1
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Wang S, Li X, Liu C, Yuan Y, Ma F. Single-cell transcriptomic analysis of the role of HPV16-positive macrophages in cervical cancer prognosis. J Med Virol 2023; 95:e28410. [PMID: 36519591 DOI: 10.1002/jmv.28410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Almost all cases of cervical cancer (CC) can be attributed to high-risk human papillomavirus (HPVs) infections in keratinocytes. However, it is unknown whether HPV invades immune cells such as macrophages and T cells. We analyzed the single-cell transcriptome of the CC and its adjacent tissues and found that HPV16 genes, including E1, E6, and E7, expressed in the macrophages and CD8+ T cells in addition to the malignant cells. HPV16+ macrophages highly expressed the genes that promote cell adhesion and the favorable genes such as WAS, IQCB1, MYO1F, and PDZD11 in CC prognosis. The transcription factor KLF5 potentially accounted for the induction of these protective genes and thus facilitated the infiltration of the immune cells in tumor tissues. Our single-cell transcriptome analysis suggests the potential value of the HPV16+ macrophage in CC prognosis. However, extensive experimental studies investigating the characteristics and functions of the HPV+ immune cells are still required.
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Affiliation(s)
- Shiyou Wang
- Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Xiaohui Li
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Research Unit of Radiation Oncology, Chinese Academy of Medical Sciences, Jinan, China
| | - Chao Liu
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Research Unit of Radiation Oncology, Chinese Academy of Medical Sciences, Jinan, China
| | - Yi Yuan
- Department of Medical Research, Jiangsu Toneker Pharmaceutical Technology Co., Ltd, Suzhou, China
| | - Feng Ma
- Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
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2
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Iida K, Kondo J, Wibisana JN, Inoue M, Okada M. ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. Bioinformatics 2022; 38:4330-4336. [PMID: 35924984 PMCID: PMC9477531 DOI: 10.1093/bioinformatics/btac541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 07/04/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) analysis reveals heterogeneity and dynamic cell transitions. However, conventional gene-based analyses require intensive manual curation to interpret biological implications of computational results. Hence, a theory for efficiently annotating individual cells remains warranted. RESULTS We present ASURAT, a computational tool for simultaneously performing unsupervised clustering and functional annotation of disease, cell type, biological process and signaling pathway activity for single-cell transcriptomic data, using a correlation graph decomposition for genes in database-derived functional terms. We validated the usability and clustering performance of ASURAT using scRNA-seq datasets for human peripheral blood mononuclear cells, which required fewer manual curations than existing methods. Moreover, we applied ASURAT to scRNA-seq and spatial transcriptome datasets for human small cell lung cancer and pancreatic ductal adenocarcinoma, respectively, identifying previously overlooked subpopulations and differentially expressed genes. ASURAT is a powerful tool for dissecting cell subpopulations and improving biological interpretability of complex and noisy transcriptomic data. AVAILABILITY AND IMPLEMENTATION ASURAT is published on Bioconductor (https://doi.org/10.18129/B9.bioc.ASURAT). The codes for analyzing data in this article are available at Github (https://github.com/keita-iida/ASURATBI) and figshare (https://doi.org/10.6084/m9.figshare.19200254.v4). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Keita Iida
- To whom correspondence should be addressed.
| | - Jumpei Kondo
- Division of Health Sciences, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan,Department of Clinical Bio-Resource Research and Development, Graduate School of Medicine Kyoto University, Kyoto 606-8501, Japan
| | | | - Masahiro Inoue
- Department of Clinical Bio-Resource Research and Development, Graduate School of Medicine Kyoto University, Kyoto 606-8501, Japan
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan,Center for Drug Design and Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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3
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Wu J, Ding Y, Wang J, Lyu F, Tang Q, Song J, Luo Z, Wan Q, Lan X, Xu Z, Chen L. Single‐cell RNA
sequencing in oral science: Current awareness and perspectives. Cell Prolif 2022; 55:e13287. [PMID: 35842899 PMCID: PMC9528768 DOI: 10.1111/cpr.13287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/10/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Abstract
The emergence of single‐cell RNA sequencing enables simultaneous sequencing of thousands of cells, making the analysis of cell population heterogeneity more efficient. In recent years, single‐cell RNA sequencing has been used in the investigation of heterogeneous cell populations, cellular developmental trajectories, stochastic gene transcriptional kinetics, and gene regulatory networks, providing strong support in life science research. However, the application of single‐cell RNA sequencing in the field of oral science has not been reviewed comprehensively yet. Therefore, this paper reviews the development and application of single‐cell RNA sequencing in oral science, including fields of tissue development, teeth and jaws diseases, maxillofacial tumors, infections, etc., providing reference and prospects for using single‐cell RNA sequencing in studying the oral diseases, tissue development, and regeneration.
