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Afrasiabi A, Ahlenstiel C, Swaminathan S, Parnell GP. The interaction between Epstein-Barr virus and multiple sclerosis genetic risk loci: insights into disease pathogenesis and therapeutic opportunities. Clin Transl Immunology 2023; 12:e1454. [PMID: 37337612 PMCID: PMC10276892 DOI: 10.1002/cti2.1454] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic neurodegenerative autoimmune disease, characterised by the demyelination of neurons in the central nervous system. Whilst it is unclear what precisely leads to MS, it is believed that genetic predisposition combined with environmental factors plays a pivotal role. It is estimated that close to half the disease risk is determined by genetic factors. However, the risk of developing MS cannot be attributed to genetic factors alone, and environmental factors are likely to play a significant role by themselves or in concert with host genetics. Epstein-Barr virus (EBV) infection is the strongest known environmental risk factor for MS. There has been increasing evidence that leaves little doubt that EBV is necessary, but not sufficient, for developing MS. One plausible explanation is EBV may alter the host immune response in the presence of MS risk alleles and this contributes to the pathogenesis of MS. In this review, we discuss recent findings regarding how EBV infection may contribute to MS pathogenesis via interactions with genetic risk loci and discuss possible therapeutic interventions.
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Affiliation(s)
- Ali Afrasiabi
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- The Graduate School of Biomedical EngineeringUniversity of New South WalesSydneyNSWAustralia
| | - Chantelle Ahlenstiel
- Kirby InstituteUniversity of New South WalesSydneyNSWAustralia
- RNA InstituteUniversity of New South WalesSydneyNSWAustralia
| | - Sanjay Swaminathan
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- Department of MedicineWestern Sydney UniversitySydneyNSWAustralia
| | - Grant P Parnell
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- Biomedical Informatics and Digital Health, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
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2
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Keane JT, Afrasiabi A, Schibeci SD, Fewings N, Parnell GP, Swaminathan S, Booth DR. Gender and the Sex Hormone Estradiol Affect Multiple Sclerosis Risk Gene Expression in Epstein-Barr Virus-Infected B Cells. Front Immunol 2021; 12:732694. [PMID: 34566997 PMCID: PMC8455923 DOI: 10.3389/fimmu.2021.732694] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022] Open
Abstract
Multiple Sclerosis (MS) is a complex immune-mediated disease of the central nervous system. Treatment is based on immunomodulation, including specifically targeting B cells. B cells are the main host for the Epstein-Barr Virus (EBV), which has been described as necessary for MS development. Over 200 genetic loci have been identified as increasing susceptibility to MS. Many MS risk genes have altered expression in EBV infected B cells, dependent on the risk genotype, and are themselves regulated by the EBV transcription factor EBNA2. Females are 2-3 times more likely to develop MS than males. We investigated if MS risk loci might mediate the gender imbalance in MS. From a large public dataset, we identified gender-specific associations with EBV traits, and MS risk SNP/gene pairs with gender differences in their associations with gene expression. Some of these genes also showed gender differences in correlation of gene expression level with Estrogen Receptor 2. To test if estrogens may drive these gender specific differences, we cultured EBV infected B cells (lymphoblastoid cell lines, LCLs), in medium depleted of serum to remove the effects of sex hormones as well as the estrogenic effect of phenol red, and then supplemented with estrogen (100 nM estradiol). Estradiol treatment altered MS risk gene expression, LCL proliferation rate, EBV DNA copy number and EBNA2 expression in a sex-dependent manner. Together, these data indicate that there are estrogen-mediated gender-specific differences in MS risk gene expression and EBV functions. This may in turn contribute to gender differences in host response to EBV and to MS susceptibility.
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Affiliation(s)
- Jeremy T. Keane
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Ali Afrasiabi
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW SYDNEY, Sydney, NSW, Australia
| | - Stephen D. Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Nicole Fewings
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Grant P. Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Sanjay Swaminathan
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
- Department of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - David R. Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
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3
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Rhodes JW, Botting RA, Bertram KM, Vine EE, Rana H, Baharlou H, Vegh P, O'Neil TR, Ashhurst AS, Fletcher J, Parnell GP, Graham JD, Nasr N, Lim JJK, Barnouti L, Haertsch P, Gosselink MP, Di Re A, Reza F, Ctercteko G, Jenkins GJ, Brooks AJ, Patrick E, Byrne SN, Hunter E, Haniffa MA, Cunningham AL, Harman AN. Human anogenital monocyte-derived dendritic cells and langerin+cDC2 are major HIV target cells. Nat Commun 2021; 12:2147. [PMID: 33846309 PMCID: PMC8042121 DOI: 10.1038/s41467-021-22375-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Tissue mononuclear phagocytes (MNP) are specialised in pathogen detection and antigen presentation. As such they deliver HIV to its primary target cells; CD4 T cells. Most MNP HIV transmission studies have focused on epithelial MNPs. However, as mucosal trauma and inflammation are now known to be strongly associated with HIV transmission, here we examine the role of sub-epithelial MNPs which are present in a diverse array of subsets. We show that HIV can penetrate the epithelial surface to interact with sub-epithelial resident MNPs in anogenital explants and define the full array of subsets that are present in the human anogenital and colorectal tissues that HIV may encounter during sexual transmission. In doing so we identify two subsets that preferentially take up HIV, become infected and transmit the virus to CD4 T cells; CD14+CD1c+ monocyte-derived dendritic cells and langerin-expressing conventional dendritic cells 2 (cDC2).
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Affiliation(s)
- Jake W Rhodes
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Rachel A Botting
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia.,Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK
| | - Kirstie M Bertram
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Erica E Vine
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Hafsa Rana
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Heeva Baharlou
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Peter Vegh
- Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK
| | - Thomas R O'Neil
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Anneliese S Ashhurst
- School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - James Fletcher
- Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK
| | - Grant P Parnell
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - J Dinny Graham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | | | | | - Peter Haertsch
- Burns Unit, Concord Repatriation General Hospital, Sydney, Australia
| | - Martijn P Gosselink
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Angelina Di Re
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Faizur Reza
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Grahame Ctercteko
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Gregory J Jenkins
- Department of Obstetrics and Gynaecology, Westmead Hospital, Westmead, NSW, Australia
| | - Andrew J Brooks
- Department of Urology, Westmead Hospital, Westmead, NSW, Australia
| | - Ellis Patrick
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Maths and Statistics, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Scott N Byrne
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | | | - Muzlifah A Haniffa
- Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK.,Wellcome Sanger Institute, Hinxton, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Anthony L Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Andrew N Harman
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia. .,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia.
