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Gondal MN, Shah SUR, Chinnaiyan AM, Cieslik M. A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations. ARXIV 2024:arXiv:2404.10545v1. [PMID: 38699169 PMCID: PMC11065044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Furthermore, we propose that bridging the gap between computational and wet lab scientists through user-friendly web-based platforms is needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.
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Affiliation(s)
- Mahnoor N. Gondal
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
| | - Saad Ur Rehman Shah
- Gies College of Business, University of Illinois Business College, Champaign, IL USA
| | - Arul M. Chinnaiyan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Urology, University of Michigan, Ann Arbor, MI USA
- Howard Hughes Medical Institute, Ann Arbor, MI USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI USA
| | - Marcin Cieslik
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Pathology, University of Michigan, Ann Arbor, MI USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI USA
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2
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Lodi MK, Lodi M, Osei K, Ranganathan V, Hwang P, Ghosh P. CHAI: Consensus Clustering Through Similarity Matrix Integration for Cell-Type Identification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585758. [PMID: 38562750 PMCID: PMC10983883 DOI: 10.1101/2024.03.19.585758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Several methods have been developed to computationally predict cell-types for single cell RNA sequencing (scRNAseq) data. As methods are developed, a common problem for investigators has been identifying the best method they should apply to their specific use-case. To address this challenge, we present CHAI (consensus Clustering tHrough similArIty matrix integratIon for single cell type identification), a wisdom of crowds approach for scRNAseq clustering. CHAI presents two competing methods which aggregate the clustering results from seven state of the art clustering methods: CHAI-AvgSim and CHAI-SNF. Both methods demonstrate improved performance on a diverse selection of benchmarking datasets, besides also outperforming a previous consensus clustering method. We demonstrate CHAI's practical use case by identifying a leader tumor cell cluster enriched with CDH3. CHAI provides a platform for multiomic integration, and we demonstrate CHAI-SNF to have improved performance when including spatial transcriptomics data. CHAI is intuitive and easily customizable; it provides a way for users to add their own clustering methods to the pipeline, or down-select just the ones they want to use for the clustering aggregation. CHAI is available as an open source R package on GitHub: https://github.com/lodimk2/chai.
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Affiliation(s)
- Musaddiq K Lodi
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA 23284
| | - Muzammil Lodi
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284
| | - Kezie Osei
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284
| | | | - Priscilla Hwang
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA 23284
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284
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3
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Yarlagadda S, Giorgio TD. A guide to single-cell RNA sequencing analysis using web-based tools for non-bioinformatician. FEBS J 2023. [PMID: 38148322 DOI: 10.1111/febs.17036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a technique that has proven to be a powerful tool for a wide range of fields and research studies. However, scRNA-seq data analysis has been dominated by scientists highly trained in bioinformatics or those with extensive computational experience and understanding. Recently, this trend has begun to shift as more user-friendly web-based scRNA-seq analysis tools have been developed that require little computational experience to use. However, barriers persist for nonbioinformaticians in using this technique. Complex, unfamiliar language and scarce comprehensive literature guidance to provide a framework for understanding scRNA-seq analysis outputs are among the obstacles. This work introduces many popular web-based tools for scRNA-seq and provides a general overview of their user interfaces and features. Then, a comprehensive start-to-finish introductory scRNA-seq analysis pipeline is described in detail, which aims to enable researchers to carry out scRNA-seq analysis, regardless of computational experience. Companion video tutorials can be found at "EasyScRNAseqTutorials" on YouTube (https://www.youtube.com/@scrnaseqtutorials). However, as scRNA-seq continues to penetrate new fields and expand in importance, there remains a need for more literature to help overcome barriers to its use by explaining further the highly complex and advanced analyses that are introduced within this paper.
