Justiz Vaillant, A.A., Goyal, A., Varacallo, M.A. Systemic Lupus Erythematosus. In StatPearls [Internet]. Treasure Island (FL) Available from: http://www.ncbi.nlm.nih.gov/books/NBK535405/ (StatPearls Publishing, 2025).
van Vollenhoven, R. F. et al. DORIS definition of remission in SLE: final recommendations from an international task force. Lupus. Sci. Med. 8(1), e000538 (2021).
Ugarte-Gil, M. F. et al. Achieving remission or low disease activity is associated with better outcomes in patients with systemic lupus erythematosus: a systematic literature review. Lupus. Sci. Med. 8(1), e000542 (2021).
Parodis, I. et al. Holistic approaches in systemic lupus erythematosus: do physicians avoid addressing difficult-to-treat but highly relevant symptoms?. RMD Open 11(1), e005400 (2025).
Miceli-Richard, C. Epigenetics and lupus. Jt. Bone Spine 82(2), 90–93 (2015).
Bose, M. & Jefferies, C. Sex bias in systemic lupus erythematosus: a molecular insight. Immunometabolism 4(3), e00004 (2022).
Horton, M. K. et al. Changes in DNA methylation are associated with systemic lupus erythematosus flare remission and clinical subtypes. Clin. Epigenet. 16(1), 181 (2024).
Javierre, B. M. et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genom. Res. 20(2), 170–179 (2010).
Ferreté-Bonastre, A. G., Cortés-Hernández, J. & Ballestar, E. What can we learn from DNA methylation studies in lupus. Clin. Immunol. 234, 108920 (2022).
Teruel, M. & Sawalha, A. H. Epigenetic variability in Systemic Lupus Erythematosus: what we learned from genome-wide DNA methylation studies. Curr. Rheumatol. Rep. 19(6), 32 (2017).
Lei, W. et al. Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythematosus, systemic sclerosis, and dermatomyositis. Scand. J. Rheumatol. 38(5), 369–374 (2009).
Li, H. et al. Precision DNA demethylation ameliorates disease in lupus-prone mice. JCI Insight. 3(16), e120880 (2018).
Zhou, H. Y. et al. Recent advances in the involvement of epigenetics in the pathogenesis of systemic lupus erythematosus. Clin. Immunol. Orlando Fla. 258, 109857 (2024).
Absher, D. M. et al. Genome-wide DNA methylation analysis of systemic lupus erythematosus reveals persistent hypomethylation of interferon genes and compositional changes to CD4+ T-cell populations. PLoS Genet. 9(8), e1003678 (2013).
Hochberg, M. C. Updating the American college of rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthr. Rheum. 40(9), 1725–1725 (1997).
Gladman, D. D., Ibañez, D. & Urowitz, M. B. Systemic lupus erythematosus disease activity index 2000. J. Rheumatol. 29(2), 288–291 (2002).
Teschendorff, A. E. et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 29(2), 189–196 (2013).
Tian, Y. et al. ChAMP: updated methylation analysis pipeline for Illumina BeadChips. Bioinformatics 33(24), 3982–3984 (2017).
Du, P. et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformat. 30(11), 587 (2010).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl. Acid. Res. 43(7), e47 (2015).
Teschendorff, A. E., Breeze, C. E., Zheng, S. C. & Beck, S. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide association studies. BMC Bioinform. 18(1), 105 (2017).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57(1), 289–300 (1995).
Thévenot, E. A., Roux, A., Xu, Y., Ezan, E. & Junot, C. Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. J. Proteom. Res. 14(8), 3322–3335 (2015).
Peters, T. J. et al. De novo identification of differentially methylated regions in the human genome. Epigenet. Chromatin. 8(1), 6 (2015).
Kolberg, L. et al. g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update). Nucl. Acid. Res. 51(W1), W207–W212 (2023).
