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Berry J, Tarn J, Lendrem D, Casement J, Ng WF. What can patients tell us in Sjögren's syndrome? Rheumatol Immunol Res 2024; 5:34-41. [PMID: 38571930 PMCID: PMC10985711 DOI: 10.1515/rir-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 10/04/2023] [Indexed: 04/05/2024]
Abstract
In Sjögren's Syndrome (SS), clinical heterogeneity and discordance between disease activity measures and patient experience are key obstacles to effective therapeutic development. Patient reported outcome measures (PROMs) are useful tools for understanding the unmet needs from the patients' perspective and therefore they are key for the development of patient centric healthcare systems. Initial concern about the subjectivity of PROMs has given way to methodological rigour and clear guidance for the development of PROMs. To date, several studies of patient stratification using PROMs have identified similar symptom-based subgroups. There is evidence to suggest that these subgroups may represent different disease endotypes with differing responses to therapeutic interventions. Stratified medicine approaches, alongside sensitive outcome measures, have the potential to improve our understanding of SS pathobiology and therapeutic development. The inclusion of PROMs is important for the success of such approaches. In this review we discuss the opportunities of using PROMs in understanding the pathogenesis of and therapeutic development for SS.
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Affiliation(s)
- Joe Berry
- Translational and Clinical Research Institute, Newcastle University, Newcastle uponTyne, UK
| | - Jessica Tarn
- Translational and Clinical Research Institute, Newcastle University, Newcastle uponTyne, UK
| | - Dennis Lendrem
- Translational and Clinical Research Institute, Newcastle University, Newcastle uponTyne, UK
| | - John Casement
- Translational and Clinical Research Institute, Newcastle University, Newcastle uponTyne, UK
| | - Wan-Fai Ng
- Translational and Clinical Research Institute, Newcastle University, Newcastle uponTyne, UK
- National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre& NIHR Newcastle Clinical Research Facility, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle uponTyne, UK
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Sadeq S, Chitcharoen S, Al-Hashimi S, Rattanaburi S, Casement J, Werner A. Significant Variations in Double-Stranded RNA Levels in Cultured Skin Cells. Cells 2024; 13:226. [PMID: 38334619 PMCID: PMC10854852 DOI: 10.3390/cells13030226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Endogenous double-stranded RNA has emerged as a potent stimulator of innate immunity. Under physiological conditions, endogenous dsRNA is maintained in the cell nucleus or the mitochondria; however, if protective mechanisms are breached, it leaches into the cytoplasm and triggers immune signaling pathways. Ectopic activation of innate immune pathways is associated with various diseases and senescence and can trigger apoptosis. Hereby, the level of cytoplasmic dsRNA is crucial. We have enriched dsRNA from two melanoma cell lines and primary dermal fibroblasts, including a competing probe, and analyzed the dsRNA transcriptome using RNA sequencing. There was a striking difference in read counts between the cell lines and the primary cells, and the effect was confirmed by northern blotting and immunocytochemistry. Both mitochondria (10-20%) and nuclear transcription (80-90%) contributed significantly to the dsRNA transcriptome. The mitochondrial contribution was lower in the cancer cells compared to fibroblasts. The expression of different transposable element families was comparable, suggesting a general up-regulation of transposable element expression rather than stimulation of a specific sub-family. Sequencing of the input control revealed minor differences in dsRNA processing pathways with an upregulation of oligoadenylate synthase and RNP125 that negatively regulates the dsRNA sensors RIG1 and MDA5. Moreover, RT-qPCR, Western blotting, and immunocytochemistry confirmed the relatively minor adaptations to the hugely different dsRNA levels. As a consequence, these transformed cell lines are potentially less tolerant to interventions that increase the formation of endogenous dsRNA.
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Affiliation(s)
- Shaymaa Sadeq
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.)
- Fallujah College of Medicine, University of Fallujah, Al-Fallujah 31002, Iraq
| | - Suwalak Chitcharoen
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Surar Al-Hashimi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.)
- College of Medicine, University of Misan, Al-Sader Teaching Hospital, Amarah 62001, Iraq
| | - Somruthai Rattanaburi
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - John Casement
- Bioinformatics Support Unit, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Andreas Werner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.)
