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Tang Y, Dou S, Wei C, Sun Z, Sun D, Zhou Q, Xie L. Single-Nuclei Characterization of Lacrimal Gland in Scopolamine-Induced Dry Eye Disease. Invest Ophthalmol Vis Sci 2024; 65:46. [PMID: 38687491 PMCID: PMC11067549 DOI: 10.1167/iovs.65.4.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/26/2024] [Indexed: 05/02/2024] Open
Abstract
Purpose The lacrimal gland (LG) is the main organ responsible for tear secretion and an important pathogenic site for dry eye disease (DED). This study aimed to comprehensively characterize LG cellular heterogeneity under normal and DED conditions using single-nucleus RNA sequencing (snRNA-seq). Methods Single LG nuclei isolated from mice with or without DED induced by scopolamine (SCOP)/desiccating stress (DS) were subjected to snRNA-seq using the 10x Genomics platform. These cells were clustered and annotated using the t-distributed stochastic neighbor embedding (t-SNE) method and unbiased computational informatic analysis. Cluster identification and functional analysis were performed based on marker gene expression and bioinformatic data mining. Results The snRNA-seq analysis of 30,351 nuclei identified eight major cell types, with acinar cells (∼72.6%) being the most abundant cell type in the LG. Subclustering analysis revealed that the LG mainly contained two acinar cell subtypes, two ductal cell subclusters, three myoepithelial cell (MECs) subtypes, and four immunocyte subclusters. In the SCOP-induced DED model, three major LG parenchymal cell types were significantly altered, characterized by a reduced proportion of acinar cells with a lowered secretion potential and an augmented proportion of ductal cells and MECs. LG immunocytes in DED scenarios showed an intensified inflammatory response and dysregulated intercellular communication with three major LG parenchymal cells. Conclusions Overall, this study offers a systemic single-nucleus transcriptomic profile of LGs in both normal and DED conditions and an atlas of the complicated interactions of immunocytes with major LG parenchymal cells. The findings also facilitate understanding the pathogenesis of DED.
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Affiliation(s)
- Yang Tang
- Shandong First Medical University, Jinan, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute of Shandong First Medical University, Qingdao, China
| | - Shengqian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute of Shandong First Medical University, Qingdao, China
| | - Chao Wei
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute of Shandong First Medical University, Qingdao, China
| | - Ziwen Sun
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Di Sun
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute of Shandong First Medical University, Qingdao, China
| | - Qingjun Zhou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute of Shandong First Medical University, Qingdao, China
| | - Lixin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute of Shandong First Medical University, Qingdao, China
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Yoshikawa T, Oguchi A, Toriu N, Sato Y, Kobayashi T, Ogawa O, Haga H, Sakurai S, Yamamoto T, Murakawa Y, Yanagita M. Tertiary Lymphoid Tissues Are Microenvironments with Intensive Interactions between Immune Cells and Proinflammatory Parenchymal Cells in Aged Kidneys. J Am Soc Nephrol 2023; 34:1687-1708. [PMID: 37548710 PMCID: PMC10561819 DOI: 10.1681/asn.0000000000000202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023] Open
Abstract
SIGNIFICANCE STATEMENT Ectopic lymphoid structures called tertiary lymphoid tissues (TLTs) develop in several kidney diseases and are associated with poor renal prognosis. However, the mechanisms underlying TLT expansion and their effect on renal regeneration remain unclear. The authors report that single-nucleus RNA sequencing and validation experiments demonstrate that TLTs potentially amplify inflammation in aged injured kidneys. Lymphocytes within TLTs promote proinflammatory phenotypes of the surrounding proximal tubules and fibroblasts within the TLTs via proinflammatory cytokine production. These proinflammatory parenchymal cells then interact with immune cells by chemokine or cytokine production. Such cell-cell interactions potentially increase inflammation, expand TLTs, and exacerbate kidney injury. These findings help illuminate renal TLT pathology and suggest potential therapeutic targets. BACKGROUND Ectopic lymphoid structures called tertiary lymphoid tissues (TLTs) develop in several kidney diseases and are associated with poor renal prognosis. However, the mechanisms that expand TLTs and underlie exacerbation of kidney injury remain unclear. METHODS We performed single-nucleus RNA sequencing (snRNA-seq) on aged mouse kidneys with TLTs after ischemia-reperfusion injury. The results were validated using immunostaining, in situ hybridization of murine and human kidneys, and in vitro experiments. RESULTS Using snRNA-seq, we identified proinflammatory and profibrotic Vcam1+ injured proximal tubules (PTs) with NF κ B and IFN-inducible transcription factor activation. VCAM1 + PTs were preferentially localized around TLTs and drove inflammation and fibrosis via the production of multiple chemokines or cytokines. Lymphocytes within TLTs expressed Tnf and Ifng at high levels, which synergistically upregulated VCAM1 and chemokine expression in cultured PT cells. In addition, snRNA-seq also identified proinflammatory and profibrotic fibroblasts, which resided within and outside TLTs, respectively. Proinflammatory fibroblasts exhibited STAT1 activation and various chemokine or cytokine production, including CXCL9/CXCL10 and B cell-activating factor, contributing to lymphocyte recruitment and survival. IFN γ upregulated the expression of these molecules in cultured fibroblasts in a STAT1-dependent manner, indicating potential bidirectional interactions between IFN γ -producing CXCR3 + T cells and proinflammatory fibroblasts within TLTs. The cellular and molecular components described in this study were confirmed in human kidneys with TLTs. CONCLUSIONS These findings suggest that TLTs potentially amplify inflammation by providing a microenvironment that allows intense interactions between renal parenchymal and immune cells. These interactions may serve as novel therapeutic targets in kidney diseases involving TLT formation.
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Affiliation(s)
- Takahisa Yoshikawa
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akiko Oguchi
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Naoya Toriu
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yuki Sato
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Kobayashi
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Ogawa
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoko Sakurai
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- IFOM-ETS, Milan, Italy
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
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3
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Quatredeniers M, Serafin AS, Benmerah A, Rausell A, Saunier S, Viau A. Meta-analysis of single-cell and single-nucleus transcriptomics reveals kidney cell type consensus signatures. Sci Data 2023; 10:361. [PMID: 37280226 DOI: 10.1038/s41597-023-02209-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 05/05/2023] [Indexed: 06/08/2023] Open
Abstract
While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching cell type. The present meta-analysis of 39 previously published datasets, from 7 independent studies, involving healthy human adult kidney samples, offers a set of 24 distinct consensus kidney cell type signatures. The use of these signatures may help to assure the reliability of cell type identification in future studies involving single-cell and single-nucleus transcriptomics while improving the reproducibility in cell type allocation.
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Affiliation(s)
- Marceau Quatredeniers
- Université de Paris Cité, Imagine Institute, Laboratory of Hereditary Kidney Diseases, Paris, INSERM UMR 1163, F-75015, France.
| | - Alice S Serafin
- Université de Paris Cité, Imagine Institute, Laboratory of Hereditary Kidney Diseases, Paris, INSERM UMR 1163, F-75015, France
| | - Alexandre Benmerah
- Université de Paris Cité, Imagine Institute, Laboratory of Hereditary Kidney Diseases, Paris, INSERM UMR 1163, F-75015, France
| | - Antonio Rausell
- Université de Paris Cité, Imagine Institute, Laboratory of Clinical Bioinformatics, Paris, INSERM UMR 1163, F-75015, France
| | - Sophie Saunier
- Université de Paris Cité, Imagine Institute, Laboratory of Hereditary Kidney Diseases, Paris, INSERM UMR 1163, F-75015, France
| | - Amandine Viau
- Université de Paris Cité, Imagine Institute, Laboratory of Hereditary Kidney Diseases, Paris, INSERM UMR 1163, F-75015, France
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4
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Shan D, Wang YY, Chang Y, Cui H, Tao M, Sheng Y, Kang H, Jia P, Song J. Dynamic cellular changes in acute kidney injury caused by different ischemia time. iScience 2023; 26:106646. [PMID: 37168554 PMCID: PMC10165188 DOI: 10.1016/j.isci.2023.106646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
Ischemia reperfusion injury (IRI), often related to surgical procedures, is one of the important causes of acute kidney injury (AKI). To decipher the dynamic process of AKI caused by IRI (with prolonged ischemia phase), we performed single-cell RNA sequencing (scRNA-seq) of clinically relevant IRI murine model with different ischemic intervals. We discovered that Slc5a2hi proximal tubular cells were susceptible to AKI and highly expressed neutral amino acid transporter gene Slc6a19, which was dramatically decreased over the time course. With the usage of mass spectrometry-based metabolomic analysis, we detected that the level of neutral amino acid isoleucine dropped off in AKI mouse plasma metabolites. And the reduction of plasma isoleucine was also verified in patients with cardiac surgery-associated acute kidney injury (CSA-AKI). The findings advanced the understanding of dynamic process of AKI and introduced reduction of isoleucine as a potential biomarker for CSA-AKI.
