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Xiao Y, Xie S, Li HD, Liu Y, Zhang H, Zuo X, Zhu H, Li Y, Luo H. Characterised intron retention profiles in muscle tissue of idiopathic inflammatory myopathy subtypes. Ann Rheum Dis 2024; 83:901-914. [PMID: 38302260 DOI: 10.1136/ard-2023-225035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
OBJECTIVES Idiopathic inflammatory myopathies (IIMs) are a group of heterogeneous autoimmune diseases. Intron retention (IR) serves as an important post-transcriptional and translational regulatory mechanism. This study aims to identify changes in IR profiles in IIM subtypes, investigating their influence on proteins and their correlations with clinical features. METHODS RNA sequencing and liquid chromatography-tandem mass spectrometry were performed on muscle tissues obtained from 174 patients with IIM and 19 controls, following QC procedures. GTFtools and iREAD software were used for IR identification. An analysis of differentially expressed IRs (DEIs), exons and proteins was carried out using edgeR or DEP. Functional analysis was performed with clusterProfiler, and SPIRON was used to assess splicing factors. RESULTS A total of 6783 IRs located in 3111 unique genes were identified in all IIM subtypes compared with controls. IIM subtype-specific DEIs were associated with the pathogenesis of respective IIM subtypes. Splicing factors YBX1 and HSPA2 exhibited the most changes in dermatomyositis and immune-mediated necrotising myopathy. Increased IR was associated with reduced protein expression. Some of the IIM-specific DEIs were correlated with clinical parameters (skin rash, MMT-8 scores and muscle enzymes) and muscle histopathological features (myofiber necrosis, regeneration and inflammation). IRs in IFIH1 and TRIM21 were strongly correlated with anti-MDA5+ antibody, while IRs in SRP14 were associated with anti-SRP+ antibody. CONCLUSION This study revealed distinct IRs and specific splicing factors associated with IIM subtypes, which might be contributing to the pathogenesis of IIM. We also emphasised the potential impact of IR on protein expression in IIM muscles.
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Affiliation(s)
- Yizhi Xiao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Shasha Xie
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China PR
| | - Yanjuan Liu
- Institute of Emergency Medicine, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China PR
| | - Huali Zhang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China PR
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Yisha Li
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China PR
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Perez-Garcia LF, Röder E, Krijthe BP, Kranenburg-van Koppen LJ, van Adrichem R, Zirkzee E, Griffioen PH, Peeters K, Lin M, Struys EA, Jansen G, van Doorn MB, de Jonge R, Dohle GR, Dolhain RJ. Is methotrexate safe for men with an immune-mediated inflammatory disease and an active desire to become a father? Results of a prospective cohort study (iFAME-MTX). Ann Rheum Dis 2023; 82:1068-1075. [PMID: 37263756 PMCID: PMC10359513 DOI: 10.1136/ard-2023-224032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/12/2023] [Indexed: 06/03/2023]
Abstract
INTRODUCTION Current scientific evidence guiding the decision whether men with an active desire to become a father should be treated with methotrexate (MTX) remains controversial. We aimed to prospectively evaluate the testicular toxicity profile of MTX focusing on several markers of male fertility, including semen parameters and sperm DNA fragmentation index (sDFI). As a secondary outcome, we aimed to evaluate whether MTX-polyglutamates can be detected in spermatozoa and seminal plasma and to evaluate the enzymatic activity in spermatozoa of folylpolyglutamate synthetase (FPGS). METHODS In a prospective cohort study, men ≥18 years who started therapy with MTX were invited to participate (MTX-starters). Participants were instructed to produce two semen samples (a pre-exposure and a post-exposure sample after 13 weeks). Healthy men ≥18 years were invited to participate as controls. Conventional semen analyses, male reproductive endocrine axis and sDFI were compared between groups. FPGS enzymatic activity and MTX-PG1-5 concentrations were determined by mass spectrometry analytical methods. RESULTS In total, 20 MTX-starters and 25 controls were included. The pre-exposure and postexposure semen parameters of MTX-starters were not statistically significant different. Compared with healthy controls, the conventional semen parameters and the sDFI of MTX-starters were not statistically significant different. These data were corroborated by the marginal accumulation of MTX-PGs in spermatozoa, consistent with the very low FPGS enzymatic activity associated with the expression of an alternative FPGS splice-variant. DISCUSSION Treatment with MTX is not associated with testicular toxicity, consistent with the very low concentration of intracellular MTX-PG. Therefore, therapy with MTX can be safely started or continued in men and with a wish to become a father.
