Assessing the potential of epigenetic targets as biomarkers in the diagnosis and treatment of rheumatoid arthritis

References

• Alamanos Y, Drosos AA. Epidemiology of adult rheumatoid arthritis. Autoimmun Rev [Internet]. 2005 [cited 2022 Apr 22];4:130–136. DOI:10.1016/j.autrev.2004.09.002.
   PubMed Web of Science ®Google Scholar
• McInnes IB, Schett G. The pathogenesis of rheumatoid arthritis. N Engl J Med [Internet]. 2011 [cited 2016 Sep 29];365:2205–2219. DOI:10.1056/NEJMra1004965.
   PubMed Web of Science ®Google Scholar
• Zhang F, Wei K, Slowikowski K, et al. Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. Nat Immunol [Internet]. 2019 [cited 2021 Jan 25];20:928–942. DOI:10.1038/s41590-019-0378-1
   PubMed Web of Science ®Google Scholar
• Plant D, Wilson AG, Barton A. Genetic and epigenetic predictors of responsiveness to treatment in RA. Nat Rev Rheumatol [Internet]. 2014 [cited 2016 Nov 1];10:329–337. DOI:10.1038/nrrheum.2014.16.
   PubMed Web of Science ®Google Scholar
• Sutcliffe M, Radley G, Barton A. Personalized medicine in rheumatic diseases: how close are we to being able to use genetic biomarkers to predict response to TNF inhibitors? Expert Rev Clin Immunol [Internet]. 2020 [cited 2022 Apr 22];16:389–396. DOI:10.1080/1744666X.2020.1740594.
   PubMed Web of Science ®Google Scholar
• Zhao SS, Moots RJ. Biomarkers for treatment response in rheumatoid arthritis: where are they? Rheumatol Immunol Res [Internet]. 2020 [cited 2022 Apr 27];1:1–3. DOI:10.2478/rir-2020-0008.
   PubMedGoogle Scholar
• Okada Y, Wu D, Trynka G, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature [Internet]. 2014 [cited 2016 Nov 2];506:376–381. DOI:10.1038/nature12873.
   PubMed Web of Science ®Google Scholar
• Okada Y, Eyre S, Suzuki A, et al. Genetics of rheumatoid arthritis: 2018 status. Ann Rheum Dis [Internet]. 2019 [cited 2022 Apr 27];78:446–453. DOI:10.1136/annrheumdis-2018-213678.
   PubMed Web of Science ®Google Scholar
• Sieberts SK, Zhu F, García-García J, et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun [Internet]. 2016 [cited 2016 Oct 3];7:12460. DOI:10.1038/ncomms12460.
   PubMed Web of Science ®Google Scholar
• Honda S, Ikari K, Yano K, et al. Association of polygenic risk scores with radiographic progression in patients with rheumatoid arthritis. Arthritis Rheumatol [Internet]. 2022 [cited 2022 Apr 27];74:791–800. DOI:10.1002/art.42051
   PubMed Web of Science ®Google Scholar
• Stricker SH, Köferle A, Beck S. From profiles to function in epigenomics. Nat Rev Genet [Internet]. 2016 [cited 2016 Nov 25];18:51–66. DOI:10.1038/nrg.2016.138.
   PubMed Web of Science ®Google Scholar
• Oliver J, Plant D, Webster AP, et al. Genetic and genomic markers of anti-TNF treatment response in rheumatoid arthritis. Biomarker Med [Internet]. 2015 [cited 2016 Nov 2];9:499–512. DOI:10.2217/bmm.15.18.
   PubMed Web of Science ®Google Scholar
• Plant D, Webster A, Nair N, et al. Differential methylation as a biomarker of response to etanercept in patients with rheumatoid arthritis. Arthritis Rheumatol (Hoboken, NJ) [Internet]. 2016 [cited 2016 Nov 4];68:1353–1360. DOI:10.1002/art.39590
   PubMed Web of Science ®Google Scholar
• Nair N, Plant D, Verstappen SM, et al. Differential DNA methylation correlates with response to methotrexate in rheumatoid arthritis. Rheumatology (Oxford) [Internet]. 2019 [cited 2020 Mar 19]. Available from: http://www.ncbi.nlm.nih.gov/pubmed/31598719
   PubMed Web of Science ®Google Scholar
• Nair N, Barton A, Wilson AG. Cell-specific epigenetic drivers of pathogenesis in rheumatoid arthritis. Epigenomics [Internet]. 2021 [cited 2022 Feb 16];13:549–560. DOI:10.2217/epi-2020-0380.