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4
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Afrasiabi A, Fewings NL, Schibeci SD, Keane JT, Booth DR, Parnell GP, Swaminathan S. The Interaction of Human and Epstein-Barr Virus miRNAs with Multiple Sclerosis Risk Loci. Int J Mol Sci 2021; 22:ijms22062927. [PMID: 33805769 PMCID: PMC8000127 DOI: 10.3390/ijms22062927] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Although the causes of Multiple Sclerosis (MS) still remain largely unknown, multiple lines of evidence suggest that Epstein–Barr virus (EBV) infection may contribute to the development of MS. Here, we aimed to identify the potential contribution of EBV-encoded and host cellular miRNAs to MS pathogenesis. We identified differentially expressed host miRNAs in EBV infected B cells (LCLs) and putative host/EBV miRNA interactions with MS risk loci. We estimated the genotype effect of MS risk loci on the identified putative miRNA:mRNA interactions in silico. We found that the protective allele of MS risk SNP rs4808760 reduces the expression of hsa-mir-3188-3p. In addition, our analysis suggests that hsa-let-7b-5p may interact with ZC3HAV1 differently in LCLs compared to B cells. In vitro assays indicated that the protective allele of MS risk SNP rs10271373 increases ZC3HAV1 expression in LCLs, but not in B cells. The higher expression for the protective allele in LCLs is consistent with increased IFN response via ZC3HAV1 and so decreased immune evasion by EBV. Taken together, this provides evidence that EBV infection dysregulates the B cell miRNA machinery, including MS risk miRNAs, which may contribute to MS pathogenesis via interaction with MS risk genes either directly or indirectly.
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Affiliation(s)
- Ali Afrasiabi
- Systems Biology and Health Data Analytics Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia;
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
| | - Nicole L. Fewings
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
| | - Stephen D. Schibeci
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
| | - Jeremy T. Keane
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
| | - David R. Booth
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
- Correspondence: (D.R.B.); (G.P.P.); (S.S.)
| | - Grant P. Parnell
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
- Correspondence: (D.R.B.); (G.P.P.); (S.S.)
| | - Sanjay Swaminathan
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia; (N.L.F.); (S.D.S.); (J.T.K.)
- Department of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Correspondence: (D.R.B.); (G.P.P.); (S.S.)
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5
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Ong LTC, Schibeci SD, Fewings NL, Booth DR, Parnell GP. Age-dependent VDR peak DNA methylation as a mechanism for latitude-dependent multiple sclerosis risk. Epigenetics Chromatin 2021; 14:9. [PMID: 33541415 PMCID: PMC7863270 DOI: 10.1186/s13072-021-00383-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/28/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The mechanisms linking UV radiation and vitamin D exposure to the risk of acquiring the latitude and critical period-dependent autoimmune disease, multiple sclerosis, is unclear. We examined the effect of vitamin D on DNA methylation and DNA methylation at vitamin D receptor binding sites in adult and paediatric myeloid cells. This was accomplished through differentiating CD34+ haematopoietic progenitors into CD14+ mononuclear phagocytes, in the presence and absence of calcitriol. RESULTS Few DNA methylation changes occurred in cells treated with calcitriol. However, several VDR-binding sites demonstrated increased DNA methylation in cells of adult origin when compared to cells of paediatric origin. This phenomenon was not observed at other transcription factor binding sites. Genes associated with these sites were enriched for intracellular signalling and cell activation pathways involved in myeloid cell differentiation and adaptive immune system regulation. CONCLUSION These results suggest vitamin D exposure at critical periods during development may contribute to latitude-related differences in autoimmune disease incidence.
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Affiliation(s)
- Lawrence T C Ong
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia. .,Department of Immunology, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, NSW, 2145, Australia.
| | - Stephen D Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Nicole L Fewings
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
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6
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Wijaya RS, Read SA, Truong NR, Han S, Chen D, Shahidipour H, Fewings NL, Schibeci S, Azardaryany MK, Parnell GP, Booth D, van der Poorten D, Lin R, George J, Douglas MW, Ahlenstiel G. HBV vaccination and HBV infection induces HBV-specific natural killer cell memory. Gut 2021; 70:357-369. [PMID: 32229546 DOI: 10.1136/gutjnl-2019-319252] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 03/02/2020] [Accepted: 03/18/2020] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Vaccination against hepatitis B virus (HBV) confers protection from subsequent infection through immunological memory that is traditionally considered the domain of the adaptive immune system. This view has been challenged following the identification of antigen-specific memory natural killer cells (mNKs) in mice and non-human primates. While the presence of mNKs has been suggested in humans based on the expansion of NK cells following pathogen exposure, evidence regarding antigen-specificity is lacking. Here, we demonstrate the existence of HBV-specific mNKs in humans after vaccination and in chronic HBV infection. DESIGN NK cell responses were evaluated by flow cytometry and ELISA following challenge with HBV antigens in HBV vaccinated, non-vaccinated and chronic HBV-infected individuals. RESULTS NK cells from vaccinated subjects demonstrated higher cytotoxic and proliferative responses against autologous hepatitis B surface antigen (HBsAg)-pulsed monocyte-derived dendritic cells (moDCs) compared with unvaccinated subjects. Moreover, NK cell lysis of HBsAg-pulsed moDCs was significantly higher than that of hepatitis B core antigen (HBcAg)-pulsed moDCs (non-vaccine antigen) or tumour necrosis factor α-activated moDCs in a NKG2D-dependent manner. The mNKs response was mediated by CD56dim NK cells coexpressing CD57, CD69 and KLRG1. Further, mNKs from chronic hepatitis B patients exhibited greater degranulation against HBcAg-pulsed moDCs compared with unvaccinated or vaccinated patients. Notably, mNK activity was negatively correlated with HBV DNA levels. CONCLUSIONS Our data support the presence of a mature mNKs following HBV antigen exposure either through vaccination or infection. Harnessing these antigen specific, functionally active mNKs provides an opportunity to develop novel treatments targeting HBV in chronic infection.
