1
|
Graham JP, Zhang Y, He L, Gonzalez-Fernandez T. CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601587. [PMID: 39005295 PMCID: PMC11244939 DOI: 10.1101/2024.07.01.601587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
CRISPR gene editing strategies are shaping cell therapies through precise and tunable control over gene expression. However, achieving reliable therapeutic effects with improved safety and efficacy requires informed target gene selection. This depends on a thorough understanding of the involvement of target genes in gene regulatory networks (GRNs) that regulate cell phenotype and function. Machine learning models have been previously used for GRN reconstruction using RNA-seq data, but current techniques are limited to single cell types and focus mainly on transcription factors. This restriction overlooks many potential CRISPR target genes, such as those encoding extracellular matrix components, growth factors, and signaling molecules, thus limiting the applicability of these models for CRISPR strategies. To address these limitations, we have developed CRISPR-GEM, a multi-layer perceptron (MLP)-based synthetic GRN constructed to accurately predict the downstream effects of CRISPR gene editing. First, input and output nodes are identified as differentially expressed genes between defined experimental and target cell/tissue types respectively. Then, MLP training learns regulatory relationships in a black-box approach allowing accurate prediction of output gene expression using only input gene expression. Finally, CRISPR-mimetic perturbations are made to each input gene individually and the resulting model predictions are compared to those for the target group to score and assess each input gene as a CRISPR candidate. The top scoring genes provided by CRISPR-GEM therefore best modulate experimental group GRNs to motivate transcriptomic shifts towards a target group phenotype. This machine learning model is the first of its kind for predicting optimal CRISPR target genes and serves as a powerful tool for enhanced CRISPR strategies across a range of cell therapies.
Collapse
Affiliation(s)
- Josh P Graham
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Yu Zhang
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
- Department of Electrical and Computer Engineering, Lehigh University, Bethlehem, PA, USA
| | - Lifang He
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA
| | | |
Collapse
|
2
|
Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nat Commun 2024; 15:4650. [PMID: 38821936 PMCID: PMC11143375 DOI: 10.1038/s41467-024-48620-7] [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: 03/29/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Collapse
Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine Division of Rheumatology and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Majd Al Suqri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| |
Collapse
|
3
|
Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536026. [PMID: 37066336 PMCID: PMC10104143 DOI: 10.1101/2023.04.07.536026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Synovial tissue inflammation is the hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. We measured genome-wide open chromatin at single cell resolution from 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identified 24 chromatin classes and predicted their associated transcription factors, including a CD8+ GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating an RA tissue transcriptional atlas, we found that the chromatin classes represented 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrated the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Collapse
Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F. M. Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H. Anolik
- Division of Allergy, Immunology and Rheumatology; Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T. Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| |
Collapse
|
4
|
Khrunin AV, Khvorykh GV, Arapova AS, Kulinskaya AE, Koltsova EA, Petrova EA, Kimelfeld EI, Limborska SA. The Study of the Association of Polymorphisms in LSP1, GPNMB, PDPN, TAGLN, TSPO, and TUBB6 Genes with the Risk and Outcome of Ischemic Stroke in the Russian Population. Int J Mol Sci 2023; 24:ijms24076831. [PMID: 37047799 PMCID: PMC10095190 DOI: 10.3390/ijms24076831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023] Open
Abstract
To date, there has been great progress in understanding the genetic basis of ischemic stroke (IS); however, several aspects of the condition remain underexplored, including the influence of genetic factors on post-stroke outcomes and the identification of causative loci. We proposed that an analysis of the results obtained from animal models of brain ischemia could be helpful. To this end, we developed a bioinformatic approach for exploring single-nucleotide polymorphisms (SNPs) in human orthologs of rat genes expressed differentially after induced brain ischemia. Using this approach, we identified and analyzed 11 SNPs from 6 genes in 553 Russian individuals (331 patients with IS and 222 controls). We assessed the association of SNPs with the risk of IS and IS outcomes. We found that the SNPs rs858239 (GPNMB), rs907611 (LSP1), and rs494356 (TAGLN) were associated with different parameters of IS functional outcomes. In addition, the SNP rs1261025 (PDPN) was associated significantly with IS itself (p = 0.0188, recessive model). All these associations were demonstrated for the first time. Analysis of the literature suggests that they should be characterized as being inflammation related. This supports the pivotal role of inflammation in both the incidence of stroke and post-stroke outcomes. We believe the findings reported here will help with stroke prognosis in the future.
Collapse
Affiliation(s)
- Andrey V. Khrunin
- National Research Centre “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia
| | - Gennady V. Khvorykh
- National Research Centre “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia
| | - Anna S. Arapova
- National Research Centre “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia
- Faculty of Biotechnology and Industrial Ecology, Mendeleev University of Chemical Technology of Russia, Miusskaya Sq. 9, Moscow 125047, Russia
| | - Anna E. Kulinskaya
- National Research Centre “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia
- Faculty of Biotechnology and Industrial Ecology, Mendeleev University of Chemical Technology of Russia, Miusskaya Sq. 9, Moscow 125047, Russia
| | - Evgeniya A. Koltsova
- Department of Neurology, Neurosurgery and Medical Genetics of Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Elizaveta A. Petrova
- Department of Neurology, Neurosurgery and Medical Genetics of Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ekaterina I. Kimelfeld
- Department of Neurology, Neurosurgery and Medical Genetics of Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Svetlana A. Limborska
- National Research Centre “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia
| |
Collapse
|
5
|
Mindikoglu AL, Park J, Opekun AR, Abdulsada MM, Wilhelm ZR, Jalal PK, Devaraj S, Jung SY. Dawn-to-dusk dry fasting induces anti-atherosclerotic, anti-inflammatory, and anti-tumorigenic proteome in peripheral blood mononuclear cells in subjects with metabolic syndrome. Metabol Open 2022; 16:100214. [PMID: 36506940 PMCID: PMC9731888 DOI: 10.1016/j.metop.2022.100214] [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: 08/17/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background Metabolic syndrome characterized by abdominal obesity, high blood pressure, elevated fasting glucose and triglyceride levels and low high-density lipoprotein cholesterol level is associated with pro-inflammatory state, increased risk for atherosclerosis, and multiple cancers. Our previous results on subjects with metabolic syndrome showed that 4-week dawn-to-dusk (sunset) dry fasting resulted in significant changes in the serum proteome and improvement in several metabolic risk factors. Peripheral blood mononuclear cells (PBMC) proteomics is a powerful tool that can provide mechanistic insights into how dawn-to-dusk dry fasting affects protein expression in metabolic pathways at cellular level. In this study, we determined whether dawn-to-dusk dry fasting would induce favorable changes in PBMC proteome in subjects with metabolic syndrome, similar to the changes induced by dawn-to-dusk dry fasting in the same subjects' serum proteome. Methods We conducted a prospective study on subjects with metabolic syndrome and collected blood specimens before 4-week dawn-to-dusk dry fasting, at the end of 4-week dawn-to-dusk dry fasting, and one week after 4-week dawn-to-dusk dry fasting. We performed untargeted proteomics using nano ultra-high performance liquid