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Berry JS, Tarn J, Casement J, Duret PM, Scott L, Wood K, Johnsen SJ, Nordmark G, Devauchelle-Pensec V, Seror R, Fisher B, Barone F, Bowman SJ, Bombardieri M, Lendrem D, Felten R, Gottenberg JE, Ng WF. Examining the biological pathways underlying clinical heterogeneity in Sjogren's syndrome: proteomic and network analysis. Ann Rheum Dis 2024; 83:88-95. [PMID: 37657927 DOI: 10.1136/ard-2023-224503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/20/2023] [Indexed: 09/03/2023]
Abstract
OBJECTIVES Stratification approaches are vital to address clinical heterogeneity in Sjogren's syndrome (SS). We previously described that the Newcastle Sjogren's Stratification Tool (NSST) identified four distinct clinical subtypes of SS. We performed proteomic and network analysis to analyse the underlying pathobiology and highlight potential therapeutic targets for different SS subtypes. METHOD We profiled serum proteins using O-link technology of 180 SS subjects. We used 5 O-link proteomics panels which included a total of 454 unique proteins. Network reconstruction was performed using the ARACNE algorithm, with differential expression estimates overlaid on these networks to reveal the key subnetworks of differential expression. Furthermore, data from a phase III trial of tocilizumab in SS were reanalysed by stratifying patients at baseline using NSST. RESULTS Our analysis highlights differential expression of chemokines, cytokines and the major autoantigen TRIM21 between the SS subtypes. Furthermore, we observe differential expression of several transcription factors associated with energy metabolism and redox balance namely APE1/Ref-1, FOXO1, TIGAR and BACH1. The differentially expressed proteins were inter-related in our network analysis, supporting the concept that distinct molecular networks underlie the clinical subtypes of SS. Stratification of patients at baseline using NSST revealed improvement of fatigue score only in the subtype expressing the highest levels of serum IL-6. CONCLUSIONS Our data provide clues to the pathways contributing to the glandular and non-glandular manifestations of SS and to potential therapeutic targets for different SS subtypes. In addition, our analysis highlights the need for further exploration of altered metabolism and mitochondrial dysfunction in the context of SS subtypes.
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Affiliation(s)
- Joe Scott Berry
- Translational and Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Jessica Tarn
- Translational and Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | - Lauren Scott
- Translational and Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Karl Wood
- Translational and Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Svein-Joar Johnsen
- Department of Rheumatology, Stavanger University Hospital, Stavanger, Norway
| | | | - Valérie Devauchelle-Pensec
- Lymphocytes B et auto-immunité, Inserm U1227, Brest university and La Cavale Blanche Hospital, Brest, France
| | - Raphaele Seror
- Centre for Immunology of Viral Infections and Autoimmune Diseases, Paris-Saclay University Faculty of Medicine, Le Kremlin-Bicetre, France
| | - Benjamin Fisher
- Institute of Inflammation and Ageing, University Hospitals Birmingham, Birmingham, UK
- Department of Rheumatology, National Institute for Health Research (NIHR), Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Fransesca Barone
- Institute of Inflammation and Ageing, University Hospitals Birmingham, Birmingham, UK
| | - Simon J Bowman
- Institute of Inflammation and Ageing, University Hospitals Birmingham, Birmingham, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, Queen Mary University of London Faculty of Medicine and Dentistry, London, UK
| | - Dennis Lendrem
- Translational and Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Renaud Felten
- Centre National de Référence des maladies auto-immunes et systémiques rares Est/Sud-Ouest (RESO), Hôpitaux universitaires de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), Strasbourg, France
| | - Jacques-Eric Gottenberg
- Centre National de Référence des maladies auto-immunes et systémiques rares Est/Sud-Ouest (RESO), Hôpitaux universitaires de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), Strasbourg, France
| | - Wan-Fai Ng
- Translational and Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
- National Institute for Health and Care Research (NIHR), Newcastle Biomedical Research Centre & NIHR Newcastle Clinical Research Facility, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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Permtermsin C, Lalchungnunga H, Nakjang S, Casement J, Ogle LF, Reeves HL, Strathdee G, Shukla R. Identification of TIAM1 as a Potential Synthetic-Lethal-like Gene in a Defined Subset of Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:6387. [PMID: 37047360 PMCID: PMC10094703 DOI: 10.3390/ijms24076387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most common type of liver cancer, has very poor outcomes. Current therapies often have low efficacy and significant toxicities. Thus, there is a critical need for the development of novel therapeutic approaches for HCC. We have developed a novel bioinformatics pipeline, which integrates genome-wide DNA methylation and gene expression data, to identify genes required for the survival of specific molecular cancer subgroups but not normal cells. Targeting these genes may induce cancer-specific "synthetic lethality". Initially, five potential HCC molecular subgroups were identified based on global DNA methylation patterns. Subgroup-2 exhibited the most unique methylation profile and two candidate subtype-specific vulnerability or SL-like genes were identified for this subgroup, including TIAM1, a guanine nucleotide exchange factor encoding gene known to activate Rac1 signalling. siRNA targeting TIAM1 inhibited cell proliferation in TIAM1-positive (subgroup-2) HCC cell lines but had no effect on the normal hepatocyte HHL5 cell line. Furthermore, TIAM1-positive/subgroup-2 cell lines were significantly more sensitive to the TIAM1/RAC1 inhibitor NSC23766 compared with TIAM1-negative HCC lines or the normal HHL5 cell line. The results are consistent with a synthetic lethal role for TIAM1 in a methylation-defined HCC subgroup and suggest it may be a viable therapeutic target in this subset of HCC patients.