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Affiliation(s)
- Dan Shan
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yin-Ying Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yuan Chang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Hao Cui
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Menghao Tao
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yixuan Sheng
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Department of Cardiovascular Surgery, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Hongen Kang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Corresponding author
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5
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Kim N, Kang H, Jo A, Yoo SA, Lee HO. Perspectives on single-nucleus RNA sequencing in different cell types and tissues. J Pathol Transl Med 2023; 57:52-59. [PMID: 36623812 PMCID: PMC9846005 DOI: 10.4132/jptm.2022.12.19] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Single-cell RNA sequencing has become a powerful and essential tool for delineating cellular diversity in normal tissues and alterations in disease states. For certain cell types and conditions, there are difficulties in isolating intact cells for transcriptome profiling due to their fragility, large size, tight interconnections, and other factors. Single-nucleus RNA sequencing (snRNA-seq) is an alternative or complementary approach for cells that are difficult to isolate. In this review, we will provide an overview of the experimental and analysis steps of snRNA-seq to understand the methods and characteristics of general and tissue-specific snRNA-seq data. Knowing the advantages and limitations of snRNA-seq will increase its use and improve the biological interpretation of the data generated using this technique.
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Affiliation(s)
- Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Huiram Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Seung-Ah Yoo
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea,Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul,
Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul,
Korea
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6
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Gaedcke S, Sinning J, Dittrich-Breiholz O, Haller H, Soerensen-Zender I, Liao CM, Nordlohne A, Sen P, von Vietinghoff S, DeLuca DS, Schmitt R. Single-Cell versus Single-Nucleus: Transcriptome differences in murine kidney after ischemia-reperfusion injury. Am J Physiol Renal Physiol 2022; 323:F171-F181. [PMID: 35635323 DOI: 10.1152/ajprenal.00453.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The kidney is a complex organ, which consists of multiple components with highly diverse cell types. A detailed understanding of these cell types in health and disease is crucial for future development of preventive and curative treatment strategies. In recent years, single cell RNA sequencing (scRNAseq) and single nucleus RNA sequencing (snRNAseq) technology has opened up completely new possibilities in investigating the variety of renal cell populations in physiological and pathological states. Here, we systematically assess differences between scRNAseq and snRNAseq approaches in transcriptome analysis of murine kidneys after ischemia reperfusion injury. We included tissues from control kidneys and from kidneys harvested one week after mild (17 minutes clamping time) and severe (27 minutes clamping time) transient unilateral ischemia. Our findings reveal important methodological differences in the discovery of inflammatory cells, tubular cells, and other specialized cell types. While the scRNAseq approach is advantageous for investigating immune cells, the snRNAseq approach allows superior insight into healthy and damaged tubular cells. Apart from differences in the quantitative discovery rate, we found important qualitative discrepancies in the captured transcriptomes with crucial consequences for the interpretation of cell states and molecular functions. Together, we provide an overview of method-dependent differences between scRNAseq and snRNAseq results from identical post-ischemic kidney tissues. Our results highlight the importance of choosing the right approach for specific research questions.