chromatography-tandem mass spectrometry to assess the impact of 4-week dawn-to-dusk dry fasting on PBMC proteome. Results There were 14 subjects with metabolic syndrome with a mean age of 59 who fasted from dawn to dusk (strict dry fasting without any liquid or food intake) for more than 14 h daily for 29 days. The quantitative proteome analysis showed that apolipoprotein B (APOB) gene protein products (GP) levels were downregulated and had the most statistical significance of the observed difference at the end of 4-week dawn-to-dusk dry fasting (P = 0.008) and one week after 4-week dawn-to-dusk dry fasting (P = 0.0004) compared with the levels before 4-week dawn-to-dusk dry fasting. The comparison between GP levels before and at the end of 4-week dawn-to-dusk dry fasting showed an alteration in the expression of genes associated with lipid and atherosclerosis pathway (P = 6.014e-4) and C-type lectin receptor signaling pathway (P = 1.064e-5). The genes that were differentially expressed in the lipid and atherosclerosis pathway were APOB (P = 0.008), CD36 (P = 0.040), CALM1, CALM2, CALM3 (P = 0.015), and HSPA8 (P = 0.047). One of the differentially expressed genes in the C-type lectin receptor signaling pathway was lymphocyte-specific protein 1 (LSP1), which showed an average of 19-fold increase at the end of 4-week dawn-to-dusk dry fasting compared with the GP levels before fasting (P = 0.004). Several GPs associated with tumor-suppressor effect (TUBB4B, LSP1, ACTR3B) were upregulated, and GPs associated with tumor-promoter effect (CD36, CALM1, CALM2, CALM3, FLOT2, PPIF) were downregulated at the end of 4-week dawn-to-dusk dry fasting or one week after 4-week dawn-to-dusk dry fasting compared with the GP levels before 4-week dawn-to-dusk dry fasting. Conclusion Based on our results, we conclude that in subjects with metabolic syndrome, 4-week dawn-to-dusk dry fasting induced anti-atherosclerotic, anti-inflammatory, and anti-tumorigenic PMBC proteome. Randomized, controlled clinical trials are needed to further investigate the effect of dawn-to-dusk dry fasting on subjects with chronic metabolic diseases and metabolic syndrome-induced cancers.
Collapse
Affiliation(s)
- Ayse L. Mindikoglu
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA,Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation, Baylor College of Medicine, Houston, TX, USA,Corresponding author. Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA.
| | - Jihwan Park
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Antone R. Opekun
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA,Department of Pediatrics, Division of Gastroenterology, Nutrition and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Mustafa M. Abdulsada
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Zoe R. Wilhelm
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Prasun K. Jalal
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA,Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation, Baylor College of Medicine, Houston, TX, USA
| | - Sridevi Devaraj
- Clinical Chemistry and Point of Care Technology, Texas Children's Hospital, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Sung Yun Jung
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
6
|
Qian Q, Cui N, Huang B, Zhao Y, Liu Q, Hu M, Li B, Wang Q, Miao Q, You Z, Ma X, Tang R. Intrahepatic activated leukocyte cell adhesion molecule induces CD6highCD4+ T cell infiltration in autoimmune hepatitis. Front Immunol 2022; 13:967944. [PMID: 36159854 PMCID: PMC9500242 DOI: 10.3389/fimmu.2022.967944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/17/2022] [Indexed: 11/28/2022] Open
Abstract
Background and objectives Autoimmune hepatitis (AIH) is characterized by the expansion and accumulation of pathogenic T cells in liver. Although CD6 and its ligand activated leukocyte cell adhesion molecule (ALCAM) are involved in the evolution of multiple inflammatory diseases, their roles in the pathogenesis of AIH remain unknown. Herein, we aimed to investigate ALCAM-CD6 axis in AIH development. Methods Immunohistochemistry was performed to examine hepatic expression of CD6 and ALCAM. The concentration of serum ALCAM was evaluated by ELISA. The phenotypes of liver infiltrating T cells were determined by flow cytometry. Primary human CD4+ T cells were used for functional studies. Results Our data showed that patients with AIH exhibited significantly higher expression of CD6 in the liver as compared to primary biliary cholangitis (PBC), chronic hepatitis B (CHB), non-alcoholic liver disease (NAFLD), and healthy controls (HC). In addition, hepatic CD6 expression was strongly correlated with disease severity of AIH. CD6 was mainly expressed on CD4+ T cells in the liver and intrahepatic CD6highCD4+ T cells demonstrated stronger proinflammatory response and proliferation features than CD6low counterparts in both AIH and HC. ALCAM, the ligand of CD6, was highly expressed in the hepatocytes of AIH and serum ALCAM was strongly associated with clinical indices of AIH. Interestingly, close spatial location between CD6+CD4+ T cells and ALCAM+ hepatocytes was observed. Finally, we found that CD6highCD4+ T cells showed enhanced capacity of trans-endothelial migration in vitro, which could be promoted by recombinant ALCAM. Conclusions Our study found that ALCAM-CD6 axis was upregulated in the AIH liver, suggesting a potential target for alleviating AIH.
Collapse
Affiliation(s)
- Qiwei Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Nana Cui
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Bingyuan Huang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yudong Zhao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaoyan Liu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Mingli Hu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Bo Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qixia Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Miao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhengrui You
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
- *Correspondence: Ruqi Tang, ; Xiong Ma, ; Zhengrui You,
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
- *Correspondence: Ruqi Tang, ; Xiong Ma, ; Zhengrui You,
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
- *Correspondence: Ruqi Tang, ; Xiong Ma, ; Zhengrui You,
| |
Collapse
|
7
|
Hilchey SP, Palshikar MG, Mendelson ES, Shen S, Rasam S, Emo JA, Qu J, Thakar J, Zand MS. Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O 2 Levels. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081284. [PMID: 36013463 PMCID: PMC9410508 DOI: 10.3390/life12081284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 12/20/2022]
Abstract
Coordinated migration of B cells within and between secondary lymphoid tissues is required for robust antibody responses to infection or vaccination. Secondary lymphoid tissues normally expose B cells to a low O2 (hypoxic) environment. Recently, we have shown that human B cell migration is modulated by an O2-dependent molecular switch, centrally controlled by the hypoxia-induced (transcription) factor-1α (HIF1A), which can be disrupted by the immunosuppressive calcineurin inhibitor, cyclosporine A (CyA). However, the mechanisms by which low O2 environments attenuate B cell migration remain poorly defined. Proteomics analysis has linked CXCR4 chemokine receptor signaling to cytoskeletal rearrangement. We now hypothesize that the pathways linking the O2 sensing molecular switch to chemokine receptor signaling and cytoskeletal rearrangement would likely contain phosphorylation events, which are typically missed in traditional transcriptomic and/or proteomic analyses. Hence, we have performed a comprehensive phosphoproteomics analysis of human B cells treated with CyA after engagement of the chemokine receptor CXCR4 with CXCL12. Statistical analysis of the separate and synergistic effects of CyA and CXCL12 revealed 116 proteins whose abundance is driven by a synergistic interaction between CyA and CXCL12. Further, we used our previously described algorithm BONITA to reveal a critical role for Lymphocyte Specific Protein 1 (LSP1) in cytoskeletal rearrangement. LSP1 is known to modulate neutrophil migration. Validating these modeling results, we show experimentally that LSP1 levels in B cells increase with low O2 exposure, and CyA treatment results in decreased LSP1 protein levels. This correlates with the increased chemotactic activity observed after CyA treatment. Lastly, we directly link LSP1 levels to chemotactic capacity, as shRNA knock-down of LSP1 results in significantly increased B cell chemotaxis at low O2 levels. These results directly link CyA to LSP1-dependent cytoskeletal regulation, demonstrating a previously unrecognized mechanism by which CyA modulates human B cell migration. Data are available via ProteomeXchange with identifier PXD036167.
