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Alves M, Gil B, Villegas-Salmerón J, Salari V, Martins-Ferreira R, Arribas Blázquez M, Menéndez Méndez A, Da Rosa Gerbatin R, Smith J, de Diego-Garcia L, Conte G, Sierra-Marquez J, Merino Serrais P, Mitra M, Fernandez Martin A, Wang Y, Kesavan J, Melia C, Parras A, Beamer E, Zimmer B, Heiland M, Cavanagh B, Parcianello Cipolat R, Morgan J, Teng X, Prehn JHM, Fabene PF, Bertini G, Artalejo AR, Ballestar E, Nicke A, Olivos-Oré LA, Connolly NMC, Henshall DC, Engel T. Opposing effects of the purinergic P2X7 receptor on seizures in neurons and microglia in male mice. Brain Behav Immun 2024; 120:121-140. [PMID: 38777288 DOI: 10.1016/j.bbi.2024.05.023] [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: 12/23/2023] [Revised: 04/28/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND The purinergic ATP-gated P2X7 receptor (P2X7R) is increasingly recognized to contribute to pathological neuroinflammation and brain hyperexcitability. P2X7R expression has been shown to be increased in the brain, including both microglia and neurons, in experimental models of epilepsy and patients. To date, the cell type-specific downstream effects of P2X7Rs during seizures remain, however, incompletely understood. METHODS Effects of P2X7R signaling on seizures and epilepsy were analyzed in induced seizure models using male mice including the kainic acid model of status epilepticus and pentylenetetrazole model and in male and female mice in a genetic model of Dravet syndrome. RNA sequencing was used to analyze P2X7R downstream signaling during seizures. To investigate the cell type-specific role of the P2X7R during seizures and epilepsy, we generated mice lacking exon 2 of the P2rx7 gene in either microglia (P2rx7:Cx3cr1-Cre) or neurons (P2rx7:Thy-1-Cre). To investigate the protective potential of overexpressing P2X7R in GABAergic interneurons, P2X7Rs were overexpressed using adeno-associated virus transduction under the mDlx promoter. RESULTS RNA sequencing of hippocampal tissue from wild-type and P2X7R knock-out mice identified both glial and neuronal genes, in particular genes involved in GABAergic signaling, under the control of the P2X7R following seizures. Mice with deleted P2rx7 in microglia displayed less severe acute seizures and developed a milder form of epilepsy, and microglia displayed an anti-inflammatory molecular profile. In contrast, mice lacking P2rx7 in neurons showed a more severe seizure phenotype when compared to epileptic wild-type mice. Analysis of single-cell expression data revealed that human P2RX7 expression is elevated in the hippocampus of patients with temporal lobe epilepsy in excitatory and inhibitory neurons. Functional studies determined that GABAergic interneurons display increased responses to P2X7R activation in experimental epilepsy. Finally, we show that viral transduction of P2X7R in GABAergic interneurons protects against evoked and spontaneous seizures in experimental temporal lobe epilepsy and in mice lacking Scn1a, a model of Dravet syndrome. CONCLUSIONS Our results suggest a dual and opposing action of P2X7R in epilepsy and suggest P2X7R overexpression in GABAergic interneurons as a novel therapeutic strategy for acquired and, possibly, genetic forms of epilepsy.
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Affiliation(s)
- Mariana Alves
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Beatriz Gil
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Javier Villegas-Salmerón
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland; The SFI Centre for Research Training in Genomics Data Science, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Valentina Salari
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, 37134 Verona, Italy
| | - Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Immunogenetics Laboratory, Molecular Pathology and Immunology, Instituto de Ciências Biomédicas Abel Salazar - Universidade do Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Autoimmunity and Neuroscience Group, UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Marina Arribas Blázquez
- Department of Pharmacology and Toxicology, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Aida Menéndez Méndez
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670, Villaviciosa de Odon, Spain
| | - Rogerio Da Rosa Gerbatin
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Jonathon Smith
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Laura de Diego-Garcia
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; Ocupharm Research Group, Faculty of Optics and Optometry, Complutense University of Madrid, Avda. Arcos de Jalon, 118 (28037), Madrid, Spain
| | - Giorgia Conte
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Juan Sierra-Marquez
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany; Laboratorio Cajal de Circuitos Corticales (CTB), Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Campus Montegancedo S/N, Pozuelo de Alarcon, 28223 Madrid, Spain; Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28002, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Paula Merino Serrais
- Laboratorio Cajal de Circuitos Corticales (CTB), Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Campus Montegancedo S/N, Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Meghma Mitra
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Ana Fernandez Martin
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Yitao Wang
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jaideep Kesavan
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Ciara Melia
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; VivoArchitect, Route de la Corniche 5, 1066 Epalinges, Vaud, Switzerland
| | - Alberto Parras
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Edward Beamer
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Béla Zimmer
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mona Heiland
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Brenton Cavanagh
- Cellular and Molecular Imaging Core, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Rafael Parcianello Cipolat
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - James Morgan
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PL, UK
| | - Xinchen Teng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jochen H M Prehn
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Paolo F Fabene
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, 37134 Verona, Italy; Section of Anatomy and Histology, Department of Neurosciences, Biomedicine, and Movement Science, Faculty of Medicine, University of Verona, Verona, Italy; Section of Innovation Biomedicine, Department of Engineering for Innovation Medicine, Faculty of Medicine, University of Verona, Verona, Italy
| | - Giuseppe Bertini
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, 37134 Verona, Italy
| | - Antonio R Artalejo
- Department of Pharmacology and Toxicology, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai 200241, China
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Luis A Olivos-Oré
- Department of Pharmacology and Toxicology, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Niamh M C Connolly
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - David C Henshall
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Tobias Engel
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland.
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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3
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Praharaj M, Shen F, Lee AJ, Zhao L, Nirschl TR, Theodros D, Singh AK, Wang X, Adusei KM, Lombardo KA, Williams RA, Sena LA, Thompson EA, Tam A, Yegnasubramanian S, Pearce EJ, Leone RD, Alt J, Rais R, Slusher BS, Pardoll DM, Powell JD, Zarif JC. Metabolic Reprogramming of Tumor-Associated Macrophages Using Glutamine Antagonist JHU083 Drives Tumor Immunity in Myeloid-Rich Prostate and Bladder Cancers. Cancer Immunol Res 2024; 12:854-875. [PMID: 38701369 PMCID: PMC11217738 DOI: 10.1158/2326-6066.cir-23-1105] [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: 12/27/2023] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Glutamine metabolism in tumor microenvironments critically regulates antitumor immunity. Using the glutamine-antagonist prodrug JHU083, we report potent tumor growth inhibition in urologic tumors by JHU083-reprogrammed tumor-associated macrophages (TAMs) and tumor-infiltrating monocytes. We show JHU083-mediated glutamine antagonism in tumor microenvironments induced by TNF, proinflammatory, and mTORC1 signaling in intratumoral TAM clusters. JHU083-reprogrammed TAMs also exhibited increased tumor cell phagocytosis and diminished proangiogenic capacities. In vivo inhibition of TAM glutamine consumption resulted in increased glycolysis, a broken tricarboxylic acid (TCA) cycle, and purine metabolism disruption. Although the antitumor effect of glutamine antagonism on tumor-infiltrating T cells was moderate, JHU083 promoted a stem cell-like phenotype in CD8+ T cells and decreased the abundance of regulatory T cells. Finally, JHU083 caused a global shutdown in glutamine-utilizing metabolic pathways in tumor cells, leading to reduced HIF-1α, c-MYC phosphorylation, and induction of tumor cell apoptosis, all key antitumor features. Altogether, our findings demonstrate that targeting glutamine with JHU083 led to suppressed tumor growth as well as reprogramming of immunosuppressive TAMs within prostate and bladder tumors that promoted antitumor immune responses. JHU083 can offer an effective therapeutic benefit for tumor types that are enriched in immunosuppressive TAMs.
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Affiliation(s)
- Monali Praharaj
- Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Fan Shen
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Alex J. Lee
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Liang Zhao
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Thomas R. Nirschl
- Pathobiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Debebe Theodros
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Alok K. Singh
- Department of Medicine, Center for Tuberculosis Research, School of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Xiaoxu Wang
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Kenneth M. Adusei
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Kara A. Lombardo
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Raekwon A. Williams
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Laura A. Sena
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Elizabeth A. Thompson
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Ada Tam
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Edward J. Pearce
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Robert D. Leone
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jesse Alt
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, Maryland.
| | - Rana Rais
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, Maryland.
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Johns Hopkins Drug Discovery, Johns Hopkins School of Medicine, Baltimore, Maryland.
| | - Drew M. Pardoll
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jonathan D. Powell
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jelani C. Zarif
- Bloomberg∼Kimmel Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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4
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Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401815. [PMID: 38887194 DOI: 10.1002/advs.202401815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Indexed: 06/20/2024]
Abstract
In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity, and confounding factors. As it is known, the cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it is not clear how it will work on the integrated single-cell multi-omics data. Here, a cell cycle-aware network (CCAN) is developed to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the outstanding performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
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Affiliation(s)
- Jiajia Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jian Ma
- Department of Electronic Information and Computer Engineering, The Engineering & Technical College of Chengdu University of Technology, Leshan, Sichuan, 614000, China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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5
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McLean AK, Reynolds G, Pratt AG. Leveraging Multi-Tissue, Single-Cell Atlases as Tools to Elucidate Shared Mechanisms of Immune-Mediated Inflammatory Diseases. Biomedicines 2024; 12:1297. [PMID: 38927506 PMCID: PMC11201400 DOI: 10.3390/biomedicines12061297] [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: 05/13/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The observation that certain therapeutic strategies for targeting inflammation benefit patients with distinct immune-mediated inflammatory diseases (IMIDs) is exemplified by the success of TNF blockade in conditions including rheumatoid arthritis, ulcerative colitis, and skin psoriasis, albeit only for subsets of individuals with each condition. This suggests intersecting "nodes" in inflammatory networks at a molecular and cellular level may drive and/or maintain IMIDs, being "shared" between traditionally distinct diagnoses without mapping neatly to a single clinical phenotype. In line with this proposition, integrative tumour tissue analyses in oncology have highlighted novel cell states acting across diverse cancers, with important implications for precision medicine. Drawing upon advances in the oncology field, this narrative review will first summarise learnings from the Human Cell Atlas in health as a platform for interrogating IMID tissues. It will then review cross-disease studies to date that inform this endeavour before considering future directions in the field.