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Affiliation(s)
- Chalermsin Permtermsin
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - H Lalchungnunga
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, Newcastle University, Newcastle NE2 4HH, UK
| | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle NE2 4HH, UK
| | - Laura Frances Ogle
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - Helen L Reeves
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
- Liver Unit, Freeman Hospital, Newcastle-Upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne NE7 7DN, UK
| | - Gordon Strathdee
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - Ruchi Shukla
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
- Department of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK
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Zadran B, Sudhindar PD, Wainwright D, Bury Y, Luli S, Howarth R, McCain MV, Watson R, Huet H, Palinkas F, Berlinguer-Palmini R, Casement J, Mann DA, Oakley F, Lunec J, Reeves H, Faulkner GJ, Shukla R. Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation. Br J Cancer 2023; 128:1236-1248. [PMID: 36707636 PMCID: PMC10050422 DOI: 10.1038/s41416-023-02154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Molecular characterisation of hepatocellular carcinoma (HCC) is central to the development of novel therapeutic strategies for the disease. We have previously demonstrated mutagenic consequences of Long-Interspersed Nuclear Element-1 (LINE1s/L1) retrotransposition. However, the role of L1 in HCC, besides somatic mutagenesis, is not well understood. METHODS We analysed L1 expression in the TCGA-HCC RNAseq dataset (n = 372) and explored potential relationships between L1 expression and clinical features. The findings were confirmed by immunohistochemical (IHC) analysis of an independent human HCC cohort (n = 48) and functional mechanisms explored using in vitro and in vivo model systems. RESULTS We observed positive associations between L1 and activated TGFβ-signalling, TP53 mutation, alpha-fetoprotein and tumour invasion. IHC confirmed a positive association between pSMAD3, a surrogate for TGFβ-signalling status, and L1 ORF1p (P < 0.0001, n = 32). Experimental modulation of L1 ORF1p levels revealed an influence of L1 ORF1p on key hepatocarcinogenesis-related pathways. Reduction in cell migration and invasive capacity was observed upon L1 ORF1 knockdown, both in vitro and in vivo. In particular, L1 ORF1p increased PIN1 cytoplasmic localisation. Blocking PIN1 activity abrogated L1 ORF1p-induced NF-κB-mediated inflammatory response genes while further activated TGFβ-signalling confirming differential alteration of PIN1 activity in cellular compartments by L1 ORF1p. DISCUSSION Our data demonstrate a causal link between L1 ORF1p and key oncogenic pathways mediated by PIN1, presenting a novel therapeutic avenue.
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Affiliation(s)
- Bassier Zadran
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Praveen Dhondurao Sudhindar
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Daniel Wainwright
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Yvonne Bury
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Saimir Luli
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Rachel Howarth
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Misti Vanette McCain
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Robyn Watson
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Hannah Huet
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Fanni Palinkas
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | | | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Derek A Mann
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Department of Gastroenterology and Hepatology, School of Medicine, Koç University, Istanbul, Turkey
| | - Fiona Oakley
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - John Lunec
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Helen Reeves
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Hepatopancreatobiliary Multidisciplinary Team, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS foundation, Newcastle-upon-Tyne, UK
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ruchi Shukla
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK.
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AL-Hashimi S, Roberts R, Weatherhead S, Rider A, Casement J, Werner A, Reynolds N. 343 Endogenous double-stranded RNA is a potential target for psoriasis therapy. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Rice SJ, Brumwell A, Falk J, Kehayova YS, Casement J, Parker E, Hofer IMJ, Shepherd C, Loughlin J. Genetic risk of osteoarthritis operates during human skeletogenesis. Hum Mol Genet 2022:6754371. [PMID: 36209419 DOI: 10.1093/hmg/ddac251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whilst methylation QTLs (mQTLs) co-localizing with OA GWAS signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. Here, for the first time, we have investigated the developmental origins of OA genetic risk at seven well-characterized OA risk loci, comprising 39 OA-mQTL CpGs, in human foetal limb (FL) and cartilage (FC) tissues using a range of molecular genetic techniques. We compared our results to aged cartilage samples (AC) and identified significant OA-mQTLs at 14 CpGs and 29 CpGs in FL and FC tissues, respectively. Differential methylation was observed at 26 sites between foetal and aged cartilage, with the majority becoming actively hypermethylated in old age. Notably, 6/9 OA effector genes showed allelic expression imbalances during foetal development. Finally, we conducted ATAC-sequencing in cartilage from the developing and aged hip and knee to identify accessible chromatin regions, and found enrichment for transcription factor binding motifs including SOX9 and FOS/JUN. For the first time, we have demonstrated the activity of OA-mQTLs and expression imbalance of OA effector genes during skeletogenesis. We show striking differences in the spatiotemporal function of these loci, contributing to our understanding of OA aetiology, with implications for the timing and strategy of pharmacological interventions.