Collapse
Affiliation(s)
- Shannon P. Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mukta G. Palshikar
- Biophysics, Structural, and Computational Biology Program, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Eric S. Mendelson
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY 14203, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY 14203, USA
| | - Sailee Rasam
- Department of Pharmaceutical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY 14203, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY 14203, USA
| | - Jason A. Emo
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY 14203, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY 14203, USA
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S. Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
- Correspondence:
| |
Collapse
|
8
|
Le NPK, do Nascimento AF, Schneberger D, Quach CC, Zhang X, Aulakh GK, Dawicki W, Liu L, Gordon JR, Singh B. Deficiency of leukocyte-specific protein 1 (LSP1) alleviates asthmatic inflammation in a mouse model. Respir Res 2022; 23:165. [PMID: 35733161 PMCID: PMC9219131 DOI: 10.1186/s12931-022-02078-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background Asthma is a major cause of morbidity and mortality in humans. The mechanisms of asthma are still not fully understood. Leukocyte-specific protein-1 (LSP-1) regulates neutrophil migration during acute lung inflammation. However, its role in asthma remains unknown. Methods An OVA-induced mouse asthma model in LSP1-deficient (Lsp1−/−) and wild-type (WT) 129/SvJ mice were used to test the hypothesis that the absence of LSP1 would inhibit airway hyperresponsiveness and lung inflammation. Results Light and electron microscopic immunocytochemistry and Western blotting showed that, compared with normal healthy lungs, the levels of LSP1 were increased in lungs of OVA-asthmatic mice. Compared to Lsp1−/− OVA mice, WT OVA mice had higher levels of leukocytes in broncho-alveolar lavage fluid and in the lung tissues (P < 0.05). The levels of OVA-specific IgE but not IgA and IgG1 in the serum of WT OVA mice was higher than that of Lsp1−/− OVA mice (P < 0.05). Deficiency of LSP1 significantly reduced the levels of IL-4, IL-5, IL-6, IL-13, and CXCL1 (P < 0.05) but not total proteins in broncho-alveolar lavage fluid in asthmatic mice. The airway hyper-responsiveness to methacholine in Lsp1−/− OVA mice was improved compared to WT OVA mice (P < 0.05). Histology revealed more inflammation (inflammatory cells, and airway and blood vessel wall thickening) in the lungs of WT OVA mice than in those of Lsp1−/− OVA mice. Finally, immunohistology showed localization of LSP1 protein in normal and asthmatic human lungs especially associated with the vascular endothelium and neutrophils. Conclusion These data show that LSP1 deficiency reduces airway hyper-responsiveness and lung inflammation, including leukocyte recruitment and cytokine expression, in a mouse model of asthma. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02078-7.
Collapse
Affiliation(s)
- Nguyen Phuong Khanh Le
- Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Canada.,Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
| | | | - David Schneberger
- Department of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Chi Cuong Quach
- Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Xiaobei Zhang
- Department of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Gurpreet K Aulakh
- Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Canada.,Small Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Wojciech Dawicki
- Department of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Lixin Liu
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, Canada
| | - John R Gordon
- Department of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Baljit Singh
- Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Canada. .,Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, S7N5B4, Canada.
| |
Collapse
|
9
|
Schmiedel BJ, Gonzalez-Colin C, Fajardo V, Rocha J, Madrigal A, Ramírez-Suástegui C, Bhattacharyya S, Simon H, Greenbaum JA, Peters B, Seumois G, Ay F, Chandra V, Vijayanand P. Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants. Sci Immunol 2022; 7:eabm2508. [PMID: 35213211 DOI: 10.1126/sciimmunol.abm2508] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The impact of genetic variants on cells challenged in biologically relevant contexts has not been fully explored. Here, we activated CD4+ T cells from 89 healthy donors and performed a single-cell RNA sequencing assay with >1 million cells to examine cell type-specific and activation-dependent effects of genetic variants. Single-cell expression quantitative trait loci (sc-eQTL) analysis of 19 distinct CD4+ T cell subsets showed that the expression of over 4000 genes is significantly associated with common genetic polymorphisms and that most of these genes show their most prominent effects in specific cell types. These genes included many that encode for molecules important for activation, differentiation, and effector functions of T cells. We also found new gene associations for disease-risk variants identified from genome-wide association studies and highlighted the cell types in which their effects are most prominent. We found that biological sex has a major influence on activation-dependent gene expression in CD4+ T cell subsets. Sex-biased transcripts were significantly enriched in several pathways that are essential for the initiation and execution of effector functions by CD4+ T cells like TCR signaling, cytokines, cytokine receptors, costimulatory, apoptosis, and cell-cell adhesion pathways. Overall, this DICE (Database of Immune Cell Expression, eQTLs, and Epigenomics) subproject highlights the power of sc-eQTL studies for simultaneously exploring the activation and cell type-dependent effects of common genetic variants on gene expression (https://dice-database.org).