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Affiliation(s)
- Svenja Gaedcke
- Department of Respiratory Medicine, German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Julius Sinning
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
| | | | - Hermann Haller
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
| | | | - Chieh Ming Liao
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
| | | | - Payel Sen
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
| | - Sibylle von Vietinghoff
- Department of Nephrology and Hypertension, Medical School Hannover, Germany.,Nephrology Section, Medical Clinic 1, University Hospital Bonn, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - David S DeLuca
- Department of Respiratory Medicine, German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Roland Schmitt
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
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7
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Zhou XJ, Zhong XH, Duan LX. Integration of Artificial Intelligence And Multi-omics in Kidney Diseases. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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8
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Bell RMB, Conway BR. Macrophages in the kidney in health, injury and repair. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 367:101-147. [PMID: 35461656 DOI: 10.1016/bs.ircmb.2022.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Macrophages are a key component of the renal mononuclear phagocyte system, playing a major role in defense against infection, renal injury and repair. Yolk sac macrophage precursors seed the early embryonic kidney and are important for renal development. Later, renal macrophages are derived from hematopoietic stem cells and in adult life, there is a significant contribution from circulating monocytes, which is enhanced in response to infection or injury. Macrophages are highly plastic and can alter their phenotype in response to cues from parenchymal renal cells. Danger-associated molecules released from injured kidney cells may activate macrophages toward a pro-inflammatory phenotype, mediating further recruitment of inflammatory cells, exacerbating renal injury and activating renal fibroblasts to promote scarring. In acute kidney injury, once the injury stimulus has abated, macrophages may adopt a more reparative phenotype, dampening the immune response and promoting repair of renal tissue. However, in chronic kidney disease ongoing activation of pro-inflammatory monocytes and persistence of reparative macrophages leads to glomerulosclerosis and tubulointerstitial fibrosis, the hallmarks of end-stage kidney disease. Several strategies to inhibit the recruitment, activation and secretory products of pro-inflammatory macrophages have proven beneficial in pre-clinical models and are now undergoing clinical trials in patients with kidney disease. In addition, macrophages may be utilized in cell therapy as a "Trojan Horse" to deliver targeted therapies to the kidney. Single-cell RNA sequencing has identified a previously unappreciated spectrum of macrophage phenotypes, which may be selectively present in injury or repair, and ongoing functional analyses of these subsets may identify more specific targets for therapeutic intervention.
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Affiliation(s)
- Rachel M B Bell
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Bryan R Conway
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom.
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9
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Tubular Cell Dropout in Preimplantation Deceased Donor Biopsies as a Predictor of Delayed Graft Function. Transplant Direct 2021; 7:e716. [PMID: 34476295 PMCID: PMC8384397 DOI: 10.1097/txd.0000000000001168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/16/2021] [Accepted: 04/01/2021] [Indexed: 12/17/2022] Open
Abstract
Supplemental Digital Content is available in the text. Background. Delayed graft function (DGF) affects over 25% of deceased donor kidney transplants (DDKTs) and is associated with increased cost, worsened graft outcomes, and mortality. While approaches to preventing DGF have focused on minimizing cold ischemia, donor factors such as acute tubular injury can influence risk. There are currently no pharmacologic therapies to modify DGF risk or promote repair, in part due to our incomplete understanding of the biology of preimplantation tubular injury. Methods. We collected intraoperative, preimplantation kidney biopsies from 11 high-risk deceased donors and 10 living donors and followed transplant recipients for graft function. We performed quantitative high-dimensional histopathologic analysis using imaging mass cytometry to determine the cellular signatures that distinguished deceased and living donor biopsies as well as deceased donor biopsies which either did or did not progress to DGF. Results. We noted decreased tubular cells (P < 0.0001) and increased macrophage infiltration (P = 0.0037) in high-risk DDKT compared with living donor biopsies. For those high-risk DDKTs that developed postimplant DGF (n = 6), quantitative imaging mass cytometry analysis showed a trend toward reduced tubular cells (P = 0.02) and increased stromal cells (P = 0.04) versus those that did not (n = 5). Notably, these differences were not identified by conventional histopathologic evaluation. Conclusions. The current study identifies donor tubular cell loss as a precursor of DGF pathogenesis and highlights an area for further investigation and potential therapeutic intervention.