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Affiliation(s)
| | - Esther Röder
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Bouwe P Krijthe
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, Netherlands
- Department of Rheumatology, Sint Franciscus Vlietland Group, Rotterdam, Netherlands
| | - Laura Jc Kranenburg-van Koppen
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, Netherlands
- Department of Rheumatology, IJsselland Hospital, Capelle aan den IJssel, Netherlands
| | | | - Els Zirkzee
- Department of Rheumatology, Maasstad Ziekenhuis, Rotterdam, Netherlands
| | - Pieter H Griffioen
- Department of Clinical Chemistry, Erasmus Medical Center, Rotterdam, Netherlands
| | - Kris Peeters
- Centre for Reproductive Medicine, University of Antwerp, Antwerpen, Belgium
| | - Marry Lin
- Department of Laboratory Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Eduard A Struys
- Department of Laboratory Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Gerrit Jansen
- Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Center, location VUmc, Amsterdam, Netherlands
| | | | - Robert de Jonge
- Department of Laboratory Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Gert R Dohle
- Department of Urology, Erasmus Medical Center, Rotterdam, Netherlands
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3
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Muller IB, Lin M, de Jonge R, Will N, López-Navarro B, van der Laken C, Struys EA, Oudejans CBM, Assaraf YG, Cloos J, Puig-Kröger A, Jansen G. Methotrexate Provokes Disparate Folate Metabolism Gene Expression and Alternative Splicing in Ex Vivo Monocytes and GM-CSF- and M-CSF-Polarized Macrophages. Int J Mol Sci 2023; 24:9641. [PMID: 37298590 PMCID: PMC10253671 DOI: 10.3390/ijms24119641] [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: 04/14/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023] Open
Abstract
Macrophages constitute important immune cell targets of the antifolate methotrexate (MTX) in autoimmune diseases, including rheumatoid arthritis. Regulation of folate/MTX metabolism remains poorly understood upon pro-inflammatory (M1-type/GM-CSF-polarized) and anti-inflammatory (M2-type/M-CSF-polarized) macrophages. MTX activity strictly relies on the folylpolyglutamate synthetase (FPGS) dependent intracellular conversion and hence retention to MTX-polyglutamate (MTX-PG) forms. Here, we determined FPGS pre-mRNA splicing, FPGS enzyme activity and MTX-polyglutamylation in human monocyte-derived M1- and M2-macrophages exposed to 50 nmol/L MTX ex vivo. Moreover, RNA-sequencing analysis was used to investigate global splicing profiles and differential gene expression in monocytic and MTX-exposed macrophages. Monocytes displayed six-eight-fold higher ratios of alternatively-spliced/wild type FPGS transcripts than M1- and M2-macrophages. These ratios were inversely associated with a six-ten-fold increase in FPGS activity in M1- and M2-macrophages versus monocytes. Total MTX-PG accumulation was four-fold higher in M1- versus M2-macrophages. Differential splicing after MTX-exposure was particularly apparent in M2-macrophages for histone methylation/modification genes. MTX predominantly induced differential gene expression in M1-macrophages, involving folate metabolic pathway genes, signaling pathways, chemokines/cytokines and energy metabolism. Collectively, macrophage polarization-related differences in folate/MTX metabolism and downstream pathways at the level of pre-mRNA splicing and gene expression may account for variable accumulation of MTX-PGs, hence possibly impacting MTX treatment efficacy.