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Affiliation(s)
- Ratna S Wijaya
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia.,Faculty of Medicine, Pelita Harapan University, Tangerang, Indonesia
| | - Scott A Read
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia.,Blacktown Medical School, Western Sydney University, Blacktown, New South Wales, Australia.,Blacktown Hospital, Blacktown, New South Wales, Australia
| | - Naomi R Truong
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Shuanglin Han
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Dishen Chen
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia.,Blacktown Medical School, Western Sydney University, Blacktown, New South Wales, Australia
| | - Haleh Shahidipour
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia.,Blacktown Medical School, Western Sydney University, Blacktown, New South Wales, Australia.,Blacktown Hospital, Blacktown, New South Wales, Australia
| | - Nicole L Fewings
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Stephen Schibeci
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Mahmoud K Azardaryany
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - David Booth
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | | | - Rita Lin
- Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Jacob George
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia.,Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Mark W Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia.,Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney at Westmead Hospital, Westmead, New South Wales, Australia
| | - Golo Ahlenstiel
- Storr Liver Centre, The Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia .,Blacktown Medical School, Western Sydney University, Blacktown, New South Wales, Australia.,Blacktown Hospital, Blacktown, New South Wales, Australia
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7
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Law SPL, Gatt PN, Schibeci SD, McKay FC, Vucic S, Hart P, Byrne SN, Brown D, Stewart GJ, Liddle C, Parnell GP, Booth DR. Expression of CYP24A1 and other multiple sclerosis risk genes in peripheral blood indicates response to vitamin D in homeostatic and inflammatory conditions. Genes Immun 2021; 22:227-233. [PMID: 34163021 PMCID: PMC8387232 DOI: 10.1038/s41435-021-00144-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Although genetic and epidemiological evidence indicates vitamin D insufficiency contributes to multiple sclerosis (MS), and serum levels of vitamin D increase on treatment with cholecalciferol, recent metanalyses indicate that this vitamin D form does not ameliorate disease. Genetic variation in genes regulating vitamin D, and regulated by vitamin D, affect MS risk. We evaluated if the expression of vitamin D responsive MS risk genes could be used to assess vitamin D response in immune cells. Peripheral blood mononuclear cells (PBMCs) were isolated from healthy controls and people with MS treated with dimethyl fumarate. We assayed changes in expression of vitamin D responsive MS risk (VDRMS) genes in response to treatment with 25 hydroxy vitamin D in the presence or absence of inflammatory stimuli. Expression of CYP24A1 and other VDRMS genes was significantly altered in PBMCs treated with vitamin D in the homeostatic and inflammatory models. Gene expression in MS samples had similar responses to controls, but lower initial expression of the risk genes. Vitamin D treatment abrogated these differences. Expression of CYP24A1 and other MS risk genes in blood immune cells indicate vitamin D response and could enable assessment of immunological response to vitamin D in clinical trials and on therapy.
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Affiliation(s)
- Samantha P. L. Law
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Prudence N. Gatt
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Stephen D. Schibeci
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Fiona C. McKay
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Steve Vucic
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Prue Hart
- grid.410667.20000 0004 0625 8600Telethon Kids Institute, Perth Children’s Hospital, Perth, WA Australia
| | - Scott N. Byrne
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - David Brown
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Graeme J. Stewart
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Christopher Liddle
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - Grant P. Parnell
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
| | - David R. Booth
- grid.1013.30000 0004 1936 834XCentre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW Australia
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8
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Ong LTC, Booth DR, Parnell GP. Vitamin D and its Effects on DNA Methylation in Development, Aging, and Disease. Mol Nutr Food Res 2020; 64:e2000437. [PMID: 33079481 DOI: 10.1002/mnfr.202000437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/04/2020] [Revised: 09/08/2020] [Indexed: 12/18/2022]
Abstract
DNA methylation is increasingly being recognized as a mechanism through which environmental exposures confer disease risk. Several studies have examined the association between vitamin D and changes in DNA methylation in areas as diverse as human and animal development, genomic stability, chronic disease risk, and malignancy. In many cases, they have demonstrated clear associations between vitamin D and DNA methylation in candidate disease pathways. Despite this, a clear understanding of the mechanisms by which these factors interact is unclear. This paper reviews the current understanding of the effects of vitamin D on DNA methylation. In light of current knowledge in the field, the potential mechanisms mediating vitamin D effects on DNA methylation are discussed, as are the limiting factors and future avenues for research into this exciting area.
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Affiliation(s)
- Lawrence T C Ong
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, New South Wales, 2145, Australia
- Department of Immunology, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, New South Wales, 2145, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, New South Wales, 2145, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, New South Wales, 2145, Australia
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9
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Ong LTC, Parnell GP, Veale K, Stewart GJ, Liddle C, Booth DR. Regulation of the methylome in differentiation from adult stem cells may underpin vitamin D risk in MS. Genes Immun 2020; 21:335-347. [PMID: 33037402 DOI: 10.1038/s41435-020-00114-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/31/2020] [Accepted: 09/28/2020] [Indexed: 01/27/2023]
Abstract
Multiple lines of evidence indicate Multiple Sclerosis (MS) is affected by vitamin D. This effect may be mediated by methylation in immune cell progenitors. We aimed to determine (1) if haematopoietic stem cell methylation constrains methylation in daughter cells and is variable between individuals, and (2) the interaction of methylation with the vitamin D receptor binding sites. We interrogated genomic methylation levels from matching purified CD34+ haematopoietic stem cells and progeny CD14+ monocytes and CD56+ NK cells from 11 individuals using modified reduced representation bisulfite sequencing. Differential methylation of Vitamin D Receptor binding sites and MS risk genes was assessed from this and using pyrosequencing for the vitamin D regulated MS risk gene ZMIZ1. Although DNA methylation states at CpG islands and other sites are almost entirely recapitulated between progenitor and progeny immune cells, significant variation was detected at some regions between cell subsets and individuals; including around the MS risk genes HLA DRB1 and the vitamin D repressor NCOR2. Methylation of the vitamin D responsive MS risk gene ZMIZ1 was associated with risk SNP and disease. We conclude that DNA methylation settings in adult haematopoietic stem cells may contribute to individual variation in vitamin D responses in immune cells.
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Affiliation(s)
- Lawrence T C Ong
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia. .,Department of Immunology, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, NSW, 2145, Australia.
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Kelly Veale
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Graeme J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
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10
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Ong LTC, Parnell GP, Afrasiabi A, Stewart GJ, Swaminathan S, Booth DR. Transcribed B lymphocyte genes and multiple sclerosis risk genes are underrepresented in Epstein-Barr Virus hypomethylated regions. Genes Immun 2020; 21:91-99. [PMID: 31619767 PMCID: PMC7182534 DOI: 10.1038/s41435-019-0089-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 11/24/2022]
Abstract
Epstein-Barr Virus (EBV) infection appears to be necessary for the development of Multiple Sclerosis (MS), although the specific mechanisms are unknown. More than 200 single-nucleotide polymorphisms (SNPs) are known to be associated with the risk of developing MS. About a quarter of these are also highly associated with proximal gene expression in B cells infected with EBV (lymphoblastoid cell lines-LCLs). The DNA of LCLs is hypomethylated compared with both uninfected and activated B cells. Since methylation can affect gene expression, and so cell differentiation and immune evasion, we hypothesised that EBV-driven hypomethylation may affect the interaction between EBV infection and MS. We interrogated an existing dataset comprising three individuals with whole-genome bisulfite sequencing data from EBV transformed B cells and CD40L-activated B cells. DNA methylation surrounding MS risk SNPs associated with gene expression in LCLs (LCLeQTL) was less likely to be hypomethylated than randomly selected chromosomal regions. Differential methylation was independent of genomic features such as promoter regions, but genes preferentially expressed in EBV-infected B cells, including the LCLeQTL genes, were underrepresented in the hypomethylated regions. Our data does not indicate MS genetic risk is affected by EBV hypomethylation.