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10
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Dissecting the human kidney allograft transcriptome: single-cell RNA sequencing. Curr Opin Organ Transplant 2021; 26:43-51. [PMID: 33315769 DOI: 10.1097/mot.0000000000000840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Single-cell RNA sequencing (scRNA-seq) has provided opportunities to interrogate kidney allografts at a hitherto unavailable molecular level of resolution. Understanding of this technology is essential to better appreciate the relevant biomedical literature. RECENT FINDINGS Sequencing is a technique to determine the order of nucleotides in a segment of RNA or DNA. RNA-seq of kidney allograft tissues has revealed novel mechanistic insights but does not provide information on individual cell types and cell states. scRNA-seq enables to study the transcriptome of individual cells and assess the transcriptional differences and similarities within a population of cells. Initial studies on rejecting kidney allograft tissues in humans have identified the transcriptional profile of the active players of the innate and adaptive immune system. Application of scRNA-seq in a preclinical model of kidney transplantation has revealed that allograft-infiltrating myeloid cells follow a trajectory of differentiation from monocytes to proinflammatory macrophages and exhibit distinct interactions with kidney allograft parenchymal cells; myeloid cell expression of Axl played a major role in promoting intragraft myeloid cell and T-cell differentiation. SUMMARY The current review discusses the technical aspects of scRNA-seq and summarizes the application of this technology to dissect the human kidney allograft transcriptome.
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11
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Zhao Y, Panzer U, Bonn S, Krebs CF. Single-cell biology to decode the immune cellular composition of kidney inflammation. Cell Tissue Res 2021; 385:435-443. [PMID: 34125286 PMCID: PMC8200789 DOI: 10.1007/s00441-021-03483-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/03/2021] [Indexed: 12/26/2022]
Abstract
Single-cell biology is transforming the ability of researchers to understand cellular signaling and identity across medical and biological disciplines. Especially for immune-mediated diseases, a single-cell look at immune cell subtypes, signaling, and activity might yield fundamental insights into the disease etiology, mechanisms, and potential therapeutic interventions. In this review, we highlight recent advances in the field of single-cell RNA profiling and their application to understand renal function in health and disease. With a focus on the immune system, in particular on T cells, we propose some key directions of understanding renal inflammation using single-cell approaches. We detail the benefits and shortcomings of the various technological approaches outlined and give advice on potential pitfalls and challenges in experimental setup and computational analysis. Finally, we conclude with a brief outlook into a promising future for single-cell technologies to elucidate kidney function.
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Affiliation(s)
- Yu Zhao
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Ulf Panzer
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian F Krebs
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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12
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Shaw R, Tian X, Xu J. Single-Cell Transcriptome Analysis in Plants: Advances and Challenges. MOLECULAR PLANT 2021; 14:115-126. [PMID: 33152518 DOI: 10.1016/j.molp.2020.10.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/08/2020] [Accepted: 10/30/2020] [Indexed: 05/22/2023]
Abstract
The rapid and enthusiastic adoption of single-cell RNA sequencing (scRNA-seq) has demonstrated that this technology is far more than just another way to perform transcriptome analysis. It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell. With this disruptive technology, it is now possible to mine heterogeneity between tissue types and within cells like never before. This enables more rapid identification of rare and novel cell types, simultaneous characterization of multiple different cell types and states, more accurate and integrated understanding of their roles in life processes, and more. However, we are only at the beginning of unlocking the full potential of scRNA-seq applications. This is particularly true for plant sciences, where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome. In this review, we compare and evaluate recent pioneering studies using the Arabidopsis root model, which has established new paradigms for scRNA-seq studies in plants. We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale. In addition, we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding.
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Affiliation(s)
- Rahul Shaw
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xin Tian
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore.
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13
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Kuppe C, Perales-Patón J, Saez-Rodriguez J, Kramann R. Experimental and computational technologies to dissect the kidney at the single-cell level. Nephrol Dial Transplant 2020; 37:628-637. [PMID: 33332571 DOI: 10.1093/ndt/gfaa233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
The field of single-cell technologies, in particular single-cell genomics with transcriptomics and epigenomics, and most recently single-cell proteomics, is rapidly growing and holds promise to advance our understanding of organ homoeostasis and disease, and facilitate the identification of novel therapeutic targets and biomarkers. This review offers an introduction to these technologies. In addition, as the size and complexity of the data require sophisticated computational methods for analysis and interpretation, we will also provide an overview of these methods and summarize the single-cell literature specifically pertaining to the kidney.
