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Skinnider MA, Gautier M, Teo AYY, Kathe C, Hutson TH, Laskaratos A, de Coucy A, Regazzi N, Aureli V, James ND, Schneider B, Sofroniew MV, Barraud Q, Bloch J, Anderson MA, Squair JW, Courtine G. Single-cell and spatial atlases of spinal cord injury in the Tabulae Paralytica. Nature 2024:10.1038/s41586-024-07504-y. [PMID: 38898272 DOI: 10.1038/s41586-024-07504-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 05/01/2024] [Indexed: 06/21/2024]
Abstract
Here, we introduce the Tabulae Paralytica-a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells, a multiome atlas pairing transcriptomic and epigenomic measurements within the same nuclei, and two spatial transcriptomic atlases of the injured spinal cord spanning four spatial and temporal dimensions. We integrated these atlases into a common framework to dissect the molecular logic that governs the responses to injury within the spinal cord1. The Tabulae Paralytica uncovered new biological principles that dictate the consequences of SCI, including conserved and divergent neuronal responses to injury; the priming of specific neuronal subpopulations to upregulate circuit-reorganizing programs after injury; an inverse relationship between neuronal stress responses and the activation of circuit reorganization programs; the necessity of re-establishing a tripartite neuroprotective barrier between immune-privileged and extra-neural environments after SCI and a failure to form this barrier in old mice. We leveraged the Tabulae Paralytica to develop a rejuvenative gene therapy that re-established this tripartite barrier, and restored the natural recovery of walking after paralysis in old mice. The Tabulae Paralytica provides a window into the pathobiology of SCI, while establishing a framework for integrating multimodal, genome-scale measurements in four dimensions to study biology and medicine.
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Affiliation(s)
- Michael A Skinnider
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Matthieu Gautier
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Alan Yue Yang Teo
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Claudia Kathe
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Thomas H Hutson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland
| | - Achilleas Laskaratos
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Alexandra de Coucy
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Nicola Regazzi
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Viviana Aureli
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicholas D James
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Bernard Schneider
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Bertarelli Platform for Gene Therapy, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Quentin Barraud
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Jocelyne Bloch
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Mark A Anderson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Jordan W Squair
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Grégoire Courtine
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
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2
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Xi NM, Huang DP. Drug safety assessment by machine learning models. J Biopharm Stat 2024:1-12. [PMID: 38888177 DOI: 10.1080/10543406.2024.2365976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
The evaluation of drug-induced Torsades de pointes (TdP) risks is crucial in drug safety assessment. In this study, we discuss machine learning approaches in the prediction of drug-induced TdP risks using preclinical data. Specifically, a random forest model was trained on the dataset generated by the rabbit ventricular wedge assay. The model prediction performance was measured on 28 drugs from the Comprehensive In Vitro Proarrhythmia Assay initiative. Leave-one-drug-out cross-validation provided an unbiased estimation of model performance. Stratified bootstrap revealed the uncertainty in the asymptotic model prediction. Our study validated the utility of machine learning approaches in predicting drug-induced TdP risks from preclinical data. Our methods can be extended to other preclinical protocols and serve as a supplementary evaluation in drug safety assessment.
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Affiliation(s)
- Nan Miles Xi
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Dalong Patrick Huang
- Office of Biostatistics, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
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3
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Palmer JA, Rosenthal N, Teichmann SA, Litvinukova M. Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics. Circ Res 2024; 134:1681-1702. [PMID: 38843288 PMCID: PMC11149945 DOI: 10.1161/circresaha.124.323672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.
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Affiliation(s)
- Jack A. Palmer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
| | - Nadia Rosenthal
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME (N.R.)
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.R.)
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory (S.A.T.), University of Cambridge, United Kingdom
| | - Monika Litvinukova
- University Hospital Würzburg, Germany (M.L.)
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany (M.L.)
- Helmholtz Pioneer Campus, Helmholtz Munich, Germany (M.L.)
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4
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Wang AZ, Mashimo BL, Schaettler MO, Sherpa ND, Leavitt LA, Livingstone AJ, Khan SM, Li M, Anzaldua-Campos MI, Bradley JD, Leuthardt EC, Kim AH, Dowling JL, Chicoine MR, Jones PS, Choi BD, Cahill DP, Carter BS, Petti AA, Johanns TM, Dunn GP. Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population. Cancer Discov 2024; 14:1106-1131. [PMID: 38416133 DOI: 10.1158/2159-8290.cd-23-0913] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
Recent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing and single-cell RNA sequencing with paired V(D)J sequencing, respectively, on TILs from two cohorts of patients totaling 15 patients with high-grade glioma, including GBM or astrocytoma, IDH-mutant, grade 4 (G4A). Analysis of the CD8+ TIL landscape reveals an enrichment of clonally expanded GZMK+ effector T cells in the tumor compared with matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+ T-cell population in GBM TIL. These data suggest that GZMK+ effector T cells represent an important T-cell subset within the GBM microenvironment and may harbor potential therapeutic implications. SIGNIFICANCE To understand the limited efficacy of immune-checkpoint blockade in GBM, we applied a multiomics approach to understand the TIL landscape. By highlighting the enrichment of GZMK+ effector T cells and the lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Anthony Z Wang
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryce L Mashimo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maximilian O Schaettler
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ngima D Sherpa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences Graduate Program, Harvard University, Cambridge, Massachusetts
| | - Lydia A Leavitt
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurosurgery, University of Louisville, Louisville, Kentucky
| | - Alexandra J Livingstone
- Department of Medicine, Division of Medical Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Saad M Khan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mao Li
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Markus I Anzaldua-Campos
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Neuroscience Undergraduate Program, Harvard University, Cambridge, Massachusetts
| | - Joseph D Bradley
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Michael R Chicoine
- Department of Neurological Surgery, University of Missouri-Columbia, Columbia, Missouri
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Allegra A Petti
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tanner M Johanns
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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Duo H, Li Y, Lan Y, Tao J, Yang Q, Xiao Y, Sun J, Li L, Nie X, Zhang X, Liang G, Liu M, Hao Y, Li B. Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios. Genome Biol 2024; 25:145. [PMID: 38831386 PMCID: PMC11149245 DOI: 10.1186/s13059-024-03290-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines. RESULTS We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe ( https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409 ), and an online tool Simsite ( https://www.ciblab.net/software/simshiny/ ) for data simulation. CONCLUSIONS No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.
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Affiliation(s)
- Hongrui Duo
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China
| | - Yinghong Li
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, People's Republic of China
| | - Yang Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Jingxin Tao
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China
| | - Qingxia Yang
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, People's Republic of China
| | - Yingxue Xiao
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China
| | - Jing Sun
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China
| | - Lei Li
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China
| | - Xiner Nie
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Xiaoxi Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Mingwei Liu
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China.
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, People's Republic of China.
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Filipovic D, Kana O, Marri D, Bhattacharya S. Unique challenges and best practices for single cell transcriptomic analysis in toxicology. CURRENT OPINION IN TOXICOLOGY 2024; 38:100475. [PMID: 38645720 PMCID: PMC11027889 DOI: 10.1016/j.cotox.2024.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The application and analysis of single-cell transcriptomics in toxicology presents unique challenges. These include identifying cell sub-populations sensitive to perturbation; interpreting dynamic shifts in cell type proportions in response to chemical exposures; and performing differential expression analysis in dose-response studies spanning multiple treatment conditions. This review examines these challenges while presenting best practices for critical single cell analysis tasks. This covers areas such as cell type identification; analysis of differential cell type abundance; differential gene expression; and cellular trajectories. Towards enhancing the use of single-cell transcriptomics in toxicology, this review aims to address key challenges in this field and offer practical analytical solutions. Overall, applying appropriate bioinformatic techniques to single-cell transcriptomic data can yield valuable insights into cellular responses to toxic exposures.
