immune response to gluten consumption. RNA-seq has led to significantly advanced research in multiple fields, particularly in CeD research. It has been instrumental in studies involving comparative transcriptomics, nutritional genomics and wheat research, cancer research in the context of CeD, genetic and noncoding RNA-mediated epigenetic insights, disease monitoring and biomarker discovery, regulation of mitochondrial functions, therapeutic target identification and drug mechanism of action, dietary factors, immune cell profiling and the immune landscape. This review offers a comprehensive examination of recent RNA-seq technology research in the field of CeD, highlighting future challenges and opportunities for its application.
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Affiliation(s)
- Maryam Shoaran
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehrnaz Mostafavi
- Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Rahimi A, Vale-Silva LA, Fälth Savitski M, Tanevski J, Saez-Rodriguez J. DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics. Nat Commun 2024; 15:4994. [PMID: 38862466 PMCID: PMC11167014 DOI: 10.1038/s41467-024-48868-z] [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: 08/07/2023] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Single-cell transcriptomics and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. However, they suffer from lack of spatial information and a trade-off of resolution and gene coverage, respectively. We propose DOT, a multi-objective optimization framework for transferring cellular features across these data modalities, thus integrating their complementary information. DOT uses genes beyond those common to the data modalities, exploits the local spatial context, transfers spatial features beyond cell-type information, and infers absolute/relative abundance of cell populations at tissue locations. Thus, DOT bridges single-cell transcriptomics data with both high- and low-resolution spatially-resolved data. Moreover, DOT combines practical aspects related to cell composition, heterogeneity, technical effects, and integration of prior knowledge. Our fast implementation based on the Frank-Wolfe algorithm achieves state-of-the-art or improved performance in localizing cell features in high- and low-resolution spatial data and estimating the expression of unmeasured genes in low-coverage spatial data.
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Affiliation(s)
- Arezou Rahimi
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | | | | | - Jovan Tanevski
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany.
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany.
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9
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Curion F, Theis FJ. Machine learning integrative approaches to advance computational immunology. Genome Med 2024; 16:80. [PMID: 38862979 PMCID: PMC11165829 DOI: 10.1186/s13073-024-01350-3] [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: 06/29/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024] Open
Abstract
The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification to encompass a more detailed view of cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements of multiple cellular components-transcriptome, proteome, chromatin, epigenetic modifications and metabolites-within single cells, including in spatial contexts within tissues. This has led to the generation of complex multiscale datasets that can include multimodal measurements from the same cells or a mix of paired and unpaired modalities. Modern machine learning (ML) techniques allow for the integration of multiple "omics" data without the need for extensive independent modelling of each modality. This review focuses on recent advancements in ML integrative approaches applied to immunological studies. We highlight the importance of these methods in creating a unified representation of multiscale data collections, particularly for single-cell and spatial profiling technologies. Finally, we discuss the challenges of these holistic approaches and how they will be instrumental in the development of a common coordinate framework for multiscale studies, thereby accelerating research and enabling discoveries in the computational immunology field.
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Affiliation(s)
- Fabiola Curion
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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10
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Yu Y, He Y, Xie Z. Accurate Identification of Spatial Domain by Incorporating Global Spatial Proximity and Local Expression Proximity. Biomolecules 2024; 14:674. [PMID: 38927077 DOI: 10.3390/biom14060674] [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: 05/03/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Accurate identification of spatial domains is essential in the analysis of spatial transcriptomics data in order to elucidate tissue microenvironments and biological functions. However, existing methods only perform domain segmentation based on local or global spatial relationships between spots, resulting in an underutilization of spatial information. To this end, we propose SECE, a deep learning-based method that captures both local and global relationships among spots and aggregates their information using expression similarity and spatial similarity. We benchmarked SECE against eight state-of-the-art methods on six real spatial transcriptomics datasets spanning four different platforms. SECE consistently outperformed other methods in spatial domain identification accuracy. Moreover, SECE produced spatial embeddings that exhibited clearer patterns in low-dimensional visualizations and facilitated a more accurate trajectory inference.
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Affiliation(s)
- Yuanyuan Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
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11
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Palmer JA, Rosenthal N, Teichmann SA, Litvinukova M. Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics. Circ Res 2024; 134:1681-1702. [PMID: 38843288 PMCID: PMC11149945 DOI: 10.1161/circresaha.124.323672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.
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Affiliation(s)
- Jack A. Palmer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
| | - Nadia Rosenthal
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME (N.R.)
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.R.)
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory (S.A.T.), University of Cambridge, United Kingdom
| | - Monika Litvinukova
- University Hospital Würzburg, Germany (M.L.)
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany (M.L.)
- Helmholtz Pioneer Campus, Helmholtz Munich, Germany (M.L.)
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12
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Lu S, Jolly AJ, Dubner AM, Strand KA, Mutryn MF, Hinthorn T, Noble T, Nemenoff RA, Moulton KS, Majesky MW, Weiser-Evans MC. KLF4 in smooth muscle cell-derived progenitor cells is essential for angiotensin II-induced cardiac inflammation and fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597485. [PMID: 38895472 PMCID: PMC11185732 DOI: 10.1101/2024.06.04.597485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Cardiac fibrosis is defined by the excessive accumulation of extracellular matrix (ECM) material resulting in cardiac tissue scarring and dysfunction. While it is commonly accepted that myofibroblasts are the major contributors to ECM deposition in cardiac fibrosis, their origin remains debated. By combining lineage tracing and RNA sequencing, our group made the paradigm-shifting discovery that a subpopulation of resident vascular stem cells residing within the aortic, carotid artery, and femoral aartery adventitia (termed AdvSca1-SM cells) originate from mature vascular smooth muscle cells (SMCs) through an in situ reprogramming process. SMC-to-AdvSca1-SM reprogramming and AdvSca1-SM cell maintenance is dependent on induction and activity of the transcription factor, KLF4. However, the molecular mechanism whereby KLF4 regulates AdvSca1-SM phenotype remains unclear. In the current study, leveraging a highly specific AdvSca1-SM cell reporter system, single-cell RNA-sequencing (scRNA-seq), and spatial transcriptomic approaches, we demonstrate the profibrotic differentiation trajectory of coronary artery-associated AdvSca1-SM cells in the setting of Angiotensin II (AngII)-induced cardiac fibrosis. Differentiation was characterized by loss of stemness-related genes, including Klf4 , but gain of expression of a profibrotic phenotype. Importantly, these changes were recapitulated in human cardiac hypertrophic tissue, supporting the translational significance of profibrotic transition of AdvSca1-SM-like cells in human cardiomyopathy. Surprisingly and paradoxically, AdvSca1-SM-specific genetic knockout of Klf4 prior to AngII treatment protected against cardiac inflammation and fibrosis, indicating that Klf4 is essential for the profibrotic response of AdvSca1-SM cells. Overall, our data reveal the contribution of AdvSca1-SM cells to myofibroblasts in the setting of AngII-induced cardiac fibrosis. KLF4 not only maintains the stemness of AdvSca1-SM cells, but also orchestrates their response to profibrotic stimuli, and may serve as a therapeutic target in cardiac fibrosis.
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13
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Ma Y, Zhou X. Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics. Nat Methods 2024:10.1038/s41592-024-02284-9. [PMID: 38844627 DOI: 10.1038/s41592-024-02284-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 04/18/2024] [Indexed: 06/23/2024]
Abstract
Spatially resolved transcriptomics (SRT) studies are becoming increasingly common and large, offering unprecedented opportunities in mapping complex tissue structures and functions. Here we present integrative and reference-informed tissue segmentation (IRIS), a computational method designed to characterize tissue spatial organization in SRT studies through accurately and efficiently detecting spatial domains. IRIS uniquely leverages single-cell RNA sequencing data for reference-informed detection of biologically interpretable spatial domains, integrating multiple SRT slices while explicitly considering correlations both within and across slices. We demonstrate the advantages of IRIS through in-depth analysis of six SRT datasets encompassing diverse technologies, tissues, species and resolutions. In these applications, IRIS achieves substantial accuracy gains (39-1,083%) and speed improvements (4.6-666.0) in moderate-sized datasets, while representing the only method applicable for large datasets including Stereo-seq and 10x Xenium. As a result, IRIS reveals intricate brain structures, uncovers tumor microenvironment heterogeneity and detects structural changes in diabetes-affected testis, all with exceptional speed and accuracy.
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Affiliation(s)
- Ying Ma
- Department of Biostatistics, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.
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14
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Williams CG, Moreira ML, Asatsuma T, Lee HJ, Li S, Barrera I, Murray E, Soon MSF, Engel JA, Khoury DS, Le S, Wanrooy BJ, Schienstock D, Alexandre YO, Skinner OP, Joseph R, Beattie L, Mueller SN, Chen F, Haque A. Plasmodium infection induces phenotypic, clonal, and spatial diversity among differentiating CD4 + T cells. Cell Rep 2024; 43:114317. [PMID: 38848213 DOI: 10.1016/j.celrep.2024.114317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/21/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
Naive CD4+ T cells must differentiate in order to orchestrate immunity to Plasmodium, yet understanding of their emerging phenotypes, clonality, spatial distributions, and cellular interactions remains incomplete. Here, we observe that splenic polyclonal CD4+ T cells differentiate toward T helper 1 (Th1) and T follicular helper (Tfh)-like states and exhibit rarer phenotypes not elicited among T cell receptor (TCR) transgenic counterparts. TCR clones present at higher frequencies exhibit Th1 skewing, suggesting that variation in major histocompatibility complex class II (MHC-II) interaction influences proliferation and Th1 differentiation. To characterize CD4+ T cell interactions, we map splenic microarchitecture, cellular locations, and molecular interactions using spatial transcriptomics at near single-cell resolution. Tfh-like cells co-locate with stromal cells in B cell follicles, while Th1 cells in red pulp co-locate with activated monocytes expressing multiple chemokines and MHC-II. Spatial mapping of individual transcriptomes suggests that proximity to chemokine-expressing monocytes correlates with stronger effector phenotypes in Th1 cells. Finally, CRISPR-Cas9 gene disruption reveals a role for CCR5 in promoting clonal expansion and Th1 differentiation. A database of cellular locations and interactions is presented: https://haquelab.mdhs.unimelb.edu.au/spatial_gui/.