Phipson, B., Maksimovic, J. & Oshlack, A. missMethyl: an R package for analyzing data from Illumina’s HumanMethylation450 platform. Bioinformatics 32(2), 286–288 (2016).
Yu, G. Gene ontology semantic similarity analysis using GOSemSim. Method. Mol. Biol. 2117, 207–215 (2020).
Gu, Z. & Hübschmann, D. simplifyEnrichment: A Bioconductor package for clustering and visualizing functional enrichment results. Genom. Proteom. Bioinform. 21(1), 190–202 (2023).
Wu, X. et al. Differential CpG DNA methylation of peripheral B cells, CD4+ T cells, and salivary gland tissues in IgG4-related disease. Arthr. Res Ther. 25(1), 4 (2023).
Zhou, Z. et al. Genome-wide DNA methylation pattern in whole blood of patients with Hashimoto thyroiditis. Front. Endocrinol. 24(14), 1259903 (2023).
Aran, D., Sabato, S. & Hellman, A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol. 14(3), R21 (2013).
Jjingo, D., Conley, A. B., Yi, S. V., Lunyak, V. V. & Jordan, I. K. On the presence and role of human gene-body DNA methylation. Oncotarget 3(4), 462–474 (2012).
Dadkhah, M., Baziar, M. & Rezaei, N. The regulatory role of BDNF in neuroimmune axis function and neuroinflammation induced by chronic stress: A new therapeutic strategies for neurodegenerative disorders. Cytokine 1(174), 156477 (2024).
Kular, L. et al. Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis. Clin. Epigenet. 30(11), 86 (2019).
Olivier, J. F. et al. CCDC88B interacts with RASAL3 and ARHGEF2 and regulates dendritic cell function in neuroinflammation and colitis. Commun. Biol. 7(1), 77 (2024).
Wang, J. et al. ADRB1 was identified as a potential biomarker for breast cancer by the co-analysis of tumor mutational burden and immune infiltration. Aging 13(1), 351–363 (2020).
Ikenouchi-Sugita, A. et al. Serum brain-derived neurotrophic factor levels as a novel biological marker for the activities of psychiatric symptoms in systemic lupus erythematosus. World J. Biol. Psychiatry 11(2), 121–128 (2010).
Tamashiro, L. F. et al. Participation of the neutrophin brain-derived neurotrophic factor in neuropsychiatric Systemic Lupus Erythematosus. Rheumatology 53(12), 2182–2190 (2014).
Alkhotani, A. Neuropsychiatric Lupus. Sultan Qaboos Univ. Med. J. 13(1), 19–25 (2013).
Zezulin, A. U. et al. RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils. Genes. Dev. 37(13–14), 605–620 (2023).
Yan, J., Li, Q., Mao, A. P., Hu, M. M. & Shu, H. B. TRIM4 modulates type I interferon induction and cellular antiviral response by targeting RIG-I for K63-linked ubiquitination. J. Mol. Cell. Biol. 6(2), 154–163 (2014).
Shao, W. H. & Cohen, P. L. Disturbances of apoptotic cell clearance in systemic lupus erythematosus. Arthr. Res. Ther. 13(1), 202 (2011).
Mathapathi, S. & Chu, C. Q. Contribution of impaired DNASE1L3 activity to Anti-DNA autoantibody production in systemic lupus erythematosus. Rheumatol. Immunol. Res. 3(1), 17–22 (2022).
Saheb Sharif-Askari, N. et al. Enhanced expression of autoantigens during SARS-CoV-2 viral infection. Front. Immunol. 12, 686462 (2021).
Stojilkovic, S. S., Sokanovic, S. J. & Constantin, S. What is known and unknown about the role of neuroendocrine genes Ptprn and Ptprn2. Front. Endocrinol. 16, 1531723 (2025).
O’Rourke, K. P. et al. High levels of Lymphotoxin-Beta (LT-Beta) gene expression in rheumatoid arthritis synovium: Clinical and cytokine correlations. Rheumatol. Int. 28(10), 979–986 (2008).