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Affiliation(s)
- Ittai B. Muller
- Department of Laboratory Medicine, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands; (I.B.M.); (M.L.); (R.d.J.); (E.A.S.); (C.B.M.O.)
| | - Marry Lin
- Department of Laboratory Medicine, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands; (I.B.M.); (M.L.); (R.d.J.); (E.A.S.); (C.B.M.O.)
| | - Robert de Jonge
- Department of Laboratory Medicine, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands; (I.B.M.); (M.L.); (R.d.J.); (E.A.S.); (C.B.M.O.)
| | - Nico Will
- Facility for Environment and Natural Science, Brandenburg Technical University Cottbus-Senftenberg, 01968 Senftenberg, Germany;
| | - Baltasar López-Navarro
- Laboratorio de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital Gregorio Marañón, 28007 Madrid, Spain; (B.L.-N.); (A.P.-K.)
| | - Conny van der Laken
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam University Medical Center–location VUmc, 1081 HV Amsterdam, The Netherlands;
| | - Eduard A. Struys
- Department of Laboratory Medicine, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands; (I.B.M.); (M.L.); (R.d.J.); (E.A.S.); (C.B.M.O.)
| | - Cees B. M. Oudejans
- Department of Laboratory Medicine, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands; (I.B.M.); (M.L.); (R.d.J.); (E.A.S.); (C.B.M.O.)
| | - Yehuda G. Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel;
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam University Medical Center–location VUmc, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Amaya Puig-Kröger
- Laboratorio de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital Gregorio Marañón, 28007 Madrid, Spain; (B.L.-N.); (A.P.-K.)
| | - Gerrit Jansen
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam University Medical Center–location VUmc, 1081 HV Amsterdam, The Netherlands;
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4
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Hebing RC, Lin M, Bulatovic Calasan M, Muller IB, Mahmoud S, Heil S, Struys EA, van den Bemt BJ, Twisk JW, Lems W, Nurmohamed MT, Jansen G, de Jonge R. Pharmacokinetics of oral and subcutaneous methotrexate in red and white blood cells in patients with early rheumatoid arthritis: the methotrexate monitoring trial. Ann Rheum Dis 2023; 82:460-467. [PMID: 36543526 DOI: 10.1136/ard-2022-223398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To investigate the pharmacokinetics of methotrexate polyglutamate (MTX-PG) accumulation in red blood cells (RBCs) and peripheral blood mononuclear cells (PBMCs) in patients with early rheumatoid arthritis (RA) after oral and subcutaneous MTX treatment. METHODS In a clinical prospective cohort study (Methotrexate Monitoring study), newly diagnosed patients with RA were randomised for oral or subcutaneous MTX. At 1, 2, 3 and 6 months after therapy initiation, blood was collected and RBCs and PBMCs were isolated. MTX-PG1-6 concentrations were determined by mass spectrometry methods using stable isotopes of MTX-PG1-6 as internal standards. RESULTS 43 patients (mean age: 58.5 years, 77% female) were included. PBMCs and RBCs revealed disparate pharmacokinetic profiles in both absolute MTX-PG accumulation levels and distribution profiles. Intracellular MTX-PG accumulation in PBMCs was significantly (p<0.001) 10-fold to 20-fold higher than RBCs at all time points, regardless of the administration route. MTX-PG distribution in PBMCs was composed of mostly MTX-PG1 (PG1>PG2>PG3). Remarkably, the distribution profile in PBMCs remained constant over 6 months. RBCs accumulated mainly MTX-PG1 and lower levels of MTX-PG2-5 at t=1 month. After 3 months, MTX-PG3 was the main PG-moiety in RBCs, a profile retained after 6 months of MTX therapy. Subcutaneous MTX administration results in higher RBC drug levels than after oral administration, especially shortly after treatment initiation. CONCLUSIONS This is the first study reporting disparate MTX-PG accumulation profiles in RBCs versus PBMCs in newly diagnosed patients with RA during 6 months oral or subcutaneous MTX administration. This analysis can contribute to improved MTX therapeutic drug monitoring for patients with RA. TRIAL REGISTRATION NUMBER NTR 7149.
