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Qi W, Bai J, Wang R, Zeng X, Zhang L. SATB1, senescence and senescence-related diseases. J Cell Physiol 2024. [PMID: 38801120 DOI: 10.1002/jcp.31327] [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: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Aging leads to an accumulation of cellular mutations and damage, increasing the risk of senescence, apoptosis, and malignant transformation. Cellular senescence, which is pivotal in aging, acts as both a guard against cellular transformation and as a check against cancer progression. It is marked by stable cell cycle arrest, widespread macromolecular changes, a pro-inflammatory profile, and altered gene expression. However, it remains to be determined whether these differing subsets of senescent cells result from unique intrinsic programs or are influenced by their environmental contexts. Multiple transcription regulators and chromatin modifiers contribute to these alterations. Special AT-rich sequence-binding protein 1 (SATB1) stands out as a crucial regulator in this process, orchestrating gene expression by structuring chromatin into loop domains and anchoring DNA elements. This review provides an overview of cellular senescence and delves into the role of SATB1 in senescence-related diseases. It highlights SATB1's potential in developing antiaging and anticancer strategies, potentially contributing to improved quality of life and addressing aging-related diseases.
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Affiliation(s)
- Wenjing Qi
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun, Jilin, China
| | - Jinping Bai
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
| | - Ruoxi Wang
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, China
| | - Xianlu Zeng
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun, Jilin, China
| | - Lihui Zhang
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
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Olecka M, van Bömmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun 2024; 15:3074. [PMID: 38594255 PMCID: PMC11004021 DOI: 10.1038/s41467-024-47316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
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Affiliation(s)
- Maja Olecka
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Alena van Bömmel
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Madlen Haase
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Silke Foerste
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Konstantin Riege
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Stefano Flor
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Marco Groth
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Steve Hoffmann
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
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Wang P, Zhang Z, Lin R, Lin J, Liu J, Zhou X, Jiang L, Wang Y, Deng X, Lai H, Xiao H. Machine learning links different gene patterns of viral infection to immunosuppression and immune-related biomarkers in severe burns. Front Immunol 2022; 13:1054407. [PMID: 36518755 PMCID: PMC9742460 DOI: 10.3389/fimmu.2022.1054407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Viral infection, typically disregarded, has a significant role in burns. However, there is still a lack of biomarkers and immunotherapy targets related to viral infections in burns. Methods Virus-related genes (VRGs) that were extracted from Gene Oncology (GO) database were included as hallmarks. Through unsupervised consensus clustering, we divided patients into two VRGs molecular patterns (VRGMPs). Weighted gene co-expression network analysis (WGCNA) was performed to study the relationship between burns and VRGs. Random forest (RF), least absolute shrinkage and selection operator (LASSO) regression, and logistic regression were used to select key genes, which were utilized to construct prognostic signatures by multivariate logistic regression. The risk score of the nomogram defined high- and low-risk groups. We compared immune cells, immune checkpoint-related genes, and prognosis between the two groups. Finally, we used network analysis and molecular docking to predict drugs targeting CD69 and SATB1. Expression of CD69 and SATB1 was validated by qPCR and microarray with the blood sample from the burn patient. Results We established two VRGMPs, which differed in monocytes, neutrophils, dendritic cells, and T cells. In WGCNA, genes were divided into 14 modules, and the black module was correlated with VRGMPs. A total of 65 genes were selected by WGCNA, STRING, and differential expression analysis. The results of GO enrichment analysis were enriched in Th1 and Th2 cell differentiation, B cell receptor signaling pathway, alpha-beta T cell activation, and alpha-beta T cell differentiation. Then the 2-gene signature was constructed by RF, LASSO, and LOGISTIC regression. The signature was an independent prognostic factor and performed well in ROC, calibration, and decision curves. Further, the expression of immune cells and checkpoint genes differed between high- and low-risk groups. CD69 and SATB1 were differentially expressed in burns. Discussion This is the first VRG-based signature (including 2 key genes validated by qPCR) for predicting survival, and it could provide vital guidance to achieve optimized immunotherapy for immunosuppression in burns.