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Affiliation(s)
- Cameron G Williams
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Marcela L Moreira
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Takahiro Asatsuma
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Hyun Jae Lee
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Irving Barrera
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Jessica A Engel
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - David S Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Shirley Le
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Brooke J Wanrooy
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Dominick Schienstock
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Yannick O Alexandre
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Oliver P Skinner
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Rainon Joseph
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Lynette Beattie
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ashraful Haque
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia.
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15
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Wischnewski S, Thäwel T, Ikenaga C, Kocharyan A, Lerma-Martin C, Zulji A, Rausch HW, Brenner D, Thomas L, Kutza M, Wick B, Trobisch T, Preusse C, Haeussler M, Leipe J, Ludolph A, Rosenbohm A, Hoke A, Platten M, Weishaupt JH, Sommer CJ, Stenzel W, Lloyd TE, Schirmer L. Cell type mapping of inflammatory muscle diseases highlights selective myofiber vulnerability in inclusion body myositis. NATURE AGING 2024:10.1038/s43587-024-00645-9. [PMID: 38834884 DOI: 10.1038/s43587-024-00645-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/03/2024] [Indexed: 06/06/2024]
Abstract
Inclusion body myositis (IBM) is the most prevalent inflammatory muscle disease in older adults with no effective therapy available. In contrast to other inflammatory myopathies such as subacute, immune-mediated necrotizing myopathy (IMNM), IBM follows a chronic disease course with both inflammatory and degenerative features of pathology. Moreover, causal factors and molecular drivers of IBM progression are largely unknown. Therefore, we paired single-nucleus RNA sequencing with spatial transcriptomics from patient muscle biopsies to map cell-type-specific drivers underlying IBM pathogenesis compared with IMNM muscles and noninflammatory skeletal muscle samples. In IBM muscles, we observed a selective loss of type 2 myonuclei paralleled by increased levels of cytotoxic T and conventional type 1 dendritic cells. IBM myofibers were characterized by either upregulation of cell stress markers featuring GADD45A and NORAD or protein degradation markers including RNF7 associated with p62 aggregates. GADD45A upregulation was preferentially seen in type 2A myofibers associated with severe tissue inflammation. We also noted IBM-specific upregulation of ACHE encoding acetylcholinesterase, which can be regulated by NORAD activity and result in functional denervation of myofibers. Our results provide promising insights into possible mechanisms of myofiber degeneration in IBM and suggest a selective type 2 fiber vulnerability linked to genomic stress and denervation pathways.
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Affiliation(s)
- Sven Wischnewski
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Thäwel
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chiseko Ikenaga
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Kocharyan
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Celia Lerma-Martin
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Amel Zulji
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hans-Werner Rausch
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Brenner
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Leonie Thomas
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Kutza
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Brittney Wick
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Tim Trobisch
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Corinna Preusse
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | | | - Jan Leipe
- Division of Rheumatology, Department of Medicine V, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Ulm, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Ulm, Germany
| | | | - Ahmet Hoke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Jochen H Weishaupt
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Clemens J Sommer
- Institute for Neuropathology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany.
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16
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Aerts T, Boonen A, Geenen L, Stulens A, Masin L, Pancho A, Francis A, Pepermans E, Baggerman G, Van Roy F, Wöhr M, Seuntjens E. Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons. Open Biol 2024; 14:240113. [PMID: 38889770 DOI: 10.1098/rsob.240113] [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: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviours. The cell adhesion molecule protocadherin10 (PCDH10) is linked to ASD in humans. Pcdh10 is expressed in the nervous system during embryonic and early postnatal development and is important for neural circuit formation. In mice, strong expression of Pcdh10 in the ganglionic eminences and in the basolateral complex (BLC) of the amygdala was observed at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressed Pcdh10 in the BLC at perinatal stages and vocalization-related genes were enriched in Pcdh10-expressing neurons in adult mice. An epitope-tagged Pcdh10-HAV5 mouse line revealed endogenous interactions of PCDH10 with synaptic proteins in the young postnatal telencephalon. Nuanced socio-affective communication changes in call emission rates, acoustic features and call subtype clustering were primarily observed in heterozygous pups of a conditional knockout (cKO) with selective deletion of Pcdh10 in Gsh2-lineage interneurons. These changes were less prominent in heterozygous ubiquitous Pcdh10 KO pups, suggesting that altered anxiety levels associated with Gsh2-lineage interneuron functioning might drive the behavioural effects. Together, loss of Pcdh10 specifically in interneurons contributes to behavioural alterations in socio-affective communication with relevance to ASD.
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Affiliation(s)
- Tania Aerts
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anneleen Boonen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Lieve Geenen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anne Stulens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Luca Masin
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Neural Circuit Development and Regeneration, KU Leuven , Leuven 3000, Belgium
| | - Anna Pancho
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- Developmental Genetics, Department of Biomedicine, University of Basel , Basel 4058, Switzerland
| | - Annick Francis
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Elise Pepermans
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
- Department of Computer Science, University of Antwerp , Antwerp, Belgium
| | - Frans Van Roy
- Faculty of Science, Department of Biomedical Molecular Biology; Inflammation Research Center, VIB, Ghent University , Cancer Research Institute Ghent (CRIG) 9000, Belgium
| | - Markus Wöhr
- Faculty of Psychology and Educational Sciences, Research Unit Brain and Cognition, Laboratory of Biological Psychology, Social and Affective Neuroscience Research Group, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- Faculty of Psychology, Experimental and Biological Psychology, Behavioral Neuroscience, Philipps-University of Marburg , Marburg 35032, Germany
- Center for Mind, Brain and Behavior, Philipps-University of Marburg , Marburg 35032, Germany
| | - Eve Seuntjens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- KU Leuven, Leuven Institute for Single Cell Omics , Leuven 3000, Belgium
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17
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Kinget L, Naulaerts S, Govaerts J, Vanmeerbeek I, Sprooten J, Laureano RS, Dubroja N, Shankar G, Bosisio FM, Roussel E, Verbiest A, Finotello F, Ausserhofer M, Lambrechts D, Boeckx B, Wozniak A, Boon L, Kerkhofs J, Zucman-Rossi J, Albersen M, Baldewijns M, Beuselinck B, Garg AD. A spatial architecture-embedding HLA signature to predict clinical response to immunotherapy in renal cell carcinoma. Nat Med 2024; 30:1667-1679. [PMID: 38773341 DOI: 10.1038/s41591-024-02978-9] [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: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 05/23/2024]
Abstract
An important challenge in the real-world management of patients with advanced clear-cell renal cell carcinoma (aRCC) is determining who might benefit from immune checkpoint blockade (ICB). Here we performed a comprehensive multiomics mapping of aRCC in the context of ICB treatment, involving discovery analyses in a real-world data cohort followed by validation in independent cohorts. We cross-connected bulk-tumor transcriptomes across >1,000 patients with validations at single-cell and spatial resolutions, revealing a patient-specific crosstalk between proinflammatory tumor-associated macrophages and (pre-)exhausted CD8+ T cells that was distinguished by a human leukocyte antigen repertoire with higher preference for tumoral neoantigens. A cross-omics machine learning pipeline helped derive a new tumor transcriptomic footprint of neoantigen-favoring human leukocyte antigen alleles. This machine learning signature correlated with positive outcome following ICB treatment in both real-world data and independent clinical cohorts. In experiments using the RENCA-tumor mouse model, CD40 agonism combined with PD1 blockade potentiated both proinflammatory tumor-associated macrophages and CD8+ T cells, thereby achieving maximal antitumor efficacy relative to other tested regimens. Thus, we present a new multiomics and spatial map of the immune-community architecture that drives ICB response in patients with aRCC.
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Affiliation(s)
- Lisa Kinget
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Stefan Naulaerts
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Isaure Vanmeerbeek
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Raquel S Laureano
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolina Dubroja
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Gautam Shankar
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca M Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Eduard Roussel
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Markus Ausserhofer
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | | | | | - Johan Kerkhofs
- Histocompatibility and Immunogenetics Laboratory, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Jessica Zucman-Rossi
- Inserm, UMRS-1138, Génomique fonctionnelle des tumeurs solides, Centre de recherche des Cordeliers, Paris, France
| | - Maarten Albersen
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | - Benoit Beuselinck
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium.
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.
| | - Abhishek D Garg
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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18
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Benjamin K, Bhandari A, Kepple JD, Qi R, Shang Z, Xing Y, An Y, Zhang N, Hou Y, Crockford TL, McCallion O, Issa F, Hester J, Tillmann U, Harrington HA, Bull KR. Multiscale topology classifies cells in subcellular spatial transcriptomics. Nature 2024; 630:943-949. [PMID: 38898271 DOI: 10.1038/s41586-024-07563-1] [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: 03/06/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Spatial transcriptomics measures in situ gene expression at millions of locations within a tissue1, hitherto with some trade-off between transcriptome depth, spatial resolution and sample size2. Although integration of image-based segmentation has enabled impactful work in this context, it is limited by imaging quality and tissue heterogeneity. By contrast, recent array-based technologies offer the ability to measure the entire transcriptome at subcellular resolution across large samples3-6. Presently, there exist no approaches for cell type identification that directly leverage this information to annotate individual cells. Here we propose a multiscale approach to automatically classify cell types at this subcellular level, using both transcriptomic information and spatial context. We showcase this on both targeted and whole-transcriptome spatial platforms, improving cell classification and morphology for human kidney tissue and pinpointing individual sparsely distributed renal mouse immune cells without reliance on image data. By integrating these predictions into a topological pipeline based on multiparameter persistent homology7-9, we identify cell spatial relationships characteristic of a mouse model of lupus nephritis, which we validate experimentally by immunofluorescence. The proposed framework readily generalizes to new platforms, providing a comprehensive pipeline bridging different levels of biological organization from genes through to tissues.