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Affiliation(s)
- Renske Cf Hebing
- Reade, Amsterdam Rheumatology and Immunology Center, Amsterdam, The Netherlands
- Rheumatology, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | - Marry Lin
- Clinical Chemistry, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | - Maja Bulatovic Calasan
- Clinical Chemistry, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
- Rheumatology and Clinical Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Ittai B Muller
- Clinical Chemistry, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | - Sohaila Mahmoud
- Reade, Amsterdam Rheumatology and Immunology Center, Amsterdam, The Netherlands
| | - Sandra Heil
- Clinical Chemistry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eduard A Struys
- Clinical Chemistry, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | | | - Jos Wr Twisk
- Methodology and Applied Biostatistics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willem Lems
- Reade, Amsterdam Rheumatology and Immunology Center, Amsterdam, The Netherlands
- Rheumatology, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | - Michael T Nurmohamed
- Reade, Amsterdam Rheumatology and Immunology Center, Amsterdam, The Netherlands
- Rheumatology, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | - Gerrit Jansen
- Rheumatology, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
| | - Robert de Jonge
- Clinical Chemistry, Amsterdam UMC VUMC Site, Amsterdam, The Netherlands
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5
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Jiang Y, Zhong S, He S, Weng J, Liu L, Ye Y, Chen H. Biomarkers (mRNAs and non-coding RNAs) for the diagnosis and prognosis of rheumatoid arthritis. Front Immunol 2023; 14:1087925. [PMID: 36817438 PMCID: PMC9929281 DOI: 10.3389/fimmu.2023.1087925] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
In recent years, diagnostic and therapeutic approaches for rheumatoid arthritis (RA) have continued to improve. However, in the advanced stages of the disease, patients are unable to achieve long-term clinical remission and often suffer from systemic multi-organ damage and severe complications. Patients with RA usually have no overt clinical manifestations in the early stages, and by the time a definitive diagnosis is made, the disease is already at an advanced stage. RA is diagnosed clinically and with laboratory tests, including the blood markers C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) and the autoantibodies rheumatoid factor (RF) and anticitrullinated protein antibodies (ACPA). However, the presence of RF and ACPA autoantibodies is associated with aggravated disease, joint damage, and increased mortality, and these autoantibodies have low specificity and sensitivity. The etiology of RA is unknown, with the pathogenesis involving multiple factors and clinical heterogeneity. The early diagnosis, subtype classification, and prognosis of RA remain challenging, and studies to develop minimally invasive or non-invasive biomarkers in the form of biofluid biopsies are becoming more common. Non-coding RNA (ncRNA) molecules are composed of long non-coding RNAs, small nucleolar RNAs, microRNAs, and circular RNAs, which play an essential role in disease onset and progression and can be used in the early diagnosis and prognosis of RA. In this review of the diagnostic and prognostic approaches to RA disease, we provide an overview of the current knowledge on the subject, focusing on recent advances in mRNA-ncRNA as diagnostic and prognostic biomarkers from the biofluid to the tissue level.