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Affiliation(s)
- Peng Wang
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Zexin Zhang
- Department of Burns and Plastic and Wound Repair Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Rongjie Lin
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Jiali Lin
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Jiaming Liu
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Xiaoqian Zhou
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Liyuan Jiang
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Yu Wang
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Xudong Deng
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Haijing Lai
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China
| | - Hou’an Xiao
- Department of Burns and Plastic and Cosmetic Surgery, Xi’an Ninth Hospital, Xi’an, China,*Correspondence: Hou’an Xiao,
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Qin R, Mahal LK, Bojar D. Deep learning explains the biology of branched glycans from single-cell sequencing data. iScience 2022; 25:105163. [PMID: 36217547 PMCID: PMC9547197 DOI: 10.1016/j.isci.2022.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/06/2022] [Accepted: 09/16/2022] [Indexed: 11/03/2022] Open
Abstract
Glycosylation is ubiquitous and often dysregulated in disease. However, the regulation and functional significance of various types of glycosylation at cellular levels is hard to unravel experimentally. Multi-omics, single-cell measurements such as SUGAR-seq, which quantifies transcriptomes and cell surface glycans, facilitate addressing this issue. Using SUGAR-seq data, we pioneered a deep learning model to predict the glycan phenotypes of cells (mouse T lymphocytes) from transcripts, with the example of predicting β1,6GlcNAc-branching across T cell subtypes (test set F1 score: 0.9351). Model interpretation via SHAP (SHapley Additive exPlanations) identified highly predictive genes, in part known to impact (i) branched glycan levels and (ii) the biology of branched glycans. These genes included physiologically relevant low-abundance genes that were not captured by conventional differential expression analysis. Our work shows that interpretable deep learning models are promising for uncovering novel functions and regulatory mechanisms of glycans from integrated transcriptomic and glycomic datasets.
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Affiliation(s)
- Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
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Nüssing S, Miosge LA, Lee K, Olshansky M, Barugahare A, Roots CM, Sontani Y, Day EB, Koutsakos M, Kedzierska K, Goodnow CC, Russ BE, Daley SR, Turner SJ. SATB1 ensures appropriate transcriptional programs within naïve CD8
+
T cells. Immunol Cell Biol 2022; 100:636-652. [PMID: 35713361 PMCID: PMC9542893 DOI: 10.1111/imcb.12566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/07/2022] [Accepted: 06/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Simone Nüssing
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Lisa A Miosge
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
| | - Kah Lee
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
| | | | - Carla M Roots
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
| | - Yovina Sontani
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
| | - E Bridie Day
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Christopher C Goodnow
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
- Garvan Institute of Medical Research & Cellular Genomics Futures Institute University of New South Wales Darlinghurst NSW Australia
| | - Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
| | - Stephen R Daley
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health Queensland University of Technology Brisbane QLD Australia
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
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He Z, Li Y, Feng G, Yuan X, Lu Z, Dai M, Hu Y, Zhang Y, Zhou Q, Li W. Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104682. [PMID: 35240008 PMCID: PMC9069193 DOI: 10.1002/advs.202104682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/27/2022] [Indexed: 05/08/2023]
Abstract
Direct cell reprogramming, also called transdifferentiation, is valuable for cell fate studies and regenerative medicine. Current approaches to transdifferentiation are usually achieved by directly targeting the nuclear functions, such as manipulating the lineage-specific transcriptional factors, microRNAs, and epigenetic modifications. Here, a robust method to convert fibroblasts to neurons through targeting the cytoskeleton followed by exposure to lineage-specification surroundings is reported. Treatment of human foreskin fibroblasts with a single molecule inhibitor of the actomyosin contraction, can disrupt the cytoskeleton, promote cell softening and nuclear export of YAP/TAZ, and induce a neuron-like state. These neuron-like cells can be further converted into mature neurons, while single-cell RNA-seq shows the homogeneity of these cells during the induction process. Finally, transcriptomic analysis shows that cytoskeletal disruption collapses the original lineage expression profile and evokes an intermediate state. These findings shed a light on the underestimated role of the cytoskeleton in maintaining cell identity and provide a paradigm for lineage conversion through the regulation of mechanical properties.
