451
|
Benitez GJ, Shinoda K. Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications. J Vis Exp 2020. [PMID: 32597862 DOI: 10.3791/61230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Brown and beige fat are specialized adipose tissues that dissipate energy for thermogenesis by UCP1 (Uncoupling Protein-1)-dependent and independent pathways. Until recently, thermogenic adipocytes were considered a homogeneous population. However, recent studies have indicated that there are multiple subtypes or subpopulations that are distinct in developmental origin, substrate use, and transcriptome. Despite advances in single-cell genomics, unbiased decomposition of adipose tissues into cellular subtypes has been challenging because of the fragile nature of lipid-filled adipocytes. The protocol presented was developed to circumvent these obstacles by effective isolation of single nuclei from adipose tissue for downstream applications, including RNA sequencing. Cellular heterogeneity can then be analyzed by RNA sequencing and bioinformatic analyses.
Collapse
Affiliation(s)
| | - Kosaku Shinoda
- Departments of Medicine, Albert Einstein College of Medicine; Departments of Molecular Pharmacology, Albert Einstein College of Medicine; Fleischer Institute of Diabetes and Metabolism;
| |
Collapse
|
452
|
Emerging technologies for systems vaccinology - multi-omics integration and single-cell (epi)genomic profiling. Curr Opin Immunol 2020; 65:57-64. [PMID: 32504952 DOI: 10.1016/j.coi.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
Systems vaccinology leverages high-throughput 'omics' technologies, such as transcriptomics, metabolomics, and mass cytometry, coupled with computational approaches to construct a global map of the complex processes that occur during an immune response to vaccination. Its goal is to define the mechanisms of protective immunity and to identify cellular and molecular correlates of vaccine efficacy. Emerging technological advances including integration of multi-omics datasets, and single-cell genomic and epigenomic profiling of immune responses, have invigorated systems vaccinology, and provide new insights into the mechanisms by which the cellular and molecular information underlying immune memory is stored in the innate and adaptive immune systems. Here, we will review these emerging directions in systems vaccinology, with a particular focus on the epigenome, and its impact on modulating vaccination induced memory in the innate and adaptive immune systems.
Collapse
|
453
|
Márquez EJ, Trowbridge J, Kuchel GA, Banchereau J, Ucar D. The lethal sex gap: COVID-19. IMMUNITY & AGEING 2020; 17:13. [PMID: 32457811 PMCID: PMC7240166 DOI: 10.1186/s12979-020-00183-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
While Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is disrupting lives across the globe for everyone, it has a more devastating impact on the health of older adults, especially that of older men. This pandemic has highlighted the crucial importance of considering an individual’s age and biological sex in the clinic in addition to other confounding diseases (Kuchel, G.A, J Am Geriatr Soc, 67, 203, 2019, Tannenbaum, C., Nature, 575 451-458, 2009) As an interdisciplinary team of scientists in immunology, hematology, genomics, bioinformatics, and geriatrics, we have been studying how age and sex shape the human immune system. Herein we reflect on how our recent findings on the alterations of the immune system in aging might contribute to our current understanding of COVID-19 infection rate and disease risk.
Collapse
Affiliation(s)
| | | | - George A Kuchel
- 3University of Connecticut Center on Aging, UConn Health Center, Farmington, CT 06030 USA
| | | | - Duygu Ucar
- 4The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030 USA
| |
Collapse
|
454
|
Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis. Commun Biol 2020; 3:213. [PMID: 32382044 PMCID: PMC7205613 DOI: 10.1038/s42003-020-0896-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
Single-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows remain expensive and complex. We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. Quantum barcoding (QBC) avoids isolation of single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. Here we show the utility of this technology in mouse and human model systems for as many as 50 antibodies to targeted proteins and, separately, >70 targeted RNA regions. We demonstrate that this method can be applied to multi-modal protein and RNA analyses. It can be scaled by expansion of the split-pool process and effectively renders sequencing instruments as versatile multi-parameter flow cytometers. Maeve O’Huallachain et al. report a method that enables simultaneous, ultra-high throughput single-cell barcoding for targeted single-cell protein and RNA analysis. They show the utility of their method in analyses of mRNA and protein expression in human and mouse cells.