Collapse
Affiliation(s)
| | - Cristian Gonzalez-Colin
- La Jolla Institute for Immunology, La Jolla, CA, USA.,Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | | | - Job Rocha
- La Jolla Institute for Immunology, La Jolla, CA, USA.,Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | | | | | | | - Hayley Simon
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Vivek Chandra
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| |
Collapse
|
10
|
Yu R, Zhang J, Zhuo Y, Hong X, Ye J, Tang S, Zhang Y. Identification of Diagnostic Signatures and Immune Cell Infiltration Characteristics in Rheumatoid Arthritis by Integrating Bioinformatic Analysis and Machine-Learning Strategies. Front Immunol 2021; 12:724934. [PMID: 34691030 PMCID: PMC8526926 DOI: 10.3389/fimmu.2021.724934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023] Open
Abstract
Background Rheumatoid arthritis (RA) refers to an autoimmune rheumatic disease that imposes a huge burden on patients and society. Early RA diagnosis is critical to preventing disease progression and selecting optimal therapeutic strategies more effectively. In the present study, the aim was at examining RA's diagnostic signatures and the effect of immune cell infiltration in this pathology. Methods Gene Expression Omnibus (GEO) database provided three datasets of gene expressions. Firstly, this study adopted R software for identifying differentially expressed genes (DEGs) and conducting functional correlation analyses. Subsequently, we integrated bioinformatic analysis and machine-learning strategies for screening and determining RA's diagnostic signatures and further verify by qRT-PCR. The diagnostic values were assessed through receiver operating characteristic (ROC) curves. Moreover, this study employed cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT) website for assessing the inflammatory state of RA, and an investigation was conducted on the relationship of diagnostic signatures and infiltrating immune cells. Results On the whole, 54 robust DEGs received the recognition. Lymphocyte-specific protein 1 (LSP1), Granulysin (GNLY), and Mesenchymal homobox 2 (MEOX2) (AUC = 0.955) were regarded as RA's diagnostic markers and showed their statistically significant difference by qRT-PCR. As indicated from the immune cell infiltration analysis, resting NK cells, neutrophils, activated NK cells, T cells CD8, memory B cells, and M0 macrophages may be involved in the development of RA. Additionally, all diagnostic signatures might be different degrees of correlation with immune cells. Conclusions In conclusion, LSP1, GNLY, and MEOX2 are likely to be available in terms of diagnosing and treating RA, and the infiltration of immune cells mentioned above may critically impact RA development and occurrence.
Collapse
Affiliation(s)
- Rongguo Yu
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Jiayu Zhang
- School of Clinical Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Youguang Zhuo
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Xu Hong
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Jie Ye
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Susu Tang
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Yiyuan Zhang
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University, Xiamen University, Xiamen, China
| |
Collapse
|
11
|
Tkachev V, Kaminski J, Potter EL, Furlan SN, Yu A, Hunt DJ, McGuckin C, Zheng H, Colonna L, Gerdemann U, Carlson J, Hoffman M, Olvera J, English C, Baldessari A, Panoskaltsis-Mortari A, Watkins B, Qayed M, Suessmuth Y, Betz K, Bratrude B, Langston A, Horan JT, Ordovas-Montanes J, Shalek AK, Blazar BR, Roederer M, Kean LS. Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8 + T cells drive gastrointestinal acute graft-versus-host disease. Sci Transl Med 2021; 13:13/576/eabc0227. [PMID: 33441422 DOI: 10.1126/scitranslmed.abc0227] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Organ infiltration by donor T cells is critical to the development of acute graft-versus-host disease (aGVHD) in recipients after allogeneic hematopoietic stem cell transplant (allo-HCT). However, deconvoluting the transcriptional programs of newly recruited donor T cells from those of tissue-resident T cells in aGVHD target organs remains a challenge. Here, we combined the serial intravascular staining technique with single-cell RNA sequencing to dissect the tightly connected processes by which donor T cells initially infiltrate tissues and then establish a pathogenic tissue residency program in a rhesus macaque allo-HCT model that develops aGVHD. Our results enabled creation of a spatiotemporal map of the transcriptional programs controlling donor CD8+ T cell infiltration into the primary aGVHD target organ, the gastrointestinal (GI) tract. We identified the large and small intestines as the only two sites demonstrating allo-specific, rather than lymphodepletion-driven, T cell infiltration. GI-infiltrating donor CD8+ T cells demonstrated a highly activated, cytotoxic phenotype while simultaneously developing a canonical tissue-resident memory T cell (TRM) transcriptional signature driven by interleukin-15 (IL-15)/IL-21 signaling. We found expression of a cluster of genes directly associated with tissue invasiveness, including those encoding adhesion molecules (ITGB2), specific chemokines (CCL3 and CCL4L1) and chemokine receptors (CD74), as well as multiple cytoskeletal proteins. This tissue invasion transcriptional signature was validated by its ability to discriminate the CD8+ T cell transcriptome of patients with GI aGVHD from those of GVHD-free patients. These results provide insights into the mechanisms controlling tissue occupancy of target organs by pathogenic donor CD8+ TRM cells during aGVHD in primate transplant recipients.
Collapse
Affiliation(s)
- Victor Tkachev
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - James Kaminski
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - E Lake Potter
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20858, USA
| | - Scott N Furlan
- Fred Hutchinson Cancer Research Center, Department of Pediatrics, University of Washington, Seattle, WA 98109, USA
| | - Alison Yu
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel J Hunt
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Connor McGuckin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hengqi Zheng
- University of Washington, Seattle, WA 98195, USA
| | - Lucrezia Colonna
- Fred Hutchinson Cancer Research Center, Department of Pediatrics, University of Washington, Seattle, WA 98109, USA
| | - Ulrike Gerdemann
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Michelle Hoffman
- Fred Hutchinson Cancer Research Center, Department of Pediatrics, University of Washington, Seattle, WA 98109, USA
| | - Joe Olvera
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chris English
- Washington National Primate Research Center, Seattle, WA 98195, USA
| | | | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55454, USA
| | | | - Muna Qayed
- Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Kayla Betz
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Brandi Bratrude
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | | | - John T Horan
- Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jose Ordovas-Montanes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Gastroenterology, Boston Children's Hospital and Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Bruce R Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55454, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20858, USA
| | - Leslie S Kean
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
12
|
Schäringer K, Maxeiner S, Schalla C, Rütten S, Zenke M, Sechi A. LSP1-myosin1e bimolecular complex regulates focal adhesion dynamics and cell migration. FASEB J 2021; 35:e21268. [PMID: 33470457 DOI: 10.1096/fj.202000740rr] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 01/22/2023]
Abstract
Several cytoskeleton-associated proteins and signaling pathways work in concert to regulate actin cytoskeleton remodeling, cell adhesion, and migration. Although the leukocyte-specific protein 1 (LSP1) has been shown to interact with the actin cytoskeleton, its function in the regulation of actin cytoskeleton dynamics is, as yet, not fully understood. We have recently demonstrated that the bimolecular complex between LSP1 and myosin1e controls actin cytoskeleton remodeling during phagocytosis. In this study, we show that LSP1 downregulation severely impairs cell migration, lamellipodia formation, and focal adhesion dynamics in macrophages. Inhibition of the interaction between LSP1 and myosin1e also impairs these processes resulting in poorly motile cells, which are characterized by few and small lamellipodia. Furthermore, cells in which LSP1-myosin1e interaction is inhibited are typically associated with inefficient focal adhesion turnover. Collectively, our findings show that the LSP1-myosin1e bimolecular complex plays a pivotal role in the regulation of actin cytoskeleton remodeling and focal adhesion dynamics required for cell migration.