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Affiliation(s)
- David Filipovic
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
| | - Omar Kana
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - Daniel Marri
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Sudin Bhattacharya
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, 48824, USA
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7
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Lin P, Gan YB, He J, Lin SE, Xu JK, Chang L, Zhao LM, Zhu J, Zhang L, Huang S, Hu O, Wang YB, Jin HJ, Li YY, Yan PL, Chen L, Jiang JX, Liu P. Advancing skeletal health and disease research with single-cell RNA sequencing. Mil Med Res 2024; 11:33. [PMID: 38816888 PMCID: PMC11138034 DOI: 10.1186/s40779-024-00538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
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Grants
- 2022YFA1103202 National Key Research and Development Program of China
- 82272507 National Natural Science Foundation of China
- 32270887 National Natural Science Foundation of China
- 32200654 National Natural Science Foundation of China
- CSTB2023NSCQ-ZDJO008 Natural Science Foundation of Chongqing
- BX20220397 Postdoctoral Innovative Talent Support Program
- SFLKF202201 Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning
- 2021-XZYG-B10 General Hospital of Western Theater Command Research Project
- 14113723 University Grants Committee, Research Grants Council of Hong Kong, China
- N_CUHK472/22 University Grants Committee, Research Grants Council of Hong Kong, China
- C7030-18G University Grants Committee, Research Grants Council of Hong Kong, China
- T13-402/17-N University Grants Committee, Research Grants Council of Hong Kong, China
- AoE/M-402/20 University Grants Committee, Research Grants Council of Hong Kong, China
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Affiliation(s)
- Peng Lin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yi-Bo Gan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian He
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
- Pancreatic Injury and Repair Key Laboratory of Sichuan Province, the General Hospital of Western Theater Command, Chengdu, 610031, China
| | - Si-En Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Jian-Kun Xu
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Li-Ming Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Sacramento, CA, 94305, USA
| | - Jun Zhu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Zhang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Sha Huang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ou Hu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ying-Bo Wang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huai-Jian Jin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yang-Yang Li
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Pu-Lin Yan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Center of Bone Metabolism and Repair, State Key Laboratory of Trauma and Chemical Poisoning, Trauma Center, Research Institute of Surgery, Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian-Xin Jiang
- Wound Trauma Medical Center, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Peng Liu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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8
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Dogga SK, Rop JC, Cudini J, Farr E, Dara A, Ouologuem D, Djimdé AA, Talman AM, Lawniczak MKN. A single cell atlas of sexual development in Plasmodium falciparum. Science 2024; 384:eadj4088. [PMID: 38696552 DOI: 10.1126/science.adj4088] [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: 07/12/2023] [Accepted: 03/14/2024] [Indexed: 05/04/2024]
Abstract
The developmental decision made by malaria parasites to become sexual underlies all malaria transmission. Here, we describe a rich atlas of short- and long-read single-cell transcriptomes of over 37,000 Plasmodium falciparum cells across intraerythrocytic asexual and sexual development. We used the atlas to explore transcriptional modules and exon usage along sexual development and expanded it to include malaria parasites collected from four Malian individuals naturally infected with multiple P. falciparum strains. We investigated genotypic and transcriptional heterogeneity within and among these wild strains at the single-cell level, finding differential expression between different strains even within the same host. These data are a key addition to the Malaria Cell Atlas interactive data resource, enabling a deeper understanding of the biology and diversity of transmission stages.
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Affiliation(s)
| | - Jesse C Rop
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Elias Farr
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Institute for Computational Biomedicine, University of Heidelberg, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany
| | - Antoine Dara
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Dinkorma Ouologuem
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Abdoulaye A Djimdé
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Arthur M Talman
- MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
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9
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Gondal MN, Shah SUR, Chinnaiyan AM, Cieslik M. A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations. ARXIV 2024:arXiv:2404.10545v1. [PMID: 38699169 PMCID: PMC11065044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Furthermore, we propose that bridging the gap between computational and wet lab scientists through user-friendly web-based platforms is needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.
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Affiliation(s)
- Mahnoor N. Gondal
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
| | - Saad Ur Rehman Shah
- Gies College of Business, University of Illinois Business College, Champaign, IL USA
| | - Arul M. Chinnaiyan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Urology, University of Michigan, Ann Arbor, MI USA
- Howard Hughes Medical Institute, Ann Arbor, MI USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI USA
| | - Marcin Cieslik
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Pathology, University of Michigan, Ann Arbor, MI USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI USA
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10
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Zhang X, Marand AP, Yan H, Schmitz RJ. scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome Biol 2024; 25:90. [PMID: 38589969 PMCID: PMC11003106 DOI: 10.1186/s13059-024-03235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called scifi-ATAC-seq, single-cell combinatorial fluidic indexing ATAC-sequencing, which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using the 10X Genomics platform. With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples can be indexed in a single emulsion reaction, representing an approximately 20-fold increase in throughput compared to the standard 10X Genomics workflow.
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Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Alexandre P Marand
- Department of Genetics, University of Georgia, Athens, GA, USA
- Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
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11
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Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. THE PLANT CELL 2024; 36:812-828. [PMID: 38231860 PMCID: PMC10980355 DOI: 10.1093/plcell/koae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 01/19/2024]
Abstract
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.
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Affiliation(s)
- Carolin Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
- VIB Single Cell Core Facility, Ghent 9052, Belgium
| | - Dongbo Shi
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Manuel Neumann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Lea S Berg
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Yuji Ke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Fabio Gomez-Cano
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Jan U Lohmann
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Olivier C Martin
- Universities of Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette 91192, France
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Michael T Raissig
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Gergo Palfalvi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marc Libault
- Division of Plant Science and Technology, Interdisciplinary Plant Group, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65201, USA
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
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12
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Jiang A, Snell RG, Lehnert K. ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells. Bioinformatics 2024; 40:btae167. [PMID: 38539041 PMCID: PMC11007236 DOI: 10.1093/bioinformatics/btae167] [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: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
MOTIVATION In recent years, improvements in throughput of single-cell RNA-seq have resulted in a significant increase in the number of cells profiled. The generation of single-cell RNA-seq datasets comprising >1 million cells is becoming increasingly common, giving rise to demands for more efficient computational workflows. RESULTS We present an update to our single-cell RNA-seq analysis web server application, ICARUS (available at https://launch.icarus-scrnaseq.cloud.edu.au) that allows effective analysis of large-scale single-cell RNA-seq datasets. ICARUS v3 utilizes the geometric cell sketching method to subsample cells from the overall dataset for dimensionality reduction and clustering that can be then projected to the large dataset. We then extend this functionality to select a representative subset of cells for downstream data analysis applications including differential expression analysis, gene co-expression network construction, gene regulatory network construction, trajectory analysis, cell-cell communication inference, and cell cluster associations to GWAS traits. We demonstrate analysis of single-cell RNA-seq datasets using ICARUS v3 of 1.3 million cells completed within the hour. AVAILABILITY AND IMPLEMENTATION ICARUS is available at https://launch.icarus-scrnaseq.cloud.edu.au.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
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13
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Zhang X, Marand AP, Yan H, Schmitz RJ. Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.17.558155. [PMID: 37786710 PMCID: PMC10541611 DOI: 10.1101/2023.09.17.558155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called single-cell combinatorial fluidic indexing ATAC-sequencing ("scifi-ATAC-seq"), which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using a widely commercialized microfluidics platform (10X Genomics). With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples in a single emulsion reaction can be indexed, representing a ~20-fold increase in throughput compared to the standard 10X Genomics workflow.
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Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Alexandre P Marand
- Department of Genetics, University of Georgia, Athens, GA, USA
- Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
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14
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Gibson A, Ram R, Gangula R, Li Y, Mukherjee E, Palubinsky AM, Campbell CN, Thorne M, Konvinse KC, Choshi P, Deshpande P, Pedretti S, O’Neil RT, Wanjalla CN, Kalams SA, Gaudieri S, Lehloenya RJ, Bailin SS, Chopra A, Mallal SA, Phillips EJ. Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.26.568771. [PMID: 38405793 PMCID: PMC10888802 DOI: 10.1101/2023.11.26.568771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCRαβ clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.
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Affiliation(s)
- Andrew Gibson
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Rama Gangula
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Yueran Li
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Eric Mukherjee
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Amy M Palubinsky
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Chelsea N Campbell
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Michael Thorne
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Katherine C Konvinse
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Phuti Choshi
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Pooja Deshpande
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Sarah Pedretti
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Richard T O’Neil
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center and Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Spyros A Kalams
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
- School of Human Sciences, The University of Western Australia, Western Australia, Australia
| | - Rannakoe J Lehloenya
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
- Division of Dermatology, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Samuel S Bailin
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Jason A Trubiano on behalf of the AUS-SCAR study group
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Victoria, Australia
| | | | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
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15
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Ledru N, Wilson PC, Muto Y, Yoshimura Y, Wu H, Li D, Asthana A, Tullius SG, Waikar SS, Orlando G, Humphreys BD. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing. Nat Commun 2024; 15:1291. [PMID: 38347009 PMCID: PMC10861555 DOI: 10.1038/s41467-024-45706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype that may promote fibrosis and chronic kidney disease. The healthy to failed repair change is marked by cell state-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq sequencing offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We develop a regularized regression approach to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generate a single nucleus multiomic dataset from seven adult human kidney samples and apply our method to study drivers of a failed injury response associated with kidney disease. We demonstrate that our approach is a highly effective tool for predicting key cis- and trans-regulatory elements underpinning the healthy to failed repair transition and use it to identify NFAT5 as a driver of the maladaptive proximal tubule state.