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Affiliation(s)
- Jie Wu
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology Sun Yat‐sen University Guangzhou China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yumei Ding
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Jinyu Wang
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Fengyuan Lyu
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
- Center of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Jiangyuan Song
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Zhiqiang Luo
- National Engineering Research Center for Nanomedicine College of Life Science and Technolog Huazhong University of Science and Technology Wuhan China
| | - Qian Wan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy Huazhong University of Science and Technology Wuhan China
- Institute of Brain Research Huazhong University of Science and Technology Wuhan China
| | - Xiaoli Lan
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Key Laboratory of Molecular Imaging Wuhan China
| | - Zhi Xu
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
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4
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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5
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Burja B, Paul D, Tastanova A, Edalat SG, Gerber R, Houtman M, Elhai M, Bürki K, Staeger R, Restivo G, Lang R, Sodin-Semrl S, Lakota K, Tomšič M, Levesque MP, Distler O, Rotar Ž, Robinson MD, Frank-Bertoncelj M. An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies. Front Cell Dev Biol 2022; 10:872688. [PMID: 35573685 PMCID: PMC9096112 DOI: 10.3389/fcell.2022.872688] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/13/2022] [Indexed: 12/16/2022] Open
Abstract
We present an optimized dissociation protocol for preparing high-quality skin cell suspensions for in-depth single-cell RNA-sequencing (scRNA-seq) analysis of fresh and cultured human skin. Our protocol enabled the isolation of a consistently high number of highly viable skin cells from small freshly dissociated punch skin biopsies, which we use for scRNA-seq studies. We recapitulated not only the main cell populations of existing single-cell skin atlases, but also identified rare cell populations, such as mast cells. Furthermore, we effectively isolated highly viable single cells from ex vivo cultured skin biopsy fragments and generated a global single-cell map of the explanted human skin. The quality metrics of the generated scRNA-seq datasets were comparable between freshly dissociated and cultured skin. Overall, by enabling efficient cell isolation and comprehensive cell mapping, our skin dissociation-scRNA-seq workflow can greatly facilitate scRNA-seq discoveries across diverse human skin pathologies and ex vivo skin explant experimentations.
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Affiliation(s)
- Blaž Burja
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Dominique Paul
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Aizhan Tastanova
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Sam G. Edalat
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Reto Gerber
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Miranda Houtman
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Muriel Elhai
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kristina Bürki
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ramon Staeger
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Gaetana Restivo
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Ramon Lang
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Snezna Sodin-Semrl
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katja Lakota
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mitchell P. Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Žiga Rotar
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mark D. Robinson
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- BioMed X Institute, Heidelberg, Germany
- *Correspondence: Mojca Frank-Bertoncelj,
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6
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Theocharidis G, Tekkela S, Veves A, McGrath JA, Onoufriadis A. Single-cell transcriptomics in human skin research: available technologies, technical considerations, and disease applications. Exp Dermatol 2022; 31:655-673. [PMID: 35196402 PMCID: PMC9311140 DOI: 10.1111/exd.14547] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/18/2022] [Indexed: 11/28/2022]
Abstract
Single‐cell technologies have revolutionized research in the last decade, including for skin biology. Single‐cell RNA sequencing has emerged as a powerful tool allowing the dissection of human disease pathophysiology at unprecedented resolution by assessing cell‐to‐cell variation, facilitating identification of rare cell populations and elucidating cellular heterogeneity. In dermatology, this technology has been widely applied to inflammatory skin disorders, fibrotic skin diseases, wound healing complications and cutaneous neoplasms. Here, we discuss the available technologies and technical considerations of single‐cell RNA sequencing and describe its applications to a broad spectrum of dermatological diseases.