   PubMed Web of Science ®Google Scholar
• Bottini N, Firestein GS. Epigenetics in rheumatoid arthritis: a primer for rheumatologists. Curr Rheumatol Rep [Internet]. 2013 [cited 2016 Nov 15];15:372. DOI:10.1007/s11926-013-0372-9.
   PubMed Web of Science ®Google Scholar
• van der Maarel SM. Epigenetic mechanisms in health and disease. Ann Rheum Dis [Internet]. 2008 [cited 2016 Nov 3];67:iii97–100. DOI:10.1136/ard.2008.098392.
   PubMed Web of Science ®Google Scholar
• Ospelt C, Gay S, Klein K. Epigenetics in the pathogenesis of RA. Semin Immunopathol [Internet]. 2017 cited 2020 Jul 28;39:409–419. Springer Verlag. DOI:10.1007/s00281-017-0621-5.
   PubMed Web of Science ®Google Scholar
• Rauluseviciute I, Drabløs F, Rye MB. DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation. BMC Med Genomics [Internet]. 2020 [cited 2022 May 1];13:1–15. DOI:10.1186/s12920-020-0657-6.
   PubMed Web of Science ®Google Scholar
• Craig G, Kenney H, Nilsson EE, et al. Epigenome association study for DNA methylation biomarkers in buccal and monocyte cells for female rheumatoid arthritis. Sci Rep [Internet]. 2021 [cited 2022 Apr 28];11:1–15. DOI:10.1038/s41598-021-03170-6.
   PubMed Web of Science ®Google Scholar
• Pitaksalee R, Burska AN, Ajaib S, et al. Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients. Clin Epigenetics [Internet]. 2020 [cited 2020 May 28];12:54. DOI:10.1186/s13148-020-00837-1
   PubMed Web of Science ®Google Scholar
• Karouzakis E, Raza K, Kolling C, et al. Analysis of early changes in DNA methylation in synovial fibroblasts of RA patients before diagnosis. Sci Rep. 2018;8. DOI:10.1038/s41598-018-24240-2.
   PubMed Web of Science ®Google Scholar
• Ai R, Hammaker D, Boyle DL, et al. Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Nat Commun. 2016;7:1–9.
   Web of Science ®Google Scholar
• de Andres MC, Perez-Pampin E, Calaza M, et al. Assessment of global DNA methylation in peripheral blood cell subpopulations of early rheumatoid arthritis before and after methotrexate. Arthritis Res Ther [Internet]. 2015 [cited 2016 Nov 4];17:233. DOI:10.1186/s13075-015-0748-5.
   PubMed Web of Science ®Google Scholar
• Glossop JR, Emes RD, Nixon NB, et al. Genome-wide DNA methylation profiling in rheumatoid arthritis identifies disease-associated methylation changes that are distinct to individual T- and B-lymphocyte populations. Epigenetics [Internet]. 2014 [cited 2014 Nov 10];9:1228–1237. DOI:10.4161/epi.29718.
   PubMed Web of Science ®Google Scholar
• Shao X, Hudson M, Colmegna I, et al. Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing. Clin Epigenetics [Internet]. 2019 [cited 2021 Jan 25];11:110. DOI:10.1186/s13148-019-0699-9
   PubMed Web of Science ®Google Scholar
• Dong X, Weng Z The correlation between histone modifications and gene expression [Internet]. Epigenomics. NIH Public Access; 2013 [cited 2020 Jul 29]. 113–116. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230708/
   PubMed Web of Science ®Google Scholar
• Eberharter A, Becker PB. Histone acetylation: a switch between repressive and permissive chromatin: second in review series on chromatin dynamics. EMBO Rep [Internet]. 2002 [cited 2020 Jul 29];3:224. DOI:10.1093/embo-reports/kvf053.
   PubMed Web of Science ®Google Scholar
• Wada TT, Araki Y, Sato K, et al. Aberrant histone acetylation contributes to elevated interleukin-6 production in rheumatoid arthritis synovial fibroblasts. Biochem Biophys Res Commun. 2014;444:682–686.