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Affiliation(s)
- Anthony K. McLean
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gary Reynolds
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Arthur G. Pratt
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
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6
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Weng W, Deng Y, Deviatiiarov R, Hamidi S, Kajikawa E, Gusev O, Kiyonari H, Zhang G, Sheng G. ETV2 induces endothelial, but not hematopoietic, lineage specification in birds. Life Sci Alliance 2024; 7:e202402694. [PMID: 38570190 PMCID: PMC10992995 DOI: 10.26508/lsa.202402694] [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: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Cardiovascular system develops from the lateral plate mesoderm. Its three primary cell lineages (hematopoietic, endothelial, and muscular) are specified by the sequential actions of conserved transcriptional factors. ETV2, a master regulator of mammalian hemangioblast development, however, is absent in the chicken genome and acts downstream of NPAS4L in zebrafish. Here, we investigated the epistatic relationship between NPAS4L and ETV2 in avian hemangioblast development. We showed that ETV2 is deleted in all 363 avian genomes analyzed. Mouse ETV2 induced LMO2, but not NPAS4L or SCL, expression in chicken mesoderm. Squamate (lizards, geckos, and snakes) genomes contain both NPAS4L and ETV2 In Madagascar ground gecko, both genes were expressed in developing hemangioblasts. Gecko ETV2 induced only LMO2 in chicken mesoderm. We propose that both NPAS4L and ETV2 were present in ancestral amniote, with ETV2 acting downstream of NPAS4L in endothelial lineage specification. ETV2 may have acted as a pioneer factor by promoting chromatin accessibility of endothelial-specific genes and, in parallel with NPAS4L loss in ancestral mammals, has gained similar function in regulating blood-specific genes.
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Affiliation(s)
- Wei Weng
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuan Deng
- Beijing Genome Institute (BGI), Shenzhen, China
| | - Ruslan Deviatiiarov
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sofiane Hamidi
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Oleg Gusev
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
| | | | - Guojie Zhang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, China
| | - Guojun Sheng
- https://ror.org/02cgss904 International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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7
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Liu Y, Carbonetto P, Willwerscheid J, Oakes SA, Macleod KF, Stephens M. Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.15.553436. [PMID: 37645713 PMCID: PMC10462040 DOI: 10.1101/2023.08.15.553436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Profiling tumors with single-cell RNA sequencing (scRNA-seq) has the potential to identify recurrent patterns of transcription variation related to cancer progression, and produce new therapeutically relevant insights. However, the presence of strong inter-tumor heterogeneity often obscures more subtle patterns that are shared across tumors, some of which may characterize clinically relevant disease subtypes. Here we introduce a new statistical method, generalized binary covariance decomposition (GBCD), to address this problem. We show that GBCD can help decompose transcriptional heterogeneity into interpretable components - including patient-specific, dataset-specific and shared components relevant to disease subtypes - and that, in the presence of strong inter-tumor heterogeneity, it can produce more interpretable results than existing methods. Applied to data from three studies on pancreatic cancer adenocarcinoma (PDAC), GBCD produces a refined characterization of existing tumor subtypes (e.g., classical vs. basal), and identifies a new gene expression program (GEP) that is prognostic of poor survival independent of established prognostic factors such as tumor stage and subtype. The new GEP is enriched for genes involved in a variety of stress responses, and suggests a potentially important role for the integrated stress response in PDAC development and prognosis.
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8
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Szabó D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A. A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593308. [PMID: 38766140 PMCID: PMC11100777 DOI: 10.1101/2024.05.10.593308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Midbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage1-3. As the synaptic and transcriptional changes that follow an acute cocaine exposure are mostly resolved within a few days4,5, the molecular changes that encode the long-term cellular memory of the exposure within DNs remain unknown. To investigate whether a single cocaine exposure induces long-term changes in the 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in the mouse midbrain. We found extensive rewiring of 3D genome architecture at 24 hours past exposure which remains or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. A single cocaine exposure triggers extensive long-lasting changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding of Rbfox1 which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a specific DN sub-type characterized by low expression of the dopamine auto-receptor Drd2, a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.
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Affiliation(s)
- Dominik Szabó
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Vedran Franke
- Bioinformatics & Omics Data Science platform, Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Eleanor J. Paul
- MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alexander Kukalev
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
| | - Ulrich G. Pfisterer
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Ibai Irastorza-Azcarate
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
| | - Andrea M. Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Samuel Demharter
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Luna Zea-Redondo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Jose P. Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Sant Joan d’Alacant, Spain
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
- Berlin Institute of Health, 10178 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics & Omics Data Science platform, Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Mark A. Ungless
- MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Toronto, Canada
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
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9
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Cui X, Chen X, Li Z, Gao Z, Chen S, Jiang R. Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. NATURE COMPUTATIONAL SCIENCE 2024; 4:346-359. [PMID: 38730185 DOI: 10.1038/s43588-024-00625-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
Single-cell epigenomic data has been growing continuously at an unprecedented pace, but their characteristics such as high dimensionality and sparsity pose substantial challenges to downstream analysis. Although deep learning models-especially variational autoencoders-have been widely used to capture low-dimensional feature embeddings, the prevalent Gaussian assumption somewhat disagrees with real data, and these models tend to struggle to incorporate reference information from abundant cell atlases. Here we propose CASTLE, a deep generative model based on the vector-quantized variational autoencoder framework to extract discrete latent embeddings that interpretably characterize single-cell chromatin accessibility sequencing data. We validate the performance and robustness of CASTLE for accurate cell-type identification and reasonable visualization compared with state-of-the-art methods. We demonstrate the advantages of CASTLE for effective incorporation of existing massive reference datasets in a weakly supervised or supervised manner. We further demonstrate CASTLE's capacity for intuitively distilling cell-type-specific feature spectra that unveil cell heterogeneity and biological implications quantitatively.
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Affiliation(s)
- Xuejian Cui
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Xiaoyang Chen
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Zhen Li
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Zijing Gao
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China.
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China.
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10
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Gaur P, Bryois J, Calini D, Foo L, Hoozemans JJM, Malhotra D, Menon V. Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590816. [PMID: 38712204 PMCID: PMC11071354 DOI: 10.1101/2024.04.23.590816] [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
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathological manifestations and is the leading cause of cognitive decline and dementia in elderly individuals. A major goal in AD research is to identify new therapeutic pathways by studying the molecular and cellular changes in the disease, either downstream or upstream of the pathological hallmarks. In this study, we present a comprehensive investigation of cellular heterogeneity from the temporal cortex region of 40 individuals, comprising healthy donors and individuals with differing tau and amyloid burden. Using single-nucleus transcriptome analysis of 430,271 nuclei from both gray and white matter of these individuals, we identified cell type-specific subclusters in both neuronal and glial cell types with varying degrees of association with AD pathology. In particular, these associations are present in layer specific glutamatergic (excitatory) neuronal types, along with GABAergic (inhibitory) neurons and glial subtypes. These associations were observed in early as well as late pathological progression. We extended this analysis by performing multiplexed in situ hybridization using the CARTANA platform, capturing 155 genes in 13 individuals with varying levels of tau pathology. By modeling the spatial distribution of these genes and their associations with the pathology, we not only replicated key findings from our snRNA data analysis, but also identified a set of cell type-specific genes that show selective enrichment or depletion near pathological inclusions. Together, our findings allow us to prioritize specific cell types and pathways for targeted interventions at various stages of pathological progression in AD.
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Affiliation(s)
- Pallavi Gaur
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
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11
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Zhang W, Cui Y, Liu B, Loza M, Park SJ, Nakai K. HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. Brief Bioinform 2024; 25:bbae152. [PMID: 38581422 PMCID: PMC10998639 DOI: 10.1093/bib/bbae152] [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: 12/19/2023] [Revised: 02/19/2024] [Accepted: 03/10/2024] [Indexed: 04/08/2024] Open
Abstract
Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels are still lacking in single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) data, because of extreme sparsity and inconsistent chromatin accessibility between datasets. Here, we present a novel automated cell annotation method that transfers cell type information from a well-labeled scRNA-seq reference to an unlabeled scATAC-seq target, via a parallel graph neural network, in a semi-supervised manner. Unlike existing methods that utilize only gene expression or gene activity features, HyGAnno leverages genome-wide accessibility peak features to facilitate the training process. In addition, HyGAnno reconstructs a reference-target cell graph to detect cells with low prediction reliability, according to their specific graph connectivity patterns. HyGAnno was assessed across various datasets, showcasing its strengths in precise cell annotation, generating interpretable cell embeddings, robustness to noisy reference data and adaptability to tumor tissues.
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Affiliation(s)
- Weihang Zhang
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yang Cui
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Bowen Liu
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Martin Loza
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Sung-Joon Park
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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12
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Günther DM, Batiuk MY, Petukhov V, De Oliveira R, Wunderle T, Buchholz CJ, Fries P, Khodosevich K. Heterogeneity of layer 4 in visual areas of rhesus macaque cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584345. [PMID: 38559123 PMCID: PMC10979896 DOI: 10.1101/2024.03.11.584345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recently, single-cell RNA-sequencing (scRNA-seq) has enabled unprecedented insights to the cellular landscape of the brains of many different species, among them the rhesus macaque as a key animal model. Building on previous, broader surveys of the macaque brain, we closely examined five immediately neighboring areas within the visual cortex of the rhesus macaque: V1, V2, V4, MT and TEO. To facilitate this, we first devised a novel pipeline for brain spatial archive - the BrainSPACE - which enabled robust archiving and sampling from the whole unfixed brain. SnRNA-sequencing of ~100,000 nuclei from visual areas V1 and V4 revealed conservation within the GABAergic neuron subtypes, while seven and one distinct principle neuron subtypes were detected in V1 and V4, respectively, all most likely located in layer 4. Moreover, using small molecule fluorescence in situ hybridization, we identified cell type density gradients across V1, V2, V4, MT, and TEO appearing to reflect the visual hierarchy. These findings demonstrate an association between the clear areal specializations among neighboring areas with the hierarchical levels within the visual cortex of the rhesus macaque.
