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Single-cell profiling of peripheral neuroblastic tumors identifies an aggressive transitional state that bridges an adrenergic-mesenchymal trajectory. Cell Rep 2022; 41:111455. [DOI: 10.1016/j.celrep.2022.111455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 04/16/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
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Richard PO, Violette PD, Bhindi B, Breau RH, Kassouf W, Lavallée LT, Jewett M, Kachura JR, Kapoor A, Noel-Lamy M, Ordon M, Pautler SE, Pouliot F, So AI, Rendon RA, Tanguay S, Collins C, Kandi M, Shayegan B, Weller A, Finelli A, Kokorovic A, Nayak J. Canadian Urological Association guideline: Management of small renal masses - Full-text. Can Urol Assoc J 2022; 16:E61-E75. [PMID: 35133268 PMCID: PMC8932428 DOI: 10.5489/cuaj.7763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Affiliation(s)
- Patrick O. Richard
- Department of Surgery, Division of Urology, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe D. Violette
- Departments of Health Research Methods Evidence and Impact (HEI) and Surgery, McMaster University, Hamilton, ON, Canada
| | - Bimal Bhindi
- Southern Alberta Institute of Urology, University of Calgary, Calgary, AB, Canada
| | - Rodney H. Breau
- Department of Surgery, Division of Urology, University of Ottawa, Ottawa, ON, Canada
| | - Wassim Kassouf
- Department of Surgery, Division of Urology, McGill University Health Centre, Montreal, QC, Canada
| | - Luke T. Lavallée
- Department of Surgery, Division of Urology, University of Ottawa, Ottawa, ON, Canada
| | - Michael Jewett
- Department of Surgical Oncology, Division of Urology, Princess Margaret Hospital, Toronto, ON, Canada
| | - John R. Kachura
- Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Anil Kapoor
- McMaster Institute of Urology, St. Joseph Healthcare, Hamilton, ON, Canada
| | - Maxime Noel-Lamy
- Department of Medical Imaging, Division of Interventional Radiology, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Michael Ordon
- Department of Surgery, Division of Urology, St. Michael’s Hospital, Toronto, ON, Canada
| | - Stephen E. Pautler
- Department of Surgery, Division of Urology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Frédéric Pouliot
- Department of Surgery, Division of Urology, Centre Hospitalier Universitaire de Québec, Quebec, QC, Canada
| | - Alan I. So
- Division of Urology, British Columbia Cancer Care, Vancouver, BC, Canada
| | - Ricardo A. Rendon
- Department of Surgery, Division of Urology, Capital Health - QEII, Halifax, NS, Canada
| | - Simon Tanguay
- Department of Surgery, Division of Urology, McGill University Health Centre, Montreal, QC, Canada
| | | | - Maryam Kandi
- Departments of Health Research Methods Evidence and Impact (HEI) and Surgery, McMaster University, Hamilton, ON, Canada
| | - Bobby Shayegan
- McMaster Institute of Urology, St. Joseph Healthcare, Hamilton, ON, Canada
| | | | - Antonio Finelli
- Department of Surgical Oncology, Division of Urology, Princess Margaret Hospital, Toronto, ON, Canada
| | - Andrea Kokorovic
- Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - Jay Nayak
- Department of Surgery, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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3
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Angius A, Scanu AM, Arru C, Muroni MR, Carru C, Porcu A, Cossu-Rocca P, De Miglio MR. A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:1257. [PMID: 34833475 PMCID: PMC8624593 DOI: 10.3390/medicina57111257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
In the study of cancer, omics technologies are supporting the transition from traditional clinical approaches to precision medicine. Intra-tumoral heterogeneity (ITH) is detectable within a single tumor in which cancer cell subpopulations with different genome features coexist in a patient in different tumor areas or may evolve/differ over time. Colorectal carcinoma (CRC) is characterized by heterogeneous features involving genomic, epigenomic, and transcriptomic alterations. The study of ITH is a promising new frontier to lay the foundation towards successful CRC diagnosis and treatment. Genome and transcriptome sequencing together with editing technologies are revolutionizing biomedical research, representing the most promising tools for overcoming unmet clinical and research challenges. Rapid advances in both bulk and single-cell next-generation sequencing (NGS) are identifying primary and metastatic intratumoral genomic and transcriptional heterogeneity. They provide critical insight in the origin and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Single-cell technologies can be used to define subpopulations within a known cell type by searching for differential gene expression within the cell population of interest and/or effectively isolating signal from rare cell populations that would not be detectable by other methods. Each single-cell sequencing analysis is driven by clustering of cells based on their differentially expressed genes. Genes that drive clustering can be used as unique markers for a specific cell population. In this review we analyzed, starting from published data, the possible achievement of a transition from clinical CRC research to precision medicine with an emphasis on new single-cell based techniques; at the same time, we focused on all approaches and issues related to this promising technology. This transition might enable noninvasive screening for early diagnosis, individualized prediction of therapeutic response, and discovery of additional novel drug targets.