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Affiliation(s)
- Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Parker C Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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16
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Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT. A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data. Genome Res 2024; 34:94-105. [PMID: 38195207 PMCID: PMC10903947 DOI: 10.1101/gr.278234.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024]
Abstract
Genetic and gene expression heterogeneity is an essential hallmark of many tumors, allowing the cancer to evolve and to develop resistance to treatment. Currently, the most commonly used data types for studying such heterogeneity are bulk tumor/normal whole-genome or whole-exome sequencing (WGS, WES); and single-cell RNA sequencing (scRNA-seq), respectively. However, tools are currently lacking to link genomic tumor subclonality with transcriptomic heterogeneity by integrating genomic and single-cell transcriptomic data collected from the same tumor. To address this gap, we developed scBayes, a Bayesian probabilistic framework that uses tumor subclonal structure inferred from bulk DNA sequencing data to determine the subclonal identity of cells from single-cell gene expression (scRNA-seq) measurements. Grouping together cells representing the same genetically defined tumor subclones allows comparison of gene expression across different subclones, or investigation of gene expression changes within the same subclone across time (i.e., progression, treatment response, or relapse) or space (i.e., at multiple metastatic sites and organs). We used simulated data sets, in silico synthetic data sets, as well as biological data sets generated from cancer samples to extensively characterize and validate the performance of our method, as well as to show improvements over existing methods. We show the validity and utility of our approach by applying it to published data sets and recapitulating the findings, as well as arriving at novel insights into cancer subclonal expression behavior in our own data sets. We further show that our method is applicable to a wide range of single-cell sequencing technologies including single-cell DNA sequencing as well as Smart-seq and 10x Genomics scRNA-seq protocols.
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Affiliation(s)
- Yi Qiao
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Xiaomeng Huang
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Philip J Moos
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jonathan M Ahmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Anthony D Pomicter
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Michael W Deininger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, Utah 84112, USA
| | - John C Byrd
- The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer A Woyach
- The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Deborah M Stephens
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Gabor T Marth
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA;
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17
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Haage V, Tuddenham JF, Comandante-Lou N, Bautista A, Monzel A, Chiu R, Fujita M, Garcia FG, Bhattarai P, Patel R, Buonfiglioli A, Idiarte J, Herman M, Rinderspacher A, Mela A, Zhao W, Argenziano MG, Furnari JL, Banu MA, Landry DW, Bruce JN, Canoll P, Zhang Y, Nuriel T, Kizil C, Sproul AA, de Witte LD, Sims PA, Menon V, Picard M, De Jager PL. A pharmacological toolkit for human microglia identifies Topoisomerase I inhibitors as immunomodulators for Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579103. [PMID: 38370689 PMCID: PMC10871172 DOI: 10.1101/2024.02.06.579103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
While efforts to identify microglial subtypes have recently accelerated, the relation of transcriptomically defined states to function has been largely limited to in silico annotations. Here, we characterize a set of pharmacological compounds that have been proposed to polarize human microglia towards two distinct states - one enriched for AD and MS genes and another characterized by increased expression of antigen presentation genes. Using different model systems including HMC3 cells, iPSC-derived microglia and cerebral organoids, we characterize the effect of these compounds in mimicking human microglial subtypes in vitro. We show that the Topoisomerase I inhibitor Camptothecin induces a CD74high/MHChigh microglial subtype which is specialized in amyloid beta phagocytosis. Camptothecin suppressed amyloid toxicity and restored microglia back to their homeostatic state in a zebrafish amyloid model. Our work provides avenues to recapitulate human microglial subtypes in vitro, enabling functional characterization and providing a foundation for modulating human microglia in vivo.
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Affiliation(s)
- Verena Haage
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - John F. Tuddenham
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Natacha Comandante-Lou
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alex Bautista
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Anna Monzel
- Department of Psychiatry, Division of Behavioral Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
| | - Rebecca Chiu
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Frankie G. Garcia
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Prabesh Bhattarai
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Ronak Patel
- Department of Pathology and Cell Biology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alice Buonfiglioli
- Department of Psychiatry, Icahn School of Medicine, 1460 Madison Avenue, New York, NY, 10029, United States
| | - Juan Idiarte
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Mathieu Herman
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | | | - Angeliki Mela
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Michael G. Argenziano
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia L. Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Donald W. Landry
- Department of Medicine, Columbia University, New York, NY 10032, United States
| | - Jeffrey N. Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ya Zhang
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Tal Nuriel
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Caghan Kizil
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Andrew A. Sproul
- Department of Pathology and Cell Biology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Lotje D. de Witte
- Department of Psychiatry, Icahn School of Medicine, 1460 Madison Avenue, New York, NY, 10029, United States
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
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18
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Geuenich MJ, Gong DW, Campbell KR. The impacts of active and self-supervised learning on efficient annotation of single-cell expression data. Nat Commun 2024; 15:1014. [PMID: 38307875 PMCID: PMC10837127 DOI: 10.1038/s41467-024-45198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
A crucial step in the analysis of single-cell data is annotating cells to cell types and states. While a myriad of approaches has been proposed, manual labeling of cells to create training datasets remains tedious and time-consuming. In the field of machine learning, active and self-supervised learning methods have been proposed to improve the performance of a classifier while reducing both annotation time and label budget. However, the benefits of such strategies for single-cell annotation have yet to be evaluated in realistic settings. Here, we perform a comprehensive benchmarking of active and self-supervised labeling strategies across a range of single-cell technologies and cell type annotation algorithms. We quantify the benefits of active learning and self-supervised strategies in the presence of cell type imbalance and variable similarity. We introduce adaptive reweighting, a heuristic procedure tailored to single-cell data-including a marker-aware version-that shows competitive performance with existing approaches. In addition, we demonstrate that having prior knowledge of cell type markers improves annotation accuracy. Finally, we summarize our findings into a set of recommendations for those implementing cell type annotation procedures or platforms. An R package implementing the heuristic approaches introduced in this work may be found at https://github.com/camlab-bioml/leader .
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Affiliation(s)
- Michael J Geuenich
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1×5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Dae-Won Gong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1×5, Canada
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1×5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Department of Statistical Sciences, University of Toronto, Toronto, ON, M5S 3G3, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada.
- Ontario Institute of Cancer Research, Toronto, ON, M5G 1M1, Canada.
- Vector Institute, Toronto, ON, M5G 1M1, Canada.
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19
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Li W, Bazaz SR, Mayoh C, Salomon R. Analytical Workflows for Single-Cell Multiomic Data Using the BD Rhapsody Platform. Curr Protoc 2024; 4:e963. [PMID: 38353375 DOI: 10.1002/cpz1.963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The conversion of raw sequencing reads to biologically relevant data in high-throughput single-cell RNA sequencing experiments is a complex and involved process. Drawing meaning from thousands of individual cells to provide biological insight requires ensuring not only that the data are of the highest quality but also that the signal can be separated from noise. In this article, we describe a detailed analytical workflow, including six pipelines, that allows high-quality data analysis in single-cell multiomics. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Image analysis Basic Protocol 2: Sequencing quality control and generation of a gene expression matrix Basic Protocol 3: Gene expression matrix data pre-processing and analysis Basic Protocol 4: Advanced analysis Basic Protocol 5: Conversion to flow cytometry standard (FCS) format Basic Protocol 6: Visualization using graphical interfaces.
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Affiliation(s)
- Wenyan Li
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Sajad Razavi Bazaz
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Robert Salomon
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
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20
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Leckie-Harre A, Silverman I, Wu H, Humphreys BD, Malone AF. Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection to Infer Contact-dependent Immune Cell Transcription. Transplantation 2024; 108:421-429. [PMID: 37638864 PMCID: PMC10798591 DOI: 10.1097/tp.0000000000004762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/25/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Rejection requires cell-cell contact involving immune cells. Inferring the transcriptional programs of cell-cell interactions from single-cell RNA-sequencing (scRNA-seq) data is challenging as spatial information is lost. METHODS We combined a CD45 pos enrichment strategy with Cellular Indexing of Transcriptomes and Epitopes by sequencing based quantification of leukocyte surface proteins to analyze cell-cell interactions in 11 human kidney transplant biopsies encompassing a spectrum of rejection diagnoses. scRNA-seq was performed using the 10X Genomics platform. We applied the sequencing physically interacting cells computational method to deconvolute the transcriptional profiles of heterotypic physically interacting cells. RESULTS The 11 human allograft biopsies generated 31 203 high-quality single-cell libraries. Clustering was further refined by combining Cellular Indexing of Transcriptomes and Epitopes by sequencing data from 6 different leukocyte-specific surface proteins. Three of 6 doublet clusters were identified as physically interacting cell complexes; macrophages or dendritic cells bound to B cells or plasma cells; natural killer (NK) or T cells bound to macrophages or dendritic cells and NK or T cells bound to endothelial cells. Myeloid-lymphocyte physically interacting cell complexes expressed activated and proinflammatory genes. Lymphocytes physically interacting with endothelial cells were enriched for NK and CD4 T cells. NK cell-endothelial cell contact caused increased expression of endothelial proinflammatory genes CXCL9 and CXCL10 and NK cell proinflammatory genes CCL3 , CCL4 , and GNLY . CONCLUSIONS The transcriptional profiles of physically interacting cells from human kidney transplant biopsies can be inferred from scRNA-seq data using the sequencing physically interacting cells method. This approach complements previous methods that estimate cell-cell physical contact from scRNA-seq data.