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Affiliation(s)
- Georgios Theocharidis
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Stavroula Tekkela
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, SE1 9RT, UK
| | - Aristidis Veves
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - John A McGrath
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, SE1 9RT, UK
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, SE1 9RT, UK
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7
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Yang F, Li R, Zhao C, Che T, Guo J, Xie Y, Wang Z, Li J, Liu Z. Single-cell sequencing reveals the new existence form of dermal papilla cells in the hair follicle regeneration of cashmere goats. Genomics 2022; 114:110316. [PMID: 35202721 DOI: 10.1016/j.ygeno.2022.110316] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 02/13/2022] [Indexed: 12/19/2022]
Abstract
The problem of human hair loss has caused widespread concern, however, such research is difficult because the periodicity is not obvious and the deeper levels knowledge of dermal papilla (DP) stem cells' differentiation are limited. Here, cashmere goats which have obvious periodicity of hair follicles were used, based on unbiased scRNA sequencing, we constructed DP cell lineage differentiation trajectory and revealed the key genes, signals and functions involved in cell fate decisions. And then we revealed the molecular landscape of hair follicle on regeneration. Revealed that DP cells differentiate into four intermediate cell states at different periodicity: Intermediate-cell-10 showed important functions in the growth and maintenance of cashmere; intermediate-cell-1 acting on apoptosis and cashmere shedding; intermediate-cell-0 initiated new follicular cycles, the migration of hair follicles and the occurrence of cashmere; and intermediate-cell-15 are suggested to be DP progenitor cells. In general, we provide new insights for hair regrowth. At the same time, it provides a new research ideas, directions and molecular landscape for the mechanism of dermal papilla cells.
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Affiliation(s)
- Feng Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of mutton sheep genetics and breeding of Ministry of Agriculture, Hohhot, 010018, China
| | - Rui Li
- China Institute of Communications, Beijing, China
| | - Cun Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tianyu Che
- Key Laboratory of mutton sheep genetics and breeding of Ministry of Agriculture, Hohhot, 010018, China
| | - Juntao Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yuchun Xie
- The Inner Mongolia Autonomous Region goat genetics and breeding Engineering Technology Research Center, Hohhot, 010018, China
| | - Zhixin Wang
- Key Laboratory of mutton sheep genetics and breeding of Ministry of Agriculture, Hohhot, 010018, China
| | - Jinquan Li
- The Inner Mongolia Autonomous Region goat genetics and breeding Engineering Technology Research Center, Hohhot, 010018, China.
| | - Zhihong Liu
- Key Laboratory of mutton sheep genetics and breeding of Ministry of Agriculture, Hohhot, 010018, China.
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8
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Ascensión AM, Araúzo-Bravo MJ, Izeta A. Challenges and Opportunities for the Translation of Single-Cell RNA Sequencing Technologies to Dermatology. Life (Basel) 2022; 12:67. [PMID: 35054460 PMCID: PMC8781146 DOI: 10.3390/life12010067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 12/19/2022] Open
Abstract
Skin is a complex and heterogeneous organ at the cellular level. This complexity is beginning to be understood through the application of single-cell genomics and computational tools. A large number of datasets that shed light on how the different human skin cell types interact in homeostasis-and what ceases to work in diverse dermatological diseases-have been generated and are publicly available. However, translation of these novel aspects to the clinic is lacking. This review aims to summarize the state-of-the-art of skin biology using single-cell technologies, with a special focus on skin pathologies and the translation of mechanistic findings to the clinic. The main implications of this review are to summarize the benefits and limitations of single-cell analysis and thus help translate the emerging insights from these novel techniques to the bedside.