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Affiliation(s)
- Sarah J Rice
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Abby Brumwell
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Julia Falk
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Yulia S Kehayova
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Casement
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Eleanor Parker
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ines M J Hofer
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Colin Shepherd
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Loughlin
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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Robinson N, Casement J, Gunter MJ, Huybrechts I, Agudo A, Barranco MR, Eichelmann F, Johnson T, Kaaks R, Pala V, Panico S, Sandanger TM, Schultze MB, Travis RC, Tumino R, Vineis P, Weiderpass E, Skinner R, Sharp L, McKay JA, Strathdee G. Anti-cancer therapy is associated with long-term epigenomic changes in childhood cancer survivors. Br J Cancer 2022; 127:288-300. [PMID: 35354948 PMCID: PMC9296636 DOI: 10.1038/s41416-022-01792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Childhood cancer survivors (CCS) exhibit significantly increased chronic diseases and premature death. Abnormalities in DNA methylation are associated with development of chronic diseases and reduced life expectancy. We investigated the hypothesis that anti-cancer treatments are associated with long-term DNA methylation changes that could be key drivers of adverse late health effects. METHODS Genome-wide DNA methylation was assessed using MethylationEPIC arrays in paired samples (before/after therapy) from 32 childhood cancer patients. Separately, methylation was determined in 32 samples from different adult CCS (mean 22-years post-diagnosis) and compared with cancer-free controls (n = 284). RESULTS Widespread DNA methylation changes were identified post-treatment in childhood cancer patients, including 146 differentially methylated regions (DMRs), which were consistently altered in the 32 post-treatment samples. Analysis of adult CCS identified matching methylation changes at 107/146 of the DMRs, suggesting potential long-term retention of post-therapy changes. Adult survivors also exhibited epigenetic age acceleration, independent of DMR methylation. Furthermore, altered methylation at the DUSP6 DMR was significantly associated with early mortality, suggesting altered methylation may be prognostic for some late adverse health effects in CCS. CONCLUSIONS These novel methylation changes could serve as biomarkers for assessing normal cell toxicity in ongoing treatments and predicting long-term health outcomes in CCS.
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Affiliation(s)
- Natassia Robinson
- Newcastle University Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Casement
- Bioinformatic Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Marc J Gunter
- Section of Nutrition and Metabolism, IARC, Lyon, France
| | | | - Antonio Agudo
- Unit of Nutrition and Cancer, Catalan Institute of Oncology - ICO, Nutrition and Cancer Group, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
| | | | - Fabian Eichelmann
- German Institute of Human Nutrition Potsdam-Rehbrücke, Heidelberg, Germany
| | - Theron Johnson
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valeria Pala
- Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | | | | | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Rosario Tumino
- Cancer Registry and Histopathology Department Azienda Sanitaria Provinciale (ASP), Ragusa, Italy
| | - Paolo Vineis
- MRC Centre for Environment and Health, Imperial College London, London, UK
| | | | - Roderick Skinner
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric and Adolescent Haematology/Oncology, Great North Children's Hospital, Newcastle, UK
| | - Linda Sharp
- Newcastle University Centre for Cancer, Population Health Sciences Institute, Newcastle upon Tyne, UK
| | - Jill A McKay
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Gordon Strathdee
- Newcastle University Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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9
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Isaacs JD, Brockbank S, Pedersen AW, Hilkens C, Anderson A, Stocks P, Lendrem D, Tarn J, Smith GR, Allen B, Casement J, Diboll J, Harry R, Cooles FAH, Cope AP, Simpson G, Toward R, Noble H, Parke A, Wu W, Clarke F, Scott D, Scott IC, Galloway J, Lempp H, Ibrahim F, Schwank S, Molyneux G, Lazarov T, Geissmann F, Goodyear CS, McInnes IB, Donnelly I, Gilmour A, Virlan AT, Porter D, Ponchel F, Emery P, El-Jawhari J, Parmar R, McDermott MF, Fisher BA, Young SP, Jones P, Raza K, Filer A, Pitzalis C, Barnes MR, Watson DS, Henkin R, Thorborn G, Fossati-Jimack L, Kelly S, Humby F, Bombardieri M, Rana S, Jia Z, Goldmann K, Lewis M, Ng S, Barbosa-Silva A, Tzanis E, Gallagher-Syed A, John CR, Ehrenstein MR, Altobelli G, Martins S, Nguyen D, Ali H, Ciurtin C, Buch M, Symmons D, Worthington J, Bruce IN, Sergeant JC, Verstappen SMM, Stirling F, Hughes-Morley A, Tom B, Farewell V, Zhong Y, Taylor PC, Buckley CD, Keidel S, Cuff C, Levesque M, Long A, Liu Z, Lipsky S, Harvey B, Macoritto M, Hong F, Kaymakcalan S, Tsuji W, Sabin T, Ward N, Talbot S, Padhji D, Sleeman M, Finch D, Herath A, Lindholm C, Jenkins M, Ho M, Hollis S, Marshall C, Parker G, Page M, Edwards H, Cuza A, Gozzard N, Pandis I, Rowe A, Capdevila FB, Loza MJ, Curran M, Verbeeck D, Dan Baker, Mela CM, Vranic I, Mela CT, Wright S, Rowell L, Vernon E, Joseph N, Payne N, Rao R, Binks M, Belson A, Ludbrook V, Hicks K, Tipney H, Ellis J, Hasan S, Didierlaurent A, Burny W, Haynes A, Larminie C, Harris R, Dastros-Pitei D, Carini C, Kola B, Jelinsky S, Hodge M, Maciejewski M, Ziemek D, Schulz-Knappe P, Zucht HD, Budde P, Coles M, Butler JA, Read S. RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients. Sci Data 2022; 9:196. [PMID: 35534493 PMCID: PMC9085807 DOI: 10.1038/s41597-022-01264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of early, drug naive RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 healthy vaccine recipients for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into immune-mediated disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.
