2,034
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome

, , , &
Pages 9313-9331 | Received 13 Sep 2021, Accepted 27 Oct 2021, Published online: 24 Nov 2021

References

  • Pillemer SR, Matteson EL, Jacobsson LT, et al. Incidence of physician-diagnosed primary Sjögren syndrome in residents of Olmsted County, Minnesota. Mayo Clin Proc. 2001;76:593–599.
  • Plesivcnik Novljan M, Rozman B, Hocevar A, et al. Incidence of primary Sjogren’s syndrome in Slovenia. Ann Rheum Dis. 2004;63:874–876.
  • Segal B, Thomas W, Rogers T, et al. Prevalence, severity, and predictors of fatigue in subjects with primary Sjögren’s syndrome. Arthritis Rheumatism. 2008;59:1780–1787.
  • Mariette X, Criswell LA. Primary Sjögren’s syndrome. N Engl J Med. 2018;379:97.
  • Baldini C, Pepe P, Quartuccio L, et al. Primary Sjogren’s syndrome as a multi-organ disease: impact of the serological profile on the clinical presentation of the disease in a large cohort of Italian patients. Rheumatology (Oxford). 2014;53:839–844.
  • Mavragani CP, Moutsopoulos HM. Sjögren syndrome. CMAJ. 2014;186:E579–86.
  • Jonsson R, Vogelsang P, Volchenkov R, et al. The complexity of Sjögren’s syndrome: novel aspects on pathogenesis. Immunol Lett. 2011;141:1–9.
  • Karameris A, Gorgoulis V, Iliopoulos A, et al. Detection of the Epstein Barr viral genome by an in situ hybridization method in salivary gland biopsies from patients with secondary Sjögren’s syndrome. Clin Exp Rheumatol. 1992;10:327–332.
  • Nakamura H, Takahashi Y, Yamamoto-Fukuda T, et al. Direct infection of primary salivary gland epithelial cells by human T lymphotropic virus type I in patients with Sjögren’s syndrome. Arthritis Rheumatol (Hoboken). 2015;67:1096–1106.
  • Ice JA, Li H, Adrianto I, et al. Genetics of Sjögren’s syndrome in the genome-wide association era. J Autoimmun. 2012;39:57–63.
  • Harley JB, Scofield RH. Systemic lupus erythematosus: RNA-protein autoantigens, models of disease heterogeneity, and theories of etiology. J Clin Immunol. 1991;11:297–316.
  • Hendrick JP, Wolin SL, Rinke J, et al. Ro small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells. Mol Cell Biol. 1981;1:1138–1149.
  • Hu S, Wang J, Meijer J, et al. Salivary proteomic and genomic biomarkers for primary Sjögren’s syndrome. Arthritis Rheumatism. 2007;56:3588–3600.
  • Miceli-Richard C, Comets E, Loiseau P, et al. Association of an IRF5 gene functional polymorphism with Sjögren’s syndrome. Arthritis Rheumatism. 2007;56:3989–3994.
  • Nordmark G, Kristjansdottir G, Theander E, et al. Additive effects of the major risk alleles of IRF5 and STAT4 in primary Sjögren’s syndrome. Genes Immun. 2009;10:68–76.
  • Miceli-Richard C, Gestermann N, Ittah M, et al. The CGGGG insertion/deletion polymorphism of the IRF5 promoter is a strong risk factor for primary Sjögren’s syndrome. Arthritis Rheumatism. 2009;60:1991–1997.
  • Sigurdsson S, Göring HH, Kristjansdottir G, et al. Comprehensive evaluation of the genetic variants of interferon regulatory factor 5 (IRF5) reveals a novel 5 bp length polymorphism as strong risk factor for systemic lupus erythematosus. Hum Mol Genet. 2008;17:872–881.
  • Nordmark G, Kristjansdottir G, Theander E, et al. Association of EBF1, FAM167A(C8orf13)-BLK and TNFSF4 gene variants with primary Sjögren’s syndrome. Genes Immun. 2011;12:100–109.
  • Korman BD, Alba MI, Le JM, et al. Variant form of STAT4 is associated with primary Sjögren’s syndrome. Genes Immun. 2008;9:267–270.
  • Nezos A, Gkioka E, Koutsilieris M. TNFAIP3 F127C coding variation in Greek primary Sjogren’s syndrome patients. J Immunol Res. 2018;2018:6923213.
  • Papageorgiou A, Mavragani CP, Nezos A, et al. A BAFF receptor His159Tyr mutation in Sjögren’s syndrome-related lymphoproliferation. Arthritis Rheumatol (Hoboken). 2015;67:2732–2741.
  • Chen S, Zhou Y, Chen Y, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–i90.
  • Cosgun E, Oh M. Exploring the consistency of the quality scores with machine learning for next-generation sequencing experiments. Biomed Res Int. 2020;2020:8531502.