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Affiliation(s)
| | - Todd D Giorgio
- Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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4
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Mullan KA, de Vrij N, Valkiers S, Meysman P. Current annotation strategies for T cell phenotyping of single-cell RNA-seq data. Front Immunol 2023; 14:1306169. [PMID: 38187377 PMCID: PMC10768068 DOI: 10.3389/fimmu.2023.1306169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a popular technique for interrogating the diversity and dynamic nature of cellular gene expression and has numerous advantages in immunology. For example, scRNA-seq, in contrast to bulk RNA sequencing, can discern cellular subtypes within a population, which is important for heterogenous populations such as T cells. Moreover, recent advancements in the technology allow the parallel capturing of the highly diverse T-cell receptor (TCR) sequence with the gene expression. However, the field of single-cell RNA sequencing data analysis is still hampered by a lack of gold-standard cell phenotype annotation. This problem is particularly evident in the case of T cells due to the heterogeneity in both their gene expression and their TCR. While current cell phenotype annotation tools can differentiate major cell populations from each other, labelling T-cell subtypes remains problematic. In this review, we identify the common automated strategy for annotating T cells and their subpopulations, and also describe what crucial information is still missing from these tools.
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Affiliation(s)
- Kerry A. Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
| | - Nicky de Vrij
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
- Clinical Immunology Unit, Department of Clinical Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Sebastiaan Valkiers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Consortium, University of Antwerp, Antwerp, Belgium
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5
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Kułak K, Wojciechowska N, Samelak-Czajka A, Jackowiak P, Bagniewska-Zadworna A. How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis. PLANT METHODS 2023; 19:129. [PMID: 37981669 PMCID: PMC10659056 DOI: 10.1186/s13007-023-01109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.
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Affiliation(s)
- Karolina Kułak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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Flora A, Jepsen R, Kozera EK, Woods JA, Cains GD, Radzieta M, Jensen SO, Malone M, Frew JW. Human dermal fibroblast subpopulations and epithelial mesenchymal transition signals in hidradenitis suppurativa tunnels are normalized by spleen tyrosine kinase antagonism in vivo. PLoS One 2023; 18:e0282763. [PMID: 37922232 PMCID: PMC10624284 DOI: 10.1371/journal.pone.0282763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/19/2023] [Indexed: 11/05/2023] Open
Abstract
Hidradenitis Suppurativa is a chronic inflammatory disease of which the pathogenesis is incompletely understood. Dermal fibroblasts have been previously identified as a major source of inflammatory cytokines, however information pertaining to the characteristics of subpopulations of fibroblasts in HS remains unexplored. Using in silico-deconvolution of whole-tissue RNAseq, Nanostring gene expression panels and confirmatory immunohistochemistry we identified fibroblast subpopulations in HS tissue and their relationship to disease severity and lesion morphology. Gene signatures of SFRP2+ fibroblast subsets were increased in lesional tissue, with gene signatures of SFRP1+ fibroblast subsets decreased. SFRP2+ and CXCL12+ fibroblast numbers, measured by IHC, were increased in HS tissue, with greater numbers associated with epithelialized tunnels and Hurley Stage 3 disease. Pro-inflammatory CXCL12+ fibroblasts were also increased, with reductions in SFRP1+ fibroblasts compared to healthy controls. Evidence of Epithelial Mesenchymal Transition was seen via altered gene expression of SNAI2 and altered protein expression of ZEB1, TWIST1, Snail/Slug, E-Cadherin and N-Cadherin in HS lesional tissue. The greatest dysregulation of EMT associated proteins was seen in biopsies containing epithelialized tunnels. The use of the oral Spleen tyrosine Kinase inhibitor Fostamatinib significantly reduced expression of genes associated with chronic inflammation, fibroblast proliferation and migration suggesting a potential role for targeting fibroblast activity in HS.