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10
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Tarn J, Lendrem D, Barnes M, Casement J, Ng WF. Comorbidities in the UK Primary Sjögren’s Syndrome Registry. Front Immunol 2022; 13:864448. [PMID: 35603172 PMCID: PMC9116135 DOI: 10.3389/fimmu.2022.864448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Primary Sjögren’s Syndrome (PSS) is a chronic disease characterised by symptoms of oral and ocular dryness, pain, fatigue, anxiety and depression. PSS patients can be subclassified by the pattern of severity of these five key symptoms using the Newcastle Sjögren’s Stratification Tool (NSST). Although PSS is often associated with one or more comorbidities, the relationship between comorbidities, polypharmacy, and PSS symptom burden is unclear. Using data from the UK Primary Sjögren’s Syndrome Registry (UKPSSR) we describe the landscape of polypharmacy and comorbidities in PSS. Methods The UKPSSR is research biobank of clinically well-defined PSS patients where clinical, demographic, comorbidities and concomitant medications data are recorded. Patients were subclassified into the four NSST subgroups: Low Symptom Burden (LSB), High Symptom Burden (HSB), Dryness Dominated Fatigue (DDF) and Pain Dominated Fatigue (PDF). Group analyses of comorbid conditions and polypharmacy scores were performed. Comorbidity and Polypharmacy Scores (CPS) were modelled as a function of age, sex, symptom duration, body mass index (BMI), current immunosuppressant and hydroxychloroquine prescriptions and NSST subgroup. Results There were marked differences in the number and the nature of comorbidities associated with the NSST subgroups. LSB and DDF patients were characterized by fewer comorbidities and medications. In contrast, HSB and PDF patients were associated with more comorbidities and were more likely to be prescribed multiple medications. Group analysis shows that HSB patients are more closely associated with peripheral vascular disease and infection whereas the PDF patients were associated with cardiovascular disease and gastrointestinal comorbidities. Comorbidity and polypharmacy scores increase with age and BMI regardless of symptom subgroup and symptom duration. In addition, the longer the reported symptom duration the higher the associated comorbidities and polypharmacy scores. Conclusion Comorbid conditions are more prevalent in some subgroups of the PSS cohort but increase with age and BMI across the entire cohort. It is unclear from these data whether specific comorbid conditions are a consequence of PSS or represent shared aetiology or pathogenetic susceptibility. Regardless, these findings may have implications for disease management and clinical trial design.
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Affiliation(s)
- Jessica Tarn
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Dennis Lendrem
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Barnes
- Centre for Translational Bioinformatics, Queen Mary, University of London (QMUL), London, United Kingdom
| | - John Casement
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wan-Fai Ng
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre & National Institute for Health and Care Research (NIHR) Newcastle Clinical Research Facility, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
- *Correspondence: Wan-Fai Ng,
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11
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Werner A, Clark JE, Samaranayake C, Casement J, Zinad HS, Sadeq S, Al-Hashimi S, Smith M, Kotaja N, Mattick JS. Widespread formation of double-stranded RNAs in testis. Genome Res 2021; 31:1174-1186. [PMID: 34158368 PMCID: PMC8256860 DOI: 10.1101/gr.265603.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022]
Abstract
The testis transcriptome is highly complex and includes RNAs that potentially hybridize to form double-stranded RNA (dsRNA). We isolated dsRNA using the monoclonal J2 antibody and deep-sequenced the enriched samples from testes of juvenile Dicer1 knockout mice, age-matched controls, and adult animals. Comparison of our data set with recently published data from mouse liver revealed that the dsRNA transcriptome in testis is markedly different from liver: In testis, dsRNA-forming transcripts derive from mRNAs including promoters and immediate downstream regions, whereas in somatic cells they originate more often from introns and intergenic transcription. The genes that generate dsRNA are significantly expressed in isolated male germ cells with particular enrichment in pachytene spermatocytes. dsRNA formation is lower on the sex (X and Y) chromosomes. The dsRNA transcriptome is significantly less complex in juvenile mice as compared to adult controls and, possibly as a consequence, the knockout of Dicer1 has only a minor effect on the total number of transcript peaks associated with dsRNA. The comparison between dsRNA-associated genes in testis and liver with a reported set of genes that produce endogenous siRNAs reveals a significant overlap in testis but not in liver. Testis dsRNAs also significantly associate with natural antisense genes-again, this feature is not observed in liver. These findings point to a testis-specific mechanism involving natural antisense transcripts and the formation of dsRNAs that feed into the RNA interference pathway, possibly to mitigate the mutagenic impacts of recombination and transposon mobilization.