  • Kim S, Scheffler K. Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods. 2018;15:591–594.
  • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
  • Xavier A, Scott RJ. TAPES: a tool for assessment and prioritisation in exome studies. PLoS Comput Biol. 2019;15:e1007453.
  • Zhao L, Liu H, Yuan X, et al. Comparative study of whole exome sequencing-based copy number variation detection tools. BMC Bioinf. 2020;21:97.
  • Samarakoon PS, Sorte HS, Stray-Pedersen A, et al. cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data. BMC Genomics. 2016;17:51.
  • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102:15545–15550.
  • Ross KA. Coherent somatic mutation in autoimmune disease. PloS One. 2014;9:e101093.
  • Song WM, Agrawal P, Von Itter R, et al. Network models of primary melanoma microenvironments identify key melanoma regulators underlying prognosis. Nat Commun. 2021;12:1214.
  • McKown RL, Wang N, Raab RW, et al. Lacritin and other new proteins of the lacrimal functional unit. Exp Eye Res. 2009;88:848–858.
  • Lyons YA, Wu SY, Overwijk WW, et al. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol. 2017;1:26.
  • Denny P, Hagen FK, Hardt M, et al. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res. 2008;7:1994–2006.
  • Johansson ME, Thomsson KA, Hansson GC. Proteomic analyses of the two mucus layers of the colon barrier reveal that their main component, the Muc2 mucin, is strongly bound to the Fcgbp protein. J Proteome Res. 2009;8:3549–3557.
  • Albert TK, Laubinger W, Müller S, et al. Human intestinal TFF3 forms disulfide-linked heteromers with the mucus-associated FCGBP protein and is released by hydrogen sulfide. J Proteome Res. 2010;9:3108–3117.
  • Valentini D, Rao M, Meng Q, et al. Identification of neoepitopes recognized by tumor-infiltrating lymphocytes (TILs) from patients with glioma. Oncotarget. 2018;9:19469–19480.
  • Huang X, Zhou Y, Liu W, et al. Identification of hub genes related to silicone-induced immune response in rats. Oncotarget. 2017;8:99772–99783.
  • Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, et al. DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus. Ann Rheumatic Dis. 2018;77:736–743.
  • Lutzow YC, Donaldson L, Gray CP, et al. Identification of immune genes and proteins involved in the response of bovine mammary tissue to Staphylococcus aureus infection. BMC Vet Res. 2008;4:18.
  • Katsiougiannis S, Tenta R, Skopouli FN. Activation of AMP-activated protein kinase by adiponectin rescues salivary gland epithelial cells from spontaneous and interferon-gamma-induced apoptosis. Arthritis Rheumatism. 2010;62:414–419.
  • Kim JW, Kim SM, Park JS, et al. Metformin improves salivary gland inflammation and hypofunction in murine Sjögren’s syndrome. Arthritis Res Ther. 2019;21:136.
  • Turkcapar N, Sak SD, Saatci M, et al. Vasculitis and expression of vascular cell adhesion molecule-1, intercellular adhesion molecule-1, and E-selectin in salivary glands of patients with Sjögren’s syndrome. J Rheumatol. 2005;32:1063–1070.
  • Youinou P, Pers JO. Disturbance of cytokine networks in Sjögren’s syndrome. Arthritis Res Ther. 2011;13:227.
  • Azuma M, Aota K, Tamatani T, et al. Suppression of tumor necrosis factor alpha-induced matrix metalloproteinase 9 production in human salivary gland acinar cells by cepharanthine occurs via down-regulation of nuclear factor kappaB: a possible therapeutic agent for preventing the destruction of the acinar structure in the salivary glands of Sjögren’s syndrome patients. Arthritis Rheumatism. 2002;46:1585–1594.
  • Koski H, Janin A, Humphreys-Beher MG, et al. Tumor necrosis factor-alpha and receptors for it in labial salivary glands in Sjögren’s syndrome. Clin Exp Rheumatol. 2001;19:131–137.
  • Baturone R, Soto MJ, Márquez M, et al. Health-related quality of life in patients with primary Sjögren’s syndrome: relationship with serum levels of proinflammatory cytokines. Scand J Rheumatol. 2009;38:386–389.
  • Stea EA, Routsias JG, Samiotaki M, et al. Analysis of parotid glands of primary Sjögren’s syndrome patients using proteomic technology reveals altered autoantigen composition and novel antigenic targets. Clin Exp Immunol. 2007;147:81–89.
  • Singh AG, Singh S, Matteson EL. Rate, risk factors and causes of mortality in patients with Sjögren’s syndrome: a systematic review and meta-analysis of cohort studies. Rheumatology (Oxford). 2016;55:450–460.
  • Pedersen AM, Bardow A, Nauntofte B. Salivary changes and dental caries as potential oral markers of autoimmune salivary gland dysfunction in primary Sjogren’s syndrome. BMC Clin Pathol. 2005;5:4.