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Affiliation(s)
- Akshay Flora
- Laboratory of Translational Cutaneous Medicine, Ingham Institute for Applied Medical Research, Sydney, Australia
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | | | - Emily K. Kozera
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Jane A. Woods
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Geoffrey D. Cains
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Slade O. Jensen
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Matthew Malone
- South West Sydney Limb Preservation and Wound Research, Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
| | - John W. Frew
- Laboratory of Translational Cutaneous Medicine, Ingham Institute for Applied Medical Research, Sydney, Australia
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
- Holdsworth House Medical Practice, Sydney, Australia
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7
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Sandoval AGW, Gim KY, Huang JT, Koehler KR. Applications of Human Pluripotent Stem Cell-Derived Skin Organoids in Dermatology. J Invest Dermatol 2023; 143:1872-1876. [PMID: 37739763 PMCID: PMC10518840 DOI: 10.1016/j.jid.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 09/24/2023]
Abstract
Pluripotent stem cells have the potential to become any cell type, and recently, they have been used to create organoids that can recapitulate several pertinent features of human organs. Skin organoids have been developed that possess many of the crucial accessory organs, including hair follicles, sebaceous glands, nerves, fat, and melanocytes. These skin organoids present the opportunity to study skin development and disease as well as perform screens to identify new drug candidates. In the future, skin organoids might augment clinical practice by serving as source material for transplantation to treat wounds or other conditions. Nevertheless, several limitations, such as the lengthy differentiation protocol, which can result in heterogeneous products, must first be addressed before the full potential of skin organoids can be realized. The purpose of this article is to provide a broad overview of skin organoids so that a broader audience can become familiar with this technology, which has important implications for dermatologic research and medicine.
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Affiliation(s)
| | - Kelly Y Gim
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Plastic & Oral Surgery, Boston Children's Hospital, Boston, Massachusetts, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer T Huang
- Dermatology Section, Division of Immunology, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA
| | - Karl R Koehler
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Plastic & Oral Surgery, Boston Children's Hospital, Boston, Massachusetts, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA.
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8
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Zhu R, Pan X, Wang S, Qiu Z, Gu C, Yao X, Li W. Updated skin transcriptomic atlas depicted by reciprocal contribution of single-nucleus RNA sequencing and single-cell RNA sequencing. J Dermatol Sci 2023; 111:22-31. [PMID: 37407342 DOI: 10.1016/j.jdermsci.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of skin biology, but its utility is restricted by the requirement of fresh samples, inadequate dissociation-induced cell loss or death, and activation during tissue digestion. Single-nucleus RNA sequencing (snRNA-seq) can use frozen, hard-to-dissociate materials, which might be a promising method to circumvent the limitations of scRNA-seq for the skin tissue. OBJECTIVE To profile skin cells using snRNA-seq in parallel with scRNA-seq. METHODS We performed snRNA-seq in parallel with scRNA-seq for the bisected skin sample of one person and integrated previously published scRNA-seq data for analysis. We comparatively analyzed the differences in cell proportions and gene expression between the two methods. The differentiation trajectories of keratinocytes and fibroblasts were analyzed by Slingshot analysis. RESULTS snRNA-seq was less susceptible to contamination from mitochondrial and ribosomal RNA, and exhibited a greater capacity to detect transcription factors. snRNA-seq identified more spatially and functionally relevant keratinocyte clusters that constitute cell trajectories with expected differentiation dynamics. Novel markers, e.g., LYPD3, EMP2, and CSTB, were revealed for different differentiation stages of keratinocytes, and NFIB and GRHL1 were identified as transcription factors involving in the proliferation and functional differentiation of keratinocytes. Fibroblasts were found in a state of activation in scRNA-seq. And scRNA-seq detected a greater number of immune cells. CONCLUSIONS We generated an updated atlas of the skin transcriptome based on the reciprocal contribution of scRNA-seq and snRNA-seq.
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Affiliation(s)
- Ronghui Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xiaoyu Pan
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Shangshang Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Zhuoqiong Qiu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Chaoying Gu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China.
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9
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Houser AE, Kazmi A, Nair AK, Ji AL. The Use of Single-Cell RNA-Sequencing and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases. JID INNOVATIONS 2023; 3:100198. [PMID: 37205302 PMCID: PMC10186616 DOI: 10.1016/j.xjidi.2023.100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 05/21/2023] Open
Abstract
The development of multiomic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) have emerged as widely adopted and powerful assays for elucidating key cellular components and their spatial arrangement within skin disease. In this paper, we review the recent biological insights gained from the use of scRNA-seq and ST and the advantages of combining both for profiling skin diseases, including aberrant wound healing, inflammatory skin diseases, and cancer. We discuss the role of scRNA-seq and ST in improving skin disease treatments and moving toward the goal of achieving precision medicine in dermatology, whereby patients can be optimally matched to treatments that maximize therapeutic response.