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Affiliation(s)
- Aidan Leckie-Harre
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Isabel Silverman
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Andrew F. Malone
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
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21
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Xiong YX, Zhang XF. scDOT: enhancing single-cell RNA-Seq data annotation and uncovering novel cell types through multi-reference integration. Brief Bioinform 2024; 25:bbae072. [PMID: 38436563 PMCID: PMC10939303 DOI: 10.1093/bib/bbae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
The proliferation of single-cell RNA-seq data has greatly enhanced our ability to comprehend the intricate nature of diverse tissues. However, accurately annotating cell types in such data, especially when handling multiple reference datasets and identifying novel cell types, remains a significant challenge. To address these issues, we introduce Single Cell annotation based on Distance metric learning and Optimal Transport (scDOT), an innovative cell-type annotation method adept at integrating multiple reference datasets and uncovering previously unseen cell types. scDOT introduces two key innovations. First, by incorporating distance metric learning and optimal transport, it presents a novel optimization framework. This framework effectively learns the predictive power of each reference dataset for new query data and simultaneously establishes a probabilistic mapping between cells in the query data and reference-defined cell types. Secondly, scDOT develops an interpretable scoring system based on the acquired probabilistic mapping, enabling the precise identification of previously unseen cell types within the data. To rigorously assess scDOT's capabilities, we systematically evaluate its performance using two diverse collections of benchmark datasets encompassing various tissues, sequencing technologies and diverse cell types. Our experimental results consistently affirm the superior performance of scDOT in cell-type annotation and the identification of previously unseen cell types. These advancements provide researchers with a potent tool for precise cell-type annotation, ultimately enriching our understanding of complex biological tissues.
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Affiliation(s)
- Yi-Xuan Xiong
- School of Mathematics and Statistics, Central China Normal University, Wuhan 430079, China
- Key Laboratory of Nonlinear Analysis & Applications (Ministry of Education), Central China Normal University, Wuhan 430079, China
| | - Xiao-Fei Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan 430079, China
- Key Laboratory of Nonlinear Analysis & Applications (Ministry of Education), Central China Normal University, Wuhan 430079, China
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22
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Cao J, Jin L, Yan ZQ, Wang XK, Li YY, Wang Z, Liu YW, Li HM, Guan Z, He ZH, Gong JS, Liu JH, Yin H, Tan YJ, Hong CG, Feng SK, Zhang Y, Wang YY, Qi LY, Chen CY, Liu ZZ, Wang ZX, Xie H. Reassessing endothelial-to-mesenchymal transition in mouse bone marrow: insights from lineage tracing models. Nat Commun 2023; 14:8461. [PMID: 38123537 PMCID: PMC10733381 DOI: 10.1038/s41467-023-44312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Endothelial cells (ECs) and bone marrow stromal cells (BMSCs) play crucial roles in supporting hematopoiesis and hematopoietic regeneration. However, whether ECs are a source of BMSCs remains unclear. Here, we evaluate the contribution of endothelial-to-mesenchymal transition to BMSC generation in postnatal mice. Single-cell RNA sequencing identifies ECs expressing BMSC markers Prrx1 and Lepr; however, this could not be validated using Prrx1-Cre and Lepr-Cre transgenic mice. Additionally, only a minority of BMSCs are marked by EC lineage tracing models using Cdh5-rtTA-tetO-Cre or Tek-CreERT2. Moreover, Cdh5+ BMSCs and Tek+ BMSCs show distinct spatial distributions and characteristic mesenchymal markers, suggestive of their origination from different progenitors rather than CDH5+ TEK+ ECs. Furthermore, myeloablation induced by 5-fluorouracil treatment does not increase Cdh5+ BMSCs. Our findings indicate that ECs hardly convert to BMSCs during homeostasis and myeloablation-induced hematopoietic regeneration, highlighting the importance of using appropriate genetic models and conducting careful data interpretation in studies concerning endothelial-to-mesenchymal transition.
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Affiliation(s)
- Jia Cao
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ling Jin
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Zi-Qi Yan
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiao-Kai Wang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - You-You Li
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Zun Wang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yi-Wei Liu
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Hong-Ming Li
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Zhe Guan
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Ze-Hui He
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Jiang-Shan Gong
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Jiang-Hua Liu
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hao Yin
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Yi-Juan Tan
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Chun-Gu Hong
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Shi-Kai Feng
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yan Zhang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yi-Yi Wang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
| | - Lu-Yue Qi
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Chun-Yuan Chen
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zheng-Zhao Liu
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhen-Xing Wang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Hui Xie
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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23
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Hornung BVH, Azmani Z, den Dekker AT, Oole E, Ozgur Z, Brouwer RWW, van den Hout MCGN, van IJcken WFJ. Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men. Genes (Basel) 2023; 14:2226. [PMID: 38137048 PMCID: PMC10743076 DOI: 10.3390/genes14122226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Single cell RNAseq has been a big leap in many areas of biology. Rather than investigating gene expression on a whole organism level, this technology enables scientists to get a detailed look at rare single cells or within their cell population of interest. The field is growing, and many new methods appear each year. We compared methods utilized in our core facility: Smart-seq3, PlexWell, FLASH-seq, VASA-seq, SORT-seq, 10X, Evercode, and HIVE. We characterized the equipment requirements for each method. We evaluated the performances of these methods based on detected features, transcriptome diversity, mitochondrial RNA abundance and multiplets, among others and benchmarked them against bulk RNA sequencing. Here, we show that bulk transcriptome detects more unique transcripts than any single cell method. While most methods are comparable in many regards, FLASH-seq and VASA-seq yielded the best metrics, e.g., in number of features. If no equipment for automation is available or many cells are desired, then HIVE or 10X yield good results. In general, more recently developed methods perform better. This also leads to the conclusion that older methods should be phased out, and that the development of single cell RNAseq methods is still progressing considerably.
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Affiliation(s)
- Bastian V. H. Hornung
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zakia Azmani
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Alexander T. den Dekker
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Edwin Oole
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zeliha Ozgur
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Mirjam C. G. N. van den Hout
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
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24
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Murphy AE, Fancy N, Skene N. Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset. eLife 2023; 12:RP90214. [PMID: 38047913 PMCID: PMC10695556 DOI: 10.7554/elife.90214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer's disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues and use best-practice approaches to snRNA-seq differential expression, resulting in 549 times fewer DEGs at a false discovery rate of 0.05. Thus, this study highlights the impact of quality control and differential analysis methods on the discovery of disease-associated genes and aims to refocus the AD research field away from spuriously identified genes.
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Affiliation(s)
- Alan E Murphy
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nurun Fancy
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nathan Skene
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
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25
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London CA, Gardner H, Zhao S, Knapp DW, Utturkar SM, Duval DL, Chambers MR, Ostrander E, Trent JM, Kuffel G. Leading the pack: Best practices in comparative canine cancer genomics to inform human oncology. Vet Comp Oncol 2023; 21:565-577. [PMID: 37778398 DOI: 10.1111/vco.12935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Pet dogs develop spontaneous cancers at a rate estimated to be five times higher than that of humans, providing a unique opportunity to study disease biology and evaluate novel therapeutic strategies in a model system that possesses an intact immune system and mirrors key aspects of human cancer biology. Despite decades of interest, effective utilization of pet dog cancers has been hindered by a limited repertoire of necessary cellular and molecular reagents for both in vitro and in vivo studies, as well as a dearth of information regarding the genomic landscape of these cancers. Recently, many of these critical gaps have been addressed through the generation of a highly annotated canine reference genome, the creation of several tools necessary for multi-omic analysis of canine tumours, and the development of a centralized repository for key genomic and associated clinical information from canine cancer patients, the Integrated Canine Data Commons. Together, these advances have catalysed multidisciplinary efforts designed to integrate the study of pet dog cancers more effectively into the translational continuum, with the ultimate goal of improving human outcomes. The current review summarizes this recent progress and provides a guide to resources and tools available for comparative study of pet dog cancers.