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Affiliation(s)
- Lawrence T C Ong
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
- Department of Clinical Immunology and Allergy, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, NSW, 2145, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Ali Afrasiabi
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Graeme J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
- Department of Clinical Immunology and Allergy, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, NSW, 2145, Australia
| | - Sanjay Swaminathan
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
- Department of Clinical Immunology and Allergy, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, NSW, 2145, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia.
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11
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Afrasiabi A, Parnell GP, Swaminathan S, Stewart GJ, Booth DR. The interaction of Multiple Sclerosis risk loci with Epstein-Barr virus phenotypes implicates the virus in pathogenesis. Sci Rep 2020; 10:193. [PMID: 31932685 PMCID: PMC6957475 DOI: 10.1038/s41598-019-55850-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022] Open
Abstract
Translating the findings of genome wide association studies (GWAS) to new therapies requires identification of the relevant immunological contexts to interrogate for genetic effects. In one of the largest GWAS, more than 200 risk loci have been identified for Multiple Sclerosis (MS) susceptibility. Infection with Epstein-Barr virus (EBV) appears to be necessary for the development of Multiple Sclerosis (MS). Many MS risk loci are associated with altered gene expression in EBV infected B cells (LCLs). We have interrogated this immunological context to identify interaction between MS risk loci and EBV DNA copy number, intrinsic growth rate and EBV encoded miRNA expression. The EBV DNA copy number was associated with significantly more risk alleles for MS than for other diseases or traits. EBV miRNAs BART4-3p and BART3-5p were highly associated with EBV DNA copy number and MS risk loci. The poliovirus receptor (PVR) risk SNP was associated with EBV DNA copy number, PVR and miRNA expression. Targeting EBV miRNAs BART4-3p and BART3-5p, and the gene PVR, may provide therapeutic benefit in MS. This study also indicates how immunological context and risk loci interactions can be exploited to validate and develop novel therapeutic approaches.
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Affiliation(s)
- Ali Afrasiabi
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Sanjay Swaminathan
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Graeme J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
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12
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Tang BM, Shojaei M, Teoh S, Meyers A, Ho J, Ball TB, Keynan Y, Pisipati A, Kumar A, Eisen DP, Lai K, Gillett M, Santram R, Geffers R, Schreiber J, Mozhui K, Huang S, Parnell GP, Nalos M, Holubova M, Chew T, Booth D, Kumar A, McLean A, Schughart K. Neutrophils-related host factors associated with severe disease and fatality in patients with influenza infection. Nat Commun 2019; 10:3422. [PMID: 31366921 PMCID: PMC6668409 DOI: 10.1038/s41467-019-11249-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
Severe influenza infection has no effective treatment available. One of the key barriers to developing host-directed therapy is a lack of reliable prognostic factors needed to guide such therapy. Here, we use a network analysis approach to identify host factors associated with severe influenza and fatal outcome. In influenza patients with moderate-to-severe diseases, we uncover a complex landscape of immunological pathways, with the main changes occurring in pathways related to circulating neutrophils. Patients with severe disease display excessive neutrophil extracellular traps formation, neutrophil-inflammation and delayed apoptosis, all of which have been associated with fatal outcome in animal models. Excessive neutrophil activation correlates with worsening oxygenation impairment and predicted fatal outcome (AUROC 0.817-0.898). These findings provide new evidence that neutrophil-dominated host response is associated with poor outcomes. Measuring neutrophil-related changes may improve risk stratification and patient selection, a critical first step in developing host-directed immune therapy.
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Affiliation(s)
- Benjamin M Tang
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia. .,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia. .,Respiratory Tract Infection Research Node, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia.
| | - Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia.,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Adrienne Meyers
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - John Ho
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - T Blake Ball
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Yoav Keynan
- Department of Internal Medicine, Medical Microbiology and Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Amarnath Pisipati
- Department of Chemistry and Biological Chemistry, Harvard University, Cambridge, MA, USA
| | - Aseem Kumar
- Department of Chemistry and Biochemistry, Laurentian University, Laurentian, Canada
| | - Damon P Eisen
- Townsville Hospital, Townsville, Queensland, Australia
| | - Kevin Lai
- Department of Emergency Medicine, Westmead Hospital, Sydney, Australia
| | - Mark Gillett
- Department of Emergency Medicine, Royal North Shore Hospital, Sydney, Australia
| | - Rahul Santram
- Department of Emergency Medicine, St. Vincent Hospital, Sydney, Australia
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jens Schreiber
- Otto-von-Guerike University of Magdeburg, Clinic of Pneumology, Magdeburg, Germany
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Centre, Memphis, TN, USA
| | - Stephen Huang
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Marek Nalos
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia.,Department of Internal Medicine, Medical Faculty Plzen, Charles University Prague, Staré Město, Czech Republic
| | - Monika Holubova
- Biomedical Centre, Medical Faculty Plzen, Charles University Prague, Staré Město, Czech Republic
| | - Tracy Chew
- Sydney Informatic Hub, The University of Sydney, Sydney, Australia
| | - David Booth
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Anand Kumar
- Section of Critical Care Medicine and Section of Infectious Diseases, Departments of Medicine, Medical Microbiology and Pharmacology, University of Manitoba, Winnipeg, Canada
| | - Anthony McLean
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,University of Veterinary Medicine, Hannover, Germany.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Centre, Memphis, TN, USA
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13
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Afrasiabi A, Parnell GP, Fewings N, Schibeci SD, Basuki MA, Chandramohan R, Zhou Y, Taylor B, Brown DA, Swaminathan S, McKay FC, Stewart GJ, Booth DR. Evidence from genome wide association studies implicates reduced control of Epstein-Barr virus infection in multiple sclerosis susceptibility. Genome Med 2019; 11:26. [PMID: 31039804 PMCID: PMC6492329 DOI: 10.1186/s13073-019-0640-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 04/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genome wide association studies have identified > 200 susceptibility loci accounting for much of the heritability of multiple sclerosis (MS). Epstein-Barr virus (EBV), a memory B cell tropic virus, has been identified as necessary but not sufficient for development of MS. The molecular and immunological basis for this has not been established. Infected B cell proliferation is driven by signalling through the EBV produced cell surface protein LMP1, a homologue of the MS risk gene CD40. METHODS We have investigated transcriptomes of B cells and EBV-infected B cells at Latency III (LCLs) and identified MS risk genes with altered expression on infection and with expression levels associated with the MS risk genotype (LCLeQTLs). The association of LCLeQTL genomic burden with EBV phenotypes in vitro and in vivo was examined. The risk genotype effect on LCL proliferation with CD40 stimulation was assessed. RESULTS These LCLeQTL MS risk SNP:gene pairs (47 identified) were over-represented in genes dysregulated between B and LCLs (p < 1.53 × 10-4), and as target loci of the EBV transcription factor EBNA2 (p < 3.17 × 10-16). Overall genetic burden of LCLeQTLs was associated with some EBV phenotypes but not others. Stimulation of the CD40 pathway by CD40L reduced LCL proliferation (p < 0.001), dependent on CD40 and TRAF3 MS risk genotypes. Both CD40 and TRAF3 risk SNPs are in binding sites for the EBV transcription factor EBNA2, with expression of each correlated with EBNA2 expression dependent on genotype. CONCLUSIONS These data indicate targeting EBV may be of therapeutic benefit in MS.