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Affiliation(s)
- Andreas Werner
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - James E Clark
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Calum Samaranayake
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - John Casement
- Bioinformatics Support Unit, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Hany S Zinad
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Shaymaa Sadeq
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
- Fallujah College of Medicine, Al-Fallujah University, Al-Fallujah, 9Q4V+H3, Iraq
| | - Surar Al-Hashimi
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Martin Smith
- CHU Sainte-Justine Research Centre, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Noora Kotaja
- Institute of Biomedicine, University of Turku, Turku, FIN-20520, Finland
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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12
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Posada J, Valadkhan S, Burge D, Davies K, Tarn J, Casement J, Jobling K, Gallagher P, Wilson D, Barone F, Fisher BA, Ng W. Improvement of Severe Fatigue Following Nuclease Therapy in Patients With Primary Sjögren's Syndrome: A Randomized Clinical Trial. Arthritis Rheumatol 2021; 73:143-150. [PMID: 32798283 PMCID: PMC7839752 DOI: 10.1002/art.41489] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To assess the safety and efficacy of RSLV-132, an RNase Fc fusion protein, in a phase II randomized, double-blind, placebo-controlled clinical trial in patients with primary Sjögren's syndrome (SS). METHODS Thirty patients with primary SS were randomized to receive treatment with RSLV-132 or placebo intravenously once per week for 2 weeks, and then every 2 weeks for 12 weeks. Eight patients received placebo and 20 patients received RSLV-132 at a dose of 10 mg/kg. Clinical efficacy measures included the European League Against Rheumatism (EULAR) Sjögren's Syndrome Disease Activity Index, EULAR Sjögren's Syndrome Patient Reported Index (ESSPRI), Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F), Profile of Fatigue (ProF), and the Digit Symbol Substitution Test (DSST). RESULTS Patients randomized to receive RSLV-132 experienced clinically meaningful improvements in the ESSPRI score (P = 0.27), FACIT-F score (P = 0.05), ProF score (P = 0.07), and DSST (P = 0.02) from baseline to day 99, whereas patients who received placebo showed no changes in any of these clinical efficacy measures. This improvement was significantly correlated with increased expression of selected interferon-inducible genes (Pearson's correlations, each P < 0.05). CONCLUSION Administration of RSLV-132 improved severe fatigue, as determined by 4 independent patient-reported measures of fatigue, in patients with primary SS.
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Affiliation(s)
| | | | | | | | | | | | - Kerry Jobling
- Newcastle Biomedical Research Centre and Newcastle upon Tyne Hospital NHS Foundation TrustNewcastle upon TyneUK
| | | | | | | | - Benjamin A. Fisher
- NIHR Birmingham Biomedical Research CentreUniversity Hospitals Birmingham NHS Foundation Trust, and University of BirminghamBirminghamUK
| | - Wan‐Fai Ng
- Newcastle UniversityNewcastle upon TyneUK
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13
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Sathasivam HP, Casement J, Bates T, Sloan P, Thomson P, Robinson M, Kist R. Gene expression changes associated with malignant transformation of oral potentially malignant disorders. J Oral Pathol Med 2020; 50:60-67. [PMID: 32740996 DOI: 10.1111/jop.13090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND A large number of oral squamous cell carcinomas (OSCCs) are believed to be preceded by oral potentially malignant disorders (OPMD) that have an increased likelihood of malignant transformation compared to clinically normal mucosa. This study was performed to identify differentially expressed genes between OPMDs that underwent malignant transformation (MT) and those that did not, termed "non-transforming" (NT) cases. METHODS Total RNA was extracted from formalin-fixed paraffin-embedded tissue biopsies of 20 OPMD cases with known clinical outcomes (10 MT vs. 10 NT). Samples were assessed for quantity, quality and integrity of RNA prior to sequencing. Analysis for differential gene expression between MT and NT was performed using statistical packages in R. Genes were considered to be significantly differentially expressed if the False Discovery Rate corrected P-value was < 0.05. RESULTS RNA yield was variable but RNA purity was good (A260/A280 > 1.90). Analysis of RNA-Sequencing outputs revealed 41 genes (34 protein-coding; 7 non-coding) that were significantly differentially expressed between MT and NT cases. The log2 fold change for the statistically significant differentially expressed genes ranged from -2.63 to 2.48, with 23 protein-coding genes being downregulated and 11 protein-coding genes being upregulated in MT cases compared to NT cases. CONCLUSION Several candidate genes that may play a role in malignant transformation of OPMD have been identified. Experiments to validate these candidates are underway. It is anticipated that this work will contribute to better understanding of the etiopathogenesis of OPMD and development of novel biomarkers.