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Affiliation(s)
- Cheryl A London
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Heather Gardner
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Shaying Zhao
- University of Georgia Cancer Center, University of Georgia, Athens, Georgia, USA
| | - Deborah W Knapp
- College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Sagar M Utturkar
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Dawn L Duval
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | | | - Elaine Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Gina Kuffel
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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26
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Jiang Z, Zheng X, Li M, Liu M. Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic challenges. Front Med 2023; 17:1135-1169. [PMID: 38151666 DOI: 10.1007/s11684-023-1050-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
Pancreatic cancer, notorious for its late diagnosis and aggressive progression, poses a substantial challenge owing to scarce treatment alternatives. This review endeavors to furnish a holistic insight into pancreatic cancer, encompassing its epidemiology, genomic characterization, risk factors, diagnosis, therapeutic strategies, and treatment resistance mechanisms. We delve into identifying risk factors, including genetic predisposition and environmental exposures, and explore recent research advancements in precursor lesions and molecular subtypes of pancreatic cancer. Additionally, we highlight the development and application of multi-omics approaches in pancreatic cancer research and discuss the latest combinations of pancreatic cancer biomarkers and their efficacy. We also dissect the primary mechanisms underlying treatment resistance in this malignancy, illustrating the latest therapeutic options and advancements in the field. Conclusively, we accentuate the urgent demand for more extensive research to enhance the prognosis for pancreatic cancer patients.
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Affiliation(s)
- Zhichen Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of General Surgery, Division of Gastroenterology and Pancreas, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, China
| | - Xiaohao Zheng
- Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Min Li
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Mingyang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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27
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Yan G, Song D, Li JJ. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nat Commun 2023; 14:7482. [PMID: 37980428 PMCID: PMC10657386 DOI: 10.1038/s41467-023-43162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/02/2023] [Indexed: 11/20/2023] Open
Abstract
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in a FASTQ or BAM file) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier (UMI) counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that UMI-tools achieves the top accuracy in scRNA-seq UMI deduplication, and HMMRATAC and MACS3 achieve the top performance in scATAC-seq peak calling.
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Affiliation(s)
- Guanao Yan
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA
| | - Dongyuan Song
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, CA, 90095-7246, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA.
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, CA, 90095-7246, USA.
- Department of Human Genetics, University of California, Los Angeles, CA, 90095-7088, USA.
- Department of Computational Medicine, University of California, Los Angeles, CA, 90095-1766, USA.
- Department of Biostatistics, University of California, Los Angeles, CA, 90095-1772, USA.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, 02138, USA.
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28
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Nakayama J, Yamamoto Y. Cancer-prone Phenotypes and Gene Expression Heterogeneity at Single-cell Resolution in Cigarette-smoking Lungs. CANCER RESEARCH COMMUNICATIONS 2023; 3:2280-2291. [PMID: 37910161 PMCID: PMC10637260 DOI: 10.1158/2767-9764.crc-23-0195] [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: 05/01/2023] [Revised: 08/16/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies have been broadly utilized to reveal molecular mechanisms of respiratory pathology and physiology at single-cell resolution. Here, we established single-cell meta-analysis (scMeta-analysis) by integrating data from eight public datasets, including 104 lung scRNA-seq samples with clinicopathologic information and designated a cigarette-smoking lung atlas. The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking. In addition, we developed two novel scMeta-analysis methods: VARIED (Visualized Algorithms of Relationships In Expressional Diversity) and AGED (Aging-related Gene Expressional Differences). VARIED analysis revealed expressional diversity associated with smoking carcinogenesis. AGED analysis revealed differences in gene expression related to both aging and smoking status. The scMeta-analysis paves the way to utilize publicly-available scRNA-seq data and provide new insights into the effects of smoking and into cellular diversity in human lungs, at single-cell resolution. SIGNIFICANCE The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking.
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Affiliation(s)
- Jun Nakayama
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
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29
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Hume DA, Millard SM, Pettit AR. Macrophage heterogeneity in the single-cell era: facts and artifacts. Blood 2023; 142:1339-1347. [PMID: 37595274 DOI: 10.1182/blood.2023020597] [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: 06/26/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
In this spotlight, we review technical issues that compromise single-cell analysis of tissue macrophages, including limited and unrepresentative yields, fragmentation and generation of remnants, and activation during tissue disaggregation. These issues may lead to a misleading definition of subpopulations of macrophages and the expression of macrophage-specific transcripts by unrelated cells. Recognition of the technical limitations of single-cell approaches is required in order to map the full spectrum of tissue-resident macrophage heterogeneity and assess its biological significance.
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Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Susan M Millard
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Allison R Pettit
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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30
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Nedwed AS, Helbich SS, Braband KL, Volkmar M, Delacher M, Marini F. Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4+ T cell clones from murine tissues. Front Immunol 2023; 14:1241283. [PMID: 37901204 PMCID: PMC10602882 DOI: 10.3389/fimmu.2023.1241283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/31/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell gene expression analysis using sequencing (scRNA-seq) has gained increased attention in the past decades for studying cellular transcriptional programs and their heterogeneity in an unbiased manner, and novel protocols allow the simultaneous measurement of gene expression, T-cell receptor clonality and cell surface protein expression. In this article, we describe the methods to isolate scRNA/TCR-seq-compatible CD4+ T cells from murine tissues, such as skin, spleen, and lymph nodes. We describe the processing of cells and quality control parameters during library preparation, protocols for multiplexing of samples, and strategies for sequencing. Moreover, we describe a step-by-step bioinformatic analysis pipeline from sequencing data generated using these protocols. This includes quality control, preprocessing of sequencing data and demultiplexing of individual samples. We perform quantification of gene expression and extraction of T-cell receptor alpha and beta chain sequences, followed by quality control and doublet detection, and methods for harmonization and integration of datasets. Next, we describe the identification of highly variable genes and dimensionality reduction, clustering and pseudotemporal ordering of data, and we demonstrate how to visualize the results with interactive and reproducible dashboards. We will combine different analytic R-based frameworks such as Bioconductor and Seurat, illustrating how these can be interoperable to optimally analyze scRNA/TCR-seq data of CD4+ T cells from murine tissues.
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Affiliation(s)
- Annekathrin Silvia Nedwed
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Sara Salome Helbich
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Kathrin Luise Braband
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Michael Volkmar
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON Mainz), Mainz, Germany
| | - Michael Delacher
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
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31
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Zhang W, Jiang R, Chen S, Wang Y. scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data. Genome Biol 2023; 24:225. [PMID: 37814314 PMCID: PMC10561408 DOI: 10.1186/s13059-023-03072-y] [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: 04/30/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
Application of the widely used droplet-based microfluidic technologies in single-cell sequencing often yields doublets, introducing bias to downstream analyses. Especially, doublet-detection methods for single-cell chromatin accessibility sequencing (scCAS) data have multiple assay-specific challenges. Therefore, we propose scIBD, a self-supervised iterative-optimizing model for boosting heterotypic doublet detection in scCAS data. scIBD introduces an adaptive strategy to simulate high-confident heterotypic doublets and self-supervise for doublet-detection in an iteratively optimizing manner. Comprehensive benchmarking on various simulated and real datasets demonstrates the outperformance and robustness of scIBD. Moreover, the downstream biological analyses suggest the efficacy of doublet-removal by scIBD.
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Affiliation(s)
- Wenhao Zhang
- Department of Automation, Xiamen University, Xiamen, 361000, Fujian, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361000, Fujian, China
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, China.
| | - Ying Wang
- Department of Automation, Xiamen University, Xiamen, 361000, Fujian, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361000, Fujian, China.
- Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen, 361005, Fujian, China.
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32
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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33
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Shiino S, Tokura M, Nakayama J, Yoshida M, Suto A, Yamamoto Y. Investigation of Tumor Heterogeneity Using Integrated Single-Cell RNA Sequence Analysis to Focus on Genes Related to Breast Cancer-, EMT-, CSC-, and Metastasis-Related Markers in Patients with HER2-Positive Breast Cancer. Cells 2023; 12:2286. [PMID: 37759508 PMCID: PMC10527746 DOI: 10.3390/cells12182286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) protein, which is characterized by the amplification of ERBB2, is a molecular target for HER2-overexpressing breast cancer. Many targeted HER2 strategies have been well developed thus far. Furthermore, intratumoral heterogeneity in HER2 cases has been observed with immunohistochemical staining and has been considered one of the reasons for drug resistance. Therefore, we conducted an integrated analysis of the breast cancer single-cell gene expression data for HER2-positive breast cancer cases from both scRNA-seq data from public datasets and data from our cohort and compared them with those for luminal breast cancer datasets. In our results, heterogeneous distribution of the expression of breast cancer-related genes (ESR1, PGR, ERBB2, and MKI67) was observed. Various gene expression levels differed at the single-cell level between the ERBB2-high group and ERBB2-low group. Moreover, molecular functions and ERBB2 expression levels differed between estrogen receptor (ER)-positive and ER-negative HER2 cases. Additionally, the gene expression levels of typical breast cancer-, CSC-, EMT-, and metastasis-related markers were also different across each patient. These results suggest that diversity in gene expression could occur not only in the presence of ERBB2 expression and ER status but also in the molecular characteristics of each patient.