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Affiliation(s)
- Yong Jiang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuxin Zhong
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
| | - Shenghua He
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Juanling Weng
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Lijin Liu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yufeng Ye
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Hanwei Chen
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Department of Radiology, GuangzhouPanyu Health Management Center (Panyu Rehabilitation Hospital), Guangzhou, China
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6
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Hariharan A, Qi W, Rehrauer H, Wu L, Ronner M, Wipplinger M, Kresoja‐Rakic J, Sun S, Oton‐Gonzalez L, Sculco M, Serre‐Beinier V, Meiller C, Blanquart C, Fonteneau J, Vrugt B, Rüschoff JH, Opitz I, Jean D, de Perrot M, Felley‐Bosco E. Heterogeneous RNA editing and influence of ADAR2 on mesothelioma chemoresistance and the tumor microenvironment. Mol Oncol 2022; 16:3949-3974. [PMID: 36221913 PMCID: PMC9718120 DOI: 10.1002/1878-0261.13322] [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: 05/17/2022] [Revised: 09/13/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
We previously observed increased levels of adenosine-deaminase-acting-on-dsRNA (Adar)-dependent RNA editing during mesothelioma development in mice exposed to asbestos. The aim of this study was to characterize and assess the role of ADAR-dependent RNA editing in mesothelioma. We found that tumors and mesothelioma primary cultures have higher ADAR-mediated RNA editing compared to mesothelial cells. Unsupervised clustering of editing in different genomic regions revealed heterogeneity between tumor samples as well as mesothelioma primary cultures. ADAR2 expression levels are higher in BRCA1-associated protein 1 wild-type tumors, with corresponding changes in RNA editing in transcripts and 3'UTR. ADAR2 knockdown and rescue models indicated a role in cell proliferation, altered cell cycle, increased sensitivity to antifolate treatment, and type-1 interferon signaling upregulation, leading to changes in the microenvironment in vivo. Our data indicate that RNA editing contributes to mesothelioma heterogeneity and highlights an important role of ADAR2 not only in growth regulation in mesothelioma but also in chemotherapy response, in addition to regulating inflammatory response downstream of sensing nucleic acid structures.
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Affiliation(s)
- Ananya Hariharan
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Weihong Qi
- Functional Genomics Center, ETH ZurichUniversity of ZurichSwitzerland
| | - Hubert Rehrauer
- Functional Genomics Center, ETH ZurichUniversity of ZurichSwitzerland
| | - Licun Wu
- Latner Thoracic Surgery Laboratories, Division of Thoracic SurgeryUniversity Health NetworkTorontoCanada
| | - Manuel Ronner
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Martin Wipplinger
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Jelena Kresoja‐Rakic
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Suna Sun
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Lucia Oton‐Gonzalez
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Marika Sculco
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | | | - Clément Meiller
- Centre de Recherche des Cordeliers, InsermSorbonne Université, Université Paris Cité, Functional Genomics of Solid TumorsFrance
| | - Christophe Blanquart
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NAFrance
| | | | - Bart Vrugt
- Institute of Pathology and Molecular PathologyUniversity Hospital ZurichSwitzerland
| | - Jan Hendrik Rüschoff
- Institute of Pathology and Molecular PathologyUniversity Hospital ZurichSwitzerland
| | - Isabelle Opitz
- Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Didier Jean
- Centre de Recherche des Cordeliers, InsermSorbonne Université, Université Paris Cité, Functional Genomics of Solid TumorsFrance
| | - Marc de Perrot
- Latner Thoracic Surgery Laboratories, Division of Thoracic SurgeryUniversity Health NetworkTorontoCanada
| | - Emanuela Felley‐Bosco