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Affiliation(s)
- Dorothee M. Günther
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, the Netherlands
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Viktor Petukhov
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Romain De Oliveira
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thomas Wunderle
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany
| | - Christian J. Buchholz
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Pascal Fries
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, the Netherlands
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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13
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Messeri L, Crockett MJ. Artificial intelligence and illusions of understanding in scientific research. Nature 2024; 627:49-58. [PMID: 38448693 DOI: 10.1038/s41586-024-07146-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Scientists are enthusiastically imagining ways in which artificial intelligence (AI) tools might improve research. Why are AI tools so attractive and what are the risks of implementing them across the research pipeline? Here we develop a taxonomy of scientists' visions for AI, observing that their appeal comes from promises to improve productivity and objectivity by overcoming human shortcomings. But proposed AI solutions can also exploit our cognitive limitations, making us vulnerable to illusions of understanding in which we believe we understand more about the world than we actually do. Such illusions obscure the scientific community's ability to see the formation of scientific monocultures, in which some types of methods, questions and viewpoints come to dominate alternative approaches, making science less innovative and more vulnerable to errors. The proliferation of AI tools in science risks introducing a phase of scientific enquiry in which we produce more but understand less. By analysing the appeal of these tools, we provide a framework for advancing discussions of responsible knowledge production in the age of AI.
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Affiliation(s)
- Lisa Messeri
- Department of Anthropology, Yale University, New Haven, CT, USA.
| | - M J Crockett
- Department of Psychology, Princeton University, Princeton, NJ, USA.
- University Center for Human Values, Princeton University, Princeton, NJ, USA.
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14
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Sun H, Qu H, Duan K, Du W. scMGCN: A Multi-View Graph Convolutional Network for Cell Type Identification in scRNA-seq Data. Int J Mol Sci 2024; 25:2234. [PMID: 38396909 PMCID: PMC10889820 DOI: 10.3390/ijms25042234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) data reveal the complexity and diversity of cellular ecosystems and molecular interactions in various biomedical research. Hence, identifying cell types from large-scale scRNA-seq data using existing annotations is challenging and requires stable and interpretable methods. However, the current cell type identification methods have limited performance, mainly due to the intrinsic heterogeneity among cell populations and extrinsic differences between datasets. Here, we present a robust graph artificial intelligence model, a multi-view graph convolutional network model (scMGCN) that integrates multiple graph structures from raw scRNA-seq data and applies graph convolutional networks with attention mechanisms to learn cell embeddings and predict cell labels. We evaluate our model on single-dataset, cross-species, and cross-platform experiments and compare it with other state-of-the-art methods. Our results show that scMGCN outperforms the other methods regarding stability, accuracy, and robustness to batch effects. Our main contributions are as follows: Firstly, we introduce multi-view learning and multiple graph construction methods to capture comprehensive cellular information from scRNA-seq data. Secondly, we construct a scMGCN that combines graph convolutional networks with attention mechanisms to extract shared, high-order information from cells. Finally, we demonstrate the effectiveness and superiority of the scMGCN on various datasets.
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Affiliation(s)
| | | | | | - Wei Du
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China; (H.S.); (H.Q.); (K.D.)
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15
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Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-aware Network for Data Integration and Label Transferring of Single-cell RNA-seq and ATAC-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578213. [PMID: 38352302 PMCID: PMC10862874 DOI: 10.1101/2024.01.31.578213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity and confounding factors. As we know, cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it's not clear how it will work on the integrated single-cell multi-omics data. Here, we developed a Cell Cycle-Aware Network (CCAN) to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the out-standing performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
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16
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Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 226] [Impact Index Per Article: 226.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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17
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Mei S, Alchahin AM, Tsea I, Kfoury Y, Hirz T, Jeffries NE, Zhao T, Xu Y, Zhang H, Sarkar H, Wu S, Subtelny AO, Johnsen JI, Zhang Y, Salari K, Wu CL, Randolph MA, Scadden DT, Dahl DM, Shin J, Kharchenko PV, Saylor PJ, Sykes DB, Baryawno N. Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions. Genome Med 2024; 16:1. [PMID: 38281962 PMCID: PMC10823713 DOI: 10.1186/s13073-023-01272-6] [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: 10/10/2022] [Accepted: 12/11/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Despite therapeutic advances, once a cancer has metastasized to the bone, it represents a highly morbid and lethal disease. One third of patients with advanced clear cell renal cell carcinoma (ccRCC) present with bone metastasis at the time of diagnosis. However, the bone metastatic niche in humans, including the immune and stromal microenvironments, has not been well-defined, hindering progress towards identification of therapeutic targets. METHODS We collected fresh patient samples and performed single-cell transcriptomic profiling of solid metastatic tissue (Bone Met), liquid bone marrow at the vertebral level of spinal cord compression (Involved), and liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal), as well as bone marrow from patients undergoing hip replacement surgery (Benign). In addition, we incorporated single-cell data from primary ccRCC tumors (ccRCC Primary) for comparative analysis. RESULTS The bone marrow of metastatic patients is immune-suppressive, featuring increased, exhausted CD8 + cytotoxic T cells, T regulatory cells, and tumor-associated macrophages (TAM) with distinct transcriptional states in metastatic lesions. Bone marrow stroma from tumor samples demonstrated a tumor-associated mesenchymal stromal cell population (TA-MSC) that appears to be supportive of epithelial-to mesenchymal transition (EMT), bone remodeling, and a cancer-associated fibroblast (CAFs) phenotype. This stromal subset is associated with poor progression-free and overall survival and also markedly upregulates bone remodeling through the dysregulation of RANK/RANKL/OPG signaling activity in bone cells, ultimately leading to bone resorption. CONCLUSIONS These results provide a comprehensive analysis of the bone marrow niche in the setting of human metastatic cancer and highlight potential therapeutic targets for both cell populations and communication channels.
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Affiliation(s)
- Shenglin Mei
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Adele M Alchahin
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Ioanna Tsea
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Youmna Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nathan Elias Jeffries
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ting Zhao
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Hirak Sarkar
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Alexander O Subtelny
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Keyan Salari
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Mark A Randolph
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Douglas M Dahl
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - John Shin
- Department of Neurosurgery, Harvard Medical School, Boston, MA, 02115, USA.
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Present: Altos Labs, San Diego, CA, 92121, USA.
| | - Philip J Saylor
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02114, USA.
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 17176, Stockholm, Sweden.
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18
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Chen L, Wan Y, Yang T, Zhang Q, Zeng Y, Zheng S, Ling Z, Xiao Y, Wan Q, Liu R, Yang C, Huang G, Zeng Q. Bibliometric and visual analysis of single-cell sequencing from 2010 to 2022. Front Genet 2024; 14:1285599. [PMID: 38274109 PMCID: PMC10808606 DOI: 10.3389/fgene.2023.1285599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/31/2023] [Indexed: 01/27/2024] Open
Abstract
Background: Single-cell sequencing (SCS) is a technique used to analyze the genome, transcriptome, epigenome, and other genetic data at the level of a single cell. The procedure is commonly utilized in multiple fields, including neurobiology, immunology, and microbiology, and has emerged as a key focus of life science research. However, a thorough and impartial analysis of the existing state and trends of SCS-related research is lacking. The current study aimed to map the development trends of studies on SCS during the years 2010-2022 through bibliometric software. Methods: Pertinent papers on SCS from 2010 to 2022 were obtained using the Web of Science Core Collection. Research categories, nations/institutions, authors/co-cited authors, journals/co-cited journals, co-cited references, and keywords were analyzed using VOSviewer, the R package "bibliometric", and CiteSpace. Results: The bibliometric analysis included 9,929 papers published between 2010 and 2022, and showed a consistent increase in the quantity of papers each year. The United States was the source of the highest quantity of articles and citations in this field. The majority of articles were published in the periodical Nature Communications. Butler A was the most frequently quoted author on this topic, and his article "Integrating single-cell transcriptome data across diverse conditions, technologies, and species" has received numerous citations to date. The literature and keyword analysis showed that studies involving single-cell RNA sequencing (scRNA-seq) were prominent in this discipline during the study period. Conclusion: This study utilized bibliometric techniques to visualize research in SCS-related domains, which facilitated the identification of emerging patterns and future directions in the field. Current hot topics in SCS research include COVID-19, tumor microenvironment, scRNA-seq, and neuroscience. Our results are significant for scholars seeking to identify key issues and generate new research ideas.
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Affiliation(s)
- Ling Chen
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yantong Wan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of BasicMedical Sciences, Southern Medical University, Guangzhou, China
| | - Tingting Yang
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qi Zhang
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Yuting Zeng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuqi Zheng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Zhishan Ling
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Yupeng Xiao
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qingyi Wan
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Ruili Liu
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Chun Yang
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, Guangdong Medical University, Dongguan, China
| | - Guozhi Huang
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qing Zeng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
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19
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Lau KEH, Nguyen NT, Kesavan JC, Langa E, Fanning K, Brennan GP, Sanz-Rodriguez A, Villegas-Salmerón J, Yan Y, Venø MT, Mills JD, Rosenow F, Bauer S, Kjems J, Henshall DC. Differential microRNA editing may drive target pathway switching in human temporal lobe epilepsy. Brain Commun 2024; 6:fcad355. [PMID: 38204971 PMCID: PMC10781512 DOI: 10.1093/braincomms/fcad355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
MicroRNAs have emerged as important regulators of the gene expression landscape in temporal lobe epilepsy. The mechanisms that control microRNA levels and influence target choice remain, however, poorly understood. RNA editing is a post-transcriptional mechanism mediated by the adenosine acting on RNA (ADAR) family of proteins that introduces base modification that diversifies the gene expression landscape. RNA editing has been studied for the mRNA landscape but the extent to which microRNA editing occurs in human temporal lobe epilepsy is unknown. Here, we used small RNA-sequencing data to characterize the identity and extent of microRNA editing in human temporal lobe epilepsy brain samples. This detected low-to-high editing in over 40 of the identified microRNAs. Among microRNA exhibiting the highest editing was miR-376a-3p, which was edited in the seed region and this was predicted to significantly change the target pool. The edited form was expressed at lower levels in human temporal lobe epilepsy samples. We modelled the shift in editing levels of miR-376a-3p in human-induced pluripotent stem cell-derived neurons. Reducing levels of the edited form of miR-376a-3p using antisense oligonucleotides resulted in extensive gene expression changes, including upregulation of mitochondrial and metabolism-associated pathways. Together, these results show that differential editing of microRNAs may re-direct targeting and result in altered functions relevant to the pathophysiology of temporal lobe epilepsy and perhaps other disorders of neuronal hyperexcitability.