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Affiliation(s)
- Sho Shiino
- Department of Breast Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan;
| | - Momoko Tokura
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (M.T.); (J.N.)
| | - Jun Nakayama
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (M.T.); (J.N.)
| | - Masayuki Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan;
| | - Akihiko Suto
- Department of Breast Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan;
| | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (M.T.); (J.N.)
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34
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Wong M, Wei Y, Ho YC. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Curr Opin HIV AIDS 2023; 18:246-256. [PMID: 37535039 PMCID: PMC10442869 DOI: 10.1097/coh.0000000000000809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
PURPOSE OF REVIEW The success of HIV-1 eradication strategies relies on in-depth understanding of HIV-1-infected cells. However, HIV-1-infected cells are extremely heterogeneous and rare. Single-cell multiomic approaches resolve the heterogeneity and rarity of HIV-1-infected cells. RECENT FINDINGS Advancement in single-cell multiomic approaches enabled HIV-1 reservoir profiling across the epigenetic (ATAC-seq), transcriptional (RNA-seq), and protein levels (CITE-seq). Using HIV-1 RNA as a surrogate, ECCITE-seq identified enrichment of HIV-1-infected cells in clonally expanded cytotoxic CD4+ T cells. Using HIV-1 DNA PCR-activated microfluidic sorting, FIND-seq captured the bulk transcriptome of HIV-1 DNA+ cells. Using targeted HIV-1 DNA amplification, PheP-seq identified surface protein expression of intact versus defective HIV-1-infected cells. Using ATAC-seq to identify HIV-1 DNA, ASAP-seq captured transcription factor activity and surface protein expression of HIV-1 DNA+ cells. Combining HIV-1 mapping by ATAC-seq and HIV-1 RNA mapping by RNA-seq, DOGMA-seq captured the epigenetic, transcriptional, and surface protein expression of latent and transcriptionally active HIV-1-infected cells. To identify reproducible biological insights and authentic HIV-1-infected cells and avoid false-positive discovery of artifacts, we reviewed current practices of single-cell multiomic experimental design and bioinformatic analysis. SUMMARY Single-cell multiomic approaches may identify innovative mechanisms of HIV-1 persistence, nominate therapeutic strategies, and accelerate discoveries.
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Affiliation(s)
- Michelle Wong
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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35
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Daniels RR, Taylor RS, Robledo D, Macqueen DJ. Single cell genomics as a transformative approach for aquaculture research and innovation. REVIEWS IN AQUACULTURE 2023; 15:1618-1637. [PMID: 38505116 PMCID: PMC10946576 DOI: 10.1111/raq.12806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/21/2024]
Abstract
Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up-step in biological information compared to long-established 'bulk' methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non-model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under-characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology.
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Affiliation(s)
- Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Richard S. Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
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36
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Speranza E. Understanding virus-host interactions in tissues. Nat Microbiol 2023; 8:1397-1407. [PMID: 37488255 DOI: 10.1038/s41564-023-01434-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to understanding how an infected cell behaves in a tissue, organ or whole organism. Infections occur in complex tissue environments, which contain a host of factors that can alter the course of the infection, including immune cells, non-immune cells and extracellular-matrix components. These factors affect how the host responds to the virus and form the basis of the protective response. To understand virus infection, tools are needed that can profile the tissue environment. This Review highlights methods to study virus-host interactions in the infection microenvironment.
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Affiliation(s)
- Emily Speranza
- Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
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37
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Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F, Schiller HB, Theis FJ. Best practices for single-cell analysis across modalities. Nat Rev Genet 2023; 24:550-572. [PMID: 37002403 PMCID: PMC10066026 DOI: 10.1038/s41576-023-00586-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 04/03/2023]
Abstract
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
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Affiliation(s)
- Lukas Heumos
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Anna C Schaar
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany
| | - Christopher Lance
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Paediatrics, Dr von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anastasia Litinetskaya
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Felix Drost
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Luke Zappia
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Malte D Lücken
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity, Helmholtz Munich, Munich, Germany
| | - Daniel C Strobl
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Juan Henao
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
| | - Fabiola Curion
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Herbert B Schiller
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany.
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Sirkis DW, Warly Solsberg C, Johnson TP, Bonham LW, Sturm VE, Lee SE, Rankin KP, Rosen HJ, Boxer AL, Seeley WW, Miller BL, Geier EG, Yokoyama JS. Single-cell RNA-seq reveals alterations in peripheral CX3CR1 and nonclassical monocytes in familial tauopathy. Genome Med 2023; 15:53. [PMID: 37464408 PMCID: PMC10354988 DOI: 10.1186/s13073-023-01205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Emerging evidence from mouse models is beginning to elucidate the brain's immune response to tau pathology, but little is known about the nature of this response in humans. In addition, it remains unclear to what extent tau pathology and the local inflammatory response within the brain influence the broader immune system. METHODS To address these questions, we performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from carriers of pathogenic variants in MAPT, the gene encoding tau (n = 8), and healthy non-carrier controls (n = 8). Primary findings from our scRNA-seq analyses were confirmed and extended via flow cytometry, droplet digital (dd)PCR, and secondary analyses of publicly available transcriptomics datasets. RESULTS Analysis of ~ 181,000 individual PBMC transcriptomes demonstrated striking differential expression in monocytes and natural killer (NK) cells in MAPT pathogenic variant carriers. In particular, we observed a marked reduction in the expression of CX3CR1-the gene encoding the fractalkine receptor that is known to modulate tau pathology in mouse models-in monocytes and NK cells. We also observed a significant reduction in the abundance of nonclassical monocytes and dysregulated expression of nonclassical monocyte marker genes, including FCGR3A. Finally, we identified reductions in TMEM176A and TMEM176B, genes thought to be involved in the inflammatory response in human microglia but with unclear function in peripheral monocytes. We confirmed the reduction in nonclassical monocytes by flow cytometry and the differential expression of select biologically relevant genes dysregulated in our scRNA-seq data using ddPCR. CONCLUSIONS Our results suggest that human peripheral immune cell expression and abundance are modulated by tau-associated pathophysiologic changes. CX3CR1 and nonclassical monocytes in particular will be a focus of future work exploring the role of these peripheral signals in additional tau-associated neurodegenerative diseases.
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Affiliation(s)
- Daniel W Sirkis
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
| | - Caroline Warly Solsberg
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, 94158, USA
| | - Taylor P Johnson
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
| | - Luke W Bonham
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, 94158, USA
| | - Virginia E Sturm
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Global Brain Health Institute, University of California, San Francisco, CA, 94158, USA
- Trinity College Dublin, Dublin, Ireland
| | - Suzee E Lee
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
| | - Katherine P Rankin
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
| | - Howard J Rosen
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Global Brain Health Institute, University of California, San Francisco, CA, 94158, USA
- Trinity College Dublin, Dublin, Ireland
| | - Adam L Boxer
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
| | - William W Seeley
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, CA, 94158, USA
| | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Global Brain Health Institute, University of California, San Francisco, CA, 94158, USA
- Trinity College Dublin, Dublin, Ireland
| | - Ethan G Geier
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA
- Transposon Therapeutics, Inc, San Diego, CA, 92122, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, 1651 4th Street, San Francisco, CA, 94158, USA.
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, 94158, USA.
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, 94158, USA.
- Global Brain Health Institute, University of California, San Francisco, CA, 94158, USA.
- Trinity College Dublin, Dublin, Ireland.
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Glasner A, Rose SA, Sharma R, Gudjonson H, Chu T, Green JA, Rampersaud S, Valdez IK, Andretta ES, Dhillon BS, Schizas M, Dikiy S, Mendoza A, Hu W, Wang ZM, Chaudhary O, Xu T, Mazutis L, Rizzuto G, Quintanal-Villalonga A, Manoj P, de Stanchina E, Rudin CM, Pe'er D, Rudensky AY. Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies. Nat Immunol 2023; 24:1020-1035. [PMID: 37127830 PMCID: PMC10232368 DOI: 10.1038/s41590-023-01504-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
While regulatory T (Treg) cells are traditionally viewed as professional suppressors of antigen presenting cells and effector T cells in both autoimmunity and cancer, recent findings of distinct Treg cell functions in tissue maintenance suggest that their regulatory purview extends to a wider range of cells and is broader than previously assumed. To elucidate tumoral Treg cell 'connectivity' to diverse tumor-supporting accessory cell types, we explored immediate early changes in their single-cell transcriptomes upon punctual Treg cell depletion in experimental lung cancer and injury-induced inflammation. Before any notable T cell activation and inflammation, fibroblasts, endothelial and myeloid cells exhibited pronounced changes in their gene expression in both cancer and injury settings. Factor analysis revealed shared Treg cell-dependent gene programs, foremost, prominent upregulation of VEGF and CCR2 signaling-related genes upon Treg cell deprivation in either setting, as well as in Treg cell-poor versus Treg cell-rich human lung adenocarcinomas. Accordingly, punctual Treg cell depletion combined with short-term VEGF blockade showed markedly improved control of PD-1 blockade-resistant lung adenocarcinoma progression in mice compared to the corresponding monotherapies, highlighting a promising factor-based querying approach to elucidating new rational combination treatments of solid organ cancers.