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Affiliation(s)
- Alex M. Ascensión
- Tissue Engineering Group, Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain;
- Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain;
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain;
- Max Planck Institute for Molecular Biomedicine, 48167 Muenster, Germany
- IKERBASQUE, Basque Foundation for Science, 48012 Bilbao, Spain
| | - Ander Izeta
- Tissue Engineering Group, Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain;
- School of Engineering, Tecnun-University of Navarra, 20009 Donostia-San Sebastián, Spain
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9
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Gu M, He T, Yuan Y, Duan S, Li X, Shen C. Single-Cell RNA Sequencing Reveals Multiple Pathways and the Tumor Microenvironment Could Lead to Chemotherapy Resistance in Cervical Cancer. Front Oncol 2021; 11:753386. [PMID: 34900703 PMCID: PMC8662819 DOI: 10.3389/fonc.2021.753386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/27/2021] [Indexed: 12/28/2022] Open
Abstract
Background Cervical cancer is one of the most common gynecological cancers worldwide. The tumor microenvironment significantly influences the therapeutic response and clinical outcome. However, the complex tumor microenvironment of cervical cancer and the molecular mechanisms underlying chemotherapy resistance are not well studied. This study aimed to comprehensively analyze cells from pretreated and chemoresistant cervical cancer tissues to generate a molecular census of cell populations. Methods Biopsy tissues collected from patients with cervical squamous cell carcinoma, cervical adenocarcinoma, and chronic cervicitis were subjected to single-cell RNA sequencing using the 10× Genomics platform. Unsupervised clustering analysis of cells was performed to identify the main cell types, and important cell clusters were reclustered into subpopulations. Gene expression profiles and functional enrichment analysis were used to explore gene expression and functional differences between cell subpopulations in cervicitis and cervical cancer samples and between chemoresistant and chemosensitive samples. Results A total of 24,371 cells were clustered into nine separate cell types, including immune and non-immune cells. Differentially expressed genes between chemoresistant and chemosensitive patients enriched in the phosphoinositide 3-kinase (PI3K)/AKT pathway were involved in tumor development, progression, and apoptosis, which might lead to chemotherapy resistance. Conclusions Our study provides a comprehensive overview of the cancer microenvironment landscape and characterizes its gene expression and functional difference in chemotherapy resistance. Consequently, our study deepens the insights into cervical cancer biology through the identification of gene markers for diagnosis, prognosis, and therapy.
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Affiliation(s)
- Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Ti He
- Department of Scientific Research & Industrial Application, Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Yuncong Yuan
- College of Life Sciences, Wuhan University, Wuhan, China.,China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Suling Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xin Li
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chao Shen
- College of Life Sciences, Wuhan University, Wuhan, China.,China Center for Type Culture Collection, Wuhan University, Wuhan, China
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10
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Shimano M, Miyauchi T, Yanagi T, Nomura T, Ujiie H. Development of Verruca Plana from Human Papillomavirus 78 Dependent on Host Immune State. Acta Derm Venereol 2021; 101:adv00608. [PMID: 34806758 PMCID: PMC9455333 DOI: 10.2340/actadv.v101.567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract is missing (Short communication)
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Affiliation(s)
| | - Toshinari Miyauchi
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-Ku, Sapporo, 060-8638, Japan .
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11
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Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma. Nat Commun 2021; 12:4821. [PMID: 34376672 PMCID: PMC8355240 DOI: 10.1038/s41467-021-25101-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/23/2021] [Indexed: 02/05/2023] Open
Abstract
Subclonal genetic heterogeneity and their diverse gene expression impose serious problems in understanding the behavior of cancers and contemplating therapeutic strategies. Here we develop and utilize a capture-based sequencing panel, which covers host hotspot genes and the full-length genome of human T-cell leukemia virus type-1 (HTLV-1), to investigate the clonal architecture of adult T-cell leukemia-lymphoma (ATL). For chronologically collected specimens from patients with ATL or pre-onset individuals, we integrate deep DNA sequencing and single-cell RNA sequencing to detect the somatic mutations and virus directly and characterize the transcriptional readouts in respective subclones. Characteristic genomic and transcriptomic patterns are associated with subclonal expansion and switches during the clinical timeline. Multistep mutations in the T-cell receptor (TCR), STAT3, and NOTCH pathways establish clone-specific transcriptomic abnormalities and further accelerate their proliferative potential to develop highly malignant clones, leading to disease onset and progression. Early detection and characterization of newly expanded subclones through the integrative analytical platform will be valuable for the development of an in-depth understanding of this disease. Characterising the clonal architecture of Adult T-cell leukemia-lymphoma (ATL) remains crucial. Here, the authors develop a capture-based sequencing panel and use deep DNA and single cell RNA sequencing and report distinct genomic and transcriptomic features associated with subclonal evolution.