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Affiliation(s)
- Aubrey E. Houser
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Abiha Kazmi
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arjun K. Nair
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew L. Ji
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Correspondence: Andrew L. Ji, Department of Dermatology, Icahn School of Medicine at Mount Sinai, 1428 Madison Avenue, Atran 7-10F, Box 1048, New York, New York 10029, USA.
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10
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Becker J, Sun B, Alammari F, Haerty W, Vance KW, Szele FG. What has single-cell transcriptomics taught us about long non-coding RNAs in the ventricular-subventricular zone? Stem Cell Reports 2022; 18:354-376. [PMID: 36525965 PMCID: PMC9860170 DOI: 10.1016/j.stemcr.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) function is mediated by the process of transcription or through transcript-dependent associations with proteins or nucleic acids to control gene regulatory networks. Many lncRNAs are transcribed in the ventricular-subventricular zone (V-SVZ), a postnatal neural stem cell niche. lncRNAs in the V-SVZ are implicated in neurodevelopmental disorders, cancer, and brain disease, but their functions are poorly understood. V-SVZ neurogenesis capacity declines with age due to stem cell depletion and resistance to neural stem cell activation. Here we analyzed V-SVZ transcriptomics by pooling current single-cell RNA-seq data. They showed consistent lncRNA expression during stem cell activation, lineage progression, and aging. In conjunction with epigenetic and genetic data, we predicted V-SVZ lncRNAs that regulate stem cell activation and differentiation. Some of the lncRNAs validate known epigenetic mechanisms, but most remain uninvestigated. Our analysis points to several lncRNAs that likely participate in key aspects of V-SVZ stem cell activation and neurogenesis in health and disease.
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Affiliation(s)
- Jemima Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia,Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Keith W. Vance
- Department of Life Sciences, University of Bath, Bath, UK
| | - Francis George Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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11
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Leyva-Castillo JM, Sun L, Wu SY, Rockowitz S, Sliz P, Geha R. Single-cell transcriptome profile of mouse skin undergoing antigen-driven allergic inflammation recapitulates findings in atopic dermatitis skin lesions. J Allergy Clin Immunol 2022; 150:373-384. [PMID: 35300986 PMCID: PMC9378429 DOI: 10.1016/j.jaci.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 02/05/2022] [Accepted: 03/03/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Allergic skin inflammation elicited in mice by epicutaneous (EC) sensitization with antigen shares characteristics with human atopic dermatitis (AD). OBJECTIVE We characterized gene expression by single cells in mouse skin undergoing antigen-driven allergic inflammation and compared the results with findings in AD skin lesions. METHODS Mice were EC sensitized by application of ovalbumin (OVA) or saline to tape-stripped skin. Single-cell RNA sequencing was performed on skin cells 12 days later. Flow cytometry analysis was performed to validate results. RESULTS Sequencing identified 7 nonhematopoietic and 6 hematopoietic cell subsets in EC-sensitized mouse skin. OVA sensitization resulted in the expansion in the skin of T cells, dendritic cells, macrophages, mast cells/basophils, fibroblasts, and myocytes cell clusters, and in upregulation of TH2 cytokine gene expression in CD4+ T cells and mast cells/basophils. Genes differentially expressed in OVA-sensitized skin included genes important for inflammation in dendritic cells and macrophages, collagen deposition, and leukocyte migration in fibroblasts, chemotaxis in endothelial cells and skin barrier integrity, and differentiation in KCs-findings that recapitulate those in AD skin lesions. Unexpectedly, mast cells/basophils, rather than T cells, were the major source of Il4 and ll13 in OVA-sensitized mouse skin. In addition, our results suggest novel pathways in fibroblast and endothelial cells that may contribute to allergic skin inflammation. CONCLUSION The gene expression profile of single cells in mouse skin undergoing antigen-driven shares many features with that in AD skin lesions and unveils novel pathways that may be involved in allergic skin inflammation.