   PubMed Web of Science ®Google Scholar
• Araki Y, Tsuzuki Wada T, Aizaki Y, et al. Histone methylation and STAT-3 differentially regulate interleukin-6-induced matrix metalloproteinase gene activation in rheumatoid arthritis synovial fibroblasts. Arthritis Rheumatol [Internet]. 2016 [cited 2020 May 20];68:1111–1123. DOI:10.1002/art.39563.
   PubMed Web of Science ®Google Scholar
• Hawtree S, Muthana M, Wilkinson JM, et al. Histone deacetylase 1 regulates tissue destruction in rheumatoid arthritis. 2015 [cited 2020 Jul 29]. Available from: https://academic.oup.com/hmg/article-abstract/24/19/5367/583607
   Google Scholar
• Angiolilli C, Kabala PA, Grabiec AM, et al. Histone deacetylase 3 regulates the inflammatory gene expression programme of rheumatoid arthritis fibroblast-like synoviocytes. [cited 2020 May 22]. Available from: 10.1136/annrheumdis-2015-209064
   Google Scholar
• Gillespie J, Savic S, Wong C, et al. Histone deacetylases are dysregulated in rheumatoid arthritis and a novel histone deacetylase 3-selective inhibitor reduces interleukin-6 production by peripheral blood mononuclear cells from rheumatoid arthritis patients. Arthritis Rheum [Internet]. 2012 [cited 2016 Nov 15];64:418–422. DOI:10.1002/art.33382.
   PubMed Web of Science ®Google Scholar
• Li Y, Zhou M, Lv X, et al. Reduced activity of HDAC3 and increased acetylation of histones H3 in peripheral blood mononuclear cells of patients with rheumatoid arthritis. J Immunol Res [Internet]. 2018 [cited 2020 Jul 30];2018:1–10. DOI:10.1155/2018/7313515.
   Web of Science ®Google Scholar
• LeRoy G, Rickards B, Flint SJ. The double Bromodomain Proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol Cell [Internet]. 2008 [cited 2020 Sep 2];30:51–60. DOI:10.1016/j.molcel.2008.01.018.
   PubMed Web of Science ®Google Scholar
• Moon KJ, Mochizuki K, Zhou M, et al. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol Cell [Internet]. 2005 [cited 2020 Sep 2];19:523–534. DOI:10.1016/j.molcel.2005.06.027.
   PubMed Web of Science ®Google Scholar
• Loh C, Park SH, Lee A, et al. TNF-induced inflammatory genes escape repression in fibroblast-like synoviocytes: transcriptomic and epigenomic analysis. Ann Rheum Dis. 2019;78:1205–1214.
   PubMed Web of Science ®Google Scholar
• Klein K, Kabala PA, Grabiec AM, et al. The bromodomain protein inhibitor I-BET151 suppresses expression of inflammatory genes and matrix degrading enzymes in rheumatoid arthritis synovial fibroblasts. Ann Rheumatic Dis. 2016 [cited 2020 May 22];75:422–429. DOI:10.1136/annrheumdis-2014-205809.
   PubMed Web of Science ®Google Scholar
• Önder Ö, Sidoli S, Carroll M, et al. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Rev Proteomics [Internet]. 2015 [cited 2022 May 10];12:499. DOI:10.1586/14789450.2015.1084231.
   PubMed Web of Science ®Google Scholar
• Taryma-Leśniak O, Sokolowska KE, Wojdacz TK. Current status of development of methylation biomarkers for in vitro diagnostic IVD applications. Clin Epigenetics [Internet]. 2020 [cited 2022 Sep 12];12:1–16. DOI:10.1186/s13148-020-00886-6.
   Web of Science ®Google Scholar
• Fatemi N, Tierling S, Es HA, et al. DNA methylation biomarkers in colorectal cancer: clinical applications for precision medicine. Int J Cancer [Internet]. 2022 [cited 2022 Sep 12];151:2068–2081. DOI:10.1002/ijc.34186.
   PubMed Web of Science ®Google Scholar
• Blair JPM, Bay-Jensen AC, Tang MH, et al. Identification of heterogenous treatment response trajectories to anti-IL6 receptor treatment in rheumatoid arthritis. Sci Rep [Internet]. 2020 [cited 2022 Apr 27];10:1–9. DOI:10.1038/s41598-020-70942-x.