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Affiliation(s)
- Hans P Sathasivam
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Malaysia
| | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | - Philip Sloan
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Newcastle upon Tyne Hospital NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter Thomson
- Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Max Robinson
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Newcastle upon Tyne Hospital NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ralf Kist
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Newcastle University Biosciences Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
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14
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Tarn JR, Howard-Tripp N, Lendrem DW, Mariette X, Saraux A, Devauchelle-Pensec V, Seror R, Skelton AJ, James K, McMeekin P, Al-Ali S, Hackett KL, Lendrem BC, Hargreaves B, Casement J, Mitchell S, Bowman SJ, Price E, Pease CT, Emery P, Lanyon P, Hunter J, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B, Johnsen SJA, Norheim KB, Omdal R, Stocken D, Everett C, Fernandez C, Isaacs JD, Gottenberg JE, Ng WF. Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials. Lancet Rheumatol 2019; 1:e85-e94. [PMID: 38229348 PMCID: PMC7134527 DOI: 10.1016/s2665-9913(19)30042-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Heterogeneity is a major obstacle to developing effective treatments for patients with primary Sjögren's syndrome. We aimed to develop a robust method for stratification, exploiting heterogeneity in patient-reported symptoms, and to relate these differences to pathobiology and therapeutic response. METHODS We did hierarchical cluster analysis using five common symptoms associated with primary Sjögren's syndrome (pain, fatigue, dryness, anxiety, and depression), followed by multinomial logistic regression to identify subgroups in the UK Primary Sjögren's Syndrome Registry (UKPSSR). We assessed clinical and biological differences between these subgroups, including transcriptional differences in peripheral blood. Patients from two independent validation cohorts in Norway and France were used to confirm patient stratification. Data from two phase 3 clinical trials were similarly stratified to assess the differences between subgroups in treatment response to hydroxychloroquine and rituximab. FINDINGS In the UKPSSR cohort (n=608), we identified four subgroups: Low symptom burden (LSB), high symptom burden (HSB), dryness dominant with fatigue (DDF), and pain dominant with fatigue (PDF). Significant differences in peripheral blood lymphocyte counts, anti-SSA and anti-SSB antibody positivity, as well as serum IgG, κ-free light chain, β2-microglobulin, and CXCL13 concentrations were observed between these subgroups, along with differentially expressed transcriptomic modules in peripheral blood. Similar findings were observed in the independent validation cohorts (n=396). Reanalysis of trial data stratifying patients into these subgroups suggested a treatment effect with hydroxychloroquine in the HSB subgroup and with rituximab in the DDF subgroup compared with placebo. INTERPRETATION Stratification on the basis of patient-reported symptoms of patients with primary Sjögren's syndrome revealed distinct pathobiological endotypes with distinct responses to immunomodulatory treatments. Our data have important implications for clinical management, trial design, and therapeutic development. Similar stratification approaches might be useful for patients with other chronic immune-mediated diseases. FUNDING UK Medical Research Council, British Sjogren's Syndrome Association, French Ministry of Health, Arthritis Research UK, Foundation for Research in Rheumatology. VIDEO ABSTRACT.