Collapse
Affiliation(s)
- Katja Schäringer
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Sebastian Maxeiner
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Carmen Schalla
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Stephan Rütten
- Electron Microscopy Facility, Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Antonio Sechi
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
13
|
Kwon R, Hong BK, Lee KG, Choi E, Sabbagh L, Cho CS, Lee N, Kim WU. Regulation of tumor growth by leukocyte-specific protein 1 in T cells. J Immunother Cancer 2020; 8:jitc-2020-001180. [PMID: 33020243 PMCID: PMC7537340 DOI: 10.1136/jitc-2020-001180] [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] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Clinical efficacy of T cell-based cancer immunotherapy is limited by the lack of T cell infiltration in the tumor mass, especially in solid tumors. Our group demonstrated previously that leukocyte-specific protein 1 (LSP1), an intracellular signal regulator, negatively regulates T cell infiltration in inflamed tissues. METHODS To determine the immuno-regulatory effects of LSP1 in T cells on tumor progression, we investigated the growth of B16 melanoma in Lsp1 knockout (KO) mice and T cell-specific Lsp1 transgenic (Tg) mice. The immune cell subpopulation infiltrated into the tumor mass as well as the expression of interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) in T cells was assessed by flow cytometry and/or immunohistochemistry. Chemotactic migration was assayed with Lsp1 KO and Lsp1 Tg T cells. Adoptive transfer of Lsp1 KO or Lsp1 Tg T cells was performed in B16 melanoma-challenged Rag1 KO mice. RESULTS Lsp1 KO mice showed decreased growth of B16 melanoma and increased infiltration of T cells in the tumor mass, which were completely reversed in T cell-specific Lsp1 Tg mice. Lsp1 KO CD8+ T cells also exhibited elevated migratory capacity in response to CXCL9 and CXCL10, whereas Lsp1 Tg CD8+ T cells did the opposite. LSP1 expression was increased in tumor-infiltrating T cells and could be induced by T cell receptor activation. Intriguingly, gene expression profiling of Lsp1 KO T cells suggested enhanced cytotoxicity. Indeed, expression of IFN-γ and TNF-α was increased in tumor-infiltrating CD4+ and CD8+ T cells of Lsp1 KO mice, while it was markedly reduced in those of Lsp1 Tg mice. Adoptive transfer of Lsp1 KO T cells to Rag1 KO mice was more effective in suppressing melanoma growth than transfer of Lsp1 Tg T cells. Of note, when treated with antiprogrammed cell death protein 1 (PD-1) antibody, inhibition of melanoma growth was more pronounced in Lsp1 KO mice than in Lsp1-sufficient mice, suggesting that Lsp1 depletion additively increases the antitumor effects of anti-PD-1 antibody. CONCLUSIONS LSP1 in T cells regulates the growth of B16 melanoma in mice, possibly by affecting migration and infiltration of T cells into the tumor and by modulating production of antitumor effector cytokines by CD8+ T cells. These findings provide evidence that LSP1 can be a target to improve the efficacy of T cell-based immunotherapy.
Collapse
Affiliation(s)
- Riri Kwon
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bong-Ki Hong
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kang-Gu Lee
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
| | - Eunbyeol Choi
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, Republic of Korea
| | - Laurent Sabbagh
- Department of Microbiology, Infectiology, and Immunology, University of Montreal, Montreal, Quebec, Canada
| | - Chul-Soo Cho
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea.,Division of Rheumatology, Department of Internal Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Naeun Lee
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea
| | - Wan-Uk Kim
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Republic of Korea .,Division of Rheumatology, Department of Internal Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
14
|
Cong P, Hou HY, Wei W, Zhou Y, Yu XM. MiR-920 and LSP1 co-regulate the growth and migration of glioblastoma cells by modulation of JAK2/STAT5 pathway. J Bioenerg Biomembr 2020; 52:311-320. [PMID: 32770294 DOI: 10.1007/s10863-020-09848-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/29/2020] [Indexed: 11/24/2022]
Abstract
This study probes the function and mechanism of lymphocyte-specific protein 1 (LSP1) in glioblastoma pathogenesis. According to the data acquired from TCGA, Oncomine and GEO databases, the expression and prognostic value of LSP1 and miR-920 in glioblastoma patients were analyzed. The expression levels of LSP1 in U251 and A172 cell lines were analyzed by qRT-PCR and western blotting. CCK8, colony formation and transwell assays were utilized to test glioblastoma cell malignant abilities. Furthermore, the associations between LSP1 and miR-920 were indentified by bioinformatics analysis and rescue assays. Moreover, the protein expression levels of p-JAK2, JAK2, p-STAT5 and STAT5, as the hallmark of JAK/STAT5 signaling, were detected by western blotting. The observations showed that LSP1 was highly augmented in glioblastoma samples. Additionally, up-regulation of LSP1 was associated with a unfavorable prognosis in glioblastoma patients. Biological experiments revealed that depletion of LSP1 significantly suppressed the proliferation, invasion and migration of U251 and A172 cells. MiR-920, as an upstream regulator of LSP1, negatively modulated LSP1 expression and promoted U251 cells malignant behaviors after miR-920 inhibitor treatment. However, together knockdown LSP1 and miR-920 inhibited these effects. Moreover, the expression levels of p-JAK2 and p-STAT5 were increased or decreased in U251 cells after transfection of miR-920 inhibitor or si-LPS1. Taken together, miR-920 might blocked the malignant development of glioblastoma cells, which is possibly realized by targeting LSP1 and modulation of JAK/STAT5 pathway. These findings implied that miR-920/LSP1 was a potential therapeutic target for glioblastoma treatment.
Collapse
Affiliation(s)
- Ping Cong
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, People's Republic of China
| | - Hua-Ying Hou
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, People's Republic of China
| | - Wei Wei
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, People's Republic of China
| | - Yong Zhou
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, People's Republic of China
| | - Xiao-Ming Yu
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, People's Republic of China.
| |
Collapse
|
15
|
Fan XX, Xu MZ, Leung ELH, Jun C, Yuan Z, Liu L. ROS-Responsive Berberine Polymeric Micelles Effectively Suppressed the Inflammation of Rheumatoid Arthritis by Targeting Mitochondria. NANO-MICRO LETTERS 2020; 12:76. [PMID: 34138288 PMCID: PMC7770724 DOI: 10.1007/s40820-020-0410-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 05/04/2023]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease, which attacks human joint system and causes lifelong inflammatory condition. To date, no cure is available for RA and even the ratio of achieving remission is very low. Hence, to enhance the efficacy of RA treatment, it is essential to develop novel approaches specifically targeting pathological tissues. In this study, we discovered that RA synovial fibroblasts exhibited higher reactive oxygen species (ROS) and mitochondrial superoxide level, which were adopted to develop ROS-responsive nano-medicines in inflammatory microenvironment for enhanced RA treatment. A selenocystamine-based polymer was synthesized as a ROS-responsive carrier nanoplatform, and berberine serves as a tool drug. By assembling, ROS-responsive berberine polymeric micelles were fabricated, which remarkably increased the uptake of berberine in RA fibroblast and improved in vitro and in vivo efficacy ten times higher. Mechanistically, the anti-RA effect of micelles was blocked by the co-treatment of AMPK inhibitor or palmitic acid, indicating that the mechanism of micelles was carried out through targeting mitochondrial, suppressing lipogenesis and finally inhibiting cellular proliferation. Taken together, our ROS-responsive nano-medicines represent an effective way of preferentially releasing prodrug at the inflammatory microenvironment and improving RA therapeutic efficacy.