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Affiliation(s)
| | - Aneesha Bhandari
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jessica D Kepple
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rui Qi
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Zhouchun Shang
- BGI Research, Riga, Latvia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Xing
- BGI Research, Riga, Latvia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Tanya L Crockford
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver McCallion
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Joanna Hester
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Ulrike Tillmann
- Mathematical Institute, University of Oxford, Oxford, UK
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Heather A Harrington
- Mathematical Institute, University of Oxford, Oxford, UK.
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Centre for Systems Biology, Dresden, Dresden, Germany.
- Faculty of Mathematics, Technische Universität Dresden, Dresden, Germany.
| | - Katherine R Bull
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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19
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Mimpen JY, Ramos-Mucci L, Paul C, Kurjan A, Hulley PA, Ikwuanusi CT, Cohen CJ, Gwilym SE, Baldwin MJ, Cribbs AP, Snelling SJB. Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon. FASEB J 2024; 38:e23629. [PMID: 38742770 DOI: 10.1096/fj.202300601rrr] [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: 03/29/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
The molecular and cellular basis of health in human tendons remains poorly understood. Among human tendons, hamstring tendon has markedly low pathology and can provide a prototypic healthy tendon reference. The aim of this study was to determine the transcriptomes and location of all cell types in healthy hamstring tendon. Using single nucleus RNA sequencing, we profiled the transcriptomes of 10 533 nuclei from four healthy donors and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and identified cell types previously unreported in tendons, including different skeletal muscle cell types, satellite cells, adipocytes, and undefined nervous system cells. The location of these cell types within tendon was defined using spatial transcriptomics and imaging, and potential transcriptional networks and cell-cell interactions were analyzed. We demonstrate that fibroblasts have the highest number of potential cell-cell interactions in our dataset, are present throughout the tendon, and play an important role in the production and organization of extracellular matrix, thus confirming their role as key regulators of hamstring tendon homeostasis. Overall, our findings underscore the complexity of the cellular networks that underpin healthy human tendon function and the central role of fibroblasts as key regulators of hamstring tendon tissue homeostasis.
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Affiliation(s)
- Jolet Y Mimpen
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lorenzo Ramos-Mucci
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Claudia Paul
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alina Kurjan
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Philippa A Hulley
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Carla J Cohen
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom of Great Britain and Northern Ireland
| | - Stephen E Gwilym
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathew J Baldwin
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sarah J B Snelling
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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20
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Mallach A, Zielonka M, van Lieshout V, An Y, Khoo JH, Vanheusden M, Chen WT, Moechars D, Arancibia-Carcamo IL, Fiers M, De Strooper B. Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer's disease mouse model, as revealed by spatial transcriptomics. Cell Rep 2024; 43:114216. [PMID: 38819990 DOI: 10.1016/j.celrep.2024.114216] [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: 06/20/2023] [Revised: 02/02/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
The amyloid plaque niche is a pivotal hallmark of Alzheimer's disease (AD). Here, we employ two high-resolution spatial transcriptomics (ST) platforms, CosMx and Spatial Enhanced Resolution Omics-sequencing (Stereo-seq), to characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model. We discover heterogeneity in the cellular composition of plaque niches, marked by an increase in microglial accumulation. We profile the transcriptomic alterations of glial cells in the vicinity of plaques and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. Meanwhile, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in hippocampal neurons. We thus show that the accumulation of microglia around hippocampal plaques disrupts astrocytic signaling, in turn inducing an imbalance in neuronal synaptic signaling.
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Affiliation(s)
- Anna Mallach
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Magdalena Zielonka
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Veerle van Lieshout
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | - Marisa Vanheusden
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Discovery Biology, Muna Therapeutics, Leuven, Belgium
| | - Wei-Ting Chen
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Discovery Biology, Muna Therapeutics, Leuven, Belgium
| | - Daan Moechars
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - I Lorena Arancibia-Carcamo
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Mark Fiers
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Bart De Strooper
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium.
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21
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Thuilliez C, Moquin-Beaudry G, Khneisser P, Marques Da Costa ME, Karkar S, Boudhouche H, Drubay D, Audinot B, Geoerger B, Scoazec JY, Gaspar N, Marchais A. CellsFromSpace: a fast, accurate, and reference-free tool to deconvolve and annotate spatially distributed omics data. BIOINFORMATICS ADVANCES 2024; 4:vbae081. [PMID: 38915885 PMCID: PMC11194756 DOI: 10.1093/bioadv/vbae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/02/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024]
Abstract
Motivation Spatial transcriptomics enables the analysis of cell crosstalk in healthy and diseased organs by capturing the transcriptomic profiles of millions of cells within their spatial contexts. However, spatial transcriptomics approaches also raise new computational challenges for the multidimensional data analysis associated with spatial coordinates. Results In this context, we introduce a novel analytical framework called CellsFromSpace based on independent component analysis (ICA), which allows users to analyze various commercially available technologies without relying on a single-cell reference dataset. The ICA approach deployed in CellsFromSpace decomposes spatial transcriptomics data into interpretable components associated with distinct cell types or activities. ICA also enables noise or artifact reduction and subset analysis of cell types of interest through component selection. We demonstrate the flexibility and performance of CellsFromSpace using real-world samples to demonstrate ICA's ability to successfully identify spatially distributed cells as well as rare diffuse cells, and quantitatively deconvolute datasets from the Visium, Slide-seq, MERSCOPE, and CosMX technologies. Comparative analysis with a current alternative reference-free deconvolution tool also highlights CellsFromSpace's speed, scalability and accuracy in processing complex, even multisample datasets. CellsFromSpace also offers a user-friendly graphical interface enabling non-bioinformaticians to annotate and interpret components based on spatial distribution and contributor genes, and perform full downstream analysis. Availability and implementation CellsFromSpace (CFS) is distributed as an R package available from github at https://github.com/gustaveroussy/CFS along with tutorials, examples, and detailed documentation.
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Affiliation(s)
- Corentin Thuilliez
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
| | - Gaël Moquin-Beaudry
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
| | - Pierre Khneisser
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif 94805, France
| | - Maria Eugenia Marques Da Costa
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif 94805, France
| | - Slim Karkar
- University Bordeaux, CNRS, IBGC, UMR, Bordeaux 33077, France
- Bordeaux Bioinformatic Center CBiB, University of Bordeaux, Bordeaux 33000, France
| | - Hanane Boudhouche
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
| | - Damien Drubay
- Office of Biostatistics and Epidemiology, Gustave Roussy, Université Paris-Saclay, Villejuif 94805, France
- Inserm, Université Paris-Saclay, CESP U1018, Oncostat, Labeled Ligue Contre le Cancer, Villejuif 94805, France
| | - Baptiste Audinot
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif 94805, France
| | - Jean-Yves Scoazec
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif 94805, France
| | - Nathalie Gaspar
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif 94805, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif F-94805, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif 94805, France
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22
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Boldrini M, Xiao Y, Sing T, Zhu C, Jabbi M, Pantazopoulos H, Gürsoy G, Martinowich K, Punzi G, Vallender EJ, Zody M, Berretta S, Hyde TM, Kleinman JE, Marenco S, Roussos P, Lewis DA, Turecki G, Lehner T, Mann JJ. Omics approaches to investigate the pathogenesis of suicide. Biol Psychiatry 2024:S0006-3223(24)01352-0. [PMID: 38821194 DOI: 10.1016/j.biopsych.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Suicide is the second leading cause of death in U.S. adolescents and young adults, and generally associated with a psychiatric disorder. Suicidal behavior has a complex etiology and pathogenesis. Moderate heritability suggests genetic causes. Associations between childhood and recent life adversity indicate contributions from epigenetic factors. Genomic contributions to suicide pathogenesis remain largely unknown. This paper is based on a workshop held to design strategies to identify molecular drivers of suicide neurobiology that would be putative new treatment targets. The panel determined that, while bulk tissue studies provide comprehensive information, single-nucleus approaches identifying cell-type specific changes are needed. While single nuclei techniques lack information on cytoplasm, processes, spines, and synapses, spatial multiomic technologies on intact tissue detect cell alterations specific to brain tissue layers and subregions. Because suicide has genetic and environmental drivers, multiomic approaches combining cell-type specific epigenome, transcriptome, and proteome provide a more complete picture of pathogenesis. To determine the direction of effect of suicide risk gene variants on RNA and protein expression, and how these interact with epigenetic marks, single nuclei and spatial multiomics quantitative trait loci maps should be integrated with whole genome sequencing and genome-wide association databases. The workshop concluded with the recommendation for the formation of an international suicide biology consortium that will bring together brain banks and investigators with expertise in cutting-edge omics technologies to delineate the biology of suicide and identify novel potential treatment targets to be tested in cellular and animal models for drug and biomarkers discovery, to guide suicide prevention.
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Affiliation(s)
- Maura Boldrini
- Department of Psychiatry, Columbia University, New York, NY; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY.