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Affiliation(s)
- Ali Afrasiabi
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Nicole Fewings
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Stephen D Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Monica A Basuki
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Ramya Chandramohan
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Yuan Zhou
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Bruce Taylor
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - David A Brown
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Sanjay Swaminathan
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Fiona C McKay
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Graeme J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
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14
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Parnell GP, Schibeci SD, Fewings NL, Afrasiabi A, Law SPL, Samaranayake S, Kh'ng JH, Fong YH, Brown DA, Liddle C, Stewart GJ, Booth DR. The latitude-dependent autoimmune disease risk genes ZMIZ1 and IRF8 regulate mononuclear phagocytic cell differentiation in response to vitamin D. Hum Mol Genet 2019; 28:269-278. [PMID: 30285234 DOI: 10.1093/hmg/ddy324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
Epidemiological, molecular and genetic studies have indicated that high serum vitamin D levels are associated with lower risk of several autoimmune diseases. The vitamin D receptor (VDR) binding sites in monocytes and dendritic cells (DCs) are more common in risk genes for diseases with latitude dependence than in risk genes for other diseases. The transcription factor genes Zinc finger MIZ domain-containing protein 1 (ZMIZ1) and interferon regulatory factor 8 (IRF8)-risk genes for many of these diseases-have VDR binding peaks co-incident with the risk single nucleotide polymorphisms (SNPs). We show these genes are responsive to vitamin D: ZMIZ1 expression increased and IRF8 expression decreased, and this response was affected by genotype in different cell subsets. The IL10/IL12 ratio in tolerogenic DCs increased with vitamin D. These data indicate that vitamin D regulation of ZMIZ1 and IRF8 in DCs and monocytes contribute to latitude-dependent autoimmune disease risk.
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Affiliation(s)
- Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Stephen D Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Nicole L Fewings
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Ali Afrasiabi
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Samantha P L Law
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Shanuka Samaranayake
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Jing Hui Kh'ng
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Yee Hsu Fong
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - David A Brown
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Christopher Liddle
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - Graeme J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead NSW, Australia
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15
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Sweeney TE, Perumal TM, Henao R, Nichols M, Howrylak JA, Choi AM, Bermejo-Martin JF, Almansa R, Tamayo E, Davenport EE, Burnham KL, Hinds CJ, Knight JC, Woods CW, Kingsmore SF, Ginsburg GS, Wong HR, Parnell GP, Tang B, Moldawer LL, Moore FE, Omberg L, Khatri P, Tsalik EL, Mangravite LM, Langley RJ. A community approach to mortality prediction in sepsis via gene expression analysis. Nat Commun 2018; 9:694. [PMID: 29449546 PMCID: PMC5814463 DOI: 10.1038/s41467-018-03078-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [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: 01/12/2017] [Accepted: 01/18/2018] [Indexed: 12/27/2022] Open
Abstract
Improved risk stratification and prognosis prediction in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate reflect global illness severity with suboptimal performance, and do not specifically reveal the underlying dysregulation of sepsis. Here, we present prognostic models for 30-day mortality generated independently by three scientific groups by using 12 discovery cohorts containing transcriptomic data collected from primarily community-onset sepsis patients. Predictive performance is validated in five cohorts of community-onset sepsis patients in which the models show summary AUROCs ranging from 0.765-0.89. Similar performance is observed in four cohorts of hospital-acquired sepsis. Combining the new gene-expression-based prognostic models with prior clinical severity scores leads to significant improvement in prediction of 30-day mortality as measured via AUROC and net reclassification improvement index These models provide an opportunity to develop molecular bedside tests that may improve risk stratification and mortality prediction in patients with sepsis.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Inflammatix Inc., Burlingame, CA, 94010, USA
| | | | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
| | - Judith A Howrylak
- Division of Pulmonary and Critical Care Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, 17033, USA
| | - Augustine M Choi
- Department of Medicine, Cornell Medical Center, New York, NY, 10065, USA
| | | | - Raquel Almansa
- Hospital Clínico Universitario de Valladolid/IECSCYL, Valladolid, 47005, Spain
| | - Eduardo Tamayo
- Hospital Clínico Universitario de Valladolid/IECSCYL, Valladolid, 47005, Spain
| | - Emma E Davenport
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Partners Center for Personalized Genetic Medicine, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Katie L Burnham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Charles J Hinds
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University, London, EC1M 6BQ, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veteran's Affairs Health Care System, Durham, NC, 27705, USA
| | | | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, OH, 45223, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Benjamin Tang
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia, Penrith, NSW, 2751, Australia
- Nepean Genomic Research Group, Nepean Clinical School, University of Sydney, Penrith, NSW, 2751, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead, NSW, 2145, Australia
| | - Lyle L Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Frederick E Moore
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | | | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veteran's Affairs Health Care System, Durham, NC, 27705, USA
| | | | - Raymond J Langley
- Department of Pharmacology, University of South Alabama, Mobile, AL, 36688, USA.