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Affiliation(s)
- Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Caterina Arru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
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4
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Single-cell chromatin state analysis with Signac. Nat Methods 2021; 18:1333-1341. [PMID: 34725479 PMCID: PMC9255697 DOI: 10.1038/s41592-021-01282-5] [Citation(s) in RCA: 460] [Impact Index Per Article: 153.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization. Through its seamless compatibility with the Seurat package, Signac facilitates the analysis of diverse multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance and mitochondrial genotype. We demonstrate scaling of the Signac framework to analyze datasets containing over 700,000 cells.
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5
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Claps F, Mir MC, Zargar H. Molecular markers of systemic therapy response in urothelial carcinoma. Asian J Urol 2021; 8:376-390. [PMID: 34765445 PMCID: PMC8566362 DOI: 10.1016/j.ajur.2021.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/07/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
Identification of reliable molecular biomarkers that can complement clinical practice represents a fascinating challenge in any cancer field. Urothelial carcinoma is a very heterogeneous disease and responses to systemic therapies, and outcomes after radical cystectomy are difficult to predict. Advances in molecular biology such as next generation sequencing and whole genome or transcriptomic analysis provide promising platforms to achieve a full understanding of the biology behind the disease and can identify emerging predictive biomarkers. Moreover, the ability to categorize patients' risk of recurrence after curative treatment, or even predict benefit from a conventional or targeted therapies, represents a compelling challenge that may reshape both selection for tailored treatment and disease monitoring. Progress has been made but currently no molecular biomarkers are used in the clinical setting to predict response to systemic agents in either neoadjuvant or adjuvant settings highlighting a relevant unmet need. Here, we aim to present the emerging role of molecular biomarkers in predicting response to systemic agents in urothelial carcinoma.
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Affiliation(s)
- Francesco Claps
- Department of Urology, Fundacion Instituto Valenciano de Oncologia, Valencia, Spain
- Urological Clinic, Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Maria Carmen Mir
- Department of Urology, Fundacion Instituto Valenciano de Oncologia, Valencia, Spain
| | - Homayoun Zargar
- Department of Urology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
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6
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Rai MF, Wu CL, Capellini TD, Guilak F, Dicks AR, Muthuirulan P, Grandi F, Bhutani N, Westendorf JJ. Single Cell Omics for Musculoskeletal Research. Curr Osteoporos Rep 2021; 19:131-140. [PMID: 33559841 PMCID: PMC8743139 DOI: 10.1007/s11914-021-00662-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW The ability to analyze the molecular events occurring within individual cells as opposed to populations of cells is revolutionizing our understanding of musculoskeletal tissue development and disease. Single cell studies have the great potential of identifying cellular subpopulations that work in a synchronized fashion to regenerate and repair damaged tissues during normal homeostasis. In addition, such studies can elucidate how these processes break down in disease as well as identify cellular subpopulations that drive the disease. This review highlights three emerging technologies: single cell RNA sequencing (scRNA-seq), Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and Cytometry by Time-Of-Flight (CyTOF) mass cytometry. RECENT FINDINGS Technological and bioinformatic tools to analyze the transcriptome, epigenome, and proteome at the individual cell level have advanced rapidly making data collection relatively easy; however, understanding how to access and interpret the data remains a challenge for many scientists. It is, therefore, of paramount significance to educate the musculoskeletal community on how single cell technologies can be used to answer research questions and advance translation. This article summarizes talks given during a workshop on "Single Cell Omics" at the 2020 annual meeting of the Orthopedic Research Society. Studies that applied scRNA-seq, ATAC-seq, and CyTOF mass cytometry to cartilage development and osteoarthritis are reviewed. This body of work shows how these cutting-edge tools can advance our understanding of the cellular heterogeneity and trajectories of lineage specification during development and disease.