Collapse
|
455
|
Yu W, Uzun Y, Zhu Q, Chen C, Tan K. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. Genome Biol 2020; 21:94. [PMID: 32312293 PMCID: PMC7169039 DOI: 10.1186/s13059-020-02008-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/02/2020] [Indexed: 02/08/2023] Open
Abstract
Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro.
Collapse
Affiliation(s)
- Wenbao Yu
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yasin Uzun
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qin Zhu
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Changya Chen
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Tan
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
456
|
Lim B, Lin Y, Navin N. Advancing Cancer Research and Medicine with Single-Cell Genomics. Cancer Cell 2020; 37:456-470. [PMID: 32289270 PMCID: PMC7899145 DOI: 10.1016/j.ccell.2020.03.008] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/01/2020] [Accepted: 03/09/2020] [Indexed: 01/21/2023]
Abstract
Single-cell sequencing (SCS) has impacted many areas of cancer research and improved our understanding of intratumor heterogeneity, the tumor microenvironment, metastasis, and therapeutic resistance. The development and refinement of SCS technologies has led to massive reductions in costs, increased cell throughput, and improved reproducibility, paving the way for clinical applications. However, before translational applications can be realized, there are a number of logistical and technical challenges that must be overcome. This review discusses past cancer research studies, emerging technologies, and future clinical applications that are bound to transform cancer medicine.
Collapse
Affiliation(s)
- Bora Lim
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiyun Lin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Navin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
457
|
Yu XX, Xu CR. Understanding generation and regeneration of pancreatic β cells from a single-cell perspective. Development 2020; 147:147/7/dev179051. [PMID: 32280064 DOI: 10.1242/dev.179051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms that underlie the generation and regeneration of β cells is crucial for developing treatments for diabetes. However, traditional research methods, which are based on populations of cells, have limitations for defining the precise processes of β-cell differentiation and trans-differentiation, and the associated regulatory mechanisms. The recent development of single-cell technologies has enabled re-examination of these processes at a single-cell resolution to uncover intermediate cell states, cellular heterogeneity and molecular trajectories of cell fate specification. Here, we review recent advances in understanding β-cell generation and regeneration, in vivo and in vitro, from single-cell technologies, which could provide insights for optimization of diabetes therapy strategies.
Collapse
Affiliation(s)
- Xin-Xin Yu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng-Ran Xu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
458
|
Stewart BJ, Clatworthy MR. Applying single-cell technologies to clinical pathology: progress in nephropathology. J Pathol 2020; 250:693-704. [PMID: 32125696 PMCID: PMC8651001 DOI: 10.1002/path.5417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022]
Abstract
Cells represent the basic building blocks of living organisms. Accurate characterisation of cellular phenotype, intercellular signalling networks, and the spatial organisation of cells within organs is crucial to deliver a better understanding of the processes underpinning physiology, and the perturbations that lead to disease. Single-cell methodologies have increased rapidly in scale and scope in recent years and are set to generate important insights into human disease. Here, we review current practices in nephropathology, which are dominated by relatively simple morphological descriptions of tissue biopsies based on their appearance using light microscopy. Bulk transcriptomics have more recently been used to explore glomerular and tubulointerstitial kidney disease, renal cancer, and the responses to injury and alloimmunity in kidney transplantation, generating novel disease insights and prognostic biomarkers. These studies set the stage for single-cell transcriptomic approaches that reveal cell-type-specific gene expression patterns in health and disease. These technologies allow genome-wide disease susceptibility genes to be interpreted with the knowledge of the specific cell populations within organs that express them, identifying candidate cell types for further study. Single-cell technologies are also moving beyond assaying individual cellular transcriptomes, to measuring the epigenetic landscape of single cells. Single-cell antigen-receptor gene sequencing also enables specific T- and B-cell clones to be tracked in different tissues and disease states. In the coming years these rich 'multi-omic' descriptions of kidney disease will enable histopathological descriptions to be comprehensively integrated with molecular phenotypes, enabling better disease classification and prognostication and the application of personalised treatment strategies. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Benjamin J Stewart
- Department of MedicineUniversity of CambridgeCambridgeUK
- Cellular GeneticsWellcome Sanger InstituteCambridgeUK
- Cambridge NIHR Biomedical Research CentreAddenbrooke's HospitalCambridgeUK
| | - Menna R Clatworthy
- Department of MedicineUniversity of CambridgeCambridgeUK
- Cellular GeneticsWellcome Sanger InstituteCambridgeUK
- Cambridge NIHR Biomedical Research CentreAddenbrooke's HospitalCambridgeUK
| |
Collapse
|
459
|
Zemmour D, Kiner E, Benoist C. CD4 + teff cell heterogeneity: the perspective from single-cell transcriptomics. Curr Opin Immunol 2020; 63:61-67. [PMID: 32259715 PMCID: PMC7198319 DOI: 10.1016/j.coi.2020.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
Single-cell transcriptomics (scRNAseq) holds the promise to generate definitive atlases of cell types. We review scRNAseq studies of conventional CD4+ αβ T cells performed in a variety of challenged contexts (infection, tumor, allergy) that aimed to parse the complexity and representativity of previously defined CD4+ T cell types, lineages, and cosmologies. With a few years' experience, the field has realized the difficulties and pitfalls of scRNAseq. With the very high-dimensionality of scRNAseq data, subset definitions based on low-dimensionality marker combinations tend to fade or blur: cell types prove more complex than expected; transcripts of key defining transcripts (cytokines, chemokines) are distributed as broad and partially overlapping continua; boundaries with innate lymphocytes are blurred. Tissue location and activation, either cytokine-driven or TCR-driven, determine Teff heterogeneity in sometimes unexpected ways. Emerging techniques for lineage and trajectory tracing, and RNA-protein connections, will further help define the space of differentiated CD4+ T cell heterogeneity.
Collapse
Affiliation(s)
- David Zemmour
- Department of Immunology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Evgeny Kiner
- Department of Immunology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christophe Benoist
- Department of Immunology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
460
|
Marx V. Cancer labs reach beyond exhausted T cells. Nat Methods 2020; 17:367-370. [PMID: 32203391 DOI: 10.1038/s41592-020-0800-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
461
|
Gibellini L, De Biasi S, Porta C, Lo Tartaro D, Depenni R, Pellacani G, Sabbatini R, Cossarizza A. Single-Cell Approaches to Profile the Response to Immune Checkpoint Inhibitors. Front Immunol 2020; 11:490. [PMID: 32265933 PMCID: PMC7100547 DOI: 10.3389/fimmu.2020.00490] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/03/2020] [Indexed: 12/26/2022] Open
Abstract
Novel treatments based upon the use of immune checkpoint inhibitors have an impressive efficacy in different types of cancer. Unfortunately, most patients do not derive benefit or lasting responses, and the reasons for the lack of therapeutic success are not known. Over the past two decades, a pressing need to deeply profile either the tumor microenvironment or cells responsible for the immune response has led investigators to integrate data obtained from traditional approaches with those obtained with new, more sophisticated, single-cell technologies, including high parameter flow cytometry, single-cell sequencing and high resolution imaging. The introduction and use of these technologies had, and still have a prominent impact in the field of cancer immunotherapy, allowing delving deeper into the molecular and cellular crosstalk between cancer and immune system, and fostering the identification of predictive biomarkers of response. In this review, besides the molecular and cellular cancer-immune system interactions, we are discussing how cutting-edge single-cell approaches are helping to point out the heterogeneity of immune cells in the tumor microenvironment and in blood.