Collapse
Affiliation(s)
- Xing-Xing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| | - Meng-Ze Xu
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| | - Cai Jun
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| | - Zhen Yuan
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China.
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China.
| |
Collapse
|
16
|
Elevated lymphocyte specific protein 1 expression is involved in the regulation of leukocyte migration and immunosuppressive microenvironment in glioblastoma. Aging (Albany NY) 2020; 12:1656-1684. [PMID: 32003759 PMCID: PMC7053627 DOI: 10.18632/aging.102706] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023]
Abstract
Immune cell infiltration mediates therapeutic response to immune therapies. The investigation on the genes regulating leukocyte migration may help us to understand the mechanisms regulating immune cell infiltration in tumor microenvironment. Here, we collected the data from Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) to analyze the expression of leukocyte migration related genes in glioblastoma (GBM). Lymphocyte specific protein 1 (LSP1) was identified as the only gene in this family which not only has an elevated expression, but also serve as an independent predictive factor for progressive malignancy in glioma. We further confirmed these results in clinical glioma samples by quantitative PCR, immunofluorescence, immunohistochemistry, and western blot. Moreover, LSP1 expression was closely related to the response to radio- and chemotherapy in GBM, and positively correlated with immunosuppressive cell populations, including M2 macrophages, neutrophil, and regulatory T cell. Additionally, elevated LSP-1 expression enhanced the expression of immunosuppression related genes like programmed cell death 1 (PD1) and leukocyte associated immunoglobulin like receptor 1 (LAIR1) in macrophages. LSP1 also promoted the migration of macrophages. Together, our study suggests a novel role of LSP1 contributing to immunosuppressive microenvironment in GBM and serving as a potential therapeutic target for it.
Collapse
|
17
|
Saeed MB, Record J, Westerberg LS. Two sides of the coin: Cytoskeletal regulation of immune synapses in cancer and primary immune deficiencies. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 356:1-97. [DOI: 10.1016/bs.ircmb.2020.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
18
|
Placental growth factor regulates the generation of T H17 cells to link angiogenesis with autoimmunity. Nat Immunol 2019; 20:1348-1359. [PMID: 31406382 DOI: 10.1038/s41590-019-0456-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
Helper T cells actively communicate with adjacent cells by secreting soluble mediators, yet crosstalk between helper T cells and endothelial cells remains poorly understood. Here we found that placental growth factor (PlGF), a homolog of the vascular endothelial growth factor that enhances an angiogenic switch in disease, was selectively secreted by the TH17 subset of helper T cells and promoted angiogenesis. Interestingly, the 'angio-lymphokine' PlGF, in turn, specifically induced the differentiation of pathogenic TH17 cells by activating the transcription factor STAT3 via binding to its receptors and replaced the activity of interleukin-6 in the production of interleukin-17, whereas it suppressed the generation of regulatory T cells. Moreover, T cell-derived PlGF was required for the progression of autoimmune diseases associated with TH17 differentiation, including experimental autoimmune encephalomyelitis and collagen-induced arthritis, in mice. Collectively, our findings provide insights into the PlGF-dictated links among angiogenesis, TH17 cell development and autoimmunity.
Collapse
|
19
|
Su Q, Jing J, Li W, Ma J, Zhang X, Wang Z, Zhou Z, Dai L, Shao L. Impaired Tip60-mediated Foxp3 acetylation attenuates regulatory T cell development in rheumatoid arthritis. J Autoimmun 2019; 100:27-39. [PMID: 30954385 DOI: 10.1016/j.jaut.2019.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/02/2019] [Accepted: 02/10/2019] [Indexed: 01/06/2023]
Abstract
In rheumatoid arthritis (RA), imbalanced T cells subsets play a critical role in sustaining chronic inflammatory responses in the synovium. Naïve T cells in RA patients undergo maldifferentiation, including an increase in the effector Th1/Th17 lineage and a reduction in regulatory T (Treg) cells. Upon stimulation, naïve CD4+CD45RO- T cells from RA patients exhibited insufficient expression of Foxp3, which induced a deficiency in Tregs production and an imbalance of Treg/Th17 differentiation. Further mechanistic study indicated that RA T cells failed to produce sufficient levels of the histone acetyltransferase Tip60, leading to reduced acetylation of Foxp3; this, in turn, decreased Foxp3 expression, impaired Treg commitment, and promoted Th17 production. Moreover, in human synovium chimeric mice, suppression of Tip60 activity in healthy T cells promoted tissue infiltration and arthritogenesis, while reconstitution of Tip60 in RA T cells suppressed synovitis and effector T cell infiltration. Our findings link T cell maldifferentiation and tissue infiltration with Tip60-mediated Foxp3 acetylation and identify Tip60 as a potential therapeutic target for suppression of tissue inflammation and autoimmunogenesis in RA.
Collapse
Affiliation(s)
- Qiao Su
- (a)The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Jun Jing
- Department of Rheumatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Wuguo Li
- (a)The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Jianda Ma
- Department of Rheumatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Xueling Zhang
- (a)The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Zongren Wang
- (a)The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China; Department of Urology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Zhongyang Zhou
- (a)The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Lie Dai
- Department of Rheumatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China.
| | - Lan Shao
- (a)The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, PR China.
| |
Collapse
|
20
|
Tang W, Pan X, Han D, Rong D, Zhang M, Yang L, Ying J, Guan H, Chen Z, Wang X. Clinical significance of CD8 + T cell immunoreceptor with Ig and ITIM domains + in locally advanced gastric cancer treated with SOX regimen after D2 gastrectomy. Oncoimmunology 2019; 8:e1593807. [PMID: 31069158 PMCID: PMC6493216 DOI: 10.1080/2162402x.2019.1593807] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/14/2019] [Accepted: 02/28/2019] [Indexed: 12/21/2022] Open
Abstract
Gastric cancer (GC) development and progression is significantly associated with tumour immune escape. T cell immunoreceptor with Ig and ITIM domains (TIGIT) inhibits T-cell responses and is associated with human cancers and T cell exhaustion phenotypes, but its role in cancers remains unclear. TIGIT and programmed cell death protein (PD)-1 levels were detected in 441 human GC specimens using histochemistry. We used flow cytometry to evaluate percentage of TIGIT+ constituting CD8+ T cells of 23 patients with GC who underwent D2 gastrectomy and the S-1 plus oxaliplatin (SOX) regimen. We investigated the influence of SOX regimen and TIGIT functional antibody on CD8 tumour-infiltrating lymphocytes (TILs). Results showed that PD-1 and TIGIT were significantly over expressed in GC and predicted poorer outcome, agreeing with bioinformatics analysis. Significantly reduced percentages of CD8+ TIGIT+ cells were observed in patients after D2 gastrectomy (pre- vs post-surgery, 38 ± 8.7% vs. 26.7% ± 5.2%, p < 0.0001). TIGIT expression on CD8+T cells was modulated by chemotherapeutics (pre- and post-chemotherapy, 31.3 ± 9% vs. 25.1 ± 4.5%, respectively, p = 0.0047) and higher TIGIT expression in post-chemotherapy group was associated with relapsed GC (p = 0.036). In vitro experiments revealed increased CD8+ TIL proliferation and interferon (IFN)-γ production following SOX regimen and TIGIT functional antibody treatments. In conclusion, TIGIT contributes to CD8+ TILs immune dysfunction in patients with GC. Combination of anti-TIGIT therapy and chemotherapy could be considered a therapy for GC.