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Affiliation(s)
- Christoph Kuppe
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Javier Perales-Patón
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Rafael Kramann
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
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14
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Conway BR, O'Sullivan ED, Cairns C, O'Sullivan J, Simpson DJ, Salzano A, Connor K, Ding P, Humphries D, Stewart K, Teenan O, Pius R, Henderson NC, Bénézech C, Ramachandran P, Ferenbach D, Hughes J, Chandra T, Denby L. Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease. J Am Soc Nephrol 2020; 31:2833-2854. [PMID: 32978267 DOI: 10.1681/asn.2020060806] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Little is known about the roles of myeloid cell subsets in kidney injury and in the limited ability of the organ to repair itself. Characterizing these cells based only on surface markers using flow cytometry might not provide a full phenotypic picture. Defining these cells at the single-cell, transcriptomic level could reveal myeloid heterogeneity in the progression and regression of kidney disease. METHODS Integrated droplet- and plate-based single-cell RNA sequencing were used in the murine, reversible, unilateral ureteric obstruction model to dissect the transcriptomic landscape at the single-cell level during renal injury and the resolution of fibrosis. Paired blood exchange tracked the fate of monocytes recruited to the injured kidney. RESULTS A single-cell atlas of the kidney generated using transcriptomics revealed marked changes in the proportion and gene expression of renal cell types during injury and repair. Conventional flow cytometry markers would not have identified the 12 myeloid cell subsets. Monocytes recruited to the kidney early after injury rapidly adopt a proinflammatory, profibrotic phenotype that expresses Arg1, before transitioning to become Ccr2 + macrophages that accumulate in late injury. Conversely, a novel Mmp12 + macrophage subset acts during repair. CONCLUSIONS Complementary technologies identified novel myeloid subtypes, based on transcriptomics in single cells, that represent therapeutic targets to inhibit progression or promote regression of kidney disease.
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Affiliation(s)
- Bryan R Conway
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Eoin D O'Sullivan
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Carolynn Cairns
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - James O'Sullivan
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel J Simpson
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Angela Salzano
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Katie Connor
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.,Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peng Ding
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Duncan Humphries
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kevin Stewart
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver Teenan
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Riinu Pius
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Cécile Bénézech
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Prakash Ramachandran
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David Ferenbach
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeremy Hughes
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Tamir Chandra
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Denby
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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15
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Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clément O, Simmons RK, Lister R, Forrest ARR. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biol 2020; 21:130. [PMID: 32487174 PMCID: PMC7265231 DOI: 10.1186/s13059-020-02048-6] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods. What has been lacking is a systematic comparison of their relative biases and benefits. RESULTS Here, we compare gene expression and cellular composition of single-cell suspensions prepared from adult mouse kidney using two tissue dissociation protocols. For each sample, we also compare fresh cells to cryopreserved and methanol-fixed cells. Lastly, we compare this single-cell data to that generated using three single-nucleus RNA sequencing workflows. Our data confirms prior reports that digestion on ice avoids the stress response observed with 37 °C dissociation. It also reveals cell types more abundant either in the cold or warm dissociations that may represent populations that require gentler or harsher conditions to be released intact. For cell storage, cryopreservation of dissociated cells results in a major loss of epithelial cell types; in contrast, methanol fixation maintains the cellular composition but suffers from ambient RNA leakage. Finally, cell type composition differences are observed between single-cell and single-nucleus RNA sequencing libraries. In particular, we note an underrepresentation of T, B, and NK lymphocytes in the single-nucleus libraries. CONCLUSIONS Systematic comparison of recovered cell types and their transcriptional profiles across the workflows has highlighted protocol-specific biases and thus enables researchers starting single-cell experiments to make an informed choice.