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Affiliation(s)
- Juan Manuel Leyva-Castillo
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA.,Corresponding authors: Juan-Manuel Leyva-Castillo, PhD. Boston Children’s Hospital, Division of Immunology, One Blackfan Circle, Boston, Massachusetts 02115, USA. Phone: 617-919-2465, Fax: 617-730-0528, Raif S. Geha, MD. Boston Children’s Hospital, Division of Immunology, One Blackfan Circle, Boston, Massachusetts 02115, USA. Phone: 617-919-2482, Fax: 617-730-0528,
| | - Liang Sun
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, USA
| | - Shih-Ying Wu
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, USA
| | - Shira Rockowitz
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, USA
| | - Piotr Sliz
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, USA.,Division of Molecular Medicine, Boston Children’s Hospital, Boston, USA
| | - Raif Geha
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA.,Corresponding authors: Juan-Manuel Leyva-Castillo, PhD. Boston Children’s Hospital, Division of Immunology, One Blackfan Circle, Boston, Massachusetts 02115, USA. Phone: 617-919-2465, Fax: 617-730-0528, Raif S. Geha, MD. Boston Children’s Hospital, Division of Immunology, One Blackfan Circle, Boston, Massachusetts 02115, USA. Phone: 617-919-2482, Fax: 617-730-0528,
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12
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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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13
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Piñeiro AJ, Houser AE, Ji AL. Research Techniques Made Simple: Spatial Transcriptomics. J Invest Dermatol 2022; 142:993-1001.e1. [PMID: 35331388 PMCID: PMC8969263 DOI: 10.1016/j.jid.2021.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 10/18/2022]
Abstract
Transcriptome profiling of tissues and single cells facilitates interrogation of gene expression changes within diverse biological contexts. However, spatial information is often lost during tissue homogenization or dissociation. Recent advances in transcriptome profiling preserve the in situ spatial contexts of RNA molecules and together comprise a group of techniques known as spatial transcriptomics (ST), enabling localization of cell types and their associated gene expression within intact tissues. In this paper, we review ST methods; summarize data analysis approaches, including integration with single-cell transcriptomics data; and discuss their applications in dermatologic research. These tools offer a promising avenue toward improving our understanding of niche patterning and cell‒cell interactions within heterogeneous tissues that encompass skin homeostasis and disease.
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14
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Onoufriadis A, McGrath JA. ESDR 50th Anniversary Lecture summary: The past and future of rare skin disease research/therapy. J Invest Dermatol 2022; 142:1010-1014. [DOI: 10.1016/j.jid.2021.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 10/19/2022]
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15
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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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16
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Zhang Y, Wang J, Yu C, Xia K, Yang B, Zhang Y, Ying L, Wang C, Huang X, Chen Q, Shen L, Li F, Liang C. Advances in single-cell sequencing and its application to musculoskeletal system research. Cell Prolif 2022; 55:e13161. [PMID: 34888976 PMCID: PMC8780907 DOI: 10.1111/cpr.13161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/30/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022] Open
Abstract
In recent years, single-cell sequencing (SCS) technologies have continued to advance with improved operating procedures and reduced cost, leading to increasing practical adoption among researchers. These emerging technologies have superior abilities to analyse cell heterogeneity at a single-cell level, which have elevated multi-omics research to a higher level. In some fields of research, application of SCS has enabled many valuable discoveries, and musculoskeletal system offers typical examples. This article reviews some major scientific issues and recent advances in musculoskeletal system. In addition, combined with SCS technologies, the research of cell or tissue heterogeneity in limb development and various musculoskeletal system clinical diseases also provides new possibilities for treatment strategies. Finally, this article discusses the challenges and future development potential of SCS and recommends the direction of future applications of SCS to musculoskeletal medicine.