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY
| | - Tarjinder Sing
- Department of Psychiatry, Columbia University, New York, NY; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY; New York Genome Center, New York, NY
| | - Chenxu Zhu
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY; New York Genome Center, New York, NY
| | - Mbemba Jabbi
- Department of Psychiatry and Behavioral Sciences, Mulva Clinics for the Neurosciences, Dell Medical School, The University of Texas at Austin, Austin, TX
| | - Harry Pantazopoulos
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS
| | - Gamze Gürsoy
- New York Genome Center, New York, NY; Departments of Biomedical Informatics and Computer Science, Columbia University, New York, NY
| | - Keri Martinowich
- Lieber Institute for Brain Development, Department of Psychiatry and Behavioral Sciences, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Giovanna Punzi
- Lieber Institute for Brain Development, Department of Psychiatry and Behavioral Sciences, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eric J Vallender
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS
| | | | - Sabina Berretta
- Department of Psychiatry, Harvard Brain Tissue Resource Center, Harvard Medical School, McLean Hospital, Belmont, MA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Department of Psychiatry and Behavioral Sciences, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Department of Psychiatry and Behavioral Sciences, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stefano Marenco
- Human Brain Collection Core (HBCC), National Institute of Mental Health's (NIMH) Division of Intramural Research Programs (DIRP), Bethesda, MD
| | - Panagiotis Roussos
- Center for Precision Medicine and Translational Therapeutics; Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - David A Lewis
- Department of Psychiatry, Douglas Institute, McGill University, Montréal, QC, Canada
| | - Gustavo Turecki
- Departments of Psychiatry and Neuroscience, University of Pittsburgh, Pittsburgh, PA
| | | | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY
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23
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Li J, Cao Q, Tong M. Deciphering anoikis resistance and identifying prognostic biomarkers in clear cell renal cell carcinoma epithelial cells. Sci Rep 2024; 14:12044. [PMID: 38802480 PMCID: PMC11130322 DOI: 10.1038/s41598-024-62978-0] [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: 01/09/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
This study tackles the persistent prognostic and management challenges of clear cell renal cell carcinoma (ccRCC), despite advancements in multimodal therapies. Focusing on anoikis, a critical form of programmed cell death in tumor progression and metastasis, we investigated its resistance in cancer evolution. Using single-cell RNA sequencing from seven ccRCC patients, we assessed the impact of anoikis-related genes (ARGs) and identified differentially expressed genes (DEGs) in Anoikis-related epithelial subclusters (ARESs). Additionally, six ccRCC RNA microarray datasets from the GEO database were analyzed for robust DEGs. A novel risk prognostic model was developed through LASSO and multivariate Cox regression, validated using BEST, ULCAN, and RT-PCR. The study included functional enrichment, immune infiltration analysis in the tumor microenvironment (TME), and drug sensitivity assessments, leading to a predictive nomogram integrating clinical parameters. Results highlighted dynamic ARG expression patterns and enhanced intercellular interactions in ARESs, with significant KEGG pathway enrichment in MYC + Epithelial subclusters indicating enhanced anoikis resistance. Additionally, all ARESs were identified in the spatial context, and their locational relationships were explored. Three key prognostic genes-TIMP1, PECAM1, and CDKN1A-were identified, with the high-risk group showing greater immune infiltration and anoikis resistance, linked to poorer prognosis. This study offers a novel ccRCC risk signature, providing innovative approaches for patient management, prognosis, and personalized treatment.
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Affiliation(s)
- Junyi Li
- Department of Urology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, Liaoning, China
| | - Qingfei Cao
- Department of Urology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, Liaoning, China
| | - Ming Tong
- Department of Urology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, Liaoning, China.
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24
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Swain AK, Pandit V, Sharma J, Yadav P. SpatialPrompt: spatially aware scalable and accurate tool for spot deconvolution and domain identification in spatial transcriptomics. Commun Biol 2024; 7:639. [PMID: 38796505 PMCID: PMC11127982 DOI: 10.1038/s42003-024-06349-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
Efficiently mapping of cell types in situ remains a major challenge in spatial transcriptomics. Most spot deconvolution tools ignore spatial coordinate information and perform extremely slow on large datasets. Here, we introduce SpatialPrompt, a spatially aware and scalable tool for spot deconvolution and domain identification. SpatialPrompt integrates gene expression, spatial location, and single-cell RNA sequencing (scRNA-seq) dataset as reference to accurately infer cell-type proportions of spatial spots. SpatialPrompt uses non-negative ridge regression and graph neural network to efficiently capture local microenvironment information. Our extensive benchmarking analysis on Visium, Slide-seq, and MERFISH datasets demonstrated superior performance of SpatialPrompt over 15 existing tools. On mouse hippocampus dataset, SpatialPrompt achieves spot deconvolution and domain identification within 2 minutes for 50,000 spots. Overall, domain identification using SpatialPrompt was 44 to 150 times faster than existing methods. We build a database housing 40 plus curated scRNA-seq datasets for seamless integration with SpatialPrompt for spot deconvolution.
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Affiliation(s)
- Asish Kumar Swain
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, 342030, India
| | - Vrushali Pandit
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, 342030, India
| | - Jyoti Sharma
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, 342030, India
| | - Pankaj Yadav
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, 342030, India.
- School of Artificial Intelligence and Data Science, Indian Institute of Technology, Jodhpur, Rajasthan, 342030, India.
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25
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Lee EJ, Suh M, Choi H, Choi Y, Hwang DW, Bae S, Lee DS. Spatial transcriptomic brain imaging reveals the effects of immunomodulation therapy on specific regional brain cells in a mouse dementia model. BMC Genomics 2024; 25:516. [PMID: 38796425 PMCID: PMC11128132 DOI: 10.1186/s12864-024-10434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
Increasing evidence of brain-immune crosstalk raises expectations for the efficacy of novel immunotherapies in Alzheimer's disease (AD), but the lack of methods to examine brain tissues makes it difficult to evaluate therapeutics. Here, we investigated the changes in spatial transcriptomic signatures and brain cell types using the 10x Genomics Visium platform in immune-modulated AD models after various treatments. To proceed with an analysis suitable for barcode-based spatial transcriptomics, we first organized a workflow for segmentation of neuroanatomical regions, establishment of appropriate gene combinations, and comprehensive review of altered brain cell signatures. Ultimately, we investigated spatial transcriptomic changes following administration of immunomodulators, NK cell supplements and an anti-CD4 antibody, which ameliorated behavior impairment, and designated brain cells and regions showing probable associations with behavior changes. We provided the customized analytic pipeline into an application named STquantool. Thus, we anticipate that our approach can help researchers interpret the real action of drug candidates by simultaneously investigating the dynamics of all transcripts for the development of novel AD therapeutics.
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Affiliation(s)
- Eun Ji Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Minseok Suh
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yoori Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cliniclal Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Do Won Hwang
- Research and Development Center, THERABEST Inc., Seocho-daero 40-gil, Seoul, 06657, Republic of Korea
| | - Sungwoo Bae
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Medical Science and Engineering, School of Convergence Science and Technology, POSTECH, Pohang, Republic of Korea.
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26
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Huuki-Myers LA, Spangler A, Eagles NJ, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR. A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science 2024; 384:eadh1938. [PMID: 38781370 DOI: 10.1126/science.adh1938] [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: 02/17/2023] [Accepted: 12/06/2023] [Indexed: 05/25/2024]
Abstract
The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally defined spatial domains that move beyond classic cytoarchitecture. We used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex. Integration with paired single-nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we mapped the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains.
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Affiliation(s)
- Louise A Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Abby Spangler
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Nicholas J Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Boyi Guo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Melissa Grant-Peters
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Chaichontat Sriworarat
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Annie B Nguyen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Prashanthi Ravichandran
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Arta Seyedian
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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27
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Tao Q, Xu Y, He Y, Luo T, Li X, Han L. Benchmarking mapping algorithms for cell-type annotating in mouse brain by integrating single-nucleus RNA-seq and Stereo-seq data. Brief Bioinform 2024; 25:bbae250. [PMID: 38796691 PMCID: PMC11128029 DOI: 10.1093/bib/bbae250] [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: 02/28/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 05/28/2024] Open
Abstract
Limited gene capture efficiency and spot size of spatial transcriptome (ST) data pose significant challenges in cell-type characterization. The heterogeneity and complexity of cell composition in the mammalian brain make it more challenging to accurately annotate ST data from brain. Many algorithms attempt to characterize subtypes of neuron by integrating ST data with single-nucleus RNA sequencing (snRNA-seq) or single-cell RNA sequencing. However, assessing the accuracy of these algorithms on Stereo-seq ST data remains unresolved. Here, we benchmarked 9 mapping algorithms using 10 ST datasets from four mouse brain regions in two different resolutions and 24 pseudo-ST datasets from snRNA-seq. Both actual ST data and pseudo-ST data were mapped using snRNA-seq datasets from the corresponding brain regions as reference data. After comparing the performance across different areas and resolutions of the mouse brain, we have reached the conclusion that both robust cell-type decomposition and SpatialDWLS demonstrated superior robustness and accuracy in cell-type annotation. Testing with publicly available snRNA-seq data from another sequencing platform in the cortex region further validated our conclusions. Altogether, we developed a workflow for assessing suitability of mapping algorithm that fits for ST datasets, which can improve the efficiency and accuracy of spatial data annotation.
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Affiliation(s)
- Quyuan Tao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310012, China
| | - Yiheng Xu
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Center of Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310058, China
| | - Youzhe He
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310012, China
| | - Ting Luo
- BGI Research, Hangzhou 310012, China
- BGI Research, Shenzhen 518103, China
| | - Xiaoming Li
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Center of Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310058, China
- Research Units for Emotion and Emotion disorders, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Lei Han
- BGI Research, Hangzhou 310012, China
- BGI Research, Shenzhen 518103, China
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28
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De Zuani M, Xue H, Park JS, Dentro SC, Seferbekova Z, Tessier J, Curras-Alonso S, Hadjipanayis A, Athanasiadis EI, Gerstung M, Bayraktar O, Cvejic A. Single-cell and spatial transcriptomics analysis of non-small cell lung cancer. Nat Commun 2024; 15:4388. [PMID: 38782901 PMCID: PMC11116453 DOI: 10.1038/s41467-024-48700-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer and the leading cause of cancer-related mortality worldwide. Tumour ecosystems feature diverse immune cell types. Myeloid cells, in particular, are prevalent and have a well-established role in promoting the disease. In our study, we profile approximately 900,000 cells from 25 treatment-naive patients with adenocarcinoma and squamous-cell carcinoma by single-cell and spatial transcriptomics. We note an inverse relationship between anti-inflammatory macrophages and NK cells/T cells, and with reduced NK cell cytotoxicity within the tumour. While we observe a similar cell type composition in both adenocarcinoma and squamous-cell carcinoma, we detect significant differences in the co-expression of various immune checkpoint inhibitors. Moreover, we reveal evidence of a transcriptional "reprogramming" of macrophages in tumours, shifting them towards cholesterol export and adopting a foetal-like transcriptional signature which promotes iron efflux. Our multi-omic resource offers a high-resolution molecular map of tumour-associated macrophages, enhancing our understanding of their role within the tumour microenvironment.