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Affiliation(s)
- Muhammad Farooq Rai
- Department of Orthopaedic Surgery, Washington University, St. Louis, MO, USA
| | - Chia-Lung Wu
- Department of Orthopaedic Surgery, Washington University and Shriners Hospitals for Children, St. Louis, MO, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University and Shriners Hospitals for Children, St. Louis, MO, USA
| | - Amanda R Dicks
- Department of Orthopaedic Surgery, Washington University and Shriners Hospitals for Children, St. Louis, MO, USA
| | | | - Fiorella Grandi
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Nidhi Bhutani
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
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7
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Navidi Z, Zhang L, Wang B. simATAC: a single-cell ATAC-seq simulation framework. Genome Biol 2021; 22:74. [PMID: 33663563 PMCID: PMC7934446 DOI: 10.1186/s13059-021-02270-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking. We hereby present the simATAC framework, an R package that generates scATAC-seq count matrices that highly resemble real scATAC-seq datasets in library size, sparsity, and chromatin accessibility signals. simATAC deploys statistical models derived from analyzing 90 real scATAC-seq cell groups. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines.
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Affiliation(s)
- Zeinab Navidi
- Peter Munk Cardiac Centre, University Health Network, Toronto, Canada
| | - Lin Zhang
- Department of Statistical Sciences, University of Toronto, Toronto, Canada
| | - Bo Wang
- Peter Munk Cardiac Centre, University Health Network, Toronto, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. .,Department of Computer Science, University of Toronto, Toronto, Canada. .,Vector Institute, Toronto, Canada.
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8
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Sinha S, Satpathy AT, Zhou W, Ji H, Stratton JA, Jaffer A, Bahlis N, Morrissy S, Biernaskie JA. Profiling Chromatin Accessibility at Single-cell Resolution. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:172-190. [PMID: 33581341 PMCID: PMC8602754 DOI: 10.1016/j.gpb.2020.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 03/04/2020] [Accepted: 08/15/2020] [Indexed: 01/22/2023]
Abstract
How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Genome-wide chromatin accessibility measurements can impart insights into regulatory sequences (in)accessible to DNA-binding proteins at a single-cell resolution. This review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies to integrate multi-omic measurements, and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.
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Affiliation(s)
- Sarthak Sinha
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jo A Stratton
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Arzina Jaffer
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nizar Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Sorana Morrissy
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeff A Biernaskie
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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9
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Yu X, Abbas-Aghababazadeh F, Chen YA, Fridley BL. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments. Methods Mol Biol 2021; 2194:143-175. [PMID: 32926366 PMCID: PMC7771369 DOI: 10.1007/978-1-0716-0849-4_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput sequencing (HTS) has revolutionized researchers' ability to study the human transcriptome, particularly as it relates to cancer. Recently, HTS technology has advanced to the point where now one is able to sequence individual cells (i.e., "single-cell sequencing"). Prior to single-cell sequencing technology, HTS would be completed on RNA extracted from a tissue sample consisting of multiple cell types (i.e., "bulk sequencing"). In this chapter, we review the various bioinformatics and statistical methods used in the processing, quality control, and analysis of bulk and single-cell RNA sequencing methods. Additionally, we discuss how these methods are also being used to study tumor heterogeneity.
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Affiliation(s)
- Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Farnoosh Abbas-Aghababazadeh
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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10
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Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T, Liu XS. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. Genome Biol 2020; 21:198. [PMID: 32767996 PMCID: PMC7412809 DOI: 10.1186/s13059-020-02116-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( http://github.com/liulab-dfci/MAESTRO ) for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for pre-processing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNA-seq and scATAC-seq. Furthermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and identifies driver regulators from differential scRNA-seq genes and scATAC-seq peaks.
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Affiliation(s)
- Chenfei Wang
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Dongqing Sun
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Changxin Wan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Ziyi Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Ya Han
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Qian Qin
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Jingyu Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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11
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Ji Z, Zhou W, Hou W, Ji H. Single-cell ATAC-seq signal extraction and enhancement with SCATE. Genome Biol 2020; 21:161. [PMID: 32620137 PMCID: PMC7333383 DOI: 10.1186/s13059-020-02075-3] [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: 10/10/2019] [Accepted: 06/15/2020] [Indexed: 01/25/2023] Open
Abstract
Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. We present a new statistical framework, SCATE, that adaptively integrates information from co-activated CREs, similar cells, and publicly available regulome data to substantially increase the accuracy for estimating activities of individual CREs. We demonstrate that SCATE can be used to better reconstruct the regulatory landscape of a heterogeneous sample.