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Affiliation(s)
- Zheng‐Quan He
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Yu‐Huan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- The First Hospital of Jilin UniversityChangchunJilin130021China
| | - Gui‐Hai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Xue‐Wei Yuan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Zong‐Bao Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
| | - Min Dai
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Yan‐Ping Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
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7
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Li Y, Liu C, Fu Y, Zhai H, Chen Z, Yang B, Zhang D. Elevated Expression of SATB1 Predicts Unfavorable Clinical Outcomes in Colon Adenocarcinoma. Appl Immunohistochem Mol Morphol 2022; 30:375-382. [PMID: 35353722 DOI: 10.1097/pai.0000000000001016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 01/24/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUNDS Special AT-rich sequence-binding protein 1 (SATB1) belongs to the chromatin-remodeling protein which regulates different genes expression. High expression of SATB1 was found to be associated with the development of certain carcinomas. However, the functions of SATB1 in colon adenocarcinoma (CAC) remains unclear yet. Our study aims to investigate the potential role of SATB1 in CAC and whether it is associated with the unfavorable symptoms of CAC patients. METHODS The expression pattern of SATB1 was measured in CAC samples and adjacent noncancerous samples through quantitative real-time polymerase chain reaction and immunohistochemistry staining. We performed univariate and multivariate analyses to evaluate the clinical role of SATB1 in enrolled patients. The Kaplan-Meier analyses and log-rank tests were carried out to assess the clinicopathologic characteristics. The effect of SATB1 in human colon cancer cells was examined through cellular experiments. RESULTS The expression level of SATB1 in CAC tissues was significantly elevated compared with adjacent control tissues. High expression of SATB1 in tumor tissue was found to be associated with lymph node metastasis and advanced TNM stage. Higher SATB1 level in CAC patients indicated a worse 5-year survival time. Moreover, high SATB1 was defined as an independent poor prognostic factor. Cellular experiments showed that inhibition of the SATB1 protein level in human colon cells could suppress the migration and invasion capabilities. CONCLUSIONS Our findings revealed that high expression of SATB1 was significantly correlated with the poor clinical features and prognosis of CAC patients. It indicated that SATB1 might serve as a potential prognostic predictor and novel drug target for CAC treatment.
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Affiliation(s)
- Yujiang Li
- Department of Gastroenterology, Taizhou People's Hospital, Taizhou, Jiangsu, China
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Abd Allah M, Soliman A. Evaluation of prolyl-4-hydroxylase subunit beta and special AT-rich region-binding protein-1 immunoexpression in bladder transitional-cell carcinoma. EGYPTIAN JOURNAL OF PATHOLOGY 2022; 42:28. [DOI: 10.4103/egjp.egjp_7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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McCaffrey TA, Toma I, Yang Z, Katz R, Reiner J, Mazhari R, Shah P, Tackett M, Jones D, Jepson T, Falk Z, Wargodsky R, Shtakalo D, Antonets D, Ertle J, Kim JH, Lai Y, Arslan Z, Aledort E, Alfaraidy M, Laurent GS. RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance. BMC Med Genomics 2021; 14:216. [PMID: 34479557 PMCID: PMC8414682 DOI: 10.1186/s12920-021-01062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019. The current standard for diagnosing coronary artery disease (CAD) is coronary angiography. Surprisingly, despite well-established clinical indications, up to 40% of the one million invasive cardiac catheterizations return a result of ‘no blockage’. The present studies employed RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD.
Methods Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by single-molecule sequencing of RNA (RNAseq) to identify transcripts associated with CAD (TRACs) in a discovery group of 96 patients presenting for elective coronary catheterization. The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs).