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16
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Wirasinha RC, Vijayan D, Smith NJ, Parnell GP, Swarbrick A, Brink R, King C, Stewart G, Booth DR, Batten M. GPR65 inhibits experimental autoimmune encephalomyelitis through CD4+
T cell independent mechanisms that include effects on iNKT cells. Immunol Cell Biol 2017; 96:128-136. [DOI: 10.1111/imcb.1031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Rushika C Wirasinha
- Immunology Division; Garvan Institute of Medical Research; Sydney NSW Australia
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
| | - Dipti Vijayan
- Immunology Division; Garvan Institute of Medical Research; Sydney NSW Australia
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
| | - Nicola J Smith
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
- Molecular Pharmacology Group; Victor Chang Cardiac Research Institute; Darlinghurst NSW Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research; Westmead Institute for Medical Research; University of Sydney; Westmead NSW Australia
| | - Alexander Swarbrick
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
- The Kinghorn Cancer Centre and Cancer Research Division; Garvan Institute of Medical Research; Darlinghurst NSW Australia
| | - Robert Brink
- Immunology Division; Garvan Institute of Medical Research; Sydney NSW Australia
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
| | - Cecile King
- Immunology Division; Garvan Institute of Medical Research; Sydney NSW Australia
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
| | - Graeme Stewart
- Centre for Immunology and Allergy Research; Westmead Institute for Medical Research; University of Sydney; Westmead NSW Australia
| | - David R Booth
- Centre for Immunology and Allergy Research; Westmead Institute for Medical Research; University of Sydney; Westmead NSW Australia
| | - Marcel Batten
- Immunology Division; Garvan Institute of Medical Research; Sydney NSW Australia
- St. Vincent's Clinical School; University of New South Wales; Sydney NSW Australia
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Tang BM, Shojaei M, Parnell GP, Huang S, Nalos M, Teoh S, O'Connor K, Schibeci S, Phu AL, Kumar A, Ho J, Meyers AFA, Keynan Y, Ball T, Pisipati A, Kumar A, Moore E, Eisen D, Lai K, Gillett M, Geffers R, Luo H, Gul F, Schreiber J, Riedel S, Booth D, McLean A, Schughart K. A novel immune biomarker IFI27 discriminates between influenza and bacteria in patients with suspected respiratory infection. Eur Respir J 2017; 49:49/6/1602098. [PMID: 28619954 DOI: 10.1183/13993003.02098-2016] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 03/15/2017] [Indexed: 11/05/2022]
Abstract
Host response biomarkers can accurately distinguish between influenza and bacterial infection. However, published biomarkers require the measurement of many genes, thereby making it difficult to implement them in clinical practice. This study aims to identify a single-gene biomarker with a high diagnostic accuracy equivalent to multi-gene biomarkers.In this study, we combined an integrated genomic analysis of 1071 individuals with in vitro experiments using well-established infection models.We identified a single-gene biomarker, IFI27, which had a high prediction accuracy (91%) equivalent to that obtained by multi-gene biomarkers. In vitro studies showed that IFI27 was upregulated by TLR7 in plasmacytoid dendritic cells, antigen-presenting cells that responded to influenza virus rather than bacteria. In vivo studies confirmed that IFI27 was expressed in influenza patients but not in bacterial infection, as demonstrated in multiple patient cohorts (n=521). In a large prospective study (n=439) of patients presented with undifferentiated respiratory illness (aetiologies included viral, bacterial and non-infectious conditions), IFI27 displayed 88% diagnostic accuracy (AUC) and 90% specificity in discriminating between influenza and bacterial infections.IFI27 represents a significant step forward in overcoming a translational barrier in applying genomic assay in clinical setting; its implementation may improve the diagnosis and management of respiratory infection.
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Affiliation(s)
- Benjamin M Tang
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia .,Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Sydney, Australia.,Respiratory Virus Infection Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia.,These authors contributed equally to the study
| | - Maryam Shojaei
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia.,Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Sydney, Australia.,These authors contributed equally to the study
| | - Grant P Parnell
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Sydney, Australia
| | - Stephen Huang
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Marek Nalos
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Sally Teoh
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Kate O'Connor
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Sydney, Australia
| | - Stephen Schibeci
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Sydney, Australia
| | - Amy L Phu
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Anand Kumar
- Section of Critical Care Medicine and Section of Infectious Diseases, Dept of Medicine, Medical Microbiology and Pharmacology, University of Manitoba, Winnipeg, Canada
| | - John Ho
- National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Adrienne F A Meyers
- National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Yoav Keynan
- Dept of Internal Medicine, University of Manitoba, Winnipeg, Canada.,Dept of Medical Microbiology, University of Manitoba, Winnipeg, Canada.,Dept of Community Health Sciences, University of Manitoba, Winnipeg, Canada.,Dept of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Terry Ball
- National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Canada.,Dept of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Amarnath Pisipati
- Dept of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Aseem Kumar
- Dept of Chemistry and Biochemistry, Laurentian University, Sudbury, Canada
| | - Elizabeth Moore
- Transfusion Research Unit, Dept of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Damon Eisen
- Dept of Infectious Diseases, Townsville Hospital, Townsville, Australia
| | - Kevin Lai
- Dept of Emergency Medicine, Westmead Hospital, Sydney, Australia
| | - Mark Gillett
- Dept of Emergency Medicine, Royal North Shore Hospital, Sydney, Australia
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hao Luo
- Nepean Clinical School, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Fahad Gul
- Nepean Clinical School, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Jens Schreiber
- Clinic of Pneumology, Otto-von-Guerike University of Magdeburg, Magdeburg, Germany
| | - Sandra Riedel
- Clinic of Pneumology, Otto-von-Guerike University of Magdeburg, Magdeburg, Germany
| | - David Booth
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Sydney, Australia
| | - Anthony McLean
- Dept of Intensive Care Medicine, Nepean Hospital, Sydney, Australia
| | - Klaus Schughart
- Dept of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,University of Veterinary Medicine, Hannover, Germany.,University of Tennessee Health Science Center, Memphis, TN, USA
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18
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Parnell GP, Booth DR. The Multiple Sclerosis (MS) Genetic Risk Factors Indicate both Acquired and Innate Immune Cell Subsets Contribute to MS Pathogenesis and Identify Novel Therapeutic Opportunities. Front Immunol 2017; 8:425. [PMID: 28458668 PMCID: PMC5394466 DOI: 10.3389/fimmu.2017.00425] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/27/2017] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is known to be a partially heritable autoimmune disease. The risk of developing MS increases from typically 1 in 1,000 in the normal population to 1 in 4 or so for identical twins where one twin is affected. Much of this heritability is now explained and is due almost entirely to genes affecting the immune response. The largest and first identified genetic risk factor is an allele from the MHC class II HLA-DRB1 gene, HLA-DRB1*15:01, which increases risk about threefold. The HLA-DRB1 gene is expressed in antigen-presenting cells, and its protein functions in presenting particular types of antigen to CD4 T cells. This discovery supported the development of the first successful immunomodulatory therapies: glatiramer acetate, which mimics the antigen presentation process, and interferon beta, which targets CD4 T cell activation. Over 200 genetic risk variants, all single nucleotide polymorphisms (SNPs), have now been described. The SNPs are located within, or close to, genes expressed predominantly in acquired and innate immune cell subsets, indicating that both contribute to MS pathogenesis. The risk alleles indicate variation in the regulation of gene expression, rather than protein variation, underpins genetic susceptibility. In this review, we discuss how the expression and function of the risk genes, as well as the effect on these of the risk SNPs, indicate specific acquired immune cell processes that are the target of current successful therapies, and also point to novel therapeutic approaches.
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Affiliation(s)
- Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
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19
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Fewings N, Gatt PN, McKay FC, Parnell GP, Schibeci SD, Edwards J, Basuki MA, Goldinger A, Fabis-Pedrini MJ, Kermode AG, Manrique CP, McCauley JL, Nickles D, Baranzini SE, Burke T, Vucic S, Stewart GJ, Booth DR. Data characterizing the ZMIZ1 molecular phenotype of multiple sclerosis. Data Brief 2017; 11:364-370. [PMID: 28275670 PMCID: PMC5329066 DOI: 10.1016/j.dib.2017.02.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 01/09/2023] Open
Abstract
The data presented in this article are related to the research article entitled "The autoimmune risk gene ZMIZ1 is a vitamin D responsived marker of a molecular phenotype of multiple sclerosis" Fewings et al. (2017) [1]. Here we identify the set of genes correlated with ZMIZ1 in multiple cohorts, provide phenotypic details on those cohorts, and identify the genes negatively correlated with ZMIZ1 and the cells predominantly expressing those genes. We identify the metabolic pathways in which the molecular phenotype genes are over-represented. Finally, we present the flow cytometry gating strategy we have used to identify the immune cells from blood which are producing ZMIZ1 and RPS6.