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Affiliation(s)
- Marco De Zuani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Haoliang Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Jun Sung Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Stefan C Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Zaira Seferbekova
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Julien Tessier
- Precision Medicine and Computational Biology, Sanofi, Cambridge, MA, USA
| | | | | | - Emmanouil I Athanasiadis
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Moritz Gerstung
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- OpenTargets, Wellcome Genome Campus, Hinxton, UK
| | - Ana Cvejic
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- OpenTargets, Wellcome Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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29
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Hegarty BE, Gruenhagen GW, Johnson ZV, Baker CM, Streelman JT. Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain. Commun Biol 2024; 7:612. [PMID: 38773256 PMCID: PMC11109250 DOI: 10.1038/s42003-024-06315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
The telencephalon has undergone remarkable diversification and expansion throughout vertebrate evolution, exhibiting striking variations in structural and functional complexity. Nevertheless, fundamental features are shared across vertebrate taxa, such as the presence of distinct regions including the pallium, subpallium, and olfactory structures. Teleost fishes have a uniquely "everted" telencephalon, which has confounded comparisons of their brain regions to other vertebrates. Here we combine spatial transcriptomics and single nucleus RNA-sequencing to generate a spatially-resolved transcriptional atlas of the Mchenga conophorus cichlid fish telencephalon. We then compare cell-types and anatomical regions in the cichlid telencephalon with those in amphibians, reptiles, birds, and mammals. We uncover striking transcriptional similarities between cell-types in the fish telencephalon and subpallial, hippocampal, and cortical cell-types in tetrapods, and find support for partial eversion of the teleost telencephalon. Ultimately, our work lends new insights into the organization and evolution of conserved cell-types and regions in the vertebrate forebrain.
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Affiliation(s)
- Brianna E Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - George W Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30329, USA
| | - Cristina M Baker
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jeffrey T Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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30
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Moreno J, Gluud LL, Galsgaard ED, Hvid H, Mazzoni G, Das V. Identification of ligand and receptor interactions in CKD and MASH through the integration of single cell and spatial transcriptomics. PLoS One 2024; 19:e0302853. [PMID: 38768139 PMCID: PMC11104622 DOI: 10.1371/journal.pone.0302853] [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: 12/22/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Chronic Kidney Disease (CKD) and Metabolic dysfunction-associated steatohepatitis (MASH) are metabolic fibroinflammatory diseases. Combining single-cell (scRNAseq) and spatial transcriptomics (ST) could give unprecedented molecular disease understanding at single-cell resolution. A more comprehensive analysis of the cell-specific ligand-receptor (L-R) interactions could provide pivotal information about signaling pathways in CKD and MASH. To achieve this, we created an integrative analysis framework in CKD and MASH from two available human cohorts. RESULTS The analytical framework identified L-R pairs involved in cellular crosstalk in CKD and MASH. Interactions between cell types identified using scRNAseq data were validated by checking the spatial co-presence using the ST data and the co-expression of the communicating targets. Multiple L-R protein pairs identified are known key players in CKD and MASH, while others are novel potential targets previously observed only in animal models. CONCLUSION Our study highlights the importance of integrating different modalities of transcriptomic data for a better understanding of the molecular mechanisms. The combination of single-cell resolution from scRNAseq data, combined with tissue slide investigations and visualization of cell-cell interactions obtained through ST, paves the way for the identification of future potential therapeutic targets and developing effective therapies.
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Affiliation(s)
- Jaime Moreno
- Digital Science and Innovation, Computational Biology – AI & Digital Research, Novo Nordisk A/S, Maløv, Denmark
| | - Lise Lotte Gluud
- Gastro Unit, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Henning Hvid
- Global Drug Discovery, Novo Nordisk A/S, Maløv, Denmark
| | - Gianluca Mazzoni
- Digital Science and Innovation, Computational Biology – AI & Digital Research, Novo Nordisk A/S, Maløv, Denmark
| | - Vivek Das
- Digital Science and Innovation, Computational Biology – AI & Digital Research, Novo Nordisk A/S, Maløv, Denmark
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31
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Haley MJ, Bere L, Minshull J, Georgaka S, Garcia-Martin N, Howell G, Coope DJ, Roncaroli F, King A, Wedge DC, Allan SM, Pathmanaban ON, Brough D, Couper KN. Hypoxia coordinates the spatial landscape of myeloid cells within glioblastoma to affect survival. SCIENCE ADVANCES 2024; 10:eadj3301. [PMID: 38758780 PMCID: PMC11100569 DOI: 10.1126/sciadv.adj3301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Myeloid cells are highly prevalent in glioblastoma (GBM), existing in a spectrum of phenotypic and activation states. We now have limited knowledge of the tumor microenvironment (TME) determinants that influence the localization and the functions of the diverse myeloid cell populations in GBM. Here, we have utilized orthogonal imaging mass cytometry with single-cell and spatial transcriptomic approaches to identify and map the various myeloid populations in the human GBM tumor microenvironment (TME). Our results show that different myeloid populations have distinct and reproducible compartmentalization patterns in the GBM TME that is driven by tissue hypoxia, regional chemokine signaling, and varied homotypic and heterotypic cellular interactions. We subsequently identified specific tumor subregions in GBM, based on composition of identified myeloid cell populations, that were linked to patient survival. Our results provide insight into the spatial organization of myeloid cell subpopulations in GBM, and how this is predictive of clinical outcome.
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Affiliation(s)
- Michael J. Haley
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
| | - Leoma Bere
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
| | - James Minshull
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Sokratia Georgaka
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, UK
| | | | - Gareth Howell
- Flow Cytometry Core Research Facility, University of Manchester, Manchester, UK
| | - David J. Coope
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - Federico Roncaroli
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - Andrew King
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - David C. Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Stuart M. Allan
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Omar N. Pathmanaban
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - David Brough
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Kevin N. Couper
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Inflammation and Immunology, University of Manchester, Manchester, UK
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32
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Steyn C, Mishi R, Fillmore S, Verhoog MB, More J, Rohlwink UK, Melvill R, Butler J, Enslin JMN, Jacobs M, Sauka-Spengler T, Greco M, Quiñones S, Dulla CG, Raimondo JV, Figaji A, Hockman D. Cell type-specific gene expression dynamics during human brain maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560114. [PMID: 37808657 PMCID: PMC10557738 DOI: 10.1101/2023.09.29.560114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The human brain undergoes protracted post-natal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell type-specific gene expression dynamics. Here, using single nucleus (sn)RNA-seq on temporal lobe tissue, including samples of African ancestry, we build a joint paediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between paediatric and adult cell types, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in paediatric tissue. The new resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map.
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Affiliation(s)
- Christina Steyn
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ruvimbo Mishi
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fillmore
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Matthijs B Verhoog
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jessica More
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ursula K Rohlwink
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Roger Melvill
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - James Butler
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Johannes M N Enslin
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Muazzam Jacobs
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Immunology, Department of Pathology University of Cape Town
- National Health Laboratory Service, South Africa
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Maria Greco
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sadi Quiñones
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Graduate School of Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Joseph V Raimondo
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anthony Figaji
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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33
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Zhang G, Sun Y, Guan M, Liu M, Sun S. Single-cell and spatial transcriptomic investigation reveals the spatiotemporal specificity of the beta-defensin gene family during mouse sperm maturation. Cell Commun Signal 2024; 22:267. [PMID: 38745232 PMCID: PMC11092205 DOI: 10.1186/s12964-024-01637-3] [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: 12/02/2023] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
Low sperm motility is a significant contributor to male infertility. beta-defensins have been implicated in host defence and the acquisition of sperm motility; however, the regulatory mechanisms governing their gene expression patterns and functions remain poorly understood. In this study, we performed single-cell RNA and spatial transcriptome sequencing to investigate the cellular composition of testicular and epididymal tissues and examined their gene expression characteristics. In the epididymis, we found that epididymal epithelial cells display a region specificity of gene expression in different epididymal segments, including the beta-defensin family genes. In particular, Defb15, Defb18, Defb20, Defb25 and Defb48 are specific to the caput; Defb22, Defb23 and Defb26 to the corpus; Defb2 and Defb9 to the cauda of the epididymis. To confirm this, we performed mRNA fluorescence in situ hybridisation (FISH) targeting certain exon region of beta-defensin genes, and found some of their expression matched the sequencing results and displayed a close connection with epididimosome marker gene Cd63. In addition, we paid attention to the Sertoli cells and Leydig cells in the testis, along with fibroblasts and smooth muscle cells in the epididymis, by demonstrating their gene expression profile and spatial information. Our study provides a single-cell and spatial landscape for analysing the gene expression characteristics of testicular and epididymal environments and has important implications for the study of spermatogenesis and sperm maturation.