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Affiliation(s)
- Yongxiang Zhang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Jingkai Wang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Chao Yu
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Kaishun Xia
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Biao Yang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Yuang Zhang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Liwei Ying
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Chenggui Wang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Xianpeng Huang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Qixin Chen
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Li Shen
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhouChina
- Hangzhou Innovation CenterZhejiang UniversityHangzhouChina
| | - Fangcai Li
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Chengzhen Liang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
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17
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Rosati D, Giordano A. Single-cell RNA sequencing and bioinformatics as tools to decipher cancer heterogenicity and mechanisms of drug resistance. Biochem Pharmacol 2021; 195:114811. [PMID: 34673017 DOI: 10.1016/j.bcp.2021.114811] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022]
Abstract
It is well known that cancer is an aggressive disease, often associated with relapse, in many cases due to drug resistance. Cancer stem cell and clonal evolution are frequently causes of innate or acquired drug resistance. Current RNA sequencing technologies do not distinguish gene expression of different cell lineages because they are based on bulk cell studies. Single-cell RNA sequencing technologies and related bioinformatics clustering and differential expression analysis represent a turning point in cancer research. They are emerging as essential tools for dissecting tumors at single-cell resolution and represent novel tools to understand carcinogenesis and drug response. In this review, we will outline the role of these new technologies in addressing cancer heterogeneity and cell lineage-dependent drug resistance.
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Affiliation(s)
- Diletta Rosati
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Antonio Giordano
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA.
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18
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An easy-to-operate method for single-cell isolation and retrieval using a microfluidic static droplet array. Mikrochim Acta 2021; 188:242. [PMID: 34226955 DOI: 10.1007/s00604-021-04897-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/12/2021] [Indexed: 10/20/2022]
Abstract
In-depth study of cellular heterogeneity of rare cells (e.g. circulating tumour cells (CTCs) and circulating foetal cells (CFCs)) is greatly needed in disease management but has never been completely explored due to the current technological limitations. We have developed a retrieval method for single-cell detection using a static droplet array (SDA) device through liquid segmentation with almost no sample loss. We explored the potential of using SDA for low sample input and retrieving the cells of interest using everyday laboratory equipment for downstream molecular analysis. This single-cell isolation and retrieval method is low-cost, rapid and provides a solution to the remaining challenge for single rare cell detection. The entire process takes less than 15 min, is easy to fabricate and allows for on-chip analysis of cells in nanolitre droplets and retrieval of desired droplets. To validate the applicability of our device and method, we mimicked detection of single CTCs by isolating and retrieving single cells and perform real-time PCR on their mRNA contents.
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19
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Abstract
Vitiligo is a disease of the skin characterized by the appearance of white spots. Significant progress has been made in understanding vitiligo pathogenesis over the past 30 years, but only through perseverance, collaboration, and open-minded discussion. Early hypotheses considered roles for innervation, microvascular anomalies, oxidative stress, defects in melanocyte adhesion, autoimmunity, somatic mosaicism, and genetics. Because theories about pathogenesis drive experimental design, focus, and even therapeutic approach, it is important to consider their impact on our current understanding about vitiligo. Animal models allow researchers to perform mechanistic studies, and the development of improved patient sample collection methods provides a platform for translational studies in vitiligo that can also be applied to understand other autoimmune diseases that are more difficult to study in human samples. Here we discuss the history of vitiligo translational research, recent advances, and their implications for new treatment approaches.
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Affiliation(s)
- Erica L Katz
- Department of Medicine, Division of Dermatology, University of Massachusetts Medical School, Worcester, MA, United States
| | - John E Harris
- Department of Medicine, Division of Dermatology, University of Massachusetts Medical School, Worcester, MA, United States
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20
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Rice G, Rompolas P. Advances in resolving the heterogeneity and dynamics of keratinocyte differentiation. Curr Opin Cell Biol 2020; 67:92-98. [PMID: 33091828 PMCID: PMC7736530 DOI: 10.1016/j.ceb.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
The mammalian skin is equipped with a highly dynamic stratified epithelium. The maintenance and regeneration of this epithelium is supported by basally located keratinocytes, which display stem cell properties, including lifelong proliferative potential and the ability to undergo diverse differentiation trajectories. Keratinocytes support not just the surface of the skin, called the epidermis, but also a range of ectodermal structures including hair follicles, sebaceous glands, and sweat glands. Recent studies have shed light on the hitherto underappreciated heterogeneity of keratinocytes by employing state-of-the-art imaging technologies and single-cell genomic approaches. In this mini review, we highlight major recent discoveries that illuminate the dynamics and cellular mechanisms that govern keratinocyte differentiation in the live mammalian skin and discuss the broader implications of these findings for our understanding of epithelial and stem cell biology in general.