Results Surprisingly, 98% of DEGs/TRACs were down-regulated ~ 1.7-fold in patients with mild to severe CAD (> 20% stenosis). The TRACs were independent of comorbid risk factors for CAD, such as sex, hypertension, and smoking. Bioinformatic analysis identified an enrichment in transcripts such as FoxP1, ICOSLG, IKZF4/Eos, SMYD3, TRIM28, and TCF3/E2A that are likely markers of regulatory T cells (Treg), consistent with known reductions in Tregs in CAD. A validation cohort of 80 patients confirmed the overall pattern (92% down-regulation) and supported many of the Treg-related changes. TRACs were enriched for transcripts associated with stress granules, which sequester RNAs, and ciliary and synaptic transcripts, possibly consistent with changes in the immune synapse of developing T cells.
Conclusions These studies identify a novel mRNA signature of a Treg-like defect in CAD patients and provides a blueprint for a diagnostic test for CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01062-2.
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Affiliation(s)
- Timothy A McCaffrey
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA. .,The St. Laurent Institute, Vancouver, WA, USA. .,Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, 20037, USA. .,True Bearing Diagnostics, Washington, DC, 20037, USA.
| | - Ian Toma
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA.,Department of Clinical Research and Leadership, The George Washington University, Washington, DC, 20037, USA.,True Bearing Diagnostics, Washington, DC, 20037, USA
| | - Zhaoquing Yang
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Richard Katz
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Jonathan Reiner
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Ramesh Mazhari
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Palak Shah
- Inova Heart and Vascular Institute, Fairfax, VA, USA
| | | | | | - Tisha Jepson
- SeqLL, Inc., Woburn, MA, USA.,The St. Laurent Institute, Vancouver, WA, USA.,True Bearing Diagnostics, Washington, DC, 20037, USA
| | - Zachary Falk
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Richard Wargodsky
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Dmitry Shtakalo
- A.P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjeva Ave, Novosibirsk, Russia, 630090
| | - Denis Antonets
- A.P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjeva Ave, Novosibirsk, Russia, 630090
| | - Justin Ertle
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Ju H Kim
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Yinglei Lai
- Department of Statistics, Biostatistics Center, The George Washington University, Washington, DC, 20037, USA
| | - Zeynep Arslan
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Emily Aledort
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Maha Alfaraidy
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
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Palacios-Pedrero MÁ, Osterhaus ADME, Becker T, Elbahesh H, Rimmelzwaan GF, Saletti G. Aging and Options to Halt Declining Immunity to Virus Infections. Front Immunol 2021; 12:681449. [PMID: 34054872 PMCID: PMC8149791 DOI: 10.3389/fimmu.2021.681449] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Immunosenescence is a process associated with aging that leads to dysregulation of cells of innate and adaptive immunity, which may become dysfunctional. Consequently, older adults show increased severity of viral and bacterial infections and impaired responses to vaccinations. A better understanding of the process of immunosenescence will aid the development of novel strategies to boost the immune system in older adults. In this review, we focus on major alterations of the immune system triggered by aging, and address the effect of chronic viral infections, effectiveness of vaccination of older adults and strategies to improve immune function in this vulnerable age group.
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Affiliation(s)
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Tanja Becker
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Husni Elbahesh
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Guus F Rimmelzwaan
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Giulietta Saletti
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
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11
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Hu Z, Leet DE, Allesøe RL, Oliveira G, Li S, Luoma AM, Liu J, Forman J, Huang T, Iorgulescu JB, Holden R, Sarkizova S, Gohil SH, Redd RA, Sun J, Elagina L, Giobbie-Hurder A, Zhang W, Peter L, Ciantra Z, Rodig S, Olive O, Shetty K, Pyrdol J, Uduman M, Lee PC, Bachireddy P, Buchbinder EI, Yoon CH, Neuberg D, Pentelute BL, Hacohen N, Livak KJ, Shukla SA, Olsen LR, Barouch DH, Wucherpfennig KW, Fritsch EF, Keskin DB, Wu CJ, Ott PA. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. Nat Med 2021; 27:515-525. [PMID: 33479501 PMCID: PMC8273876 DOI: 10.1038/s41591-020-01206-4] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2022]
Abstract
Personal neoantigen vaccines have been envisioned as an effective approach to induce, amplify and diversify antitumor T cell responses. To define the long-term effects of such a vaccine, we evaluated the clinical outcome and circulating immune responses of eight patients with surgically resected stage IIIB/C or IVM1a/b melanoma, at a median of almost 4 years after treatment with NeoVax, a long-peptide vaccine targeting up to 20 personal neoantigens per patient ( NCT01970358 ). All patients were alive and six were without evidence of active disease. We observed long-term persistence of neoantigen-specific T cell responses following vaccination, with ex vivo detection of neoantigen-specific T cells exhibiting a memory phenotype. We also found diversification of neoantigen-specific T cell clones over time, with emergence of multiple T cell receptor clonotypes exhibiting distinct functional avidities. Furthermore, we detected evidence of tumor infiltration by neoantigen-specific T cell clones after vaccination and epitope spreading, suggesting on-target vaccine-induced tumor cell killing. Personal neoantigen peptide vaccines thus induce T cell responses that persist over years and broaden the spectrum of tumor-specific cytotoxicity in patients with melanoma.