Collapse
Affiliation(s)
- Weiwei Tang
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiongxiong Pan
- Department of Anesthesiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Di Han
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Dawei Rong
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Minghui Zhang
- Department of Clinical skill Center, Medical School, Southeast University, Nanjing, Jiangsu, China
| | - Lulu Yang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Ying
- Department of Clinical Research Center, Xuyi People's Hospital, Xuyi, Jiangsu, China
| | - Hua Guan
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Ziyi Chen
- Department of General Surgery, Zhongda Hospital, Medical School, Southeast University, Nanjing, Jiangsu, China
| | - Xuehao Wang
- Hepatobiliary/Liver Transplantation Center, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| |
Collapse
|
21
|
Buckley CD, McGettrick HM. Leukocyte trafficking between stromal compartments: lessons from rheumatoid arthritis. Nat Rev Rheumatol 2018; 14:476-487. [DOI: 10.1038/s41584-018-0042-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
22
|
Abstract
Europe and North America have been leaders in rheumatology for many years. However, for more than a decade now the East Asian region has been catching up dramatically. Some aspects of rheumatology in East Asia are now almost comparable to those in the European League Against Rheumatism (EULAR) and the American College of Rheumatology (ACR). In this article, we describe recent progress in rheumatology in East Asia, focusing specifically on Japan, Korea, and China.
Collapse
Affiliation(s)
- Kazuhiko Yamamoto
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Yeong-Wook Song
- Seoul National University Medical Research Center, Seoul, South Korea
| | - Zhan-Guo Li
- Peking University People's Hospital, Peking, China
| |
Collapse
|
23
|
Lymphocyte-specific protein 1 regulates mechanosensory oscillation of podosomes and actin isoform-based actomyosin symmetry breaking. Nat Commun 2018; 9:515. [PMID: 29410425 PMCID: PMC5802837 DOI: 10.1038/s41467-018-02904-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/05/2018] [Indexed: 01/06/2023] Open
Abstract
Subcellular fine-tuning of the actomyosin cytoskeleton is a prerequisite for polarized cell migration. We identify LSP (lymphocyte-specific protein) 1 as a critical regulator of actomyosin contractility in primary macrophages. LSP1 regulates adhesion and migration, including the parameters cell area and speed, and also podosome turnover, oscillation and protrusive force. LSP1 recruits myosin IIA and its regulators, including myosin light chain kinase and calmodulin, and competes with supervillin, a myosin hyperactivator, for myosin regulators, and for actin isoforms, notably β-actin. Actin isoforms are anisotropically distributed in myosin IIA-expressing macrophages, and contribute to the differential recruitment of LSP1 and supervillin, thus enabling an actomyosin symmetry break, analogous to the situation in cells expressing two myosin II isoforms. Collectively, these results show that the cellular pattern of actin isoforms builds the basis for the differential distribution of two actomyosin machineries with distinct properties, leading to the establishment of discrete zones of actomyosin contractility. The actomyosin cytoskeleton plays an important role in polarised cell migration. Here the authors identify lymphocyte-specific protein (LSP)-1 as a regulator of actomyosin contractility in macrophages, by competing with supervillin for myosin IIA activators acting specifically on the β-actin isoform.
Collapse
|
24
|
Kringelbach TM, Glintborg B, Hogdall EV, Johansen JS, Hetland ML. Identification of new biomarkers to promote personalised treatment of patients with inflammatory rheumatic disease: protocol for an open cohort study. BMJ Open 2018; 8:e019325. [PMID: 29391382 PMCID: PMC5829933 DOI: 10.1136/bmjopen-2017-019325] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/13/2017] [Accepted: 12/04/2017] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The introduction of biological disease-modifying antirheumatic drugs (bDMARDs) has improved the treatment of inflammatory rheumatic diseases dramatically. However, bDMARD treatment failure occurs in 30%-40% of patients due to lack of effect or adverse events, and the tools to predict treatment outcomes in individual patients are currently limited. The objective of the present study is to identify diagnostic, prognostic and predictive biomarkers, which can be used to (1) diagnose inflammatory rheumatic diseases early in the disease course with high sensitivity and specificity, (2) improve prognostication or (3) predict and monitor treatment effectiveness and tolerability for the individual patient. METHODS AND ANALYSIS The present study is an observational and translational open cohort study with prospective collection of clinical data and biological materials (primarily blood) in patients with inflammatory rheumatic diseases treated in routine care. Patients contribute with one cross-sectional blood sample and/or are enrolled for longitudinal follow-up on initiation of a new DMARD (blood sampling after 0, 3, 6, 12, 24, 36, 48, 60 months of treatment). Other biological materials will be collected when accessible and relevant. Demographics, disease characteristics, comorbidities and lifestyle factors are registered at inclusion; DMARD treatment and outcomes are collected repeatedly during follow-up. Currently (July 2017), >5000 samples from approximately 3000 patients have been collected. Data will be analysed using appropriate statistical analyses. ETHICS AND DISSEMINATION The protocol is approved by the Danish Ethics Committee and the Danish Data Protection Agency. Participants give written and oral informed consent. Biomarkers will be evaluated and published according to the Reporting Recommendations for Tumour Marker (REMARK) prognostic studies, Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) and the Standards for Reporting of Diagnostic Accuracy (STARD) guidelines. Results will be published in peer-reviewed scientific journals and presented at international conferences. TRIAL REGISTRATION NUMBER NCT03214263.