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
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7
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Wang J, Zhang SX, Chang JS, Cheng T, Jiang XJ, Su QY, Zhang JQ, Luo J, Li XF. Low-dose IL-2 improved clinical symptoms by restoring reduced regulatory T cells in patients with refractory rheumatoid arthritis: A randomized controlled trial. Front Immunol 2022; 13:947341. [PMID: 36524114 PMCID: PMC9744779 DOI: 10.3389/fimmu.2022.947341] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
Background Regulatory T cells (Tregs) have been found to play crucial roles in immune tolerance. However, the status of Tregs in refractory rheumatoid arthritis (RA) is still unclear. Moreover, low-dose interleukin-2 (IL-2) has been reported to selectively promote the expansion of Tregs. This study investigated the status of CD4+ Tregs and low-dose IL-2 therapy in patients with refractory RA. Methods The absolute number of CD4+CD25+FOXP3+ Treg (CD4 Treg), CD4+IL17+ T (Th17), and other subsets in peripheral blood (PB) from 41 patients with refractory RA and 40 healthy donors was characterized by flow cytometry combined with an internal microsphere counting standard. Twenty-six patients with refractory RA were treated with daily subcutaneous injections of 0.5 million IU of human IL-2 for five consecutive days. Then, its effects on CD4 Treg and Th17 cells in PB were analyzed. Results A decrease in the absolute number of PB CD4 Tregs rather than the increase in the number of Th17 was found to contribute to an imbalance between Th17 and CD4 Tregs in these patients, suggesting an essential role of CD4 Tregs in sustained high disease activity. Low-dose IL-2 selectively increased the number of CD4 Tregs and rebalanced the ratio of Th17 and CD4 Tregs, leading to increased clinical symptom remission without the observed side effects. Conclusions An absolute decrease of PB CD4 Tregs in patients with refractory RA was associated with continuing disease activation but not the increase of Th17 cells. Low-dose IL-2, a potential therapeutic candidate, restored decreased CD4 Tregs and promoted the rapid remission of patients with refractory RA without overtreatment and the observed side effects. Clinical trial registration http://www.chictr.org.cn/showproj.aspx?proj=13909, identifier ChiCTR-INR-16009546.
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Affiliation(s)
- Jia Wang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Jia-Song Chang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ting Cheng
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Xiao-Jing Jiang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Qin-Yi Su
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Jia-Qi Zhang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Jing Luo
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Xiao-Feng Li
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China,Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China,*Correspondence: Xiao-Feng Li,
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8
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Cavalli M, Eriksson N, Sundbaum JK, Wallenberg M, Kohnke H, Baecklund E, Hallberg P, Wadelius M. Genome-wide association study of liver enzyme elevation in an extended cohort of rheumatoid arthritis patients starting low-dose methotrexate. Pharmacogenomics 2022; 23:813-820. [PMID: 36070248 DOI: 10.2217/pgs-2022-0074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: A follow-up genome-wide association study (GWAS) in an extended cohort of rheumatoid arthritis (RA) patients starting low-dose methotrexate (MTX) treatment was performed to identify further genetic variants associated with alanine aminotransferase (ALT) elevation. Patients & methods: A GWAS was performed on 346 RA patients. Two outcomes within the first 6 months of MTX treatment were assessed: ALT >1.5-times the upper level of normal (ULN) and maximum level of ALT. Results: SPATA9 (rs72783407) was significantly associated with maximum level of ALT (p = 2.58 × 10-8) and PLCG2 (rs60427389) was tentatively associated with ALT >1.5 × ULN. Conclusion: Associations with SNPs in genes related to male fertility (SPATA9) and inflammatory processes (PLCG2) were identified.