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Affiliation(s)
| | - Yuanchao Sun
- Qingdao Agricultural University, Qingdao, China
- Qingdao University, Qingdao, China
| | - Minkai Guan
- Qingdao Agricultural University, Qingdao, China
| | | | - Shiduo Sun
- Northwest A&F University, Yangling, China
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34
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Kang J, Lee JH, Cha H, An J, Kwon J, Lee S, Kim S, Baykan MY, Kim SY, An D, Kwon AY, An HJ, Lee SH, Choi JK, Park JE. Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types. Nat Commun 2024; 15:4067. [PMID: 38744958 PMCID: PMC11094150 DOI: 10.1038/s41467-024-48310-4] [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: 05/26/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
The complexity of the tumor microenvironment poses significant challenges in cancer therapy. Here, to comprehensively investigate the tumor-normal ecosystems, we perform an integrative analysis of 4.9 million single-cell transcriptomes from 1070 tumor and 493 normal samples in combination with pan-cancer 137 spatial transcriptomics, 8887 TCGA, and 1261 checkpoint inhibitor-treated bulk tumors. We define a myriad of cell states constituting the tumor-normal ecosystems and also identify hallmark gene signatures across different cell types and organs. Our atlas characterizes distinctions between inflammatory fibroblasts marked by AKR1C1 or WNT5A in terms of cellular interactions and spatial co-localization patterns. Co-occurrence analysis reveals interferon-enriched community states including tertiary lymphoid structure (TLS) components, which exhibit differential rewiring between tumor, adjacent normal, and healthy normal tissues. The favorable response of interferon-enriched community states to immunotherapy is validated using immunotherapy-treated cancers (n = 1261) including our lung cancer cohort (n = 497). Deconvolution of spatial transcriptomes discriminates TLS-enriched from non-enriched cell types among immunotherapy-favorable components. Our systematic dissection of tumor-normal ecosystems provides a deeper understanding of inter- and intra-tumoral heterogeneity.
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Affiliation(s)
- Junho Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jun Hyeong Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinhyeon An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Joonha Kwon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Division of Cancer Data Science, National Cancer Center, Bioinformatics Branch, Goyang, Republic of Korea
| | - Seongwoo Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seongryong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Mert Yakup Baykan
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - So Yeon Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dohyeon An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ah-Young Kwon
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
- Biomedical Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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Gupta T, Antanaviciute A, Hyun-Jung Lee C, Ottakandathil Babu R, Aulicino A, Christoforidou Z, Siejka-Zielinska P, O'Brien-Ball C, Chen H, Fawkner-Corbett D, Geros AS, Bridges E, McGregor C, Cianci N, Fryer E, Alham NK, Jagielowicz M, Santos AM, Fellermeyer M, Davis SJ, Parikh K, Cheung V, Al-Hillawi L, Sasson S, Slevin S, Brain O, Fernandes RA, Koohy H, Simmons A. Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis. Cancer Cell 2024; 42:797-814.e15. [PMID: 38744246 DOI: 10.1016/j.ccell.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8+ T cells, but how these arise is unclear. Here, we track CPI-bound T cells in intestinal tissue using multimodal single-cell and subcellular spatial transcriptomics (ST). Target occupancy was increased in inflamed tissue, with drug-bound T cells located in distinct microdomains distinguished by specific intercellular signaling and transcriptional gradients. CPI-bound cells were largely CD4+ T cells, including enrichment in CPI-bound peripheral helper, follicular helper, and regulatory T cells. IFNγ CD8+ T cells emerged from both tissue-resident memory (TRM) and peripheral populations, displayed more restricted target occupancy profiles, and co-localized with damaged epithelial microdomains lacking effective regulatory cues. Our multimodal analysis identifies causal pathways and constitutes a resource to inform novel preventive strategies.
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Affiliation(s)
- Tarun Gupta
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Chloe Hyun-Jung Lee
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rosana Ottakandathil Babu
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Anna Aulicino
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Zoe Christoforidou
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Paulina Siejka-Zielinska
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Caitlin O'Brien-Ball
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hannah Chen
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - David Fawkner-Corbett
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Ana Sousa Geros
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Esther Bridges
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Colleen McGregor
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Nicole Cianci
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Eve Fryer
- Pathology, Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Nasullah Khalid Alham
- Nuffield Department of Surgical Sciences and Oxford NIHR Biomedical Research Centre (BRC), University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ana Mafalda Santos
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Martin Fellermeyer
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Simon J Davis
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Vincent Cheung
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lulia Al-Hillawi
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sarah Sasson
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Stephanie Slevin
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Oliver Brain
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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36
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Wang W, Li T, Cheng Y, Li F, Qi S, Mao M, Wu J, Liu Q, Zhang X, Li X, Zhang L, Qi H, Yang L, Yang K, He Z, Ding S, Qin Z, Yang Y, Yang X, Luo C, Guo Y, Wang C, Liu X, Zhou L, Liu Y, Kong W, Miao J, Ye S, Luo M, An L, Wang L, Che L, Niu Q, Ma Q, Zhang X, Zhang Z, Hu R, Feng H, Ping YF, Bian XW, Shi Y. Identification of hypoxic macrophages in glioblastoma with therapeutic potential for vasculature normalization. Cancer Cell 2024; 42:815-832.e12. [PMID: 38640932 DOI: 10.1016/j.ccell.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/21/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
Monocyte-derived tumor-associated macrophages (Mo-TAMs) intensively infiltrate diffuse gliomas with remarkable heterogeneity. Using single-cell transcriptomics, we chart a spatially resolved transcriptional landscape of Mo-TAMs across 51 patients with isocitrate dehydrogenase (IDH)-wild-type glioblastomas or IDH-mutant gliomas. We characterize a Mo-TAM subset that is localized to the peri-necrotic niche and skewed by hypoxic niche cues to acquire a hypoxia response signature. Hypoxia-TAM destabilizes endothelial adherens junctions by activating adrenomedullin paracrine signaling, thereby stimulating a hyperpermeable neovasculature that hampers drug delivery in glioblastoma xenografts. Accordingly, genetic ablation or pharmacological blockade of adrenomedullin produced by Hypoxia-TAM restores vascular integrity, improves intratumoral concentration of the anti-tumor agent dabrafenib, and achieves combinatorial therapeutic benefits. Increased proportion of Hypoxia-TAM or adrenomedullin expression is predictive of tumor vessel hyperpermeability and a worse prognosis of glioblastoma. Our findings highlight Mo-TAM diversity and spatial niche-steered Mo-TAM reprogramming in diffuse gliomas and indicate potential therapeutics targeting Hypoxia-TAM to normalize tumor vasculature.
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Affiliation(s)
- Wenying Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Tianran Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Yue Cheng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Fei Li
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Shuhong Qi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P.R. China
| | - Min Mao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Jingjing Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Qing Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xiaoning Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xuegang Li
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Lu Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Haoyue Qi
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lan Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Kaidi Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Zhicheng He
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Shuaishuai Ding
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Zhongyi Qin
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Ying Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xi Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Chunhua Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Ying Guo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Chao Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xindong Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lei Zhou
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Yuqi Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Weikai Kong
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Jingya Miao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Shuanghui Ye
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Min Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lele An
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Lujing Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Linrong Che
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Qin Niu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Qinghua Ma
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Xia Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China
| | - Zhihong Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P.R. China
| | - Rong Hu
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Hua Feng
- Department of Neurosurgery and Glioma Medical Research Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Yi-Fang Ping
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 400039, P. R. China; Yu-Yue Scientific Research Center for Pathology, Jinfeng Laboratory, Chongqing 400039, P.R. China.
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 400039, P. R. China; Yu-Yue Scientific Research Center for Pathology, Jinfeng Laboratory, Chongqing 400039, P.R. China.
| | - Yu Shi
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Amy Medical University), and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing 400038, P.R. China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 400039, P. R. China; Yu-Yue Scientific Research Center for Pathology, Jinfeng Laboratory, Chongqing 400039, P.R. China.
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37
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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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38
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Greenwald AC, Darnell NG, Hoefflin R, Simkin D, Mount CW, Gonzalez Castro LN, Harnik Y, Dumont S, Hirsch D, Nomura M, Talpir T, Kedmi M, Goliand I, Medici G, Laffy J, Li B, Mangena V, Keren-Shaul H, Weller M, Addadi Y, Neidert MC, Suvà ML, Tirosh I. Integrative spatial analysis reveals a multi-layered organization of glioblastoma. Cell 2024; 187:2485-2501.e26. [PMID: 38653236 PMCID: PMC11088502 DOI: 10.1016/j.cell.2024.03.029] [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: 06/16/2023] [Revised: 01/11/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics, spatial proteomics, and computational approaches to define glioma cellular states and uncover their organization. We find three prominent modes of organization. First, gliomas are composed of small local environments, each typically enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. This pairing of states is consistent across tumors. Third, these pairwise interactions collectively define a global architecture composed of five layers. Hypoxia appears to drive the layers, as it is associated with a long-range organization that includes all cancer cell states. Accordingly, tumor regions distant from any hypoxic/necrotic foci and tumors that lack hypoxia such as low-grade IDH-mutant glioma are less organized. In summary, we provide a conceptual framework for the organization of cellular states in glioma, highlighting hypoxia as a long-range tissue organizer.
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Affiliation(s)
- Alissa C Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Galili Darnell
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dor Simkin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Christopher W Mount
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Nicolas Gonzalez Castro
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sydney Dumont
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dana Hirsch
- Immunohistochemistry Unit, Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Masashi Nomura
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tom Talpir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Goliand
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Gioele Medici
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julie Laffy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Vamsi Mangena
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Weller
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Marian C Neidert
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Mario L Suvà
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Ramnauth AD, Tippani M, Divecha HR, Papariello AR, Miller RA, Nelson ED, Pattie EA, Kleinman JE, Maynard KR, Collado-Torres L, Hyde TM, Martinowich K, Hicks SC, Page SC. Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567883. [PMID: 38045413 PMCID: PMC10690172 DOI: 10.1101/2023.11.20.567883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The dentate gyrus of the hippocampus is important for many cognitive functions, including learning, memory, and mood. Here, we investigated age-associated changes in transcriptome-wide spatial gene expression in the human dentate gyrus across the lifespan. Genes associated with neurogenesis and the extracellular matrix were enriched in infants, while gene markers of inhibitory neurons and cell proliferation showed increases and decreases in post-infancy, respectively. While we did not find evidence for neural proliferation post-infancy, we did identify molecular signatures supporting protracted maturation of granule cells. We also identified a wide-spread hippocampal aging signature and an age-associated increase in genes related to neuroinflammation. Our findings suggest major changes to the putative neurogenic niche after infancy and identify molecular foci of brain aging in glial and neuropil enriched tissue.