Collapse
Affiliation(s)
- Lara Gibellini
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Camillo Porta
- Department of Internal Medicine and Therapeutics, Division of Translational Oncology, IRCCS Istituti Clinici Scientifici Maugeri, University of Pavia, Pavia, Italy
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Depenni
- Department of Oncology, Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Giovanni Pellacani
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberto Sabbatini
- Department of Oncology, Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy.,Section of Modena, Istituto Nazionale per le Ricerche Cardiovascolari, Bologna, Italy
| |
Collapse
|
462
|
Wang W, Fasolino M, Cattau B, Goldman N, Kong W, Frederick MA, McCright SJ, Kiani K, Fraietta JA, Vahedi G. Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels. Proc Natl Acad Sci U S A 2020; 117:5442-5452. [PMID: 32094195 PMCID: PMC7071901 DOI: 10.1073/pnas.1919259117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chimeric antigen receptor (CAR)-T immunotherapy has yielded impressive results in several B cell malignancies, establishing itself as a powerful means to redirect the natural properties of T lymphocytes. In this strategy, the T cell genome is modified by the integration of lentiviral vectors encoding CAR that direct tumor cell killing. However, this therapeutic approach is often limited by the extent of CAR-T cell expansion in vivo. A major outstanding question is whether or not CAR-T integration itself enhances the proliferative competence of individual T cells by rewiring their regulatory landscape. To address this question, it is critical to define the identity of an individual CAR-T cell and simultaneously chart where the CAR-T vector integrates into the genome. Here, we report the development of a method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.
Collapse
Affiliation(s)
- Wenliang Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Maria Fasolino
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Benjamin Cattau
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Naomi Goldman
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Weimin Kong
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Megan A Frederick
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Sam J McCright
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Karun Kiani
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Joseph A Fraietta
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104;
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| |
Collapse
|
463
|
Zhang JD, Sach-Peltason L, Kramer C, Wang K, Ebeling M. Multiscale modelling of drug mechanism and safety. Drug Discov Today 2020; 25:519-534. [DOI: 10.1016/j.drudis.2019.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/06/2019] [Accepted: 12/23/2019] [Indexed: 12/19/2022]
|
464
|
Efremova M, Vento-Tormo R, Park JE, Teichmann SA, James KR. Immunology in the Era of Single-Cell Technologies. Annu Rev Immunol 2020; 38:727-757. [PMID: 32075461 DOI: 10.1146/annurev-immunol-090419-020340] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immune cells are characterized by diversity, specificity, plasticity, and adaptability-properties that enable them to contribute to homeostasis and respond specifically and dynamically to the many threats encountered by the body. Single-cell technologies, including the assessment of transcriptomics, genomics, and proteomics at the level of individual cells, are ideally suited to studying these properties of immune cells. In this review we discuss the benefits of adopting single-cell approaches in studying underappreciated qualities of immune cells and highlight examples where these technologies have been critical to advancing our understanding of the immune system in health and disease.
Collapse
Affiliation(s)
- Mirjana Efremova
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| | - Jong-Eun Park
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; , .,Theory of Condensed Matter, Department of Physics, University of Cambridge, Cambridgeshire CB3 0HE, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Kylie R James
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| |
Collapse
|
465
|
Lareau CA, Ma S, Duarte FM, Buenrostro JD. Inference and effects of barcode multiplets in droplet-based single-cell assays. Nat Commun 2020; 11:866. [PMID: 32054859 PMCID: PMC7018801 DOI: 10.1038/s41467-020-14667-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/23/2020] [Indexed: 12/12/2022] Open
Abstract
A widespread assumption for single-cell analyses specifies that one cell's nucleic acids are predominantly captured by one oligonucleotide barcode. Here, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call "barcode multiplets". We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that approximately 4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that approximately 5% of beads may contain detectable levels of multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.
Collapse
Affiliation(s)
- Caleb A Lareau
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA.
| | - Sai Ma
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| |
Collapse
|
466
|
Single-cell genomic approaches for developing the next generation of immunotherapies. Nat Med 2020; 26:171-177. [PMID: 32015555 DOI: 10.1038/s41591-019-0736-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/10/2019] [Indexed: 01/22/2023]
Abstract
Recent progress in single-cell genomics urges its application in drug development, particularly of cancer immunotherapies. Current immunotherapy pipelines are focused on functional outcome and simple cellular and molecular readouts. A thorough mechanistic understanding of the cells and pathways targeted by immunotherapy agents is lacking, which limits the success rate of clinical trials. A large leap forward can be made if the immunotherapy target cells and pathways are characterized at high resolution before and after treatment, in clinical cohorts and model systems. This will enable rapid development of effective immunotherapies and data-driven design of synergistic drug combinations. In this Perspective, we discuss how emerging single-cell genomic technologies can serve as an engine for target identification and drug development.