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Affiliation(s)
- Kelvin E How Lau
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Ngoc T Nguyen
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Jaideep C Kesavan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Elena Langa
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Kevin Fanning
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Gary P Brennan
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Amaya Sanz-Rodriguez
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Javier Villegas-Salmerón
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway H91 TK33, Ireland
| | - Yan Yan
- Omiics ApS, 8200 Aarhus N, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Morten T Venø
- Omiics ApS, 8200 Aarhus N, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - James D Mills
- Department of Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
- Chalfont Centre for Epilepsy, Chalfont St.Peter SL9 0RJ, UK
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Felix Rosenow
- Goethe-University Frankfurt, Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, University Hospital, 60590 Frankfurt, Germany
- Goethe-University Frankfurt, LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60590 Frankfurt, Germany
| | - Sebastian Bauer
- Goethe-University Frankfurt, Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, University Hospital, 60590 Frankfurt, Germany
- Goethe-University Frankfurt, LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60590 Frankfurt, Germany
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
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20
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Hu T, Allam M, Cai S, Henderson W, Yueh B, Garipcan A, Ievlev AV, Afkarian M, Beyaz S, Coskun AF. Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology. Nat Commun 2023; 14:8260. [PMID: 38086839 PMCID: PMC10716522 DOI: 10.1038/s41467-023-43917-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet's ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.
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Affiliation(s)
- Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mayar Allam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Walter Henderson
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian Yueh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Anton V Ievlev
- Oak Ridge National Laboratory, Center for Nanophase Materials Sciences, Oak Ridge, TN, USA
| | - Maryam Afkarian
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, CA, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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21
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López-Tobón A, Shyti R, Villa CE, Cheroni C, Fuentes-Bravo P, Trattaro S, Caporale N, Troglio F, Tenderini E, Mihailovich M, Skaros A, Gibson WT, Cuomo A, Bonaldi T, Mercurio C, Varasi M, Osborne L, Testa G. GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders. SCIENCE ADVANCES 2023; 9:eadh2726. [PMID: 38019906 PMCID: PMC10686562 DOI: 10.1126/sciadv.adh2726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome featuring hypersociability, while duplication causes 7q11.23 microduplication syndrome (7Dup), frequently exhibiting autism spectrum disorder (ASD). Converging evidence indicates GTF2I as key mediator of the cognitive-behavioral phenotypes, yet its role in cortical development and behavioral hallmarks remains largely unknown. We integrated proteomic and transcriptomic profiling of patient-derived cortical organoids, including longitudinally at single-cell resolution, to dissect 7q11.23 dosage-dependent and GTF2I-specific disease mechanisms. We observed dosage-dependent impaired dynamics of neural progenitor proliferation, transcriptional imbalances, and highly specific alterations in neuronal output, leading to precocious excitatory neuron production in 7Dup, which was rescued by restoring physiological GTF2I levels. Transgenic mice with Gtf2i duplication recapitulated progenitor proliferation and neuronal differentiation defects alongside ASD-like behaviors. Consistently, inhibition of lysine demethylase 1 (LSD1), a GTF2I effector, was sufficient to rescue ASD-like phenotypes in transgenic mice, establishing GTF2I-LSD1 axis as a molecular pathway amenable to therapeutic intervention in ASD.
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Affiliation(s)
- Alejandro López-Tobón
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Carlo Emanuele Villa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Patricio Fuentes-Bravo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Flavia Troglio
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Erika Tenderini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Adrianos Skaros
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - William T. Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Lucy Osborne
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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22
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Dong M, Kluger Y. Deep identifiable modeling of single-cell atlases enables zero-shot query of cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566161. [PMID: 38014345 PMCID: PMC10680588 DOI: 10.1101/2023.11.11.566161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
With the emerging single-cell RNA-seq datasets at atlas levels, the potential of a universal model built on existing atlas that can extrapolate to new data remains unclear. A fundamental yet challenging problem for such a model is to identify the underlying biological and batch variations in a zero-shot manner, which is crucial for characterizing scRNA-seq datasets with new biological states. In this work, we present scShift, a mechanistic model that learns batch and biological patterns from atlas-level scRNA-seq data as well as perturbation scRNA-seq data. scShift models genes as functions of latent biological processes, with sparse shifts induced by batch effects and biological perturbations, leveraging recent advances of causal representation learning. Through benchmarking in holdout real datasets, we show scShift reveals unified cell type representations as well as underlying biological variations for query data in zero-shot manners, outperforming widely-used atlas integration, batch correction, and perturbation modeling approaches. scShift enables mapping of gene expression profiles to perturbation labels, and predicts meaningful targets for exhausted T cells as well as a list of diseases in the CellxGene blood atlas.
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23
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Zhang M, Ceyhan Y, Mei S, Hirz T, Sykes DB, Agoulnik IU. Regulation of EZH2 Expression by INPP4B in Normal Prostate and Primary Prostate Cancer. Cancers (Basel) 2023; 15:5418. [PMID: 38001678 PMCID: PMC10670027 DOI: 10.3390/cancers15225418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
The phosphatases INPP4B and PTEN are tumor suppressors that are lost in nearly half of advanced metastatic cancers. The loss of PTEN in prostate epithelium initially leads to an upregulation of several tumor suppressors that slow the progression of prostate cancer in mouse models. We tested whether the loss of INPP4B elicits a similar compensatory response in prostate tissue and whether this response is distinct from the one caused by the loss of PTEN. Knockdown of INPP4B but not PTEN in human prostate cancer cell lines caused a decrease in EZH2 expression. In Inpp4b-/- mouse prostate epithelium, EZH2 levels were decreased, as were methylation levels of histone H3. In contrast, Ezh2 levels were increased in the prostates of Pten-/- male mice. Contrary to PTEN, there was a positive correlation between INPP4B and EZH2 expression in normal human prostates and early-stage prostate tumors. Analysis of single-cell transcriptomic data demonstrated that a subset of EZH2-positive cells expresses INPP4B or PTEN, but rarely both, consistent with their opposing correlation with EZH2 expression. Unlike PTEN, INPP4B did not affect the levels of SMAD4 protein expression or Pml mRNA expression. Like PTEN, p53 protein expression and phosphorylation of Akt in Inpp4b-/- murine prostates were elevated. Taken together, the loss of INPP4B in the prostate leads to overlapping and distinct changes in tumor suppressor and oncogenic downstream signaling.
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Affiliation(s)
- Manqi Zhang
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC 27708, USA;
| | - Yasemin Ceyhan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA;
| | - Shenglin Mei
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (S.M.); (T.H.); (D.B.S.)
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (S.M.); (T.H.); (D.B.S.)
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David B. Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (S.M.); (T.H.); (D.B.S.)
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Irina U. Agoulnik
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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24
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Leduc A, Harens H, Slavov N. Modeling and interpretation of single-cell proteogenomic data. ARXIV 2023:arXiv:2308.07465v2. [PMID: 37645043 PMCID: PMC10462161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable data-driven modeling of the molecular mechanisms coordinating proteins and nucleic acids at single-cell resolution. This promising potential requires estimating the reliability of measurements and computational analysis so that models can distinguish biological regulation from technical artifacts. We highlight different measurement modes that can support single-cell proteogenomic analysis and how to estimate their reliability. We then discuss approaches for developing both abstract and mechanistic models that aim to biologically interpret the measured differences across modalities, including specific applications to directed stem cell differentiation and to inferring protein interactions in cancer cells from the buffing of DNA copy-number variations. Single-cell proteogenomic data will support mechanistic models of direct molecular interactions that will provide generalizable and predictive representations of biological systems.
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Affiliation(s)
- Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
| | - Hannah Harens
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
- Parallel Squared Technology Institute, Watertown, MA 02472, USA
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25
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Chaudagar K, Rameshbabu S, Mei S, Hirz T, Hu YM, Argulian A, Labadie B, Desai K, Grimaldo S, Kahramangil D, Nair R, DSouza S, Zhou D, Li M, Doughan F, Chen R, Shafran J, Loyd M, Xia Z, Sykes DB, Moran A, Patnaik A. Androgen blockade primes NLRP3 in macrophages to induce tumor phagocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557996. [PMID: 37904975 PMCID: PMC10614738 DOI: 10.1101/2023.09.15.557996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Immune-based therapies induce durable remissions in subsets of patients across multiple malignancies. However, there is limited efficacy of immunotherapy in metastatic castrate-resistant prostate cancer (mCRPC), manifested by an enrichment of immunosuppressive (M2) tumor- associated macrophages (TAM) in the tumor immune microenvironment (TME). Therefore, therapeutic strategies to overcome TAM-mediated immunosuppression are critically needed in mCRPC. Here we discovered that NLR family pyrin domain containing 3 (NLRP3), an innate immune sensing protein, is highly expressed in TAM from metastatic PC patients treated with standard-of-care androgen deprivation therapy (ADT). Importantly, ex vivo studies revealed that androgen receptor (AR) blockade in TAM upregulates NLRP3 expression, but not inflammasome activity, and concurrent AR blockade/NLRP3 agonist (NLRP3a) treatment promotes cancer cell phagocytosis by immunosuppressive M2 TAM. In contrast, NLRP3a monotherapy was sufficient to enhance phagocytosis of cancer cells in anti-tumor (M1) TAM, which exhibit high de novo NLRP3 expression. Critically, combinatorial treatment with ADT/NLRP3a in a murine model of advanced PC resulted in significant tumor control, with tumor clearance in 55% of mice via TAM phagocytosis. Collectively, our results demonstrate NLRP3 as an AR-regulated "macrophage phagocytic checkpoint", inducibly expressed in TAM by ADT and activated by NLRP3a treatment, the combination resulting in TAM-mediated phagocytosis and tumor control.