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Affiliation(s)
- Zhuting Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna E Leet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Rosa L Allesøe
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Juliet Forman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Teddy Huang
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Rebecca Holden
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Academic Haematology, University College London, London, UK
| | - Robert A Redd
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Zoe Ciantra
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Oriol Olive
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keerthi Shetty
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mohamed Uduman
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick C Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Pavan Bachireddy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth I Buchbinder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Charles H Yoon
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Donna Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley L Pentelute
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nir Hacohen
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lars Rønn Olsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagan, Denmark
| | - Dan H Barouch
- Harvard Medical School, Boston, MA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kai W Wucherpfennig
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward F Fritsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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12
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Feng D, Li Z, Qin L, Hao B. The role of chromatin organizer Satb1 in shaping TCR repertoire in adult thymus. Genome 2021; 64:821-832. [PMID: 33617384 DOI: 10.1139/gen-2020-0139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
T cells recognize the universe of foreign antigens with a diverse repertoire of T cell receptors generated by V(D)J recombination. Special AT-rich binding protein 1 (Satb1) is a chromatin organizer that plays an essential role in T cell development. Previous study has shown that Satb1 regulates the re-induction of recombinase Rag1 and Rag2 in CD4+CD8+ thymocytes, affecting the secondary rearrangement of the Tcra gene. Here, we detected the repertoires of four TCR genes, Tcrd, Tcrg, Tcrb, and Tcra, in the adult thymus, and explored the role of the Satb1 in shaping the TCR repertoires. We observed a strong bias in the V and J gene usages of the Tcrd and Tcrg repertoires in WT and Satb1-deleted thymocytes. Satb1 deletion had few effects on the V(D)J rearrangement and repertoire of the Tcrg, Tcrd, and Tcrb genes. The Tcra repertoire was severely impaired in Satb1-deleted thymocytes, while the primary rearrangement was relatively normal. We also found the CDR3 length of TCRα chain was significantly longer in Satb1-deleted thymocytes, which can be explained by the strong bias of the proximal Jα usage. Our results showed that Satb1 plays an essential role in shaping TCR repertoires in αβ T cells.
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Affiliation(s)
- Delong Feng
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhaoqiang Li
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 450003, P.R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, Henan 450003, P.R. China
| | - Bingtao Hao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Medical Genetic Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 450003, P.R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, Henan 450003, P.R. China
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13
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Zheng HY, Xu M, Yang CX, Tian RR, Zhang M, Li JJ, Wang XC, Ding ZL, Li GM, Li XL, He YQ, Dong XQ, Yao YG, Zheng YT. Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19. Signal Transduct Target Ther 2020; 5:294. [PMID: 33361761 PMCID: PMC7758413 DOI: 10.1038/s41392-020-00457-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022] Open
Abstract
Understanding the processes of immune regulation in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for improving treatment. Here, we performed longitudinal whole-transcriptome RNA sequencing on peripheral blood mononuclear cell (PBMC) samples from 18 patients with coronavirus disease 2019 (COVID-19) during their treatment, convalescence, and rehabilitation. After analyzing the regulatory networks of differentially expressed messenger RNAs (mRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) between the different clinical stages, we found that humoral immunity and type I interferon response were significantly downregulated, while robust T-cell activation and differentiation at the whole transcriptome level constituted the main events that occurred during recovery from COVID-19. The formation of this T cell immune response might be driven by the activation of activating protein-1 (AP-1) related signaling pathway and was weakly affected by other clinical features. These findings uncovered the dynamic pattern of immune responses and indicated the key role of T cell immunity in the creation of immune protection against this disease.