Collapse
|
467
|
Rai V, Quang DX, Erdos MR, Cusanovich DA, Daza RM, Narisu N, Zou LS, Didion JP, Guan Y, Shendure J, Parker SCJ, Collins FS. Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. Mol Metab 2020; 32:109-121. [PMID: 32029221 PMCID: PMC6961712 DOI: 10.1016/j.molmet.2019.12.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/12/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Type 2 diabetes (T2D) is a complex disease characterized by pancreatic islet dysfunction, insulin resistance, and disruption of blood glucose levels. Genome-wide association studies (GWAS) have identified > 400 independent signals that encode genetic predisposition. More than 90% of associated single-nucleotide polymorphisms (SNPs) localize to non-coding regions and are enriched in chromatin-defined islet enhancer elements, indicating a strong transcriptional regulatory component to disease susceptibility. Pancreatic islets are a mixture of cell types that express distinct hormonal programs, so each cell type may contribute differentially to the underlying regulatory processes that modulate T2D-associated transcriptional circuits. Existing chromatin profiling methods such as ATAC-seq and DNase-seq, applied to islets in bulk, produce aggregate profiles that mask important cellular and regulatory heterogeneity. METHODS We present genome-wide single-cell chromatin accessibility profiles in >1,600 cells derived from a human pancreatic islet sample using single-cell combinatorial indexing ATAC-seq (sci-ATAC-seq). We also developed a deep learning model based on U-Net architecture to accurately predict open chromatin peak calls in rare cell populations. RESULTS We show that sci-ATAC-seq profiles allow us to deconvolve alpha, beta, and delta cell populations and identify cell-type-specific regulatory signatures underlying T2D. Particularly, T2D GWAS SNPs are significantly enriched in beta cell-specific and across cell-type shared islet open chromatin, but not in alpha or delta cell-specific open chromatin. We also demonstrate, using less abundant delta cells, that deep learning models can improve signal recovery and feature reconstruction of rarer cell populations. Finally, we use co-accessibility measures to nominate the cell-specific target genes at 104 non-coding T2D GWAS signals. CONCLUSIONS Collectively, we identify the islet cell type of action across genetic signals of T2D predisposition and provide higher-resolution mechanistic insights into genetically encoded risk pathways.
Collapse
Affiliation(s)
- Vivek Rai
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Daniel X Quang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Darren A Cusanovich
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Luli S Zou
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John P Didion
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuanfang Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA
| | - Stephen C J Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
468
|
Solier S, Müller S, Rodriguez R. Whole-genome mapping of small-molecule targets for cancer medicine. Curr Opin Chem Biol 2020; 56:42-50. [PMID: 31978625 DOI: 10.1016/j.cbpa.2019.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 12/18/2022]
Abstract
Cancers display intratumoral and intertumoral heterogeneity, which poses challenges to small-molecule intervention. Studying drug responses on a whole-genome and transcriptome level using next-generation sequencing has revolutionized our understanding of how small molecules intervene in cells, which helps us to study and potentially predict treatment outcomes. Some small molecules act directly at the genomic level by targeting DNA or chromatin proteins. Here, we review recent advances in establishing whole-genome and transcriptome maps of small-molecule targets, comprising chromatin components or downstream events. We also describe recent advances in studying drug responses using single-cell RNA and DNA sequencing. Furthermore, we discuss how this fundamental research can be taken forward to devise innovative personalized treatment modalities.