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26
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Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biol 2023; 24:236. [PMID: 37858253 PMCID: PMC10588049 DOI: 10.1186/s13059-023-03067-9] [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: 03/03/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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Affiliation(s)
- Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Research Computing Center, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Vesalius Therapeutics, Cambridge, MA, USA
| | - Anthony Hung
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Statistics, University of Chicago, Chicago, IL, USA.
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27
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Parry EM, Lemvigh CK, Deng S, Dangle N, Ruthen N, Knisbacher BA, Broséus J, Hergalant S, Guièze R, Li S, Zhang W, Johnson C, Long JM, Yin S, Werner L, Anandappa A, Purroy N, Gohil S, Oliveira G, Bachireddy P, Shukla SA, Huang T, Khoury JD, Thakral B, Dickinson M, Tam C, Livak KJ, Getz G, Neuberg D, Feugier P, Kharchenko P, Wierda W, Olsen LR, Jain N, Wu CJ. ZNF683 marks a CD8 + T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome. Cancer Cell 2023; 41:1803-1816.e8. [PMID: 37738974 PMCID: PMC10618915 DOI: 10.1016/j.ccell.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 05/30/2023] [Accepted: 08/30/2023] [Indexed: 09/24/2023]
Abstract
Unlike many other hematologic malignancies, Richter syndrome (RS), an aggressive B cell lymphoma originating from indolent chronic lymphocytic leukemia, is responsive to PD-1 blockade. To discover the determinants of response, we analyze single-cell transcriptome data generated from 17 bone marrow samples longitudinally collected from 6 patients with RS. Response is associated with intermediate exhausted CD8 effector/effector memory T cells marked by high expression of the transcription factor ZNF683, determined to be evolving from stem-like memory cells and divergent from terminally exhausted cells. This signature overlaps with that of tumor-infiltrating populations from anti-PD-1 responsive solid tumors. ZNF683 is found to directly target key T cell genes (TCF7, LMO2, CD69) and impact pathways of T cell cytotoxicity and activation. Analysis of pre-treatment peripheral blood from 10 independent patients with RS treated with anti-PD-1, as well as patients with solid tumors treated with anti-PD-1, supports an association of ZNF683high T cells with response.
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Affiliation(s)
- Erin M Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Camilla K Lemvigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Stephanie Deng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan Dangle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Neil Ruthen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Julien Broséus
- Inserm UMRS1256 Nutrition-Génétique et Exposition Aux Risques Environnementaux (N-GERE), Université de Lorraine, 54000 Nancy, France; Université de Lorraine, CHRU-Nancy, Service d'hématologie Biologique, Pôle Laboratoires, 54000 Nancy, France
| | - Sébastien Hergalant
- Inserm UMRS1256 Nutrition-Génétique et Exposition Aux Risques Environnementaux (N-GERE), Université de Lorraine, 54000 Nancy, France
| | - Romain Guièze
- CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; EA 7453 (CHELTER), Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Connor Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jaclyn M Long
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lillian Werner
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Annabelle Anandappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Satyen Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Pavan Bachireddy
- Department of Hematopoietic Biology and Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sachet A Shukla
- Department of Hematopoietic Biology and Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joseph D Khoury
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Beenu Thakral
- Department of Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Michael Dickinson
- Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Constantine Tam
- Alfred Health, Melbourne, VIC, Australia; Monash University, Melbourne, VIC, Australia
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Pierre Feugier
- Inserm UMRS1256 Nutrition-Génétique et Exposition Aux Risques Environnementaux (N-GERE), Université de Lorraine, 54000 Nancy, France; Université de Lorraine, CHRU Nancy, service d'hématologie clinique, Nancy, France
| | - Peter Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA
| | - William Wierda
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Nitin Jain
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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28
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Ben-Kiki O, Bercovich A, Lifshitz A, Raz O, Brook D, Tanay A. MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases. Genome Biol 2023; 24:220. [PMID: 37798781 PMCID: PMC10552220 DOI: 10.1186/s13059-023-03069-7] [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: 12/04/2022] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
We describe MCProj-an algorithm for analyzing query scRNA-seq data by projections over reference single-cell atlases. We represent the reference as a manifold of annotated metacell gene expression distributions. We then interpret query metacells as mixtures of atlas distributions while correcting for technology-specific gene biases. This approach distinguishes and tags query cells that are consistent with atlas states from unobserved (novel or artifactual) behaviors. It also identifies expression differences observed in successfully mapped query states. We showcase MCProj functionality by projecting scRNA-seq data on a blood cell atlas, deriving precise, quantitative, and interpretable results across technologies and datasets.
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Affiliation(s)
- Oren Ben-Kiki
- Department of Applied Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Akhiad Bercovich
- Department of Applied Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Aviezer Lifshitz
- Department of Applied Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Ofir Raz
- Department of Applied Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Dror Brook
- Department of Applied Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Applied Math and Computer Science, Weizmann Institute of Science, Rehovot, Israel.
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29
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Li Y, Zhang D, Yang M, Peng D, Yu J, Liu Y, Lv J, Chen L, Peng X. scBridge embraces cell heterogeneity in single-cell RNA-seq and ATAC-seq data integration. Nat Commun 2023; 14:6045. [PMID: 37770437 PMCID: PMC10539354 DOI: 10.1038/s41467-023-41795-5] [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: 01/17/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
Single-cell multi-omics data integration aims to reduce the omics difference while keeping the cell type difference. However, it is daunting to model and distinguish the two differences due to cell heterogeneity. Namely, even cells of the same omics and type would have various features, making the two differences less significant. In this work, we reveal that instead of being an interference, cell heterogeneity could be exploited to improve data integration. Specifically, we observe that the omics difference varies in cells, and cells with smaller omics differences are easier to be integrated. Hence, unlike most existing works that homogeneously treat and integrate all cells, we propose a multi-omics data integration method (dubbed scBridge) that integrates cells in a heterogeneous manner. In brief, scBridge iterates between i) identifying reliable scATAC-seq cells that have smaller omics differences, and ii) integrating reliable scATAC-seq cells with scRNA-seq data to narrow the omics gap, thus benefiting the integration for the rest cells. Extensive experiments on seven multi-omics datasets demonstrate the superiority of scBridge compared with six representative baselines.
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Affiliation(s)
- Yunfan Li
- School of Computer Science, Sichuan University, Chengdu, Sichuan, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Mouxing Yang
- School of Computer Science, Sichuan University, Chengdu, Sichuan, China
| | - Dezhong Peng
- School of Computer Science, Sichuan University, Chengdu, Sichuan, China
| | - Jun Yu
- School of Computer Science, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Yu Liu
- School of Electronic and Information Engineering, Naval Aviation University, Yantai, Shandong, China
| | - Jiancheng Lv
- School of Computer Science, Sichuan University, Chengdu, Sichuan, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xi Peng
- School of Computer Science, Sichuan University, Chengdu, Sichuan, China.
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30
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Yu H, Usoskin D, Nagi SS, Hu Y, Kupari J, Bouchatta O, Cranfill SL, Gautam M, Su Y, Lu Y, Wymer J, Glanz M, Albrecht P, Song H, Ming GL, Prouty S, Seykora J, Wu H, Ma M, Rice FL, Olausson H, Ernfors P, Luo W. Single-Soma Deep RNA sequencing of Human DRG Neurons Reveals Novel Molecular and Cellular Mechanisms Underlying Somatosensation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533207. [PMID: 36993480 PMCID: PMC10055202 DOI: 10.1101/2023.03.17.533207] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The versatility of somatosensation arises from heterogeneous dorsal root ganglion (DRG) neurons. However, soma transcriptomes of individual human DRG (hDRG) neurons-critical in-formation to decipher their functions-are lacking due to technical difficulties. Here, we developed a novel approach to isolate individual hDRG neuron somas for deep RNA sequencing (RNA-seq). On average, >9,000 unique genes per neuron were detected, and 16 neuronal types were identified. Cross-species analyses revealed remarkable divergence among pain-sensing neurons and the existence of human-specific nociceptor types. Our deep RNA-seq dataset was especially powerful for providing insight into the molecular mechanisms underlying human somatosensation and identifying high potential novel drug targets. Our dataset also guided the selection of molecular markers to visualize different types of human afferents and the discovery of novel functional properties using single-cell in vivo electrophysiological recordings. In summary, by employing a novel soma sequencing method, we generated an unprecedented hDRG neuron atlas, providing new insights into human somatosensation, establishing a critical foundation for translational work, and clarifying human species-species properties.
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31
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Tian L, Xie Y, Xie Z, Tian J, Tian W. AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data. Brief Bioinform 2023; 24:bbad268. [PMID: 37497729 DOI: 10.1093/bib/bbad268] [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: 03/14/2023] [Revised: 06/14/2023] [Accepted: 07/04/2023] [Indexed: 07/28/2023] Open
Abstract
Here, we present AtacAnnoR, a two-round annotation method for scATAC-seq data using well-annotated scRNA-seq data as reference. We evaluate AtacAnnoR's performance against six competing methods on 11 benchmark datasets. Our results show that AtacAnnoR achieves the highest mean accuracy and the highest mean balanced accuracy and performs particularly well when unpaired scRNA-seq data are used as the reference. Furthermore, AtacAnnoR implements a 'Combine and Discard' strategy to further improve annotation accuracy when annotations of multiple references are available. AtacAnnoR has been implemented in an R package and can be directly integrated into currently popular scATAC-seq analysis pipelines.