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Affiliation(s)
- Ariella Glasner
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Rose
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herman Gudjonson
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tinyi Chu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse A Green
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sham Rampersaud
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Izabella K Valdez
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emma S Andretta
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bahawar S Dhillon
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michail Schizas
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stanislav Dikiy
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alejandra Mendoza
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Hu
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhong-Min Wang
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Linas Mazutis
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology & Laboratory Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, New York, NY, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Y Rudensky
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, Li Y, Gao N, Jung SY, Creighton CJ, Li JJ, Cui Y, Arimura S, Lei Y, Li W, Shen L. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res 2023; 42:113. [PMID: 37143122 PMCID: PMC10157929 DOI: 10.1186/s13046-023-02689-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Methylation of the p16 promoter resulting in epigenetic gene silencing-known as p16 epimutation-is frequently found in human colorectal cancer and is also common in normal-appearing colonic mucosa of aging individuals. Thus, to improve clinical care of colorectal cancer (CRC) patients, we explored the role of age-related p16 epimutation in intestinal tumorigenesis. METHODS We established a mouse model that replicates two common genetic and epigenetic events observed in human CRCs: Apc mutation and p16 epimutation. We conducted long-term survival and histological analysis of tumor development and progression. Colonic epithelial cells and tumors were collected from mice and analyzed by RNA sequencing (RNA-seq), quantitative PCR, and flow cytometry. We performed single-cell RNA sequencing (scRNA-seq) to characterize tumor-infiltrating immune cells throughout tumor progression. We tested whether anti-PD-L1 immunotherapy affects overall survival of tumor-bearing mice and whether inhibition of both epigenetic regulation and immune checkpoint is more efficacious. RESULTS Mice carrying combined Apc mutation and p16 epimutation had significantly shortened survival and increased tumor growth compared to those with Apc mutation only. Intriguingly, colon tumors with p16 epimutation exhibited an activated interferon pathway, increased expression of programmed death-ligand 1 (Pdl1), and enhanced infiltration of immune cells. scRNA-seq further revealed the presence of Foxp3+ Tregs and γδT17 cells, which contribute to an immunosuppressive tumor microenvironment (TME). Furthermore, we showed that a combined therapy using an inhibitor of DNA methylation and a PD-L1 immune checkpoint inhibitor is more effective for improving survival in tumor-bearing mice than blockade of either pathway alone. CONCLUSIONS Our study demonstrated that age-dependent p16 epimutation creates a permissive microenvironment for malignant transformation of polyps to colon cancer. Our findings provide a mechanistic rationale for future targeted therapy in patients with p16 epimutation.
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Affiliation(s)
- Li Yang
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Xiaomin Chen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Christy Lee
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Jiejun Shi
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
- Present address: Department of General Surgery, Shanghai Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Emily B Lawrence
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Lanjing Zhang
- Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA
- Department of Chemical Biology, Earnest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Sumimasa Arimura
- Department of Medicine and Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA.
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Liu Z, Kong X, Long Y, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J, Yan Z. Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. NATURE PLANTS 2023; 9:515-524. [PMID: 37055554 DOI: 10.1038/s41477-023-01387-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule development, and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.
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Affiliation(s)
- Zhijian Liu
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiangying Kong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Long
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Sirui Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Hong Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jinbu Jia
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenhui Cui
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Zunmian Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Zhe Yan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
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Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023; 3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
Abstract
Individual cells within an otherwise genetically homogenous population constantly undergo fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity is being increasingly implicated in cancer therapy resistance and metastasis. Identifying the origins of non-genetic heterogeneity is therefore crucial for making clinical breakthroughs. We discuss with examples how dynamical models and computational tools have provided critical multiscale insights into the nature and consequences of non-genetic heterogeneity in cancer. We demonstrate how mechanistic modeling has been pivotal in establishing key concepts underlying non-genetic diversity at various biological scales, from population dynamics to gene regulatory networks. We discuss advances in single-cell longitudinal profiling techniques to reveal patterns of non-genetic heterogeneity, highlighting the ongoing efforts and challenges in statistical frameworks to robustly interpret such multimodal datasets. Moving forward, we stress the need for data-driven statistical and mechanistically motivated dynamical frameworks to come together to develop predictive cancer models and inform therapeutic strategies.
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Affiliation(s)
- Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Emilia Hojel
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA.
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Crowell HL, Morillo Leonardo SX, Soneson C, Robinson MD. The shaky foundations of simulating single-cell RNA sequencing data. Genome Biol 2023; 24:62. [PMID: 36991470 PMCID: PMC10061781 DOI: 10.1186/s13059-023-02904-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND With the emergence of hundreds of single-cell RNA-sequencing (scRNA-seq) datasets, the number of computational tools to analyze aspects of the generated data has grown rapidly. As a result, there is a recurring need to demonstrate whether newly developed methods are truly performant-on their own as well as in comparison to existing tools. Benchmark studies aim to consolidate the space of available methods for a given task and often use simulated data that provide a ground truth for evaluations, thus demanding a high quality standard results credible and transferable to real data. RESULTS Here, we evaluated methods for synthetic scRNA-seq data generation in their ability to mimic experimental data. Besides comparing gene- and cell-level quality control summaries in both one- and two-dimensional settings, we further quantified these at the batch- and cluster-level. Secondly, we investigate the effect of simulators on clustering and batch correction method comparisons, and, thirdly, which and to what extent quality control summaries can capture reference-simulation similarity. CONCLUSIONS Our results suggest that most simulators are unable to accommodate complex designs without introducing artificial effects, they yield over-optimistic performance of integration and potentially unreliable ranking of clustering methods, and it is generally unknown which summaries are important to ensure effective simulation-based method comparisons.
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Affiliation(s)
- Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Charlotte Soneson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Current address: Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
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Naydenov DD, Vashukova ES, Barbitoff YA, Nasykhova YA, Glotov AS. Current Status and Prospects of the Single-Cell Sequencing Technologies for Revealing the Pathogenesis of Pregnancy-Associated Disorders. Genes (Basel) 2023; 14:756. [PMID: 36981026 PMCID: PMC10048492 DOI: 10.3390/genes14030756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a method that focuses on the analysis of gene expression profile in individual cells. This method has been successfully applied to answer the challenging questions of the pathogenesis of multifactorial diseases and open up new possibilities in the prognosis and prevention of reproductive diseases. In this article, we have reviewed the application of scRNA-seq to the analysis of the various cell types and their gene expression changes in normal pregnancy and pregnancy complications. The main principle, advantages, and limitations of single-cell technologies and data analysis methods are described. We discuss the possibilities of using the scRNA-seq method for solving the fundamental and applied tasks related to various pregnancy-associated disorders. Finally, we provide an overview of the scRNA-seq findings for the common pregnancy-associated conditions, such as hyperglycemia in pregnancy, recurrent pregnancy loss, preterm labor, polycystic ovary syndrome, and pre-eclampsia.
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Affiliation(s)
- Dmitry D. Naydenov
- Faculty of Biology, St. Petersburg State University, 199034 Saint-Petersburg, Russia
| | - Elena S. Vashukova
- D. O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - Yury A. Barbitoff
- Faculty of Biology, St. Petersburg State University, 199034 Saint-Petersburg, Russia
- D. O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - Yulia A. Nasykhova
- D. O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - Andrey S. Glotov
- Faculty of Biology, St. Petersburg State University, 199034 Saint-Petersburg, Russia
- D. O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, 199034 Saint-Petersburg, Russia
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Zhu J, Shang L, Zhou X. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics. Genome Biol 2023; 24:39. [PMID: 36869394 PMCID: PMC9983268 DOI: 10.1186/s13059-023-02879-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.