Collapse
Affiliation(s)
- Stéphanie Solier
- Institut Curie, 26 rue d'Ulm, 75248, Paris, Cedex 05, France; PSL Université Paris, France; Chemical Biology of Cancer Laboratory, CNRS UMR 3666, INSERM U1143, France
| | - Sebastian Müller
- Institut Curie, 26 rue d'Ulm, 75248, Paris, Cedex 05, France; PSL Université Paris, France; Chemical Biology of Cancer Laboratory, CNRS UMR 3666, INSERM U1143, France.
| | - Raphaël Rodriguez
- Institut Curie, 26 rue d'Ulm, 75248, Paris, Cedex 05, France; PSL Université Paris, France; Chemical Biology of Cancer Laboratory, CNRS UMR 3666, INSERM U1143, France.
| |
Collapse
|
469
|
Sabbagh MF, Nathans J. A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture. eLife 2020; 9:e51276. [PMID: 31913116 PMCID: PMC6948952 DOI: 10.7554/elife.51276] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
Vascular endothelial cells (ECs) derived from the central nervous system (CNS) variably lose their unique barrier properties during in vitro culture, hindering the development of robust assays for blood-brain barrier (BBB) function, including drug permeability and extrusion assays. In previous work (Sabbagh et al., 2018) we characterized transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs. In this report, we compare transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs versus mouse CNS ECs in short-term in vitro culture. We observe that standard culture conditions are associated with a rapid and selective loss of BBB transcripts and chromatin features, as well as a greatly reduced level of beta-catenin signaling. Interestingly, forced expression of a stabilized derivative of beta-catenin, which in vivo leads to a partial conversion of non-BBB CNS ECs to a BBB-like state, has little or no effect on gene expression or chromatin accessibility in vitro.
Collapse
Affiliation(s)
- Mark F Sabbagh
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Jeremy Nathans
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of OphthalmologyJohns Hopkins University School of MedicineBaltimoreUnited States
- Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| |
Collapse
|
470
|
Al-Ali R, Bauer K, Park JW, Al Abdulla R, Fermi V, von Deimling A, Herold-Mende C, Mallm JP, Herrmann C, Wick W, Turcan Ş. Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas. Acta Neuropathol Commun 2019; 7:201. [PMID: 31806013 PMCID: PMC6896263 DOI: 10.1186/s40478-019-0851-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
The presence of genome-wide DNA hypermethylation is a hallmark of lower grade gliomas (LGG) with isocitrate dehydrogenase (IDH) mutations. Further molecular classification of IDH mutant gliomas is defined by the presence (IDHmut-codel) or absence (IDHmut-noncodel) of hemizygous codeletion of chromosome arms 1p and 19q. Despite the DNA hypermethylation seen in bulk tumors, intra-tumoral heterogeneity at the epigenetic level has not been thoroughly analyzed. To address this question, we performed the first epigenetic profiling of single cells in a cohort of 5 gliomas with IDH1 mutation using single nucleus Assay for Transposase-Accessible Chromatin with high-throughput sequencing (snATAC-seq). Using the Fluidigm HT IFC microfluidics platform, we generated chromatin accessibility maps from 336 individual nuclei, and identified variable promoter accessibility of non-coding RNAs in LGGs. Interestingly, local chromatin structures of several non-coding RNAs are significant factors that contribute to heterogeneity, and show increased promoter accessibility in IDHmut-noncodel samples. As an example for clinical significance of this result, we identify CYTOR as a poor prognosis factor in gliomas with IDH mutation. Open chromatin assay points to differential accessibility of non-coding RNAs as an important source of epigenetic heterogeneity within individual tumors and between molecular subgroups. Rare populations of nuclei that resemble either IDH mutant molecular group co-exist within IDHmut-noncodel and IDHmut-codel groups, and along with non-coding RNAs may be an important issue to consider for future studies, as they may help guide predict treatment response and relapse. A web-based explorer for the data is available at shiny.turcanlab.org.