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Affiliation(s)
- Lejin Tian
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yunxiao Xie
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhaobin Xie
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
- Children's Hospital of Fudan University, Shanghai, China
- Children's Hospital of Shandong University, Jinan, China
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32
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Fouché A, Chadoutaud L, Delattre O, Zinovyev A. Transmorph: a unifying computational framework for modular single-cell RNA-seq data integration. NAR Genom Bioinform 2023; 5:lqad069. [PMID: 37448589 PMCID: PMC10336778 DOI: 10.1093/nargab/lqad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/02/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023] Open
Abstract
Data integration of single-cell RNA-seq (scRNA-seq) data describes the task of embedding datasets gathered from different sources or experiments into a common representation so that cells with similar types or states are embedded close to one another independently from their dataset of origin. Data integration is a crucial step in most scRNA-seq data analysis pipelines involving multiple batches. It improves data visualization, batch effect reduction, clustering, label transfer, and cell type inference. Many data integration tools have been proposed during the last decade, but a surge in the number of these methods has made it difficult to pick one for a given use case. Furthermore, these tools are provided as rigid pieces of software, making it hard to adapt them to various specific scenarios. In order to address both of these issues at once, we introduce the transmorph framework. It allows the user to engineer powerful data integration pipelines and is supported by a rich software ecosystem. We demonstrate transmorph usefulness by solving a variety of practical challenges on scRNA-seq datasets including joint datasets embedding, gene space integration, and transfer of cycle phase annotations. transmorph is provided as an open source python package.
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Affiliation(s)
- Aziz Fouché
- To whom correspondence should be addressed. Tel: +33 156246989;
| | - Loïc Chadoutaud
- Institut Curie, PSL Research University, 75005 Paris, France
- INSERM, 75005 Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75005 Paris, France
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Andrei Zinovyev
- Correspondence may also be addressed to Andrei Zinovyev. Tel: +33 156246989;
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33
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Itai Y, Rappoport N, Shamir R. Integration of gene expression and DNA methylation data across different experiments. Nucleic Acids Res 2023; 51:7762-7776. [PMID: 37395437 PMCID: PMC10450176 DOI: 10.1093/nar/gkad566] [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: 11/16/2022] [Revised: 06/04/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it. Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on 11 TCGA (The Cancer Genome Atlas) cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared with four state-of-the-art integration algorithms. We also demonstrate INTEND's ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND's data-driven approach makes it a valuable multi-omic data integration tool. The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.
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Affiliation(s)
- Yonatan Itai
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nimrod Rappoport
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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34
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Fouché A, Zinovyev A. Omics data integration in computational biology viewed through the prism of machine learning paradigms. FRONTIERS IN BIOINFORMATICS 2023; 3:1191961. [PMID: 37600970 PMCID: PMC10436311 DOI: 10.3389/fbinf.2023.1191961] [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: 03/22/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023] Open
Abstract
Important quantities of biological data can today be acquired to characterize cell types and states, from various sources and using a wide diversity of methods, providing scientists with more and more information to answer challenging biological questions. Unfortunately, working with this amount of data comes at the price of ever-increasing data complexity. This is caused by the multiplication of data types and batch effects, which hinders the joint usage of all available data within common analyses. Data integration describes a set of tasks geared towards embedding several datasets of different origins or modalities into a joint representation that can then be used to carry out downstream analyses. In the last decade, dozens of methods have been proposed to tackle the different facets of the data integration problem, relying on various paradigms. This review introduces the most common data types encountered in computational biology and provides systematic definitions of the data integration problems. We then present how machine learning innovations were leveraged to build effective data integration algorithms, that are widely used today by computational biologists. We discuss the current state of data integration and important pitfalls to consider when working with data integration tools. We eventually detail a set of challenges the field will have to overcome in the coming years.
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Affiliation(s)
- Aziz Fouché
- Institut Curie, PSL Research University, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- CBIO-Centre for Computational Biology, ParisTech, PSL Research University, Paris, France
- Ecole Normale Supérieure Paris-Saclay, Cachan, France
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35
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Eckenrode KB, Righelli D, Ramos M, Argelaguet R, Vanderaa C, Geistlinger L, Culhane AC, Gatto L, Carey V, Morgan M, Risso D, Waldron L. Curated single cell multimodal landmark datasets for R/Bioconductor. PLoS Comput Biol 2023; 19:e1011324. [PMID: 37624866 PMCID: PMC10497156 DOI: 10.1371/journal.pcbi.1011324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 09/12/2023] [Accepted: 07/03/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes. RESULTS We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor's Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor's ecosystem of hundreds of packages for single-cell and multimodal data. CONCLUSIONS We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.
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Affiliation(s)
- Kelly B. Eckenrode
- Graduate School of Public Health and Health Policy, City University of New York, NY, NY, United States of America
- Institute for Implementation Science in Public Health, City University of New York, NY, NY, United States of America
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Marcel Ramos
- Graduate School of Public Health and Health Policy, City University of New York, NY, NY, United States of America
- Institute for Implementation Science in Public Health, City University of New York, NY, NY, United States of America
- Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Ricard Argelaguet
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | | | - Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Laurent Gatto
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Vincent Carey
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Martin Morgan
- Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, NY, NY, United States of America
- Institute for Implementation Science in Public Health, City University of New York, NY, NY, United States of America
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36
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Wang H, Fu T, Du Y, Gao W, Huang K, Liu Z, Chandak P, Liu S, Van Katwyk P, Deac A, Anandkumar A, Bergen K, Gomes CP, Ho S, Kohli P, Lasenby J, Leskovec J, Liu TY, Manrai A, Marks D, Ramsundar B, Song L, Sun J, Tang J, Veličković P, Welling M, Zhang L, Coley CW, Bengio Y, Zitnik M. Scientific discovery in the age of artificial intelligence. Nature 2023; 620:47-60. [PMID: 37532811 DOI: 10.1038/s41586-023-06221-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2023] [Indexed: 08/04/2023]
Abstract
Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment and accelerate research, helping scientists to generate hypotheses, design experiments, collect and interpret large datasets, and gain insights that might not have been possible using traditional scientific methods alone. Here we examine breakthroughs over the past decade that include self-supervised learning, which allows models to be trained on vast amounts of unlabelled data, and geometric deep learning, which leverages knowledge about the structure of scientific data to enhance model accuracy and efficiency. Generative AI methods can create designs, such as small-molecule drugs and proteins, by analysing diverse data modalities, including images and sequences. We discuss how these methods can help scientists throughout the scientific process and the central issues that remain despite such advances. Both developers and users of AI toolsneed a better understanding of when such approaches need improvement, and challenges posed by poor data quality and stewardship remain. These issues cut across scientific disciplines and require developing foundational algorithmic approaches that can contribute to scientific understanding or acquire it autonomously, making them critical areas of focus for AI innovation.
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Affiliation(s)
- Hanchen Wang
- Department of Engineering, University of Cambridge, Cambridge, UK
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
- Department of Research and Early Development, Genentech Inc, South San Francisco, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Tianfan Fu
- Department of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuanqi Du
- Department of Computer Science, Cornell University, Ithaca, NY, USA
| | - Wenhao Gao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kexin Huang
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziming Liu
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Payal Chandak
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - Shengchao Liu
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Peter Van Katwyk
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
- Data Science Institute, Brown University, Providence, RI, USA
| | - Andreea Deac
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Anima Anandkumar
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
- NVIDIA, Santa Clara, CA, USA
| | - Karianne Bergen
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
- Data Science Institute, Brown University, Providence, RI, USA
| | - Carla P Gomes
- Department of Computer Science, Cornell University, Ithaca, NY, USA
| | - Shirley Ho
- Center for Computational Astrophysics, Flatiron Institute, New York, NY, USA
- Department of Astrophysical Sciences, Princeton University, Princeton, NJ, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Physics and Center for Data Science, New York University, New York, NY, USA
| | | | - Joan Lasenby
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Arjun Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Le Song
- BioMap, Beijing, China
- Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates
| | - Jimeng Sun
- University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jian Tang
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- HEC Montréal, Montreal, Quebec, Canada
- CIFAR AI Chair, Toronto, Ontario, Canada
| | - Petar Veličković
- Google DeepMind, London, UK
- Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Max Welling
- University of Amsterdam, Amsterdam, Netherlands
- Microsoft Research Amsterdam, Amsterdam, Netherlands
| | - Linfeng Zhang
- DP Technology, Beijing, China
- AI for Science Institute, Beijing, China
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yoshua Bengio
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Data Science Initiative, Cambridge, MA, USA.
- Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Cambridge, MA, USA.
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37
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Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB, Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S. An atlas of healthy and injured cell states and niches in the human kidney. Nature 2023; 619:585-594. [PMID: 37468583 PMCID: PMC10356613 DOI: 10.1038/s41586-023-05769-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/30/2023] [Indexed: 07/21/2023]
Abstract
Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
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Affiliation(s)
- Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Seth Winfree
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ricardo Melo Ferreira
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kian Kalhor
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Daria Barwinska
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edgar A Otto
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Michael Ferkowicz
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sarah Urata
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit S Naik
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Bo Zhang
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Diane Salamon
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James C Williams
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xin Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Paul J Hoover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Teia Noel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anitha Vijayan
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Sylvia E Rosas
- Kidney and Hypertension Unit, Joslin Diabetes Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Francis P Wilson
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Paul M Palevsky
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - John R Sedor
- Lerner Research and Glickman Urology and Kidney Institutes, Cleveland Clinic, Cleveland, OH, USA
| | - Robert D Toto
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eric H Kim
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | | | - Anna Greka
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Pierre C Dagher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Tarek M El-Achkar
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA.
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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38
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Zhou Y, Sheng Q, Qi J, Hua J, Yang B, Wan L, Jin S. Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation. Genome Res 2023; 33:750-762. [PMID: 37308294 PMCID: PMC10317120 DOI: 10.1101/gr.277522.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/03/2023] [Indexed: 06/14/2023]
Abstract
For most biological and medical applications of single-cell transcriptomics, an integrative study of multiple heterogeneous single-cell RNA sequencing (scRNA-seq) data sets is crucial. However, present approaches are unable to integrate diverse data sets from various biological conditions effectively because of the confounding effects of biological and technical differences. We introduce single-cell integration (scInt), an integration method based on accurate, robust cell-cell similarity construction and unified contrastive biological variation learning from multiple scRNA-seq data sets. scInt provides a flexible and effective approach to transfer knowledge from the already integrated reference to the query. We show that scInt outperforms 10 other cutting-edge approaches using both simulated and real data sets, particularly in the case of complex experimental designs. Application of scInt to mouse developing tracheal epithelial data shows its ability to integrate development trajectories from different developmental stages. Furthermore, scInt successfully identifies functionally distinct condition-specific cell subpopulations in single-cell heterogeneous samples from a variety of biological conditions.