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Affiliation(s)
- Jiaqiang Zhu
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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46
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Fonseca MAS, Haro M, Wright KN, Lin X, Abbasi F, Sun J, Hernandez L, Orr NL, Hong J, Choi-Kuaea Y, Maluf HM, Balzer BL, Fishburn A, Hickey R, Cass I, Goodridge HS, Truong M, Wang Y, Pisarska MD, Dinh HQ, El-Naggar A, Huntsman DG, Anglesio MS, Goodman MT, Medeiros F, Siedhoff M, Lawrenson K. Single-cell transcriptomic analysis of endometriosis. Nat Genet 2023; 55:255-267. [PMID: 36624343 PMCID: PMC10950360 DOI: 10.1038/s41588-022-01254-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/28/2022] [Indexed: 01/11/2023]
Abstract
Endometriosis is a common condition in women that causes chronic pain and infertility and is associated with an elevated risk of ovarian cancer. We profiled transcriptomes of >370,000 individual cells from endometriomas (n = 8), endometriosis (n = 28), eutopic endometrium (n = 10), unaffected ovary (n = 4) and endometriosis-free peritoneum (n = 4), generating a cellular atlas of endometrial-type epithelial cells, stromal cells and microenvironmental cell populations across tissue sites. Cellular and molecular signatures of endometrial-type epithelium and stroma differed across tissue types, suggesting a role for cellular restructuring and transcriptional reprogramming in the disease. Epithelium, stroma and proximal mesothelial cells of endometriomas showed dysregulation of pro-inflammatory pathways and upregulation of complement proteins. Somatic ARID1A mutation in epithelial cells was associated with upregulation of pro-angiogenic and pro-lymphangiogenic factors and remodeling of the endothelial cell compartment, with enrichment of lymphatic endothelial cells. Finally, signatures of ciliated epithelial cells were enriched in ovarian cancers, reinforcing epidemiologic associations between these two diseases.
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Affiliation(s)
- Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcela Haro
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kelly N Wright
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Abbasi
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer Sun
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lourdes Hernandez
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Natasha L Orr
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
| | - Jooyoon Hong
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
| | - Yunhee Choi-Kuaea
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Horacio M Maluf
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bonnie L Balzer
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Aaron Fishburn
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ryan Hickey
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ilana Cass
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mireille Truong
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yemin Wang
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Margareta D Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Amal El-Naggar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - David G Huntsman
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- British Columbia's Gynecological Cancer Research (OVCARE) Program, University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, British Columbia, Canada
| | - Marc T Goodman
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabiola Medeiros
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew Siedhoff
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Drake RS, Villanueva MA, Vilme M, Russo DD, Navia A, Love JC, Shalek AK. Profiling Transcriptional Heterogeneity with Seq-Well S 3: A Low-Cost, Portable, High-Fidelity Platform for Massively Parallel Single-Cell RNA-Seq. Methods Mol Biol 2023; 2584:57-104. [PMID: 36495445 DOI: 10.1007/978-1-0716-2756-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Seq-Well is a high-throughput, picowell-based single-cell RNA-seq technology that can be used to simultaneously profile the transcriptomes of thousands of cells (Gierahn et al. Nat Methods 14(4):395-398, 2017). Relative to its reverse-emulsion-droplet-based counterparts, Seq-Well addresses key cost, portability, and scalability limitations. Recently, we introduced an improved molecular biology for Seq-Well to enhance the information content that can be captured from individual cells using the platform. This update, which we call Seq-Well S3 (S3: Second-Strand Synthesis), incorporates a second-strand-synthesis step after reverse transcription to boost the detection of cellular transcripts normally missed when running the original Seq-Well protocol (Hughes et al. Immunity 53(4):878-894.e7, 2020). This chapter provides details and tips on how to perform Seq-Well S3, along with general pointers on how to subsequently analyze the resultant single-cell RNA-seq data.
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Affiliation(s)
- Riley S Drake
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin Arreola Villanueva
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Mike Vilme
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniela D Russo
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Navia
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Alex K Shalek
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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48
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Schriever H, Kostka D. Vaeda computationally annotates doublets in single-cell RNA sequencing data. Bioinformatics 2023; 39:6808614. [PMID: 36342203 PMCID: PMC9805559 DOI: 10.1093/bioinformatics/btac720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/23/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) continues to expand our knowledge by facilitating the study of transcriptional heterogeneity at the level of single cells. Despite this technology's utility and success in biomedical research, technical artifacts are present in scRNA-seq data. Doublets/multiplets are a type of artifact that occurs when two or more cells are tagged by the same barcode, and therefore they appear as a single cell. Because this introduces non-existent transcriptional profiles, doublets can bias and mislead downstream analysis. To address this limitation, computational methods to annotate and remove doublets form scRNA-seq datasets are needed. RESULTS We introduce vaeda (Variational Auto-Encoder for Doublet Annotation), a new approach for computational annotation of doublets in scRNA-seq data. Vaeda integrates a variational auto-encoder and Positive-Unlabeled learning to produce doublet scores and binary doublet calls. We apply vaeda, along with seven existing doublet annotation methods, to 16 benchmark datasets and find that vaeda performs competitively in terms of doublet scores and doublet calls. Notably, vaeda outperforms other python-based methods for doublet annotation. Altogether, vaeda is a robust and competitive method for scRNA-seq doublet annotation and may be of particular interest in the context of python-based workflows. AVAILABILITY AND IMPLEMENTATION Vaeda is available at https://github.com/kostkalab/vaeda, and the version used for the results we present here is archived at zenodo (https://doi.org/10.5281/zenodo.7199783). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hannah Schriever
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA
- Canegie Mellon—University of Pittsburgh Joint PhD Program, University of Pittsburgh, Pittsburgh, PA 15201, USA
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49
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Umu SU, Rapp Vander-Elst K, Karlsen VT, Chouliara M, Bækkevold ES, Jahnsen FL, Domanska D. Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis. Gigascience 2022; 12:giad091. [PMID: 37889009 PMCID: PMC10603768 DOI: 10.1093/gigascience/giad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, nonexpert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines. RESULTS We have developed cellsnake, a comprehensive, reproducible, and accessible single-cell data analysis workflow, to overcome these problems. Cellsnake offers advanced features for standard users and facilitates downstream analyses in both R and Python environments. It is also designed for easy integration into existing workflows, allowing for rapid analyses of multiple samples. CONCLUSION As an open-source tool, cellsnake is accessible through Bioconda, PyPi, Docker, and GitHub, making it a cost-effective and user-friendly option for researchers. By using cellsnake, researchers can streamline the analysis of scRNA-seq data and gain insights into the complex biology of single cells.
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Affiliation(s)
- Sinan U Umu
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo 0372, Norway
| | | | - Victoria T Karlsen
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
| | - Manto Chouliara
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
| | - Espen Sønderaal Bækkevold
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
- Institute of Oral Biology, University of Oslo, Oslo 0372, Norway
| | - Frode Lars Jahnsen
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo 0372, Norway
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
| | - Diana Domanska
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
- Department of Microbiology, University of Oslo, Rikshospitalet, Oslo 0372, Norway
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50
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Salcher S, Sturm G, Horvath L, Untergasser G, Kuempers C, Fotakis G, Panizzolo E, Martowicz A, Trebo M, Pall G, Gamerith G, Sykora M, Augustin F, Schmitz K, Finotello F, Rieder D, Perner S, Sopper S, Wolf D, Pircher A, Trajanoski Z. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell 2022; 40:1503-1520.e8. [PMID: 36368318 PMCID: PMC9767679 DOI: 10.1016/j.ccell.2022.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/26/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and resistance. However, full understanding of how immune cell phenotypes vary across different patient subgroups is lacking. Here, we dissect the NSCLC tumor microenvironment at high resolution by integrating 1,283,972 single cells from 556 samples and 318 patients across 29 datasets, including our dataset capturing cells with low mRNA content. We stratify patients into immune-deserted, B cell, T cell, and myeloid cell subtypes. Using bulk samples with genomic and clinical information, we identify cellular components associated with tumor histology and genotypes. We then focus on the analysis of tissue-resident neutrophils (TRNs) and uncover distinct subpopulations that acquire new functional properties in the tissue microenvironment, providing evidence for the plasticity of TRNs. Finally, we show that a TRN-derived gene signature is associated with anti-programmed cell death ligand 1 (PD-L1) treatment failure.
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Affiliation(s)
- Stefan Salcher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lena Horvath
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Christiane Kuempers
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Elisa Panizzolo
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Agnieszka Martowicz
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria; Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
| | - Manuel Trebo
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Pall
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriele Gamerith
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Sykora
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Augustin
- Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Innsbruck, Austria
| | - Katja Schmitz
- Tyrolpath Obrist Brunhuber GmbH, Zams, Austria; INNPATH GmbH, Institute of Pathology, Innsbruck, Austria
| | - Francesca Finotello
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria; Digital Science Center, University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany; Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Lung Research (DZL), Luebeck and Borstel, Germany
| | - Sieghart Sopper
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Pircher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria.
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
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