Collapse
|
471
|
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol 2019; 37:1458-1465. [PMID: 31792411 DOI: 10.1038/s41587-019-0332-7] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/29/2019] [Indexed: 12/28/2022]
Abstract
Identifying the causes of human diseases requires deconvolution of abnormal molecular phenotypes spanning DNA accessibility, gene expression and protein abundance1-3. We present a single-cell framework that integrates highly multiplexed protein quantification, transcriptome profiling and analysis of chromatin accessibility. Using this approach, we establish a normal epigenetic baseline for healthy blood development, which we then use to deconvolve aberrant molecular features within blood from patients with mixed-phenotype acute leukemia4,5. Despite widespread epigenetic heterogeneity within the patient cohort, we observe common malignant signatures across patients as well as patient-specific regulatory features that are shared across phenotypic compartments of individual patients. Integrative analysis of transcriptomic and chromatin-accessibility maps identified 91,601 putative peak-to-gene linkages and transcription factors that regulate leukemia-specific genes, such as RUNX1-linked regulatory elements proximal to the marker gene CD69. These results demonstrate how integrative, multiomic analysis of single cells within the framework of normal development can reveal both distinct and shared molecular mechanisms of disease from patient samples.
Collapse
|
472
|
Matuła K, Rivello F, Huck WTS. Single-Cell Analysis Using Droplet Microfluidics. ACTA ACUST UNITED AC 2019; 4:e1900188. [PMID: 32293129 DOI: 10.1002/adbi.201900188] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Droplet microfluidics has revolutionized the study of single cells. The ability to compartmentalize cells within picoliter droplets in microfluidic devices has opened up a wide range of strategies to extract information at the genomic, transcriptomic, proteomic, or metabolomic level from large numbers of individual cells. Studying the different molecular landscapes at single-cell resolution has provided the authors with a detailed picture of intracellular heterogeneity and the resulting changes in cellular phenotypes. In addition, these technologies have aided in the discovery of rare cells in tumors or in the immune system, and left the authors with a deeper understanding of the fundamental biological processes that determine cell fate. This review aims to provide a detailed overview of the various droplet microfluidic strategies reported in the literature, taking into account the sometimes subtle differences in workflow or reagents that enable or improve certain protocols. Specifically, approaches to targeted- and whole-genome analysis, as well as whole-transcriptome profiling techniques, are reviewed. In addition, an up-to-date overview of new methods to characterize and quantify single-cell protein levels, and of developments to screen secreted molecules such as antibodies, cytokines, or metabolites at the single-cell level, is provided.
Collapse
Affiliation(s)
- Kinga Matuła
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Francesca Rivello
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| |
Collapse
|
473
|
Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L. Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biol 2019; 20:241. [PMID: 31739806 PMCID: PMC6859644 DOI: 10.1186/s13059-019-1854-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique methodological challenges. scATAC-seq experiments sample DNA, which, due to low copy numbers (diploid in humans), lead to inherent data sparsity (1-10% of peaks detected per cell) compared to transcriptomic (scRNA-seq) data (10-45% of expressed genes detected per cell). Such challenges in data generation emphasize the need for informative features to assess cell heterogeneity at the chromatin level. RESULTS We present a benchmarking framework that is applied to 10 computational methods for scATAC-seq on 13 synthetic and real datasets from different assays, profiling cell types from diverse tissues and organisms. Methods for processing and featurizing scATAC-seq data were compared by their ability to discriminate cell types when combined with common unsupervised clustering approaches. We rank evaluated methods and discuss computational challenges associated with scATAC-seq analysis including inherently sparse data, determination of features, peak calling, the effects of sequencing coverage and noise, and clustering performance. Running times and memory requirements are also discussed. CONCLUSIONS This reference summary of scATAC-seq methods offers recommendations for best practices with consideration for both the non-expert user and the methods developer. Despite variation across methods and datasets, SnapATAC, Cusanovich2018, and cisTopic outperform other methods in separating cell populations of different coverages and noise levels in both synthetic and real datasets. Notably, SnapATAC is the only method able to analyze a large dataset (> 80,000 cells).
Collapse
Affiliation(s)
- Huidong Chen
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Caleb Lareau
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Tommaso Andreani
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
- Faculty of Biology, Computational Biology and Data Mining Lab, Johannes Gutenberg University of Mainz, 55128, Mainz, Germany
| | - Michael E Vinyard
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02142, USA
| | - Sara P Garcia
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA
| | - Kendell Clement
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Computational Biology and Data Mining Lab, Johannes Gutenberg University of Mainz, 55128, Mainz, Germany
| | - Jason D Buenrostro
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA, 02129, USA.
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| |
Collapse
|