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Mongia A, Zohora FT, Burget NG, Zhou Y, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW, Faryabi RB. AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics. Nat Commun 2024; 15:3744. [PMID: 38702321 PMCID: PMC11068798 DOI: 10.1038/s41467-024-47334-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 03/25/2024] [Indexed: 05/06/2024] Open
Abstract
Cellular composition and anatomical organization influence normal and aberrant organ functions. Emerging spatial single-cell proteomic assays such as Image Mass Cytometry (IMC) and Co-Detection by Indexing (CODEX) have facilitated the study of cellular composition and organization by enabling high-throughput measurement of cells and their localization directly in intact tissues. However, annotation of cell types and quantification of their relative localization in tissues remain challenging. To address these unmet needs for atlas-scale datasets like Human Pancreas Analysis Program (HPAP), we develop AnnoSpat (Annotator and Spatial Pattern Finder) that uses neural network and point process algorithms to automatically identify cell types and quantify cell-cell proximity relationships. Our study of data from IMC and CODEX shows the higher performance of AnnoSpat in rapid and accurate annotation of cell types compared to alternative approaches. Moreover, the application of AnnoSpat to type 1 diabetic, non-diabetic autoantibody-positive, and non-diabetic organ donor cohorts recapitulates known islet pathobiology and shows differential dynamics of pancreatic polypeptide (PP) cell abundance and CD8+ T cells infiltration in islets during type 1 diabetes progression.
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Affiliation(s)
- Aanchal Mongia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Fatema Tuz Zohora
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Vector Institute, University of Toronto, Toronto, ON, Canada
| | - Noah G Burget
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Diane C Saunders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yue J Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marcela Brissova
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alvin C Powers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- VA Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Klaus H Kaestner
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ali Naji
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory W Schwartz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Vector Institute, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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41
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Laury AR, Zheng S, Aho N, Fallegger R, Hänninen S, Saez-Rodriguez J, Tanevski J, Youssef O, Tang J, Carpén OM. Opening the Black Box: Spatial Transcriptomics and the Relevance of Artificial Intelligence-Detected Prognostic Regions in High-Grade Serous Carcinoma. Mod Pathol 2024; 37:100508. [PMID: 38704029 DOI: 10.1016/j.modpat.2024.100508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Image-based deep learning models are used to extract new information from standard hematoxylin and eosin pathology slides; however, biological interpretation of the features detected by artificial intelligence (AI) remains a challenge. High-grade serous carcinoma of the ovary (HGSC) is characterized by aggressive behavior and chemotherapy resistance, but also exhibits striking variability in outcome. Our understanding of this disease is limited, partly due to considerable tumor heterogeneity. We previously trained an AI model to identify HGSC tumor regions that are highly associated with outcome status but are indistinguishable by conventional morphologic methods. Here, we applied spatially resolved transcriptomics to further profile the AI-identified tumor regions in 16 patients (8 per outcome group) and identify molecular features related to disease outcome in patients who underwent primary debulking surgery and platinum-based chemotherapy. We examined formalin-fixed paraffin-embedded tissue from (1) regions identified by the AI model as highly associated with short or extended chemotherapy response, and (2) background tumor regions (not identified by the AI model as highly associated with outcome status) from the same tumors. We show that the transcriptomic profiles of AI-identified regions are more distinct than background regions from the same tumors, are superior in predicting outcome, and differ in several pathways including those associated with chemoresistance in HGSC. Further, we find that poor outcome and good outcome regions are enriched by different tumor subpopulations, suggesting distinctive interaction patterns. In summary, our work presents proof of concept that AI-guided spatial transcriptomic analysis improves recognition of biologic features relevant to patient outcomes.
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Affiliation(s)
- Anna Ray Laury
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland.
| | - Shuyu Zheng
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Niina Aho
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robin Fallegger
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | - Satu Hänninen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | - Jovan Tanevski
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany; Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Omar Youssef
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Jing Tang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Olli Mikael Carpén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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42
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Schmauch E, Piening B, Mohebnasab M, Xia B, Zhu C, Stern J, Zhang W, Dowdell AK, Kim JI, Andrijevic D, Khalil K, Jaffe IS, Loza BL, Gragert L, Camellato BR, Oliveira MF, O'Brien DP, Chen HM, Weldon E, Gao H, Gandla D, Chang A, Bhatt R, Gao S, Lin X, Reddy KP, Kagermazova L, Habara AH, Widawsky S, Liang FX, Sall J, Loupy A, Heguy A, Taylor SEB, Zhu Y, Michael B, Jiang L, Jian R, Chong AS, Fairchild RL, Linna-Kuosmanen S, Kaikkonen MU, Tatapudi V, Lorber M, Ayares D, Mangiola M, Narula N, Moazami N, Pass H, Herati RS, Griesemer A, Kellis M, Snyder MP, Montgomery RA, Boeke JD, Keating BJ. Integrative multi-omics profiling in human decedents receiving pig heart xenografts. Nat Med 2024; 30:1448-1460. [PMID: 38760586 DOI: 10.1038/s41591-024-02972-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/03/2024] [Indexed: 05/19/2024]
Abstract
In a previous study, heart xenografts from 10-gene-edited pigs transplanted into two human decedents did not show evidence of acute-onset cellular- or antibody-mediated rejection. Here, to better understand the detailed molecular landscape following xenotransplantation, we carried out bulk and single-cell transcriptomics, lipidomics, proteomics and metabolomics on blood samples obtained from the transplanted decedents every 6 h, as well as histological and transcriptomic tissue profiling. We observed substantial early immune responses in peripheral blood mononuclear cells and xenograft tissue obtained from decedent 1 (male), associated with downstream T cell and natural killer cell activity. Longitudinal analyses indicated the presence of ischemia reperfusion injury, exacerbated by inadequate immunosuppression of T cells, consistent with previous findings of perioperative cardiac xenograft dysfunction in pig-to-nonhuman primate studies. Moreover, at 42 h after transplantation, substantial alterations in cellular metabolism and liver-damage pathways occurred, correlating with profound organ-wide physiological dysfunction. By contrast, relatively minor changes in RNA, protein, lipid and metabolism profiles were observed in decedent 2 (female) as compared to decedent 1. Overall, these multi-omics analyses delineate distinct responses to cardiac xenotransplantation in the two human decedents and reveal new insights into early molecular and immune responses after xenotransplantation. These findings may aid in the development of targeted therapeutic approaches to limit ischemia reperfusion injury-related phenotypes and improve outcomes.
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Affiliation(s)
- Eloi Schmauch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Brian Piening
- Earle A. Chiles Research Institute, Providence Cancer Center, Portland, OR, USA
| | - Maedeh Mohebnasab
- Division of Molecular Genetics Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Bo Xia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jeffrey Stern
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Alexa K Dowdell
- Earle A. Chiles Research Institute, Providence Cancer Center, Portland, OR, USA
| | - Jacqueline I Kim
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - David Andrijevic
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Karen Khalil
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
| | - Ian S Jaffe
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Bao-Li Loza
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Loren Gragert
- Division of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | | | | | - Han M Chen
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Elaina Weldon
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Hui Gao
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Divya Gandla
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Chang
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Riyana Bhatt
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Gao
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiangping Lin
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kriyana P Reddy
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Alawi H Habara
- Department of Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Sophie Widawsky
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Feng-Xia Liang
- DART Microscopy Laboratory, NYU Langone Health, New York, NY, USA
| | - Joseph Sall
- DART Microscopy Laboratory, NYU Langone Health, New York, NY, USA
| | - Alexandre Loupy
- Université Paris Cité, Paris Institute for Transplantation and Organ Regeneration, Paris, France
| | - Adriana Heguy
- Genome Technology Center, NYU Langone Health, New York, NY, USA
| | | | - Yinan Zhu
- Division of Molecular Genetics Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Basil Michael
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anita S Chong
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Robert L Fairchild
- Department of Inflammation and Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Suvi Linna-Kuosmanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vasishta Tatapudi
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | | | | | - Massimo Mangiola
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
| | - Navneet Narula
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Nader Moazami
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
| | - Harvey Pass
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
| | - Ramin S Herati
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Adam Griesemer
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | | | - Robert A Montgomery
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Brendan J Keating
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY, USA.
- Department of Surgery, NYU Grossman School of Medicine, New York, NY, USA.