Tumanov, A. V., Kuprash, D. V. & Nedospasov, S. A. The role of lymphotoxin in development and maintenance of secondary lymphoid tissues. Cytokine Growth. Factor. Rev. 14(3–4), 275–288 (2003).
Yin, C. et al. Pathological significance and regulatory mechanism of lymphotoxin β receptor overexpression in T cells of patients with systemic lupus erythematosus. J. Biomed. Res. 32(2), 113–122 (2018).
Fehmi, J. et al. Contactin-1 links autoimmune neuropathy and membranous glomerulonephritis. PLoS ONE 18(3), e0281156 (2023).
Sarwar, S. et al. Neuropsychiatric systemic lupus erythematosus: a 2021 update on diagnosis, management, and current challenges. Cureus 13(9), e17969 (2021).
Cho, H. J. et al. POU6F2 mutation in humans with pubertal failure alters GnRH transcript expression. Front. Endocrinol. 14, 1203542 (2023).
Sowers, L. P. et al. Disruption of the non-canonical Wnt gene PRICKLE2 leads to autism-like behaviors with evidence for hippocampal synaptic dysfunction. Mol. Psychiatr. 18(10), 1077–1089 (2013).
Folke, J. et al. DNAJB6b is downregulated in synucleinopathies. J. Parkinson. Dis. 11(4), 1791–1803 (2021).
Bonnert, T. P. et al. theta, a novel gamma-aminobutyric acid type A receptor subunit. Proc. Natl. Acad. Sci. U S A. 96(17), 9891–9896 (1999).
Pinna, G. Targeting neurosteroidogenesis as therapy for PTSD. Front. Pharmacol. 6(4), 166 (2014).
Singh, K. et al. The IgLON family of cell adhesion molecules expressed in developing neural circuits ensure the proper functioning of the sensory system in mice. Sci. Rep. 14(1), 22593 (2024).
Tovey, C. A. & Conduit, P. T. Microtubule nucleation by γ-tubulin complexes and beyond. Essay. Biochem. 62(6), 765–780 (2018).
Papa, R., Penco, F., Volpi, S. & Gattorno, M. Actin remodeling defects leading to autoinflammation and immune dysregulation. Front. Immunol. 7(11), 604206 (2021).
Alblas, J., Ulfman, L., Hordijk, P. & Koenderman, L. Activation of Rhoa and ROCK are essential for detachment of migrating leukocytes. Mol. Biol. Cell. 12(7), 2137–2145 (2001).
Houy, S. et al. Doc2B acts as a calcium sensor for vesicle priming requiring synaptotagmin-1, Munc13-2 and SNAREs. Elife 6, e27000 (2017).
Amalraj, J., Cutler, S. J., Ghazawi, I., Boyle, G. M. & Ralph, S. J. REST negatively and ISGF3 positively regulate the human STAT1 gene in melanoma. Mol. Cancer Ther. 12(7), 1288–1298 (2013).
Magin, A., Lietz, M., Cibelli, G. & Thiel, G. RE-1 silencing transcription factor-4 (REST4) is neither a transcriptional repressor nor a de-repressor. Neurochem. Int. 40(3), 195–202 (2002).
Otto, S. J. et al. A new binding motif for the transcriptional repressor REST uncovers large gene networks devoted to neuronal functions. J. Neurosci. Off. J. Soc. Neurosci. 27(25), 6729–6739 (2007).
Silva, C. T. et al. Distinct sex-specific DNA methylation differences in Alzheimer’s disease. Alzheimer. Res. Ther. 14(1), 133 (2022).
Kim, J. W., Kim, H. A., Suh, C. H. & Jung, J. Y. Sex hormones affect the pathogenesis and clinical characteristics of systemic lupus erythematosus. Front. Med. 9, 906475 (2022).
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