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Affiliation(s)
- N Fewings
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - P N Gatt
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - F C McKay
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - G P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - S D Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - J Edwards
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - M A Basuki
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - A Goldinger
- University of Queensland Diamantina Institute, Translational Research Institute, Australia; The Queensland Brain Institute, University of Queensland, Australia
| | - M J Fabis-Pedrini
- Western Australian Neuroscience Research Institute, University of Western Australia, Nedlands, Western Australia, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - A G Kermode
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - C P Manrique
- John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - J L McCauley
- John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - D Nickles
- Department of Neurology, University of California San Francisco, USA
| | - S E Baranzini
- Department of Neurology, University of California San Francisco, USA
| | - T Burke
- Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - S Vucic
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - G J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - D R Booth
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
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20
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Fewings NL, Gatt PN, McKay FC, Parnell GP, Schibeci SD, Edwards J, Basuki MA, Goldinger A, Fabis-Pedrini MJ, Kermode AG, Manrique CP, McCauley JL, Nickles D, Baranzini SE, Burke T, Vucic S, Stewart GJ, Booth DR. The autoimmune risk gene ZMIZ1 is a vitamin D responsive marker of a molecular phenotype of multiple sclerosis. J Autoimmun 2017; 78:57-69. [PMID: 28063629 DOI: 10.1016/j.jaut.2016.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 11/02/2016] [Revised: 12/22/2016] [Accepted: 12/24/2016] [Indexed: 01/08/2023]
Abstract
Multiple Sclerosis (MS) is a neurological condition driven in part by immune cells from the peripheral circulation, the targets for current successful therapies. The autoimmune and MS risk gene ZMIZ1 is underexpressed in blood in people with MS. We show that, from three independent sets of transcriptomic data, expression of ZMIZ1 is tightly correlated with that of hundreds of other genes. Further we show expression is partially heritable (heritability 0.26), relatively stable over time, predominantly in plasmacytoid dendritic cells and non-classical monocytes, and that levels of ZMIZ1 protein expression are reduced in MS. ZMIZ1 gene expression is increased in response to calcipotriol (1,25 Vitamin D3) (p < 0.0003) and associated with Epstein Barr Virus (EBV) EBNA-1 antibody titre (p < 0.004). MS therapies fingolimod and dimethyl fumarate altered blood ZMIZ1 gene expression compared to untreated MS. The phenotype indicates susceptibility to MS, and may correspond with clinical response and represent a novel clinical target.
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Affiliation(s)
- N L Fewings
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - P N Gatt
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - F C McKay
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - G P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - S D Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - J Edwards
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - M A Basuki
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - A Goldinger
- University of Queensland, Diamantina Institute, Translational Research Institute, The Queensland Brain Institute, University of Queensland, Australia
| | - M J Fabis-Pedrini
- Western Australian Neuroscience Research Institute, University of Western Australia, Nedlands, Western Australia, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - A G Kermode
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - C P Manrique
- John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - J L McCauley
- John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - D Nickles
- Department of Neurology, University of California San Francisco, USA
| | - S E Baranzini
- Department of Neurology, University of California San Francisco, USA
| | - T Burke
- Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - S Vucic
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - G J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - D R Booth
- Western Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia.
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21
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Booth DR, Fewings NL, Parnell GP, McKay FC, Stewart GJ. Differences in common heritable blood immune cell populations may underlie MS susceptibility and progression. Mult Scler J Exp Transl Clin 2016; 2:2055217316637087. [PMID: 28607721 PMCID: PMC5433329 DOI: 10.1177/2055217316637087] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A promising new avenue of MS research that may lead to a better understanding of pathogenesis, progression and therapeutic response, and to development of new therapies, comes from the recent identification of defined immune cell populations that are highly heritable. Such stable populations have been identified in three recent papers using extensive flow cytometric panels to investigate twin and family cohorts. They showed that while most of the variation in immune cell populations between individuals was not heritable, some was. This heritability was sometimes very high, and the authors concluded that it likely contributes to variability in response among individuals for disease and drug response traits.
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Affiliation(s)
- David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Australia
| | - Nicole L Fewings
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Australia
| | - Fiona C McKay
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Australia
| | - Graeme J Stewart
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Australia
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22
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Abstract
Since most immunological and hematological conditions might be expected to alter whole blood gene expression, its examination can lead to insights into disease processes, and biomarkers to assess molecular phenotypes, disease states, progression and response to therapy. In this chapter we describe collection and storage of RNA from whole blood, techniques to measure gene expression, and analytical approaches to identify the dysregulated gene expression using pathway and clustering analysis, gene set enrichment, heat map approaches, and cell subset deconvolution.
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Affiliation(s)
- Grant P Parnell
- Westmead Millennium Institute, University of Sydney, Hawkesbury Road, Sydney, NSW, 2145, Australia
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23
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Parnell GP, Gatt PN, Krupa M, Nickles D, McKay FC, Schibeci SD, Batten M, Baranzini S, Henderson A, Barnett M, Slee M, Vucic S, Stewart GJ, Booth DR. The autoimmune disease-associated transcription factors EOMES and TBX21 are dysregulated in multiple sclerosis and define a molecular subtype of disease. Clin Immunol 2014; 151:16-24. [PMID: 24495857 DOI: 10.1016/j.clim.2014.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [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: 12/02/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 12/22/2022]
Abstract
We have identified a marked over-representation of transcription factors controlling differentiation of T, B, myeloid and NK cells among the 110 MS genes now known to be associated with multiple sclerosis (MS). To test if the expression of these genes might define molecular subtypes of MS, we interrogated their expression in blood in three independent cohorts of untreated MS (from Sydney and Adelaide) or clinically isolated syndrome (CIS, from San Francisco) patients. Expression of the transcription factors (TF) controlling T and NK cell differentiation, EOMES, TBX21 and other TFs was significantly lower in MS/CIS compared to healthy controls in all three cohorts. Expression was tightly correlated between these TFs, with other T/NK cell TFs, and to another downregulated gene, CCL5. Expression was stable over time, but did not predict disease phenotype. Optimal response to therapy might be indicated by normalization of expression of these genes in blood.