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12
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Zou D, Qi J, Wu W, Xu D, Tu Y, Liu T, Zhang J, Li X, Lu F, He L. Applications of Single-Cell Sequencing in Dermatology. Med Sci Monit 2021; 27:e931862. [PMID: 34011922 PMCID: PMC8147034 DOI: 10.12659/msm.931862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-cell sequencing (SCS) is a promising new technique used to assess the genomics, transcriptomics, epigenetics, and other multi-omics at the single-cell level. In addition to elucidating the immune microenvironment and revealing the pathomechanisms of disease and drug resistance, SCS can profile the actual state of an individual cell and identify a novel cell type and differentiation trajectories, which cannot be achieved by bulk tissue sequencing technique. SCS technique serves as powerful tools to explore more meaningful biomarkers of diagnosis, prognosis, and new therapeutic targets in clinical practice. The SCS technique has been widely applied in the field of dermatology. In this review, we summarize the advances of SCS in dermatology.
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Affiliation(s)
- Dandan Zou
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Jue Qi
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Dan Xu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Ying Tu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Tongyun Liu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Juan Zhang
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Xing Li
- Department of Dermatology, People's Hospital of Chuxiong Yi Autonomous Prefecture, Chuxiong, Yunnan, China (mainland)
| | - Fengyan Lu
- Qujing Affiliated Hospital of Kunming Medical University and Department of Dermatology, The First People's Hospital of Qujing, Qujing, Yunnan, China (mainland)
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
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13
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Kim J, Lee J, Kim HJ, Kameyama N, Nazarian R, Der E, Cohen S, Guttman-Yassky E, Putterman C, Krueger JG. Single-cell transcriptomics applied to emigrating cells from psoriasis elucidate pathogenic versus regulatory immune cell subsets. J Allergy Clin Immunol 2021; 148:1281-1292. [PMID: 33932468 DOI: 10.1016/j.jaci.2021.04.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/16/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND In previous human skin single-cell data, inflammatory cells constituted only a small fraction of the overall cell population, such that functional subsets were difficult to ascertain. OBJECTIVE Our aims were to overcome the aforesaid limitation by applying single-cell transcriptomics to emigrating cells from skin and elucidate ex vivo gene expression profiles of pathogenic versus regulatory immune cell subsets in the skin of individuals with psoriasis. METHODS We harvested emigrating cells from human psoriasis skin after incubation in culture medium without enzyme digestion or cell sorting and analyzed cells with single-cell RNA sequencing and flow cytometry simultaneously. RESULTS Unsupervised clustering of harvested cells from psoriasis skin and control skin identified natural killer cells, T-cell subsets, dendritic cell subsets, melanocytes, and keratinocytes in different layers. Comparison between psoriasis cells and control cells within each cluster revealed that (1) cutaneous type 17 T cells display highly differing transcriptome profiles depending on IL-17A versus IL-17F expression and IFN-γ versus IL-10 expression; (2) semimature dendritic cells are regulatory dendritic cells with high IL-10 expression, but a subset of semimature dendritic cells expresses IL-23A and IL-36G in psoriasis; and (3) CCL27-CCR10 interaction is potentially impaired in psoriasis because of decreased CCL27 expression in basal keratinocytes. CONCLUSION We propose that single-cell transcriptomics applied to emigrating cells from human skin provides an innovative study platform to compare gene expression profiles of heterogenous immune cells in various inflammatory skin diseases.
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Affiliation(s)
- Jaehwan Kim
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY; Department of Medicine, Division of Dermatology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY.
| | - Jongmi Lee
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY
| | - Hyun Je Kim
- Department of Dermatology, and Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Dermatology, Samsung Medical Center, Seoul, Korea
| | - Naoya Kameyama
- Department of Dermatology, and Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Roya Nazarian
- Department of Medicine, Division of Dermatology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Evan Der
- Department of Medicine, Division of Rheumatology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Steven Cohen
- Department of Medicine, Division of Dermatology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Emma Guttman-Yassky
- Department of Dermatology, and Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Chaim Putterman
- Department of Medicine, Division of Rheumatology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY; Azrieli School of Medicine, Safed, Israel; Research Institute, Galillee Medical Center, Nahariya, Israel
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY.