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Affiliation(s)
- Marco Cavalli
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.,Department of Immunology, Genetics & Pathology, & Science for Life Laboratory, Uppsala University, SE-751 22, Uppsala, Sweden
| | - Niclas Eriksson
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.,Uppsala Clinical Research Center, SE-751 85, Uppsala, Sweden
| | - Johanna Karlsson Sundbaum
- Department of Medical Sciences, Rheumatology, Uppsala University, SE-751 85, Uppsala, Sweden.,Department of Health Sciences, Luleå University of Technology, SE-971 87, Luleå, Sweden
| | - Matilda Wallenberg
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.,Svensk Dos AB, Box 2, SE-751 03, Uppsala, Sweden
| | - Hugo Kohnke
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Eva Baecklund
- Department of Medical Sciences, Rheumatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Pär Hallberg
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
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9
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Cao X, Li P, Song X, Shi L, Qin L, Chen D, Chu T, Cheng Y. PCBP1 is associated with rheumatoid arthritis by affecting RNA products of genes involved in immune response in Th1 cells. Sci Rep 2022; 12:8398. [PMID: 35589811 PMCID: PMC9120163 DOI: 10.1038/s41598-022-12594-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by persistent synovitis, in which T helper 1 (Th1) can promote the development of a pro-inflammatory microenvironment. Poly(rC)-binding protein 1 (PCBP1) has been identified as a promising biomarker of RA, while its molecular mechanisms in RA development are unknown. As a canonical RNA binding protein, we propose that PCBP1 could play roles in RA by affecting both expression and alternative splicing levels in Th1 cells. Here, microarray datasets (GSE15573 and GSE23561), including 102 peripheral blood mononuclear cell samples from 39 RA patients and 63 controls, were used to evaluate the PCBP1 expression changes in RA patients. High throughput sequencing data (GSE84702) of iron driven pathogenesis in Th1 cells were downloaded and reanalyzed, including two Pcbp1 deficiency samples and two control samples in Th1 cells. In addition, CLIP-seq data of PCBP1 in Jurkat T cells was also analyzed to investigate the regulatory mechanisms of PCBP1. We found PCBP1 were down-regulated in RA specimens compared with control. The result of differentially expressed genes (DEGs) showed that Pcbp1 silencing in Th1 cells affected the expression of genes involved in immune response pathway. Alternative splicing analysis also revealed that PCBP1-regulated alternative splicing genes (RASGs) were enriched in TNF-a/NF-κB signaling pathway, T cell activation, T cell differentiation and T cell differentiation associated immune response pathways, which were highly associated with RA. DEGs and RASGs by Pcbp1 deficiency in mice were validated in PBMCs specimens of RA patients by RT-qPCR. Investigation of the CLIP-seq data revealed PCBP1 preferred to bind to 3′UTR and intron regions. PCBP1-bound genes were also significantly associated with RASGs, identifying 102 overlapped genes of these two gene sets. These genes were significantly enriched in several immune response related pathways, including myeloid cell differentiation and positive regulation of NF-κB transcription factor activity. Two RA-related genes, PML and IRAK1, were screened from the above immune related pathways. These results together support our hypothesis that PCBP1 can regulate the expression of genes involved in immune response pathway, and can bind to and regulate the alternative splicing of immune response related genes in immune T cells, and ultimately participate in the molecular mechanism of RA, providing new research ideas and directions for clinical diagnosis and treatment.
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Affiliation(s)
- Xue Cao
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Panlong Li
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Xiaojuan Song
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lipu Shi
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijie Qin
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, China
| | - Tianshu Chu
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China.
| | - Yanwei Cheng
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China.
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10
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Georgiou M, Ntavelou P, Stokes W, Roy R, Maher GJ, Stoilova T, Rakhit CP, Martins M, Ajuh P, Horowitz N, Berkowitz RS, Elias K, Seckl MJ, Pardo OE. ATR and CDK4/6 inhibition target the growth of methotrexate-resistant choriocarcinoma. Oncogene 2022; 41:2540-2554. [PMID: 35301407 PMCID: PMC9054653 DOI: 10.1038/s41388-022-02251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/12/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022]
Abstract
Low-risk gestational trophoblastic neoplasia including choriocarcinoma is often effectively treated with Methotrexate (MTX) as a first line therapy. However, MTX resistance (MTX-R) occurs in at least ≈33% of cases. This can sometimes be salvaged with actinomycin-D but often requires more toxic combination chemotherapy. Moreover, additional therapy may be needed and, for high-risk patients, 5% still die from the multidrug-resistant disease. Consequently, new treatments that are less toxic and could reverse MTX-R are needed. Here, we compared the proteome/phosphoproteome of MTX-resistant and sensitive choriocarcinoma cells using quantitative mass-spectrometry to identify therapeutically actionable molecular changes associated with MTX-R. Bioinformatics analysis of the proteomic data identified cell cycle and DNA damage repair as major pathways associated with MTX-R. MTX-R choriocarcinoma cells undergo cell cycle delay in G1 phase that enables them to repair DNA damage more efficiently through non-homologous end joining in an ATR-dependent manner. Increased expression of cyclin-dependent kinase 4 (CDK4) and loss of p16Ink4a in resistant cells suggested that CDK4 inhibition may be a strategy to treat MTX-R choriocarcinoma. Indeed, inhibition of CDK4/6 using genetic silencing or the clinically relevant inhibitor, Palbociclib, induced growth inhibition both in vitro and in an orthotopic in vivo mouse model. Finally, targeting the ATR pathway, genetically or pharmacologically, re-sensitised resistant cells to MTX in vitro and potently prevented the growth of MTX-R tumours in vivo. In short, we identified two novel therapeutic strategies to tackle MTX-R choriocarcinoma that could rapidly be translated into the clinic.