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Affiliation(s)
- Yang Zhou
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
| | - Qiongyu Sheng
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
| | - Jing Qi
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
| | - Jiao Hua
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
| | - Bo Yang
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
| | - Lei Wan
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
| | - Shuilin Jin
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China, 150001
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39
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Brase L, You SF, D'Oliveira Albanus R, Del-Aguila JL, Dai Y, Novotny BC, Soriano-Tarraga C, Dykstra T, Fernandez MV, Budde JP, Bergmann K, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Goate AM, Farlow M, Sutherland GT, Kipnis J, Karch CM, Benitez BA, Harari O. Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers. Nat Commun 2023; 14:2314. [PMID: 37085492 PMCID: PMC10121712 DOI: 10.1038/s41467-023-37437-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/15/2023] [Indexed: 04/23/2023] Open
Abstract
Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell-specific effect of variants in these genes is not fully understood. Here, we perform single-nucleus RNA-sequencing (snRNA-seq) on nearly 300,000 nuclei from the parietal cortex of AD autosomal dominant (APP and PSEN1) and risk-modifying variant (APOE, TREM2 and MS4A) carriers. Within individual cell types, we capture genes commonly dysregulated across variant groups. However, specific transcriptional states are more prevalent within variant carriers. TREM2 oligodendrocytes show a dysregulated autophagy-lysosomal pathway, MS4A microglia have dysregulated complement cascade genes, and APOEε4 inhibitory neurons display signs of ferroptosis. All cell types have enriched states in autosomal dominant carriers. We leverage differential expression and single-nucleus ATAC-seq to map GWAS signals to effector cell types including the NCK2 signal to neurons in addition to the initially proposed microglia. Overall, our results provide insights into the transcriptional diversity resulting from AD genetic architecture and cellular heterogeneity. The data can be explored on the online browser ( http://web.hararilab.org/SNARE/ ).
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Affiliation(s)
- Logan Brase
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Shih-Feng You
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Ricardo D'Oliveira Albanus
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Yaoyi Dai
- Baylor College of Medicine, Houston, TX, USA
| | - Brenna C Novotny
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Carolina Soriano-Tarraga
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Taitea Dykstra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John C Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Randall J Bateman
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Richard J Perrin
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Eric McDade
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Chengjie Xiong
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Greg T Sutherland
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jonathan Kipnis
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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40
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Reich M, Tabor T, Liefeld J, Joshi J, Kim F, Thorvaldsdottir H, Blankenberg D, Mesirov JP. Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535621. [PMID: 37066251 PMCID: PMC10104038 DOI: 10.1101/2023.04.04.535621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
We present Genomics to Notebook (g2nb), an environment that combines the JupyterLab notebook system with widely-used bioinformatics platforms. Galaxy, GenePattern, and the JavaScript versions of IGV and Cytoscape are currently available within g2nb. The analyses and visualizations within those platforms are presented as cells in a notebook, making thousands of genomics methods available within the notebook metaphor and allowing notebooks to contain workflows utilizing multiple software packages on remote servers, all without the need for programming. The g2nb environment is, to our knowledge, the only notebook-based system that incorporates multiple bioinformatics analysis platforms into a notebook interface.
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Affiliation(s)
- Michael Reich
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thorin Tabor
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John Liefeld
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jayadev Joshi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Forrest Kim
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Daniel Blankenberg
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jill P Mesirov
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
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41
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Xu Y, Zang Z, Xia J, Tan C, Geng Y, Li SZ. Structure-preserving visualization for single-cell RNA-Seq profiles using deep manifold transformation with batch-correction. Commun Biol 2023; 6:369. [PMID: 37016133 PMCID: PMC10073100 DOI: 10.1038/s42003-023-04662-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Dimensionality reduction and visualization play an important role in biological data analysis, such as data interpretation of single-cell RNA sequences (scRNA-seq). It is desired to have a visualization method that can not only be applicable to various application scenarios, including cell clustering and trajectory inference, but also satisfy a variety of technical requirements, especially the ability to preserve inherent structure of data and handle with batch effects. However, no existing methods can accommodate these requirements in a unified framework. In this paper, we propose a general visualization method, deep visualization (DV), that possesses the ability to preserve inherent structure of data and handle batch effects and is applicable to a variety of datasets from different application domains and dataset scales. The method embeds a given dataset into a 2- or 3-dimensional visualization space, with either a Euclidean or hyperbolic metric depending on a specified task type with type static (at a time point) or dynamic (at a sequence of time points) scRNA-seq data, respectively. Specifically, DV learns a structure graph to describe the relationships between data samples, transforms the data into visualization space while preserving the geometric structure of the data and correcting batch effects in an end-to-end manner. The experimental results on nine datasets in complex tissue from human patients or animal development demonstrate the competitiveness of DV in discovering complex cellular relations, uncovering temporal trajectories, and addressing complex batch factors. We also provide a preliminary attempt to pre-train a DV model for visualization of new incoming data.
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Affiliation(s)
- Yongjie Xu
- Zhejiang University, Hangzhou, 310058, China
- AI Division, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Zelin Zang
- Zhejiang University, Hangzhou, 310058, China
- AI Division, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Jun Xia
- Zhejiang University, Hangzhou, 310058, China
- AI Division, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Cheng Tan
- Zhejiang University, Hangzhou, 310058, China
- AI Division, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Yulan Geng
- AI Division, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Stan Z Li
- AI Division, School of Engineering, Westlake University, Hangzhou, 310024, China.
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42
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Huebner AJ, Gorelov RA, Deviatiiarov R, Demharter S, Kull T, Walsh RM, Taylor MS, Steiger S, Mullen JT, Kharchenko PV, Hochedlinger K. Dissection of gastric homeostasis in vivo facilitates permanent capture of isthmus-like stem cells in vitro. Nat Cell Biol 2023; 25:390-403. [PMID: 36717627 DOI: 10.1038/s41556-022-01079-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 12/12/2022] [Indexed: 02/01/2023]
Abstract
The glandular stomach is composed of two regenerative compartments termed corpus and antrum, and our understanding of the transcriptional networks that maintain these tissues is incomplete. Here we show that cell types with equivalent functional roles in the corpus and antrum share similar transcriptional states including the poorly characterized stem cells of the isthmus region. To further study the isthmus, we developed a monolayer two-dimensional (2D) culture system that is continually maintained by Wnt-responsive isthmus-like cells capable of differentiating into several gastric cell types. Importantly, 2D cultures can be converted into conventional three-dimensional organoids, modelling the plasticity of gastric epithelial cells in vivo. Finally, we utilized the 2D culture system to show that Sox2 is both necessary and sufficient to generate enterochromaffin cells. Together, our data provide important insights into gastric homeostasis, establish a tractable culture system to capture isthmus cells and uncover a role for Sox2 in enterochromaffin cells.
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Affiliation(s)
- Aaron J Huebner
- Massachusetts General Hospital Department of Molecular Biology, Boston, MA, USA
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Rebecca A Gorelov
- Massachusetts General Hospital Department of Molecular Biology, Boston, MA, USA
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Ruslan Deviatiiarov
- Institute of Fundamental Medicine and Biology, Kazan Feberal University, Kazan, Russia
| | - Samuel Demharter
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tobias Kull
- Massachusetts General Hospital Department of Molecular Biology, Boston, MA, USA
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Ryan M Walsh
- Massachusetts General Hospital Department of Molecular Biology, Boston, MA, USA
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Marty S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Simon Steiger
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John T Mullen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Peter V Kharchenko
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- San Diego Institute, Altos Labs, San Diego, CA, USA.
| | - Konrad Hochedlinger
- Massachusetts General Hospital Department of Molecular Biology, Boston, MA, USA.
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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43
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Gao T, Soldatov R, Sarkar H, Kurkiewicz A, Biederstedt E, Loh PR, Kharchenko PV. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nat Biotechnol 2023; 41:417-426. [PMID: 36163550 PMCID: PMC10289836 DOI: 10.1038/s41587-022-01468-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 08/11/2022] [Indexed: 11/09/2022]
Abstract
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq) has the potential to investigate both genetic and nongenetic sources of tumor heterogeneity in a single assay. Here we present a computational method, Numbat, that integrates haplotype information obtained from population-based phasing with allele and expression signals to enhance detection of copy number variations from scRNA-seq. Numbat exploits the evolutionary relationships between subclones to iteratively infer single-cell copy number profiles and tumor clonal phylogeny. Analysis of 22 tumor samples, including multiple myeloma, gastric, breast and thyroid cancers, shows that Numbat can reconstruct the tumor copy number profile and precisely identify malignant cells in the tumor microenvironment. We identify genetic subpopulations with transcriptional signatures relevant to tumor progression and therapy resistance. Numbat requires neither sample-matched DNA data nor a priori genotyping, and is applicable to a wide range of experimental settings and cancer types.
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Affiliation(s)
- Teng Gao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ruslan Soldatov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hirak Sarkar
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Adam Kurkiewicz
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Evan Biederstedt
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Altos Labs, San Diego, CA, USA.
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44
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Ryu Y, Han GH, Jung E, Hwang D. Integration of Single-Cell RNA-Seq Datasets: A Review of Computational Methods. Mol Cells 2023; 46:106-119. [PMID: 36859475 PMCID: PMC9982060 DOI: 10.14348/molcells.2023.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
With the increased number of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, integrative analysis of multiple scRNA-seq datasets has become commonplace. Batch effects among different datasets are inevitable because of differences in cell isolation and handling protocols, library preparation technology, and sequencing platforms. To remove these batch effects for effective integration of multiple scRNA-seq datasets, a number of methodologies have been developed based on diverse concepts and approaches. These methods have proven useful for examining whether cellular features, such as cell subpopulations and marker genes, identified from a certain dataset, are consistently present, or whether their condition-dependent variations, such as increases in cell subpopulations in particular disease-related conditions, are consistently observed in different datasets generated under similar or distinct conditions. In this review, we summarize the concepts and approaches of the integration methods and their pros and cons as has been reported in previous literature.