   PubMed Web of Science ®Google Scholar
• Balsa A, García de Yébenes MJ, Carmona L. Multilevel factors predict medication adherence in rheumatoid arthritis: a 6-month cohort study. Ann Rheum Dis [Internet]. 2022 [cited 2022 May 3];81:327–334. DOI:10.1136/annrheumdis-2021-221163.
   PubMed Web of Science ®Google Scholar
• Stylianou E. Epigenetics of chronic inflammatory diseases. J Inflamm Res [Internet]. 2019 [cited 2022 May 10];12:1. DOI:10.2147/JIR.S129027.
   PubMed Web of Science ®Google Scholar
• Nair N, Wilson AG, Barton A. DNA methylation as a marker of response in rheumatoid arthritis. Pharmacogenomics. 2017;18:1323–1332. Future Medicine Ltd.
   PubMed Web of Science ®Google Scholar
• Guo S, Xu L, Chang C, et al. Epigenetic regulation mediated by methylation in the pathogenesis and precision medicine of rheumatoid arthritis. Front Genet. 2020;11:811.
   PubMed Web of Science ®Google Scholar
• Atzeni F, Talotta R, Masala IF, et al. Biomarkers in rheumatoid arthritis. Cureus [Internet]. 2021 [cited 2022 May 3];13:512–516. Available from: /pmc/articles/PMC8205440/
   Web of Science ®Google Scholar
• Mun S, Lee J, Park M, et al. Serum biomarker panel for the diagnosis of rheumatoid arthritis. Arthritis Res Ther [Internet]. 2021 [cited 2022 May 3];23:1–10. DOI:10.1186/s13075-020-02405-7
   PubMed Web of Science ®Google Scholar
• Yoosuf N, Maciejewski M, Ziemek D, et al. Early prediction of clinical response to anti-TNF treatment using multi-omics and machine learning in rheumatoid arthritis. Rheumatology (Oxford) [Internet]. 2022 [cited 2022 May 3];61:1680–1689. DOI:10.1093/rheumatology/keab521.
   PubMed Web of Science ®Google Scholar
• Maciejewski M, Sands C, Nair N, et al. Prediction of response of methotrexate in patients with rheumatoid arthritis using serum lipidomics. Sci Rep [Internet]. 2021 [cited 2022 May 3];11. DOI:10.1038/s41598-021-86729-7.
   Web of Science ®Google Scholar
• Guan Y, Zhang H, Quang D, et al. Machine learning to predict anti-tumor necrosis factor drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers. Arthritis Rheumatol [Internet]. 2019 [cited 2019 Sep 18];71:art.41056. DOI:10.1002/art.41056.
   Web of Science ®Google Scholar
• Kalweit M, Walker UA, Finckh A, et al. Personalized prediction of disease activity in patients with rheumatoid arthritis using an adaptive deep neural network. PLoS ONE [Internet]. 2021 [cited 2022 May 3];16:e0252289. DOI:10.1371/journal.pone.0252289
   PubMed Web of Science ®Google Scholar
• Nair N, Wilson AG. Can machine learning predict responses to TNF inhibitors? Nat Rev Rheumatol [Internet]. 2019 [cited 2022 May 3];15:702–704. DOI:10.1038/s41584-019-0320-9.
   PubMed Web of Science ®Google Scholar
• Hensor EMA, McKeigue P, Ling SF, et al. Validity of a two-component imaging-derived disease activity score for improved assessment of synovitis in early rheumatoid arthritis. Rheumatology [Internet]. 2019 [cited 2019 Aug 19];58:1400–1409. DOI:10.1093/rheumatology/kez049
   PubMed Web of Science ®Google Scholar
• Ha E, Bae SC, Kim K. Large-scale meta-analysis across East Asian and European populations updated genetic architecture and variant-driven biology of rheumatoid arthritis, identifying 11 novel susceptibility loci. Ann Rheum Dis [Internet]. 2021 [cited 2022 May 3];80:558–565. DOI:10.1136/annrheumdis-2020-219065.
   PubMed Web of Science ®Google Scholar
• Breeze CE, Batorsky A, Lee MK, et al. Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci. Genome Med [Internet]. 2021 [cited 2022 May 3];13:1–16. DOI:10.1186/s13073-021-00877-z.
   PubMed Web of Science ®Google Scholar