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Affiliation(s)
- Gabriella Rice
- Department of Dermatology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Panteleimon Rompolas
- Department of Dermatology, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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21
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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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22
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Shangguan Y, Li C, Lin H, Ou M, Tang D, Dai Y, Yan Q. Application of single-cell RNA sequencing in embryonic development. Genomics 2020; 112:4547-4551. [PMID: 32781204 DOI: 10.1016/j.ygeno.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Embryonic development is a complex process that is regulated by a series of precise cellular behaviours. The limited number of cells in the early stages of embryonic development represents a challenge for studying early gene regulation and maintaining cell sternness. Single-cell sequencing is a new technology for high-throughput sequencing analysis at the single-cell level that not only reflects the heterogeneity between cells but also reveals gene expression characteristics in different cells from limited samples. Currently, the widespread application of single-cell RNA sequencing technology is gradually changing our understanding of disease pathogenesis. This article reviews the application of single-cell RNA sequencing in embryonic development in recent years and provides innovative ideas for research on embryonic development and the treatment of diseases related to embryonic development.
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Affiliation(s)
- Yu Shangguan
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Chunhong Li
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Hua Lin
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China
| | - Minglin Ou
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China
| | - Donge Tang
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Yong Dai
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Qiang Yan
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China.
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23
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Yao Y, Liu Q, Adrianto I, Wu X, Glassbrook J, Khalasawi N, Yin C, Yi Q, Dong Z, Geissmann F, Zhou L, Mi QS. Histone deacetylase 3 controls lung alveolar macrophage development and homeostasis. Nat Commun 2020; 11:3822. [PMID: 32732898 PMCID: PMC7393351 DOI: 10.1038/s41467-020-17630-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/03/2020] [Indexed: 12/21/2022] Open
Abstract
Alveolar macrophages (AMs) derived from embryonic precursors seed the lung before birth and self-maintain locally throughout adulthood, but are regenerated by bone marrow (BM) under stress conditions. However, the regulation of AM development and maintenance remains poorly understood. Here, we show that histone deacetylase 3 (HDAC3) is a key epigenetic factor required for AM embryonic development, postnatal homeostasis, maturation, and regeneration from BM. Loss of HDAC3 in early embryonic development affects AM development starting at E14.5, while loss of HDAC3 after birth affects AM homeostasis and maturation. Single-cell RNA sequencing analyses reveal four distinct AM sub-clusters and a dysregulated cluster-specific pathway in the HDAC3-deficient AMs. Moreover, HDAC3-deficient AMs exhibit severe mitochondrial oxidative dysfunction and deteriorative cell death. Mechanistically, HDAC3 directly binds to Pparg enhancers, and HDAC3 deficiency impairs Pparg expression and its signaling pathway. Our findings identify HDAC3 as a key epigenetic regulator of lung AM development and homeostasis. Alveolar macrophages are known to derive from embryonic precursors although the regulation of this process is poorly understood. Here the authors propose a key role for histone deacetylase 3 as an epigenetic regulator of lung alveolar macrophage development.
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Affiliation(s)
- Yi Yao
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Queping Liu
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA.,Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Indra Adrianto
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA.,Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, 48202, USA.,Center for Bioinformatics, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Xiaojun Wu
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA
| | - James Glassbrook
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA.,Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI, 48202, USA
| | - Namir Khalasawi
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Congcong Yin
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Qijun Yi
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA.,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, 30912, USA
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Li Zhou
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA. .,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA. .,Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI, 48202, USA. .,Department of Internal Medicine, Henry Ford Health System, Detroit, MI, 48202, USA.
| | - Qing-Sheng Mi
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health System, Detroit, MI, 48202, USA. .,Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, 48202, USA. .,Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI, 48202, USA. .,Department of Internal Medicine, Henry Ford Health System, Detroit, MI, 48202, USA.