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Affiliation(s)
- Zhicheng Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205 USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205 USA
| | - Wenpin Hou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205 USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205 USA
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12
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Baek S, Lee I. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. Comput Struct Biotechnol J 2020; 18:1429-1439. [PMID: 32637041 PMCID: PMC7327298 DOI: 10.1016/j.csbj.2020.06.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 12/21/2022] Open
Abstract
Most genetic variations associated with human complex traits are located in non-coding genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a comprehensive catalog of functional non-coding genomic elements, most of which are involved in epigenetic regulation of gene expression. Genome-wide maps of open chromatin regions can facilitate functional analysis of cis- and trans-regulatory elements via their connections with trait-associated sequence variants. Currently, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is considered the most accessible and cost-effective strategy for genome-wide profiling of chromatin accessibility. Single-cell ATAC-seq (scATAC-seq) technology has also been developed to study cell type-specific chromatin accessibility in tissue samples containing a heterogeneous cellular population. However, due to the intrinsic nature of scATAC-seq data, which are highly noisy and sparse, accurate extraction of biological signals and devising effective biological hypothesis are difficult. To overcome such limitations in scATAC-seq data analysis, new methods and software tools have been developed over the past few years. Nevertheless, there is no consensus for the best practice of scATAC-seq data analysis yet. In this review, we discuss scATAC-seq technology and data analysis methods, ranging from preprocessing to downstream analysis, along with an up-to-date list of published studies that involved the application of this method. We expect this review will provide a guideline for successful data generation and analysis methods using appropriate software tools and databases for the study of chromatin accessibility at single-cell resolution.
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Affiliation(s)
- Seungbyn Baek
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul 03722, Korea
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Vodiasova EA, Chelebieva ES, Kuleshova ON. The new technologies of high-throughput single-cell RNA sequencing. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A wealth of genome and transcriptome data obtained using new generation sequencing (NGS) technologies for whole organisms could not answer many questions in oncology, immunology, physiology, neurobiology, zoology and other fields of science and medicine. Since the cell is the basis for the living of all unicellular and multicellular organisms, it is necessary to study the biological processes at its level. This understanding gave impetus to the development of a new direction – the creation of technologies that allow working with individual cells (single-cell technology). The rapid development of not only instruments, but also various advanced protocols for working with single cells is due to the relevance of these studies in many fields of science and medicine. Studying the features of various stages of ontogenesis, identifying patterns of cell differentiation and subsequent tissue development, conducting genomic and transcriptome analyses in various areas of medicine (especially in demand in immunology and oncology), identifying cell types and states, patterns of biochemical and physiological processes using single cell technologies, allows the comprehensive research to be conducted at a new level. The first RNA-sequencing technologies of individual cell transcriptomes (scRNA-seq) captured no more than one hundred cells at a time, which was insufficient due to the detection of high cell heterogeneity, existence of the minor cell types (which were not detected by morphology) and complex regulatory pathways. The unique techniques for isolating, capturing and sequencing transcripts of tens of thousands of cells at a time are evolving now. However, new technologies have certain differences both at the sample preparation stage and during the bioinformatics analysis. In the paper we consider the most effective methods of multiple parallel scRNA-seq using the example of 10XGenomics, as well as the specifics of such an experiment, further bioinformatics analysis of the data, future outlook and applications of new high-performance technologies.
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Affiliation(s)
- E. A. Vodiasova
- A.O. Kovalevsky Institute of Biology of the Southern Seas, RAS
| | | | - O. N. Kuleshova
- A.O. Kovalevsky Institute of Biology of the Southern Seas, RAS
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Santoni M, Cimadamore A, Cheng L, Lopez-Beltran A, Battelli N, Massari F, Scarpelli M, Galosi AB, Bracarda S, Montironi R. Circulating Tumor Cells in Renal Cell Carcinoma: Recent Findings and Future Challenges. Front Oncol 2019; 9:228. [PMID: 31024837 PMCID: PMC6460373 DOI: 10.3389/fonc.2019.00228] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/14/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
| | - Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, Ancona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | | | | | | | - Andrea Benedetto Galosi
- Department of Urology, School of Medicine, United Hospitals, Marche Polytechnic University, Ancona, Italy
| | - Sergio Bracarda
- Medical Oncology, Department of Oncology, Azienda Ospedaliera S. Maria, Terni, Italy
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15
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Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nat Methods 2019; 16:323-325. [PMID: 30923384 DOI: 10.1038/s41592-019-0361-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/20/2019] [Indexed: 12/17/2022]
Abstract
Our method for analyzing histone modifications, scChIC-seq (single-cell chromatin immunocleavage sequencing), involves targeting of the micrococcal nuclease (MNase) to a histone mark of choice by tethering to a specific antibody. Cleaved target sites are then selectively PCR amplified. We show that scChIC-seq reliably detects H3K4me3 and H3K27me3 target sites in single human white blood cells. The resulting data are used for clustering of blood cell types.