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14
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Abstract
The skin is an ecosystem composed of specialized cell types that work together to serve as a physical protective barrier. Single-cell resolution is therefore essential to deconvolve skin's heterogeneity by identifying novel, distinct cell subsets in health and disease. Single-cell RNA sequencing is a highly meticulous methodology used to study the distinct transcriptional profiles of each cell within large tissue libraries at uniquely high resolution. The investigative capabilities achieved by this methodology allow previously unattainable analyses, including identification of rare cell populations, evaluation of cell-to-cell variation, and the ability to track trajectories of distinct cell lineages through development. In the past decade, application of transcriptomic analysis to skin biology and dermatology has greatly advanced understanding of homeostatic physiology in the skin, as well as a multitude of dermatologic diseases. Single-cell RNA sequencing offers tremendous promise for identification of novel therapeutic targets in dermatologic diseases, with broad implications of improving therapeutic interventions.
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Affiliation(s)
- Alana Deutsch
- Division of Dermatology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Beth N. McLellan
- Division of Dermatology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Kosaku Shinoda
- Division of Endocrinology and Diabetes, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York
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15
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O'Sullivan JDB, Nicu C, Picard M, Chéret J, Bedogni B, Tobin DJ, Paus R. The biology of human hair greying. Biol Rev Camb Philos Soc 2020; 96:107-128. [PMID: 32965076 DOI: 10.1111/brv.12648] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
Hair greying (canities) is one of the earliest, most visible ageing-associated phenomena, whose modulation by genetic, psychoemotional, oxidative, senescence-associated, metabolic and nutritional factors has long attracted skin biologists, dermatologists, and industry. Greying is of profound psychological and commercial relevance in increasingly ageing populations. In addition, the onset and perpetuation of defective melanin production in the human anagen hair follicle pigmentary unit (HFPU) provides a superb model for interrogating the molecular mechanisms of ageing in a complex human mini-organ, and greying-associated defects in bulge melanocyte stem cells (MSCs) represent an intriguing system of neural crest-derived stem cell senescence. Here, we emphasize that human greying invariably begins with the gradual decline in melanogenesis, including reduced tyrosinase activity, defective melanosome transfer and apoptosis of HFPU melanocytes, and is thus a primary event of the anagen hair bulb, not the bulge. Eventually, the bulge MSC pool becomes depleted as well, at which stage greying becomes largely irreversible. There is still no universally accepted model of human hair greying, and the extent of genetic contributions to greying remains unclear. However, oxidative damage likely is a crucial driver of greying via its disruption of HFPU melanocyte survival, MSC maintenance, and of the enzymatic apparatus of melanogenesis itself. While neuroendocrine factors [e.g. alpha melanocyte-stimulating hormone (α-MSH), adrenocorticotropic hormone (ACTH), ß-endorphin, corticotropin-releasing hormone (CRH), thyrotropin-releasing hormone (TRH)], and micropthalmia-associated transcription factor (MITF) are well-known regulators of human hair follicle melanocytes and melanogenesis, how exactly these and other factors [e.g. thyroid hormones, hepatocyte growth factor (HGF), P-cadherin, peripheral clock activity] modulate greying requires more detailed study. Other important open questions include how HFPU melanocytes age intrinsically, how psychoemotional stress impacts this process, and how current insights into the gerontobiology of the human HFPU can best be translated into retardation or reversal of greying.
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Affiliation(s)
- James D B O'Sullivan
- Dr. Philip Frost Department for Dermatology and Cutaneous Surgery, University of Miami, Miami, Florida, 33136, U.S.A
| | - Carina Nicu
- Dr. Philip Frost Department for Dermatology and Cutaneous Surgery, University of Miami, Miami, Florida, 33136, U.S.A
| | - Martin Picard
- Departments of Psychiatry and Neurology, Columbia University Irving Medical Center, 622 W 168th Street, PH1540N, New York, 10032, U.S.A
| | - Jérémy Chéret
- Dr. Philip Frost Department for Dermatology and Cutaneous Surgery, University of Miami, Miami, Florida, 33136, U.S.A
| | - Barbara Bedogni
- Dr. Philip Frost Department for Dermatology and Cutaneous Surgery, University of Miami, Miami, Florida, 33136, U.S.A
| | - Desmond J Tobin
- Charles Institute of Dermatology, University College Dublin, Dublin 4, Ireland
| | - Ralf Paus
- Dr. Philip Frost Department for Dermatology and Cutaneous Surgery, University of Miami, Miami, Florida, 33136, U.S.A.,Monasterium Laboratory, Skin & Hair Research Solutions GmbH, Münster, D-48149, Germany.,Centre for Dermatology Research, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, M13 9PT, U.K
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16