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Wang Y, Jiang Y, Ni G, Li S, Balderson B, Zou Q, Liu H, Jiang Y, Sun J, Ding X. Integrating Single-Cell and Spatial Transcriptomics Reveals Heterogeneity of Early Pig Skin Development and a Subpopulation with Hair Placode Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306703. [PMID: 38561967 PMCID: PMC11132071 DOI: 10.1002/advs.202306703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The dermis and epidermis, crucial structural layers of the skin, encompass appendages, hair follicles (HFs), and intricate cellular heterogeneity. However, an integrated spatiotemporal transcriptomic atlas of embryonic skin has not yet been described and would be invaluable for studying skin-related diseases in humans. Here, single-cell and spatial transcriptomic analyses are performed on skin samples of normal and hairless fetal pigs across four developmental periods. The cross-species comparison of skin cells illustrated that the pig epidermis is more representative of the human epidermis than mice epidermis. Moreover, Phenome-wide association study analysis revealed that the conserved genes between pigs and humans are strongly associated with human skin-related diseases. In the epidermis, two lineage differentiation trajectories describe hair follicle (HF) morphogenesis and epidermal development. By comparing normal and hairless fetal pigs, it is found that the hair placode (Pc), the most characteristic initial structure in HFs, arises from progenitor-like OGN+/UCHL1+ cells. These progenitors appear earlier in development than the previously described early Pc cells and exhibit abnormal proliferation and migration during differentiation in hairless pigs. The study provides a valuable resource for in-depth insights into HF development, which may serve as a key reference atlas for studying human skin disease etiology using porcine models.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yao Jiang
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Guiyan Ni
- Division of Genetics and GenomicsInstitute for Molecular BioscienceThe University of QueenslandBrisbane4072Australia
| | - Shujuan Li
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Brad Balderson
- School of Chemistry & Molecular BiosciencesThe University of QueenslandBrisbane4067Australia
| | - Quan Zou
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Huatao Liu
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yifan Jiang
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Jingchun Sun
- Key Laboratory of Animal GeneticsBreeding and Reproduction of Shaanxi ProvinceLaboratory of Animal Fat Deposition & Muscle DevelopmentCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China
| | - Xiangdong Ding
- State Key Laboratory of Animal Biotech BreedingNational Engineering Laboratory for Animal BreedingLaboratory of Animal GeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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45
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Khatri R, Machart P, Bonn S. DISSECT: deep semi-supervised consistency regularization for accurate cell type fraction and gene expression estimation. Genome Biol 2024; 25:112. [PMID: 38689377 PMCID: PMC11061925 DOI: 10.1186/s13059-024-03251-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Cell deconvolution is the estimation of cell type fractions and cell type-specific gene expression from mixed data. An unmet challenge in cell deconvolution is the scarcity of realistic training data and the domain shift often observed in synthetic training data. Here, we show that two novel deep neural networks with simultaneous consistency regularization of the target and training domains significantly improve deconvolution performance. Our algorithm, DISSECT, outperforms competing algorithms in cell fraction and gene expression estimation by up to 14 percentage points. DISSECT can be easily adapted to other biomedical data types, as exemplified by our proteomic deconvolution experiments.
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Affiliation(s)
- Robin Khatri
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pierre Machart
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Nelson ED, Tippani M, Ramnauth AD, Divecha HR, Miller RA, Eagles NJ, Pattie EA, Kwon SH, Bach SV, Kaipa UM, Yao J, Kleinman JE, Collado-Torres L, Han S, Maynard KR, Hyde TM, Martinowich K, Page SC, Hicks SC. An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.590643. [PMID: 38712198 PMCID: PMC11071618 DOI: 10.1101/2024.04.26.590643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The hippocampus contains many unique cell types, which serve the structure's specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and infer the expression of these patterns in the SRT data. With this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.
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Licón-Muñoz Y, Avalos V, Subramanian S, Granger B, Martinez F, Varela S, Moore D, Perkins E, Kogan M, Berto S, Chohan M, Bowers C, Piccirillo S. Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590852. [PMID: 38712234 PMCID: PMC11071523 DOI: 10.1101/2024.04.24.590852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The sub-ventricular zone (SVZ) is the most well-characterized neurogenic area in the mammalian brain. We previously showed that in 65% of patients with glioblastoma (GBM), the SVZ is a reservoir of cancer stem-like cells that contribute to treatment resistance and emergence of recurrence. Here, we built a single-nucleus RNA-sequencing-based microenvironment landscape of the tumor mass (T_Mass) and the SVZ (T_SVZ) of 15 GBM patients and 2 histologically normal SVZ (N_SVZ) samples as controls. We identified a mesenchymal signature in the T_SVZ of GBM patients: tumor cells from the T_SVZ relied on the ZEB1 regulatory network, whereas tumor cells in the T_Mass relied on the TEAD1 regulatory network. Moreover, the T_SVZ microenvironment was predominantly characterized by tumor-supportive microglia, which spatially co-exist and establish heterotypic interactions with tumor cells. Lastly, differential gene expression analyses, predictions of ligand-receptor and incoming/outgoing interactions, and functional assays revealed that the IL-1β/IL-1RAcP and Wnt-5a/Frizzled-3 pathways are therapeutic targets in the T_SVZ microenvironment. Our data provide insights into the biology of the SVZ in GBM patients and identify specific targets of this microenvironment.
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Affiliation(s)
- Y. Licón-Muñoz
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - V. Avalos
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - S. Subramanian
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - B. Granger
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - F. Martinez
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - S. Varela
- University of New Mexico School of Medicine, Albuquerque, NM
| | - D. Moore
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - E. Perkins
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS
| | - M. Kogan
- Department of Neurosurgery, University of New Mexico Hospital, Albuquerque, NM
| | - S. Berto
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - M.O. Chohan
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS
| | - C.A. Bowers
- Department of Neurosurgery, University of New Mexico Hospital, Albuquerque, NM
| | - S.G.M. Piccirillo
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
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48
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Matchett KP, Paris J, Teichmann SA, Henderson NC. Spatial genomics: mapping human steatotic liver disease. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00915-2. [PMID: 38654090 DOI: 10.1038/s41575-024-00915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as non-alcoholic fatty liver disease) is a leading cause of chronic liver disease worldwide. MASLD can progress to metabolic dysfunction-associated steatohepatitis (MASH, formerly known as non-alcoholic steatohepatitis) with subsequent liver cirrhosis and hepatocellular carcinoma formation. The advent of current technologies such as single-cell and single-nuclei RNA sequencing have transformed our understanding of the liver in homeostasis and disease. The next frontier is contextualizing this single-cell information in its native spatial orientation. This understanding will markedly accelerate discovery science in hepatology, resulting in a further step-change in our knowledge of liver biology and pathobiology. In this Review, we discuss up-to-date knowledge of MASLD development and progression and how the burgeoning field of spatial genomics is driving exciting new developments in our understanding of human liver disease pathogenesis and therapeutic target identification.
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Affiliation(s)
- Kylie P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Jasmin Paris
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Neil C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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49
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Rossi M, Radisky DC. Multiplex Digital Spatial Profiling in Breast Cancer Research: State-of-the-Art Technologies and Applications across the Translational Science Spectrum. Cancers (Basel) 2024; 16:1615. [PMID: 38730568 PMCID: PMC11083340 DOI: 10.3390/cancers16091615] [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: 03/21/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
While RNA sequencing and multi-omic approaches have significantly advanced cancer diagnosis and treatment, their limitation in preserving critical spatial information has been a notable drawback. This spatial context is essential for understanding cellular interactions and tissue dynamics. Multiplex digital spatial profiling (MDSP) technologies overcome this limitation by enabling the simultaneous analysis of transcriptome and proteome data within the intact spatial architecture of tissues. In breast cancer research, MDSP has emerged as a promising tool, revealing complex biological questions related to disease evolution, identifying biomarkers, and discovering drug targets. This review highlights the potential of MDSP to revolutionize clinical applications, ranging from risk assessment and diagnostics to prognostics, patient monitoring, and the customization of treatment strategies, including clinical trial guidance. We discuss the major MDSP techniques, their applications in breast cancer research, and their integration in clinical practice, addressing both their potential and current limitations. Emphasizing the strategic use of MDSP in risk stratification for women with benign breast disease, we also highlight its transformative potential in reshaping the landscape of breast cancer research and treatment.
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Affiliation(s)
| | - Derek C. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
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50
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Zhou B, Feng C, Sun S, Chen X, Zhuansun D, Wang D, Yu X, Meng X, Xiao J, Wu L, Wang J, Wang J, Chen K, Li Z, You J, Mao H, Yang S, Zhang J, Jiao C, Li Z, Yu D, Wu X, Zhu T, Yang J, Xiang L, Liu J, Chai T, Shen J, Mao CX, Hu J, Hao X, Xiong B, Zheng S, Liu Z, Feng J. Identification of signaling pathways that specify a subset of migrating enteric neural crest cells at the wavefront in mouse embryos. Dev Cell 2024:S1534-5807(24)00202-8. [PMID: 38636517 DOI: 10.1016/j.devcel.2024.03.034] [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: 07/25/2023] [Revised: 01/17/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
During enteric nervous system (ENS) development, pioneering wavefront enteric neural crest cells (ENCCs) initiate gut colonization. However, the molecular mechanisms guiding their specification and niche interaction are not fully understood. We used single-cell RNA sequencing and spatial transcriptomics to map the spatiotemporal dynamics and molecular landscape of wavefront ENCCs in mouse embryos. Our analysis shows a progressive decline in wavefront ENCC potency during migration and identifies transcription factors governing their specification and differentiation. We further delineate key signaling pathways (ephrin-Eph, Wnt-Frizzled, and Sema3a-Nrp1) utilized by wavefront ENCCs to interact with their surrounding cells. Disruptions in these pathways are observed in human Hirschsprung's disease gut tissue, linking them to ENS malformations. Additionally, we observed region-specific and cell-type-specific transcriptional changes in surrounding gut tissues upon wavefront ENCC arrival, suggesting their role in shaping the gut microenvironment. This work offers a roadmap of ENS development, with implications for understanding ENS disorders.
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Affiliation(s)
- Bingyan Zhou
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Chenzhao Feng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Song Sun
- Department of Pediatric Surgery, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Ministry of Health, Shanghai 201102, China
| | - Xuyong Chen
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Didi Zhuansun
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Di Wang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Xiaosi Yu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Xinyao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jun Xiao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Luyao Wu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jing Wang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jing Wang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Ke Chen
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Zejian Li
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jingyi You
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Handan Mao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Shimin Yang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jiaxin Zhang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Chunlei Jiao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Zhi Li
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Donghai Yu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Xiaojuan Wu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Tianqi Zhu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jixin Yang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Lei Xiang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China
| | - Jiazhe Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518081, China
| | | | - Juan Shen
- BGI-Shenzhen, Shenzhen, Guangdong 518081, China
| | - Chuan-Xi Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Juncheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Bo Xiong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Institute for Brain Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shan Zheng
- Department of Pediatric Surgery, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Ministry of Health, Shanghai 201102, China
| | - Zhihua Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China.
| | - Jiexiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, Hubei 430030, China.
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