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Dahl JA, Gilfillan GD. How low can you go? Pushing the limits of low-input ChIP-seq. Brief Funct Genomics 2019; 17:89-95. [PMID: 29087438 DOI: 10.1093/bfgp/elx037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past decade, chromatin immunoprecipitation sequencing (ChIP-seq) has emerged as the dominant technique for those wishing to perform genome-wide protein:DNA profiling. Owing to the tissue- and cell-type-specific nature of epigenetic marks, the field has been driven towards obtaining data from ever-lower cell numbers. In this review, we focus on the methodological developments that have lowered input requirements and the biological findings they have enabled, as we strive towards the ultimate goal of robust single-cell ChIP-seq.
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AlJanahi AA, Danielsen M, Dunbar CE. An Introduction to the Analysis of Single-Cell RNA-Sequencing Data. Mol Ther Methods Clin Dev 2018; 10:189-196. [PMID: 30094294 PMCID: PMC6072887 DOI: 10.1016/j.omtm.2018.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The recent development of single-cell RNA sequencing has deepened our understanding of the cell as a functional unit, providing new insights based on gene expression profiles of hundreds to hundreds of thousands of individual cells, and revealing new populations of cells with distinct gene expression profiles previously hidden within analyses of gene expression performed on bulk cell populations. However, appropriate analysis and utilization of the massive amounts of data generated from single-cell RNA sequencing experiments are challenging and require an understanding of the experimental and computational pathways taken between preparation of input cells and output of interpretable data. In this review, we will discuss the basic principles of these new technologies, focusing on concepts important in the analysis of single-cell RNA-sequencing data. Specifically, we summarize approaches to quality-control measures for determination of which single cells to include for further examination, methods of data normalization and scaling to overcome the relatively inefficient capture rate of mRNA from each cell, and clustering and visualization algorithms used for dimensional reduction of the data to a two-dimensional plot.
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Affiliation(s)
- Aisha A. AlJanahi
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Mark Danielsen
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
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18
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Circulating Tumor Cells for the Management of Renal Cell Carcinoma. Diagnostics (Basel) 2018; 8:diagnostics8030063. [PMID: 30177639 PMCID: PMC6164661 DOI: 10.3390/diagnostics8030063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 12/17/2022] Open
Abstract
Renal cell carcinoma is a highly malignant cancer that would benefit from non-invasive innovative markers providing early diagnosis and recurrence detection. Circulating tumor cells are a particularly promising marker of tumor invasion that could be used to improve the management of patients with RCC. However, the extensive genetic and immunophenotypic heterogeneity of cells from RCC and their trend to transition to the mesenchymal phenotype when they circulate in blood constitute a challenge for their sensitive and specific detection. This review analyzes published studies targeting CTC in patients with RCC, in the context of the biological, pathological, and molecular complexity of this particular cancer. Although further analytical and clinical studies are needed to pinpoint the most suitable approach for highly sensitive CTC detection in RCC patients, it is clear that this field can bring a relevant guide to clinicians and help to RCC patients. Furthermore, as described, a particular subtype of RCC-the ccRCC-can be used as a model to study the relationship between cytomorphological and genetic cellular markers of malignancy, an important issue for the study of CTC from any type of solid cancer.
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Zappia L, Phipson B, Oshlack A. Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLoS Comput Biol 2018; 14:e1006245. [PMID: 29939984 PMCID: PMC6034903 DOI: 10.1371/journal.pcbi.1006245] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 07/06/2018] [Accepted: 05/30/2018] [Indexed: 01/19/2023] Open
Abstract
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time.
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Affiliation(s)
- Luke Zappia
- Bioinformatics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- School of Biosciences, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Belinda Phipson
- Bioinformatics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Alicia Oshlack
- Bioinformatics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- School of Biosciences, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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20
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Single Cell Genetics and Epigenetics in Early Embryo: From Oocyte to Blastocyst. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:103-117. [DOI: 10.1007/978-981-13-0502-3_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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