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Affiliation(s)
- Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
| | - Belinda B. Guo
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
| | - Matthew Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
| | - Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
| | - Leanne de Kock
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
| | - Timo Lassmann
- Telethon Kids Institute, Perth’s Children Hospital, the University of Western Australia, 15 Hospital Avenue, Nedlands, Perth, Western Australia 6009 Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, 35 Stirling Hwy, Crawley, Perth, Western Australia 6009 Australia
| | - Olivier Clément
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
| | - Rebecca K. Simmons
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, 35 Stirling Hwy, Crawley, Perth, Western Australia 6009 Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, 35 Stirling Hwy, Crawley, Perth, Western Australia 6009 Australia
| | - Alistair R. R. Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6009 Australia
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Pyle MP, Hoa M. Applications of single-cell sequencing for the field of otolaryngology: A contemporary review. Laryngoscope Investig Otolaryngol 2020; 5:404-431. [PMID: 32596483 PMCID: PMC7314468 DOI: 10.1002/lio2.388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Single-cell RNA sequencing (scRNA-Seq) is a new technique used to interrogate the transcriptome of individual cells within native tissues that have already resulted in key discoveries in auditory basic science research. Rapid advances in scRNA-Seq make it likely that it will soon be translated into clinical medicine. The goal of this review is to inspire the use of scRNA-Seq in otolaryngology by giving examples of how it can be applied to patient samples and how this information can be used clinically. METHODS Studies were selected based on the scientific quality and relevance to scRNA-Seq. In addition to mouse auditory system (inner ear including hair cells and supporting cells, spiral ganglion neurons, and inner ear organoids), recent studies using human primary cell samples are discussed. We also perform our own analysis on publicly available, published scRNA-Seq data from oral head and neck squamous cell carcinoma (HNSCC) samples to serve as an example of a clinically relevant application of scRNA-Seq. RESULTS Studies focusing on patient tissues show that scRNA-Seq reveals tissue heterogeneity and rare-cell types responsible for disease pathogenesis. The heterogeneity detected by scRNA-Seq can result in both the identification of known or novel disease biomarkers and drug targets. Our analysis of HNSCC data gives an example for how otolaryngologists can use scRNA-Seq for clinical use. CONCLUSIONS Although there are limitations to the translation of scRNA-Seq to the clinic, we show that its use in otolaryngology can give physicians insight into the tissue heterogeneity within their patient's diseased tissue giving them information on disease pathogenesis, novel disease biomarkers or druggable targets, and aid in selecting patient-specific drug cocktails.
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Affiliation(s)
- Madeline P. Pyle
- Division of Intramural Research, Section on Auditory Development and Restoration, National Institute on Deafness and Other Communication Disorders (NIDCD) Otolaryngology Surgeon‐Scientist ProgramNational Institutes of HealthBethesdaMarylandUSA
| | - Michael Hoa
- Division of Intramural Research, Section on Auditory Development and Restoration, National Institute on Deafness and Other Communication Disorders (NIDCD) Otolaryngology Surgeon‐Scientist ProgramNational Institutes of HealthBethesdaMarylandUSA
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Singh N, Avigan ZM, Kliegel JA, Shuch BM, Montgomery RR, Moeckel GW, Cantley LG. Development of a 2-dimensional atlas of the human kidney with imaging mass cytometry. JCI Insight 2019; 4:129477. [PMID: 31217358 DOI: 10.1172/jci.insight.129477] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022] Open
Abstract
An incomplete understanding of the biology of the human kidney, including the relative abundances of and interactions between intrinsic and immune cells, has long constrained the development of therapies for kidney disease. The small amount of tissue obtained by renal biopsy has previously limited the ability to use patient samples for discovery purposes. Imaging mass cytometry (IMC) is an ideal technology for quantitative interrogation of scarce samples, permitting concurrent analysis of more than 40 markers on a single tissue section. Using a validated panel of metal-conjugated antibodies designed to confer unique signatures on the structural and infiltrating cells comprising the human kidney, we performed simultaneous multiplexed imaging with IMC in 23 channels on 16 histopathologically normal human samples. We devised a machine-learning pipeline (Kidney-MAPPS) to perform single-cell segmentation, phenotyping, and quantification, thus creating a spatially preserved quantitative atlas of the normal human kidney. These data define selected baseline renal cell types, respective numbers, organization, and variability. We demonstrate the utility of IMC coupled to Kidney-MAPPS to qualitatively and quantitatively distinguish individual cell types and reveal expected as well as potentially novel abnormalities in diseased versus normal tissue. Our studies define a critical baseline data set for future quantitative analysis of human kidney disease.
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Affiliation(s)
- Nikhil Singh
- Section of Nephrology, Department of Internal Medicine
| | | | | | | | | | - Gilbert W Moeckel
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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18
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine and
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine and
| | | | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine and .,Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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