Collapse
Affiliation(s)
- Tina Marie Kringelbach
- The Danish Rheumatologic Biobank, Capital Region, Denmark
- Bio- and Genome Bank Denmark, The Molecular Unit, Department of Pathology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Bente Glintborg
- The Danish Rheumatologic Biobank, Capital Region, Denmark
- Copenhagen Centre for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- The Danish DANBIO Registry, Rigshospitalet, Glostrup, Denmark
| | - Estrid V Hogdall
- The Danish Rheumatologic Biobank, Capital Region, Denmark
- Bio- and Genome Bank Denmark, The Molecular Unit, Department of Pathology, Copenhagen University Hospital Herlev, Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julia Sidenius Johansen
- The Danish Rheumatologic Biobank, Capital Region, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Copenhagen University Hospital Herlev, Herlev, Denmark
- Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denamrk
| | - Merete Lund Hetland
- The Danish Rheumatologic Biobank, Capital Region, Denmark
- Copenhagen Centre for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- The Danish DANBIO Registry, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
25
|
IL-4 driven transcription factor FoxQ1 is expressed by monocytes in atopic dermatitis and stimulates monocyte migration. Sci Rep 2017; 7:16847. [PMID: 29203829 PMCID: PMC5715145 DOI: 10.1038/s41598-017-17307-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 11/22/2017] [Indexed: 12/18/2022] Open
Abstract
Monocytes are actively recruited at sites of chronic inflammation. However, molecular factors involved in this process are not fully elucidated. Here, we show that cytokine IL-4 which is implicated in the development of chronic inflammatory disease atopic dermatitis (AD) induces expression of transcription factor FoxQ1 in human monocytes and macrophages. FoxQ1 mRNA levels were elevated in monocytes of AD patients compared to healthy donors. Overexpression of FoxQ1 in RAW 264.7 monocytic cells facilitated their migration towards MCP-1 and was associated with decreased expression of migration-regulating genes (claudin 11 and plexin C1). Furthermore, FoxQ1 overexpression in RAW cells accelerated TNFα secretion after LPS challenge. Overall, our results indicate that FoxQ1 stimulates monocyte motility, increases pro-inflammatory potential, and directs monocyte migration towards MCP-1 that is crucial for monocyte influx into inflammatory sites. This mechanism could contribute to the pathogenesis of chronic inflammatory disorders such as AD.
Collapse
|
26
|
Shen Y, Wen Z, Li Y, Matteson EL, Hong J, Goronzy JJ, Weyand CM. Metabolic control of the scaffold protein TKS5 in tissue-invasive, proinflammatory T cells. Nat Immunol 2017; 18:1025-1034. [PMID: 28737753 PMCID: PMC5568495 DOI: 10.1038/ni.3808] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/28/2017] [Indexed: 12/13/2022]
Abstract
Pathogenic T cells in individuals with rheumatoid arthritis (RA) infiltrate non-lymphoid tissue sites, maneuver through extracellular matrix and form lasting inflammatory microstructures. Here we found that RA T cells abundantly express the podosome scaffolding protein TKS5, which enables them to form tissue-invasive membrane structures. TKS5 overexpression was regulated by the intracellular metabolic environment of RA T cells-specifically, by reduced glycolytic flux that led to deficiencies in ATP and pyruvate. ATPlopyruvatelo conditions triggered fatty acid biosynthesis and the formation of cytoplasmic lipid droplets. Restoration of pyruvate production or inhibition of fatty acid synthesis corrected the tissue-invasiveness of RA T cells in vivo and reversed their proarthritogenic behavior. Thus, metabolic control of T cell locomotion provides new opportunities to interfere with T cell invasion into specific tissue sites.
Collapse
Affiliation(s)
- Yi Shen
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhenke Wen
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yinyin Li
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric L. Matteson
- Division of Rheumatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Jison Hong
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
27
|
Zhang H, Wang Y, Liu Z, Yao B, Dou C, Xu M, Li Q, Jia Y, Wu S, Tu K, Liu Q. Lymphocyte-specific protein 1 inhibits the growth of hepatocellular carcinoma by suppressing ERK1/2 phosphorylation. FEBS Open Bio 2016; 6:1227-1237. [PMID: 28255535 PMCID: PMC5324767 DOI: 10.1002/2211-5463.12139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/29/2016] [Accepted: 09/27/2016] [Indexed: 12/13/2022] Open
Abstract
Lymphocyte‐specific protein 1 (LSP1) has been reported to regulate cell biology in several human cancers including lymphoma and breast cancer. However, the functions of LSP1 in human hepatocellular carcinoma (HCC) are still unknown. In this study, we found that LSP1 expression was downregulated in HCC tissues and cell lines, and lower LSP1 expression was correlated with poor clinicopathological features including large tumor size, high Edmondson–Steiner grading and advanced tumor–node–metastasis (TNM) stage. Additionally, we demonstrated that patients with high LSP1 expression had significantly better overall survival and disease‐free survival. Moreover, LSP1 was found to be an independent factor for predicting the prognosis of HCC patients. In vitro and in vivo assays showed that overexpressing LSP1 inhibited HCC growth by inducing both apoptosis and growth arrest. Mechanistically, we found that expression of phosphorylated extracellular regulated protein kinases 1 and 2 (ERK1/2) was downregulated after LSP1 overexpression, indicating LSP1 could suppress HCC growth by inhibiting the ERK pathway in HCC cells. Taken together, these results indicate that LSP1 may serve as a prognostic marker and a potential therapeutic target in human HCC.
Collapse
Affiliation(s)
- Hongyong Zhang
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Yufeng Wang
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Zhikui Liu
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Bowen Yao
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Changwei Dou
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Meng Xu
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Qing Li
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Yuli Jia
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Shengli Wu
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| | - Qingguang Liu
- Department of Hepatobiliary Surgery The First Affiliated Hospital of Xi'an Jiaotong University China
| |
Collapse
|
28
|
Li Y, Shen Y, Hohensinner P, Ju J, Wen Z, Goodman SB, Zhang H, Goronzy JJ, Weyand CM. Deficient Activity of the Nuclease MRE11A Induces T Cell Aging and Promotes Arthritogenic Effector Functions in Patients with Rheumatoid Arthritis. Immunity 2016; 45:903-916. [PMID: 27742546 DOI: 10.1016/j.immuni.2016.09.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/08/2023]
Abstract
Immune aging manifests with a combination of failing adaptive immunity and insufficiently restrained inflammation. In patients with rheumatoid arthritis (RA), T cell aging occurs prematurely, but the mechanisms involved and their contribution to tissue-destructive inflammation remain unclear. We found that RA CD4+ T cells showed signs of aging during their primary immune responses and differentiated into tissue-invasive, proinflammatory effector cells. RA T cells had low expression of the double-strand-break repair nuclease MRE11A, leading to telomeric damage, juxtacentromeric heterochromatin unraveling, and senescence marker upregulation. Inhibition of MRE11A activity in healthy T cells induced the aging phenotype, whereas MRE11A overexpression in RA T cells reversed it. In human-synovium chimeric mice, MRE11Alow T cells were tissue-invasive and pro-arthritogenic, and MRE11A reconstitution mitigated synovitis. Our findings link premature T cell aging and tissue-invasiveness to telomere deprotection and heterochromatin unpacking, identifying MRE11A as a therapeutic target to combat immune aging and suppress dysregulated tissue inflammation.
Collapse
Affiliation(s)
- Yinyin Li
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Shen
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Philipp Hohensinner
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Internal Medicine II/Cardiology, Medical University of Vienna, 1090 Vienna, Austria
| | - Jihang Ju
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhenke Wen
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart B Goodman
- Department of Orthopedic Surgery and Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hui Zhang
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|