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Budhwani M, Lukowski SW, Porceddu SV, Frazer IH, Chandra J. Dysregulation of Stemness Pathways in HPV Mediated Cervical Malignant Transformation Identifies Potential Oncotherapy Targets. Front Cell Infect Microbiol 2020; 10:307. [PMID: 32670895 PMCID: PMC7330094 DOI: 10.3389/fcimb.2020.00307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/20/2020] [Indexed: 12/11/2022] Open
Abstract
Human papillomavirus (HPV) infection is associated with a range of malignancies that affect anogenital and oropharyngeal sites. α-HPVs dominantly infect basal epithelial cells of mucosal tissues, where they dysregulate cell division and local immunity. The cervix is one of the mucosal sites most susceptible to HPV infections. It consists of anatomically diverse regions, and the majority of cervical intraepithelial neoplasia and cancers arise within the cervical squamo-columnar junction where undifferentiated basal progenitor cells with stem cell properties are found. The cancer stem cell theory particularly associates tumorigenesis, invasion, dissemination, and metastasis with cancer cells exhibiting stem cell properties. In this perspective, we discuss evidence of a cervical cancer stem cell niche and explore the association of stemness related genes with 5-year survival using a publicly available transcriptomic dataset of a cervical cancer cohort. We report that poor prognosis in this cohort correlates with overexpression of a subset of stemness pathway genes, a majority of which regulate the central Focal Adhesion pathway, and are also found to be enriched in the HPV infection pathway. These observations support therapeutic targeting of stemness genes overexpressed by mucosal cells infected with high-risk HPVs.
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Affiliation(s)
- Megha Budhwani
- Diamantina Institute, Translational Research Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Sandro V Porceddu
- Cancer Services, Princess Alexandra Hospital, Woolloongabba, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ian H Frazer
- Diamantina Institute, Translational Research Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Janin Chandra
- Diamantina Institute, Translational Research Institute, The University of Queensland, Woolloongabba, QLD, Australia
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17
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Kim D, Chung KB, Kim TG. Application of single-cell RNA sequencing on human skin: Technical evolution and challenges. J Dermatol Sci 2020; 99:74-81. [PMID: 32593488 DOI: 10.1016/j.jdermsci.2020.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022]
Abstract
The bulk tissue RNA sequencing technique measures the average gene expression of potentially heterogeneous cellular subsets of human skin. However, single-cell RNA sequencing (scRNA-seq) enables both profiling of gene expression measurements at a single-cell resolution and identification of cellular heterogeneity. This recent technical advance has broadened the understanding of many aspects of skin biology, such as development, oncogenesis, and immunopathogenesis. However, due to the low number of mRNAs detectable in an individual cell and the alteration of transcriptomes during sample preparation, scRNA-seq data are often extremely noisy. Moreover, unstandardized methodologies for sample preparation, capturing, and bioinformatic analysis (e.g., batch correction or integration) hamper reliable inter-study comparisons. Nevertheless, sophisticated bioinformatic analysis and integrative omics-based approaches are making up for these limitations. Here, we discuss both the advantages and technical challenges of scRNA-seq, a promising tool opening new horizons in dermatological research.
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Affiliation(s)
- Doyoung Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Kyung Bae Chung
- Department of Dermatology and Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae-Gyun Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Republic of Korea.
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18
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Liu W, He H, Zheng SY. Microfluidics in Single-Cell Virology: Technologies and Applications. Trends Biotechnol 2020; 38:1360-1372. [PMID: 32430227 DOI: 10.1016/j.tibtech.2020.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
Abstract
Microfluidics has proven to be a powerful tool for probing biology at the single-cell level. However, it is only in the past 5 years that single-cell microfluidics has been used in the field of virology. An array of strategies based on microwells, microvalves, and droplets is now available for tracking viral infection dynamics, identifying cell subpopulations with particular phenotypes, as well as high-throughput screening. The insights into the virus-host interactions gained at the single-cell level are unprecedented and usually inaccessible by population-based experiments. Therefore, single-cell microfluidics, which opens new avenues for mechanism elucidation and development of antiviral therapeutics, would be a valuable tool for the study of viral pathogenesis.
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Affiliation(s)
- Wu Liu
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Hongzhang He
- Captis Diagnostics Inc., Pittsburgh, PA 15213, USA
| | - Si-Yang Zheng
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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