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Affiliation(s)
- Grant P Parnell
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia
| | - Prudence N Gatt
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia
| | - Malgorzata Krupa
- School of Medicine, Flinders University of South Australia, South Australia 5042, Australia
| | - Dorothee Nickles
- Department of Neurology, University of California at San Francisco, CA 94158, USA
| | - Fiona C McKay
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia
| | - Stephen D Schibeci
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia
| | - Marcel Batten
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Sergio Baranzini
- Department of Neurology, University of California at San Francisco, CA 94158, USA
| | - Andrew Henderson
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia
| | - Michael Barnett
- Brain and Mind Research Institute, University of Sydney, Sydney, NSW 2050 Australia
| | - Mark Slee
- School of Medicine, Flinders University of South Australia, South Australia 5042, Australia
| | - Steve Vucic
- Westmead Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales 2145, Australia
| | - Graeme J Stewart
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia
| | - David R Booth
- Institute for Immunology and Allergy Research, Westmead Millennium Institute University of Sydney, Sydney, New South Wales 2145, Australia.
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24
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Shahijanian F, Parnell GP, McKay FC, Gatt PN, Shojoei M, O'Connor KS, Schibeci SD, Brilot F, Liddle C, Batten M, Stewart GJ, Booth DR. The CYP27B1 variant associated with an increased risk of autoimmune disease is underexpressed in tolerizing dendritic cells. Hum Mol Genet 2013; 23:1425-34. [PMID: 24158849 DOI: 10.1093/hmg/ddt529] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies have identified a linkage disequilibrium (LD) block on chromosome 12 associated with multiple sclerosis (MS), type 1 diabetes and other autoimmune diseases. This block contains CYP27B1, which catalyzes the conversion of 25 vitamin D3 (VitD3) to 1,25VitD3. Fine-mapping analysis has failed to identify which of the 17 genes in this block is most associated with MS. We have previously used a functional approach to identify the causal gene. We showed that the expression of several genes in this block in whole blood is highly associated with the MS risk allele, but not CYP27B1. Here, we show that CYP27B1 is predominantly expressed in dendritic cells (DCs). Its expression in these cells is necessary for their response to VitD, which is known to upregulate pathways involved in generating a tolerogenic DC phenotype. Here, we utilize a differentiation protocol to generate inflammatory (DC1) and tolerogenic (DC2) DCs, and show that for the MS risk allele CYP27B1 is underexpressed in DCs, especially DC2s. Of the other Chr12 LD block genes expressed in these cells, only METT21B expression was as affected by the genotype. Another gene associated with autoimmune diseases, CYP24A1, catabolizes 1,25 VitD3, and is predominantly expressed in DCs, but equally between DC1s and DC2s. Overall, these data are consistent with the hypothesis that reduced VitD pathway gene upregulation in DC2s of carriers of the risk haplotype of CYP27B1 contributes to autoimmune diseases. These data support therapeutic approaches aimed at targeting VitD effects on DCs.
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25
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Parnell GP, Gatt PN, McKay FC, Schibeci S, Krupa M, Powell JE, Visscher PM, Montgomery GW, Lechner-Scott J, Broadley S, Liddle C, Slee M, Vucic S, Stewart GJ, Booth DR. Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season. Mult Scler 2013; 20:675-85. [DOI: 10.1177/1352458513507819] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background: Multiple Sclerosis (MS) is an immune-mediated disease of the central nervous system which responds to therapies targeting circulating immune cells. Objective: Our aim was to test if the T-cell activation gene expression pattern (TCAGE) we had previously described from whole blood was replicated in an independent cohort. Methods: We used RNA-seq to interrogate the whole blood transcriptomes of 72 individuals (40 healthy controls, 32 untreated MS). A cohort of 862 control individuals from the Brisbane Systems Genetics Study (BSGS) was used to assess heritability and seasonal expression. The effect of interferon beta (IFNB) therapy on expression was evaluated. Results: The MS/TCAGE association was replicated and rationalized to a single marker, ribosomal protein S6 (RPS6). Expression of RPS6 was higher in MS than controls ( p<0.0004), and lower in winter than summer ( p<4.6E-06). The seasonal pattern correlated with monthly UV light index ( R=0.82, p<0.002), and was also identified in the BSGS cohort ( p<0.0016). Variation in expression of RPS6 was not strongly heritable. RPS6 expression was reduced by IFNB therapy. Conclusions: These data support investigation of RPS6 as a potential therapeutic target and candidate biomarker for measuring clinical response to IFNB and other MS therapies, and of MS disease heterogeneity.
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Affiliation(s)
- Grant P Parnell
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Prudence N Gatt
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Fiona C McKay
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Stephen Schibeci
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Malgorzata Krupa
- School of Medicine, Flinders University of South Australia, South Australia, Australia
| | - Joseph E Powell
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | | | | | - Christopher Liddle
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Mark Slee
- School of Medicine, Flinders University of South Australia, South Australia, Australia
| | - Steve Vucic
- Westmead Clinical School, University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Graeme J Stewart
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - David R Booth
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
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Parnell GP, McLean AS, Booth DR, Armstrong NJ, Nalos M, Huang SJ, Manak J, Tang W, Tam OY, Chan S, Tang BM. A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia. Crit Care 2012; 16:R157. [PMID: 22898401 PMCID: PMC3580747 DOI: 10.1186/cc11477] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 08/15/2012] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Diagnosis of severe influenza pneumonia remains challenging because of a lack of correlation between the presence of influenza virus and clinical status. We conducted gene-expression profiling in the whole blood of critically ill patients to identify a gene signature that would allow clinicians to distinguish influenza infection from other causes of severe respiratory failure, such as bacterial pneumonia, and noninfective systemic inflammatory response syndrome. METHODS Whole-blood samples were collected from critically ill individuals and assayed on Illumina HT-12 gene-expression beadarrays. Differentially expressed genes were determined by linear mixed-model analysis and overrepresented biological pathways determined by using GeneGo MetaCore. RESULTS The gene-expression profile of H1N1 influenza A pneumonia was distinctly different from those of bacterial pneumonia and systemic inflammatory response syndrome. The influenza gene-expression profile is characterized by upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways. In contrast, no distinctive gene-expression signature was found in patients with bacterial pneumonia or systemic inflammatory response syndrome. The gene-expression profile of influenza infection persisted through 5 days of follow-up. Furthermore, in patients with primary H1N1 influenza A infection in whom bacterial co-infection subsequently developed, the influenza gene-expression signature remained unaltered, despite the presence of a superimposed bacterial infection. CONCLUSIONS The whole-blood expression-profiling data indicate that the host response to influenza pneumonia is distinctly different from that caused by bacterial pathogens. This information may speed the identification of the cause of infection in patients presenting with severe respiratory failure, allowing appropriate patient care to be undertaken more rapidly.
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Parnell GP. Employee motivation: mixing the ingredients. Exec Housekeeper 1979; 26:20-2. [PMID: 10239947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Parnell GP. Your department--disordered or disciplined? Exec Housekeeper 1978; 25:10-2. [PMID: 10307948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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