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Affiliation(s)
- Marina Georgiou
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Panagiota Ntavelou
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - William Stokes
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Rajat Roy
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Geoffrey J Maher
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Tsvetana Stoilova
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | | | - Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Neil Horowitz
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ross S Berkowitz
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kevin Elias
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michael J Seckl
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK.
| | - Olivier E Pardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK.
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11
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Muller IB, Meijers S, Kampstra P, van Dijk S, van Elswijk M, Lin M, Wojtuszkiewicz AM, Jansen G, de Jonge R, Cloos J. Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers. BMC Bioinformatics 2021; 22:347. [PMID: 34174808 PMCID: PMC8236165 DOI: 10.1186/s12859-021-04263-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/11/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Computational tools analyzing RNA-sequencing data have boosted alternative splicing research by identifying and assessing differentially spliced genes. However, common alternative splicing analysis tools differ substantially in their statistical analyses and general performance. This report compares the computational performance (CPU utilization and RAM usage) of three event-level splicing tools; rMATS, MISO, and SUPPA2. Additionally, concordance between tool outputs was investigated. RESULTS Log-linear relations were found between job times and dataset size in all splicing tools and all virtual machine (VM) configurations. MISO had the highest job times for all analyses, irrespective of VM size, while MISO analyses also exceeded maximum CPU utilization on all VM sizes. rMATS and SUPPA2 load averages were relatively low in both size and replicate comparisons, not nearing maximum CPU utilization in the VM simulating the lowest computational power (D2 VM). RAM usage in rMATS and SUPPA2 did not exceed 20% of maximum RAM in both size and replicate comparisons while MISO reached maximum RAM usage in D2 VM analyses for input size. Correlation coefficients of differential splicing analyses showed high correlation (β > 80%) between different tool outputs with the exception of comparisons of retained intron (RI) events between rMATS/MISO and rMATS/SUPPA2 (β < 60%). CONCLUSIONS Prior to RNA-seq analyses, users should consider job time, amount of replicates and splice event type of interest to determine the optimal alternative splicing tool. In general, rMATS is superior to both MISO and SUPPA2 in computational performance. Analysis outputs show high concordance between tools, with the exception of RI events.
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Affiliation(s)
- Ittai B Muller
- Department of Clinical Chemistry, Amsterdam UMC - location VUmc, Amsterdam, The Netherlands
| | | | | | | | | | - Marry Lin
- Department of Clinical Chemistry, Amsterdam UMC - location VUmc, Amsterdam, The Netherlands
| | - Anna M Wojtuszkiewicz
- Department of Hematology, Cancer Center Amsterdam, Rm CCA 4.24, Amsterdam UMC - location VUmc, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Gerrit Jansen
- Amsterdam Rheumatology and immunology Center, Amsterdam UMC - location VUmc, Amsterdam, The Netherlands
| | - Robert de Jonge
- Department of Clinical Chemistry, Amsterdam UMC - location VUmc, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, Cancer Center Amsterdam, Rm CCA 4.24, Amsterdam UMC - location VUmc, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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