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Affiliation(s)
- Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Cui-Xian Yang
- Yunnan Infectious Disease Hospital, Kunming, 650301, China
| | - Ren-Rong Tian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Mi Zhang
- Yunnan Infectious Disease Hospital, Kunming, 650301, China
| | - Jian-Jian Li
- Yunnan Infectious Disease Hospital, Kunming, 650301, China
| | - Xi-Cheng Wang
- Yunnan Infectious Disease Hospital, Kunming, 650301, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xiao-Lu Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Yu-Qi He
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xing-Qi Dong
- Yunnan Infectious Disease Hospital, Kunming, 650301, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
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14
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Running to Stand Still: Naive CD8 + T Cells Actively Maintain a Program of Quiescence. Int J Mol Sci 2020; 21:ijms21249773. [PMID: 33371448 PMCID: PMC7767439 DOI: 10.3390/ijms21249773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
CD8+ T cells play a pivotal role in clearing intracellular pathogens and combatting tumours. Upon infection, naïve CD8+ T cells differentiate into effector and memory cells, and this program is underscored by large-scale and coordinated changes in the chromatin architecture and gene expression. Importantly, recent evidence demonstrates that the epigenetic mechanisms that regulate the capacity for rapid effector function of memory T cells are shared by innate immune cells such as natural killer (NK) cells. Thus, it appears that the crucial difference between innate and adaptive immunity is the presence of the naïve state. This important distinction raises an intriguing new hypothesis, that the naïve state was evolutionary installed to restrain a default program of effector and memory differentiation in response to antigen recognition. We argue that the hallmark of adaptive T immunity is therefore the naïve program, which actively maintains CD8+ T cell quiescence until receipt of appropriate activation signals. In this review, we examine the mechanistic control of naïve CD8+ T cell quiescence and summarise the multiple levels of restraint imposed in naïve cells in to limit spontaneous and inappropriate activation. This includes epigenetic mechanisms and transcription factor (TF) regulation of gene expression, in addition to novel inhibitory receptors, abundance of RNA, and protein degradation.
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15
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Salou M, Legoux F, Lantz O. MAIT cell development in mice and humans. Mol Immunol 2020; 130:31-36. [PMID: 33352411 DOI: 10.1016/j.molimm.2020.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/02/2020] [Indexed: 01/11/2023]
Abstract
MAIT cells arise in the thymus following rearrangement of a T cell receptor (TCR) reactive against microbial vitamin B2-derived metabolites presented by the MHC-Ib molecule, MR1. Mechanisms that are conserved in mammals ensure the frequent production of MR1-restricted TCRs and the intra-thymic differentiation of MR1-restricted thymocytes into effector cells. Upon thymic egress and migration into non-lymphoid tissues, additional signals modulate MAIT cell functions according to each local tissue environment. Here, we review the recent progress made towards a better understanding of the establishment of this major immune cell subset.
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Affiliation(s)
- Marion Salou
- INSERM U932, PSL University, Institut Curie, Paris, 75005, France
| | - François Legoux
- INSERM U932, PSL University, Institut Curie, Paris, 75005, France
| | - Olivier Lantz
- INSERM U932, PSL University, Institut Curie, Paris, 75005, France; Laboratoire d'immunologie clinique, Institut Curie, Paris, 75005, France; Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, 75005, France.