  • Shi H, Cao N, Pu Y, et al. Long non-coding RNA expression profile in minor salivary gland of primary Sjögren’s syndrome. Arthritis Res Ther. 2016;18:109.
  • Fallarino F, Vacca C, Orabona C, et al. Functional expression of indoleamine 2,3-dioxygenase by murine CD8 alpha(+) dendritic cells. Int Immunol. 2002;14:65–68.
  • Orabona C, Puccetti P, Vacca C, et al. Toward the identification of a tolerogenic signature in IDO-competent dendritic cells. Blood. 2006;107:2846–2854.
  • Hildner K, Edelson BT, Purtha WE, et al. Batf3 deficiency reveals a critical role for CD8alpha+ dendritic cells in cytotoxic T cell immunity. Science (New York, NY). 2008;322:1097–1100.
  • Martínez-López M, Iborra S, Conde-Garrosa R, et al. Batf3-dependent CD103+ dendritic cells are major producers of IL-12 that drive local Th1 immunity against Leishmania major infection in mice. Eur J Immunol. 2015;45:119–129.
  • Törőcsik D, Kovács D, Póliska S, et al. Genome wide analysis of TLR1/2- and TLR4-activated SZ95 sebocytes reveals a complex immune-competence and identifies serum amyloid A as a marker for activated sebaceous glands. PloS One. 2018;13:e0198323.
  • Williams KL, Nanda I, Lyons GE, et al. Characterization of murine BATF: a negative regulator of activator protein-1 activity in the thymus. Eur J Immunol. 2001;31:1620–1627.
  • Schraml BU, Hildner K, Ise W, et al. The AP-1 transcription factor Batf controls T(H)17 differentiation. Nature. 2009;460:405–409.
  • Geissmann F, Manz MG, Jung S, et al. Development of monocytes, macrophages, and dendritic cells. Science (New York, NY). 2010;327:656–661.
  • Yao Q, Song Z, Wang B, et al. Identifying key genes and functionally enriched pathways in Sjögren’s syndrome by weighted gene co-expression network analysis. Front Genet. 2019;10:1142.
  • Kitada S, Kayama H. BATF2 inhibits immunopathological Th17 responses by suppressing Il23a expression during Trypanosoma cruzi infection. J Exp Med. 2017;214:1313–1331.
  • Koraka P, Martina BEE, van den Ham HJ, et al. Analysis of mouse brain transcriptome after experimental duvenhage virus infection shows activation of innate immune response and pyroptotic cell death pathway. Front Microbiol. 2018;9:397.
  • Pontarini E, Lucchesi D, Bombardieri M. Current views on the pathogenesis of Sjögren’s syndrome. Curr Opin Rheumatol. 2018;30:215–221.
  • Niu T, Li J, Wang J, et al. Identification of novel signal transduction, immune function, and oxidative stress genes and pathways by topiramate for treatment of methamphetamine dependence based on secondary outcomes. Front Psychiatry. 2017;8:271.
  • Shi H, Liu C, Tan H, et al. Hippo kinases Mst1 and Mst2 sense and amplify IL-2R-STAT5 signaling in regulatory T cells to establish stable regulatory activity. Immunity. 2018;49:899–914.e6.
  • Daniels PJ, McArthur CP, Heruth DP, et al. Cytokine-mediated stimulation of laminin expression and cell-growth arrest in a human submandibular gland duct-cell line (HSG). Arch Oral Biol. 1999;44:603–615.
  • Daniels PJ, Gustafson SA, French D, et al. Interferon-mediated block in cell cycle and altered integrin expression in a differentiated salivary gland cell line (HSG) cultured on Matrigel. J Interferon Cytokine Res. 2000;20:1101–1109.
  • Boehm N, Riechardt AI, Wiegand M, et al. Proinflammatory cytokine profiling of tears from dry eye patients by means of antibody microarrays. Invest Ophthalmol Vis Sci. 2011;52:7725–7730.
  • de Oliveira FR, Fantucci MZ, Adriano L, et al. Neurological and inflammatory manifestations in Sjögren’s syndrome: the role of the kynurenine metabolic pathway. Int J Mol Sci. 2018;19.
  • Brkic Z, Maria NI, van Helden-meeuwsen CG, et al. Prevalence of interferon type I signature in CD14 monocytes of patients with Sjogren’s syndrome and association with disease activity and BAFF gene expression. Ann Rheum Dis. 2013;72:728–735.
  • Hall JC, Casciola-Rosen L, Berger AE, et al. Precise probes of type II interferon activity define the origin of interferon signatures in target tissues in rheumatic diseases. Proc Natl Acad Sci USA. 2012;109:17609–17614.
  • Gottenberg JE, Cagnard N, Lucchesi C, et al. Activation of IFN pathways and plasmacytoid dendritic cell recruitment in target organs of primary Sjögren’s syndrome. Proc Natl Acad Sci USA. 2006;103:2770–2775.