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Affiliation(s)
- Yeonjae Ryu
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Geun Hee Han
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eunsoo Jung
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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45
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Pavillon N, Smith NI. Non-invasive monitoring of T cell differentiation through Raman spectroscopy. Sci Rep 2023; 13:3129. [PMID: 36813799 PMCID: PMC9947172 DOI: 10.1038/s41598-023-29259-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
The monitoring of dynamic cellular behaviors remains a technical challenge for most established techniques used nowadays for single-cell analysis, as most of them are either destructive, or rely on labels that can affect the long-term functions of cells. We employ here label-free optical techniques to non-invasively monitor the changes that occur in murine naive T cells upon activation and subsequent differentiation into effector cells. Based on spontaneous Raman single-cell spectra, we develop statistical models that allow the detection of activation, and employ non-linear projection methods to delineate the changes occurring over a several day period spanning early differentiation. We show that these label-free results have very high correlation with known surface markers of activation and differentiation, while also providing spectral models that allow the identification of the underlying molecular species that are representative of the biological process under study.
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Affiliation(s)
- Nicolas Pavillon
- Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan.
| | - Nicholas I. Smith
- grid.136593.b0000 0004 0373 3971Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Open and Transdisciplinary Research Institute (OTRI), Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 Japan
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46
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Yu X, Xu X, Zhang J, Li X. Batch alignment of single-cell transcriptomics data using deep metric learning. Nat Commun 2023; 14:960. [PMID: 36810607 PMCID: PMC9944958 DOI: 10.1038/s41467-023-36635-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
scRNA-seq has uncovered previously unappreciated levels of heterogeneity. With the increasing scale of scRNA-seq studies, the major challenge is correcting batch effect and accurately detecting the number of cell types, which is inevitable in human studies. The majority of scRNA-seq algorithms have been specifically designed to remove batch effect firstly and then conduct clustering, which may miss some rare cell types. Here we develop scDML, a deep metric learning model to remove batch effect in scRNA-seq data, guided by the initial clusters and the nearest neighbor information intra and inter batches. Comprehensive evaluations spanning different species and tissues demonstrated that scDML can remove batch effect, improve clustering performance, accurately recover true cell types and consistently outperform popular methods such as Seurat 3, scVI, Scanorama, BBKNN, Harmony et al. Most importantly, scDML preserves subtle cell types in raw data and enables discovery of new cell subtypes that are hard to extract by analyzing each batch individually. We also show that scDML is scalable to large datasets with lower peak memory usage, and we believe that scDML offers a valuable tool to study complex cellular heterogeneity.
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Affiliation(s)
- Xiaokang Yu
- Center for Applied Statistics, School of Statistics, Renmin University of China, 100872, Beijing, China
| | - Xinyi Xu
- School of Statistics and Mathematics, Central University of Finance and Economics, 100081, Beijing, China
| | - Jingxiao Zhang
- Center for Applied Statistics, School of Statistics, Renmin University of China, 100872, Beijing, China.
| | - Xiangjie Li
- Changping Laboratory, 102206, Beijing, China.
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47
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Hirz T, Mei S, Sarkar H, Kfoury Y, Wu S, Verhoeven BM, Subtelny AO, Zlatev DV, Wszolek MW, Salari K, Murray E, Chen F, Macosko EZ, Wu CL, Scadden DT, Dahl DM, Baryawno N, Saylor PJ, Kharchenko PV, Sykes DB. Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nat Commun 2023; 14:663. [PMID: 36750562 PMCID: PMC9905093 DOI: 10.1038/s41467-023-36325-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
The treatment of low-risk primary prostate cancer entails active surveillance only, while high-risk disease requires multimodal treatment including surgery, radiation therapy, and hormonal therapy. Recurrence and development of metastatic disease remains a clinical problem, without a clear understanding of what drives immune escape and tumor progression. Here, we comprehensively describe the tumor microenvironment of localized prostate cancer in comparison with adjacent normal samples and healthy controls. Single-cell RNA sequencing and high-resolution spatial transcriptomic analyses reveal tumor context dependent changes in gene expression. Our data indicate that an immune suppressive tumor microenvironment associates with suppressive myeloid populations and exhausted T-cells, in addition to high stromal angiogenic activity. We infer cell-to-cell relationships from high throughput ligand-receptor interaction measurements within undissociated tissue sections. Our work thus provides a highly detailed and comprehensive resource of the prostate tumor microenvironment as well as tumor-stromal cell interactions.
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Affiliation(s)
- Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Shenglin Mei
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Hirak Sarkar
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Youmna Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bronte M Verhoeven
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Alexander O Subtelny
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dimitar V Zlatev
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew W Wszolek
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Keyan Salari
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Douglas M Dahl
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Philip J Saylor
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Peter V Kharchenko
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Altos Labs, San Diego, CA, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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48
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Mishra S, Pandey N, Chawla S, Sharma M, Chandra O, Jha IP, SenGupta D, Natarajan KN, Kumar V. Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis. Genome Res 2023; 33:218-231. [PMID: 36653120 PMCID: PMC10069468 DOI: 10.1101/gr.277015.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
The true benefits of large single-cell transcriptome and epigenome data sets can be realized only with the development of new approaches and search tools for annotating individual cells. Matching a single-cell epigenome profile to a large pool of reference cells remains a major challenge. Here, we present scEpiSearch, which enables searching, comparison, and independent classification of single-cell open-chromatin profiles against a large reference of single-cell expression and open-chromatin data sets. Across performance benchmarks, scEpiSearch outperformed multiple methods in accuracy of search and low-dimensional coembedding of single-cell profiles, irrespective of platforms and species. Here we also demonstrate the unconventional utilities of scEpiSearch by applying it on single-cell epigenome profiles of K562 cells and samples from patients with acute leukaemia to reveal different aspects of their heterogeneity, multipotent behavior, and dedifferentiated states. Applying scEpiSearch on our single-cell open-chromatin profiles from embryonic stem cells (ESCs), we identified ESC subpopulations with more activity and poising for endoplasmic reticulum stress and unfolded protein response. Thus, scEpiSearch solves the nontrivial problem of amalgamating information from a large pool of single cells to identify and study the regulatory states of cells using their single-cell epigenomes.
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Affiliation(s)
- Shreya Mishra
- Department for Computational Biology, IIIT Delhi 110020, India
| | - Neetesh Pandey
- Department for Computational Biology, IIIT Delhi 110020, India
| | - Smriti Chawla
- Department for Computational Biology, IIIT Delhi 110020, India
| | - Madhu Sharma
- Department for Computational Biology, IIIT Delhi 110020, India
| | - Omkar Chandra
- Department for Computational Biology, IIIT Delhi 110020, India
| | | | - Debarka SenGupta
- Department for Computational Biology, IIIT Delhi 110020, India.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4001, Australia
| | - Kedar Nath Natarajan
- DTU Bioengineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Vibhor Kumar
- Department for Computational Biology, IIIT Delhi 110020, India;
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49
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Hsu LL, Culhane AC. Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data. Sci Rep 2023; 13:1197. [PMID: 36681709 PMCID: PMC9867729 DOI: 10.1038/s41598-022-26434-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 01/22/2023] Open
Abstract
Effective dimension reduction is essential for single cell RNA-seq (scRNAseq) analysis. Principal component analysis (PCA) is widely used, but requires continuous, normally-distributed data; therefore, it is often coupled with log-transformation in scRNAseq applications, which can distort the data and obscure meaningful variation. We describe correspondence analysis (CA), a count-based alternative to PCA. CA is based on decomposition of a chi-squared residual matrix, avoiding distortive log-transformation. To address overdispersion and high sparsity in scRNAseq data, we propose five adaptations of CA, which are fast, scalable, and outperform standard CA and glmPCA, to compute cell embeddings with more performant or comparable clustering accuracy in 8 out of 9 datasets. In particular, we find that CA with Freeman-Tukey residuals performs especially well across diverse datasets. Other advantages of the CA framework include visualization of associations between genes and cell populations in a "CA biplot," and extension to multi-table analysis; we introduce corralm for integrative multi-table dimension reduction of scRNAseq data. We implement CA for scRNAseq data in corral, an R/Bioconductor package which interfaces directly with single cell classes in Bioconductor. Switching from PCA to CA is achieved through a simple pipeline substitution and improves dimension reduction of scRNAseq datasets.
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Affiliation(s)
- Lauren L Hsu
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aedín C Culhane
- Limerick Digital Cancer Research Centre, Health Research Institute, School of Medicine, University of Limerick, Limerick, Ireland.
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50
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Xu X, Li X. Structure-preserved dimension reduction using joint triplets sampling for multi-batch integration of single-cell transcriptomic data. Brief Bioinform 2023; 24:6982727. [PMID: 36627114 DOI: 10.1093/bib/bbac608] [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: 09/14/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
Dimension reduction (DR) plays an important role in single-cell RNA sequencing (scRNA-seq), such as data interpretation, visualization and other downstream analysis. A desired DR method should be applicable to various application scenarios, including identifying cell types, preserving the inherent structure of data and handling with batch effects. However, most of the existing DR methods fail to accommodate these requirements simultaneously, especially removing batch effects. In this paper, we develop a novel structure-preserved dimension reduction (SPDR) method using intra- and inter-batch triplets sampling. The constructed triplets jointly consider each anchor's mutual nearest neighbors from inter-batch, k-nearest neighbors from intra-batch and randomly selected cells from the whole data, which capture higher order structure information and meanwhile account for batch information of the data. Then we minimize a robust loss function for the chosen triplets to obtain a structure-preserved and batch-corrected low-dimensional representation. Comprehensive evaluations show that SPDR outperforms other competing DR methods, such as INSCT, IVIS, Trimap, Scanorama, scVI and UMAP, in removing batch effects, preserving biological variation, facilitating visualization and improving clustering accuracy. Besides, the two-dimensional (2D) embedding of SPDR presents a clear and authentic expression pattern, and can guide researchers to determine how many cell types should be identified. Furthermore, SPDR is robust to complex data characteristics (such as down-sampling, duplicates and outliers) and varying hyperparameter settings. We believe that SPDR will be a valuable tool for characterizing complex cellular heterogeneity.
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Affiliation(s)
- Xinyi Xu
- School of Statistics and Mathematics, Central University of Finance and Economics, Beijing, 100081, China
| | - Xiangjie Li
- Changping Laboratory, Beijing, 102206, China
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