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16
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Zilenaite D, Rasmusson A, Augulis R, Besusparis J, Laurinaviciene A, Plancoulaine B, Ostapenko V, Laurinavicius A. Independent Prognostic Value of Intratumoral Heterogeneity and Immune Response Features by Automated Digital Immunohistochemistry Analysis in Early Hormone Receptor-Positive Breast Carcinoma. Front Oncol 2020; 10:950. [PMID: 32612954 PMCID: PMC7308549 DOI: 10.3389/fonc.2020.00950] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Immunohistochemistry (IHC) for ER, PR, HER2, and Ki67 is used to predict outcome and therapy response in breast cancer patients. The current IHC assessment, visual or digital, is based mostly on global biomarker expression levels in the tissue sample. In our study, we explored the prognostic value of digital image analysis of conventional breast cancer IHC biomarkers supplemented with their intratumoral heterogeneity and tissue immune response indicators. Surgically excised tumor samples from 101 female patients with hormone receptor-positive breast cancer (HRBC) were stained for ER, PR, HER2, Ki67, SATB1, CD8, and scanned at 20x. Digital image analysis was performed using the HALO™ platform. Subsequently, hexagonal tiling was used to compute intratumoral heterogeneity indicators for ER, PR and Ki67 expression. Multiple Cox regression analysis revealed three independent predictors of the patient's overall survival: Haralick's texture entropy of PR (HR = 0.19, p = 0.0005), Ki67 Ashman's D bimodality (HR = 3.0, p = 0.01), and CD8+SATB1+ cell density in tumor tissue (HR = 0.32, p = 0.02). Remarkably, the PR and Ki67 intratumoral heterogeneity indicators were prognostically more informative than the rates of their expression. In particular, a distinct non-linear relationship between the rate of PR expression and its intratumoral heterogeneity was observed and revealed a non-linear prognostic effect of PR expression. The independent prognostic significance of CD8+SATB1+ cells infiltrating the tumor could indicate their role in anti-tumor immunity. In conclusion, we suggest that prognostic modeling, based entirely on the computational image-based IHC biomarkers, is possible in HRBC patients. The intratumoral heterogeneity and immune response indicators outperformed both conventional breast cancer IHC and clinicopathological variables while markedly increasing the power of the model.
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Affiliation(s)
- Dovile Zilenaite
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Allan Rasmusson
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Renaldas Augulis
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Justinas Besusparis
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Aida Laurinaviciene
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Benoit Plancoulaine
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,ANTICIPE, Inserm (UMR 1086), Cancer Center F. Baclesse, Normandy University, Caen, France
| | - Valerijus Ostapenko
- Department of Breast Surgery and Oncology, National Cancer Institute, Vilnius, Lithuania
| | - Arvydas Laurinavicius
- Department of Pathology, Forensic Medicine and Pharmacology, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.,National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
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17
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Koay HF, Su S, Amann-Zalcenstein D, Daley SR, Comerford I, Miosge L, Whyte CE, Konstantinov IE, d'Udekem Y, Baldwin T, Hickey PF, Berzins SP, Mak JYW, Sontani Y, Roots CM, Sidwell T, Kallies A, Chen Z, Nüssing S, Kedzierska K, Mackay LK, McColl SR, Deenick EK, Fairlie DP, McCluskey J, Goodnow CC, Ritchie ME, Belz GT, Naik SH, Pellicci DG, Godfrey DI. A divergent transcriptional landscape underpins the development and functional branching of MAIT cells. Sci Immunol 2019; 4:eaay6039. [PMID: 31757835 PMCID: PMC10627559 DOI: 10.1126/sciimmunol.aay6039] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022]
Abstract
MR1-restricted mucosal-associated invariant T (MAIT) cells play a unique role in the immune system. These cells develop intrathymically through a three-stage process, but the events that regulate this are largely unknown. Here, using bulk and single-cell RNA sequencing-based transcriptomic analysis in mice and humans, we studied the changing transcriptional landscape that accompanies transition through each stage. Many transcripts were sharply modulated during MAIT cell development, including SLAM (signaling lymphocytic activation molecule) family members, chemokine receptors, and transcription factors. We also demonstrate that stage 3 "mature" MAIT cells comprise distinct subpopulations including newly arrived transitional stage 3 cells, interferon-γ-producing MAIT1 cells and interleukin-17-producing MAIT17 cells. Moreover, the validity and importance of several transcripts detected in this study are directly demonstrated using specific mutant mice. For example, MAIT cell intrathymic maturation was found to be halted in SLAM-associated protein (SAP)-deficient and CXCR6-deficient mouse models, providing clear evidence for their role in modulating MAIT cell development. These data underpin a model that maps the changing transcriptional landscape and identifies key factors that regulate the process of MAIT cell differentiation, with many parallels between mice and humans.