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Affiliation(s)
- Jessica R Tarn
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Nadia Howard-Tripp
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Dennis W Lendrem
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Xavier Mariette
- Université Paris-Sud, AP-HP Université Paris-Saclay, Hôpital Bicêtre, Department of Rheumatology, INSERM UMR1184, Le Kremlin-Bicêtre, France
| | - Alain Saraux
- Lymphocytes B et auto-immunité, Inserm U1227, University of Brest, Brest, France; Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Valerie Devauchelle-Pensec
- Lymphocytes B et auto-immunité, Inserm U1227, University of Brest, Brest, France; Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Raphaele Seror
- Université Paris-Sud, AP-HP Université Paris-Saclay, Hôpital Bicêtre, Department of Rheumatology, INSERM UMR1184, Le Kremlin-Bicêtre, France
| | - Andrew J Skelton
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine James
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Peter McMeekin
- Faculty of Health and Life Science, Northumbria University, Newcastle upon Tyne, UK
| | - Shereen Al-Ali
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Department of Pathological Analyses, College of Science, University of Basrah, Basrah, Iraq
| | - Katie L Hackett
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Faculty of Health and Life Science, Northumbria University, Newcastle upon Tyne, UK
| | - B Clare Lendrem
- National Institute for Health Research Newcastle In Vitro Diagnostics Co-operative, NewcastleUniversity, Newcastle upon Tyne, UK
| | - Ben Hargreaves
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - John Casement
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sheryl Mitchell
- Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | - Colin T Pease
- Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust Leeds, Leeds, UK
| | - Paul Emery
- Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust Leeds, Leeds, UK
| | - Peter Lanyon
- Nottingham University Hospitals NHS Trust, Rheumatology, Derby Road, Nottingham, UK
| | | | | | - Michele Bombardieri
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | | | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | | | | | - Marian Regan
- University Hospitals of Derby and Burton, Derby, UK
| | - Ian Giles
- Centre for Rheumatology, University College London, London, UK
| | - David Isenberg
- Centre for Rheumatology, University College London, London, UK
| | | | - David Coady
- City Hospitals Sunderland NHS Foundation Trust, Sunderland, UK
| | - Bhaskar Dasgupta
- Southend University Hospital NHS Foundation Trust, Westcliff-on-Sea, UK
| | - Neil McHugh
- Department of Pharmacy and Pharmacology, University of Bath, Bath, UK
| | | | - Robert Moots
- University Hospital Aintree, University of Liverpool, Liverpool, UK
| | - Nagui Gendi
- Basildon and Thurrock University Hospitals NHS Foundation Trust, Basildon, UK
| | - Mohammed Akil
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Bridget Griffiths
- Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | | | - Deborah Stocken
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Colin Everett
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Catherine Fernandez
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - John D Isaacs
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Jacques-Eric Gottenberg
- Department of Rheumatology, Centre de Référence National Pour les Maladies Auto-Immunes Systémiques Rares, CNRS, Strasbourg, France; Institut de Biologie Moléculaire et Cellulaire, Immunopathologie et Chimie Thérapeutique, Université de Strasbourg, Strasbourg, France
| | - Wan-Fai Ng
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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Guyet A, Dade-Robertson M, Wipat A, Casement J, Smith W, Mitrani H, Zhang M. Mild hydrostatic pressure triggers oxidative responses in Escherichia coli. PLoS One 2018; 13:e0200660. [PMID: 30016375 PMCID: PMC6049941 DOI: 10.1371/journal.pone.0200660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/30/2018] [Indexed: 11/24/2022] Open
Abstract
Hydrostatic pressure is an important physical stimulus which can cause various responses in bacterial cells. The survival and cellular processes of Escherichia coli under hydrostatic pressures between 10 MPa and 110 MPa have been studied. However, understanding bacterial responses to moderately elevated pressure of up to 10 MPa is useful for a range of different applications including for example in smart and responsive materials. In this study, the genetic responses of E. coli K-12 MG1655 to 1 MPa pressure was examined using transcriptomic analysis by RNA-Seq. The results show that 101 genes were differentially expressed under 1 MPa pressure in E. coli cells, with 85 of them up-regulated. The analysis suggested that some genes were over expressed to adapt the increase of oxygen levels in our system, and several functional categories are involved including oxidative stress responses, Fe-S cluster assembly and iron acquisition. Two differentially expressed genes azuC and entC were further investigated using RT-qPCR, and GFP reported strains of those two genes were created, AG1319 (PazuCazuC-msfgfp) and AG1321 (PentCentC-msfgfp). A linear response of azuC expression was observed between 0 MPa to 1 MPa by monitoring the fluorescence signal of strain AG1319 (PazuCazuC-msfgfp). This study is the first report to demonstrate the genetic response of bacterial cells under 1 MPa hydrostatic pressure, and provides preliminary data for creating pressure sensing bacterial strains for a wide range of applications.
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Affiliation(s)
- Aurelie Guyet
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martyn Dade-Robertson
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
- School of Architecture Planning and Landscape, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John Casement
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wendy Smith
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen Mitrani
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Meng Zhang
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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Robinson J, Rostami N, Casement J, Vollmer W, Rickard A, Jakubovics N. ArcR modulates biofilm formation in the dental plaque colonizerStreptococcus gordonii. Mol Oral Microbiol 2018; 33:143-154. [DOI: 10.1111/omi.12207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 01/20/2023]
Affiliation(s)
- J.C. Robinson
- School of Dental Sciences; Newcastle University; Newcastle upon Tyne UK
| | - N. Rostami
- School of Dental Sciences; Newcastle University; Newcastle upon Tyne UK
| | - J. Casement
- Bioinformatics Support Unit; Newcastle University; Newcastle upon Tyne UK
| | - W. Vollmer
- Centre for Bacterial Cell Biology; Newcastle University; Newcastle upon Tyne UK
| | - A.H. Rickard
- Department of Epidemiology; School of Public Health; University of Michigan; Ann Arbor MI USA
| | - N.S. Jakubovics
- School of Dental Sciences; Newcastle University; Newcastle upon Tyne UK
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Carr R, Casement J. What stress ulcer prophylaxis do you use? Br J Anaesth 2000. [DOI: 10.1093/bja/84.5.686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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