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24
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Dubois A, Gopee N, Olabi B, Haniffa M. Defining the Skin Cellular Community Using Single-Cell Genomics to Advance Precision Medicine. J Invest Dermatol 2020; 141:255-264. [PMID: 32713511 DOI: 10.1016/j.jid.2020.05.104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 11/24/2022]
Abstract
Single-cell genomics has revolutionized biological science, enabling high-resolution analysis of human tissues. The ability to demonstrate the role and function of distinct cell types comprising human tissues paves the way for a new understanding of cellular pathways, interactions, and future research directions. The skin, easily accessible and possessing a diverse and complex role in defending us both physically and immunologically from the outside world, lends itself ideally to single-cell genomics analysis. Here, we outline the benefits of single-cell RNA sequencing while also highlighting the challenges in achieving a meaningful result from its use. Key milestones relating to the study of skin in this way are introduced, covering both healthy and diseased states, and we discuss the potential promise of single-cell RNA sequencing to result in tangible medical advances, with a particular focus on precision medicine.
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Affiliation(s)
- Anna Dubois
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Nusayhah Gopee
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Bayanne Olabi
- Department of Dermatology, Lauriston Building, Lauriston Place, Edinburgh, United Kingdom
| | - Muzlifah Haniffa
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Lavker RM, Kaplan N, Wang J, Peng H. Corneal epithelial biology: Lessons stemming from old to new. Exp Eye Res 2020; 198:108094. [PMID: 32697979 DOI: 10.1016/j.exer.2020.108094] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
The anterior surface of the eye functions as a barrier to the external environment and protects the delicate underlying tissues from injury. Central to this protection are the corneal, limbal and conjunctival epithelia. The corneal epithelium is a self-renewing stratified squamous epithelium that protects the underlying delicate structures of the eye, supports a tear film and maintains transparency so that light can be transmitted to the interior of the eye (Basu et al., 2014; Cotsarelis et al., 1989; Funderburgh et al., 2016; Lehrer et al., 1998; Pajoohesh-Ganji and Stepp, 2005; Parfitt et al., 2015; Peng et al., 2012b; Stepp and Zieske, 2005). In this review, dedicated to James Funderburgh and his contributions to visual science, in particular the limbal niche, corneal stroma and corneal stromal stem cells, we will focus on recent data on the identification of novel regulators in corneal epithelial cell biology, their roles in stem cell homeostasis, wound healing, limbal/corneal boundary maintenance and the utility of single cell RNA sequencing (scRNA-seq) in vision biology studies.
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Affiliation(s)
- Robert M Lavker
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Nihal Kaplan
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Junyi Wang
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Ophthalmology, The First Center of the PLA General Hospital, Haidian District, Beijing, China
| | - Han Peng
- Departments of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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An Evaluation of the Information Technology of Gene Expression Profiles Processing Stability for Different Levels of Noise Components. DATA 2018. [DOI: 10.3390/data3040048] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This paper presents the results of research concerning the evaluation of stability of information technology of gene expression profiles processing with the use of gene expression profiles, which contain different levels of noise components. The information technology is presented as a structural block-chart, which contains all stages of the studied data processing. The hybrid model of objective clustering based on the SOTA algorithm and the technology of gene regulatory networks reconstruction have been investigated to evaluate the stability to the level of the noise components. The results of the simulation have shown that the hybrid model of the objective clustering has high level of stability to noise components and vice versa, the technology of gene regulatory networks reconstruction is rather sensitive to the level of noise component. The obtained results indicate the importance of gene expression profiles preprocessing at the early stage of the gene regulatory network reconstruction in order to remove background noise and non-informative genes in terms of the used criteria.
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27
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Johnson JL. The Value and Process of Authoring a "Research Techniques Made Simple" Article. J Invest Dermatol 2018; 138:2091-2092. [PMID: 30244717 DOI: 10.1016/j.jid.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Jodi L Johnson
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA; Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.
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