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Affiliation(s)
- H-F Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - S Su
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - D Amann-Zalcenstein
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - S R Daley
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - I Comerford
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - L Miosge
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - C E Whyte
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - I E Konstantinov
- Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
- Melbourne Children's Centre for Cardiovascular Genomics and Regenerative Medicine, Murdoch Children's Research Institute, Victoria 3052, Australia
- Murdoch Children's Research Institute, Victoria 3052, Australia
| | - Y d'Udekem
- Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
- Melbourne Children's Centre for Cardiovascular Genomics and Regenerative Medicine, Murdoch Children's Research Institute, Victoria 3052, Australia
- Murdoch Children's Research Institute, Victoria 3052, Australia
| | - T Baldwin
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
- Blood Cells and Blood Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - P F Hickey
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - S P Berzins
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Federation University Australia, Ballarat, Victoria 3350, Australia
- Fiona Elsey Cancer Research Institute, Ballarat, Victoria 3350, Australia
| | - J Y W Mak
- Division of Chemistry and Structural Biology, and Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Y Sontani
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - C M Roots
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - T Sidwell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - A Kallies
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Z Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - S Nüssing
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - K Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - L K Mackay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - S R McColl
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - E K Deenick
- Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Sydney, Australia
| | - D P Fairlie
- Division of Chemistry and Structural Biology, and Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - J McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - C C Goodnow
- Garvan Institute of Medical Research, Sydney, Australia
- UNSW Cellular Genomics Futures Institute, UNSW, Sydney, Australia
| | - M E Ritchie
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - G T Belz
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - S H Naik
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - D G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
- Murdoch Children's Research Institute, Victoria 3052, Australia
| | - D I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
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Glatzel-Plucińska N, Piotrowska A, Dzięgiel P, Podhorska-Okołów M. The Role of SATB1 in Tumour Progression and Metastasis. Int J Mol Sci 2019; 20:E4156. [PMID: 31450715 PMCID: PMC6747166 DOI: 10.3390/ijms20174156] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
Carcinogenesis is a long-drawn, multistep process, in which metastatic spread is an unequivocal hallmark of a poor prognosis. The progression and dissemination of epithelial cancers is commonly thought to rely on the epidermal-mesenchymal transition (EMT) process. During EMT, epithelial cells lose their junctions and apical-basal polarity, and they acquire a mesenchymal phenotype with its migratory and invasive capabilities. One of the proteins involved in cancer progression and EMT may be SATB1 (Special AT-Rich Binding Protein 1)-a chromatin organiser and a global transcriptional regulator. SATB1 organizes chromatin into spatial loops, providing a "docking site" necessary for the binding of further transcription factors and chromatin modifying enzymes. SATB1 has the ability to regulate whole sets of genes, even those located on distant chromosomes. SATB1 was found to be overexpressed in numerous malignancies, including lymphomas, breast, colorectal, prostate, liver, bladder and ovarian cancers. In the solid tumours, an elevated SATB1 level was observed to be associated with an aggressive phenotype, presence of lymph node, distant metastases, and a poor prognosis. In this review, we briefly describe the prognostic significance of SATB1 expression in most common human cancers, and analyse its impact on EMT and metastasis.
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Affiliation(s)
- Natalia Glatzel-Plucińska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland.
| | - Aleksandra Piotrowska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
- Department of Physiotherapy, Wroclaw University School of Physical Education, 51-612 Wroclaw, Poland
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