[1] O. M. Steinmetz, J. E. Turner, H. J. Paust, M. Lindner, A. Peters, K. Heiss, J. Velden, H. Hopfer, S. Fehr, T. Krieger, C. Meyer-Schwesinger, T. N. Meyer, U. Helmchen, H. W. Mittrucker, R. A. Stahl, U. Panzer, CXCR3 mediates renal Th1 and Th17 immune response in murine lupus nephritis, J Immunol 183(7) (2009) 4693–704.
[2] F. Yu, M. Haas, R. Glassock, M. H. Zhao, Redefining lupus nephritis: clinical implications of pathophysiologic subtypes, Nat Rev Nephrol 13(8) (2017) 483–495.
[3] M. Dall’Era, Treatment of lupus nephritis: current paradigms and emerging strategies, Curr Opin Rheumatol 29(3) (2017) 241–247.
[4] D. A. Forero, G. P. Guio-Vega, Y. Gonzalez-Giraldo, A comprehensive regional analysis of genome-wide expression profiles for major depressive disorder, Journal of affective disorders 218 (2017) 86–92.
[5] M. I. Khan, K. J. Debski, M. Dabrowski, A.M. Czarnecka, C. Szczylik, Gene set enrichment analysis and ingenuity pathway analysis of metastatic clear cell renal cell carcinoma cell line, Am J Physiol Renal Physiol 311(2) (2016) F424–36.
[6] P. F. Bing, W. Xia, L. Wang, Y. H. Zhang, S. F. Lei, F. Y. Deng, Common Marker Genes Identified from Various Sample Types for Systemic Lupus Erythematosus, PLoS One 11(6) (2016) e0156234.
[7] T. Sezin, A. Vorobyev, C. D. Sadik, D. Zillikens, Y. Gupta, R. J. Ludwig, Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4(+) T Cells, Front Immunol 8 (2017) 1992.
[8] P. Coit, M. Jeffries, N. Altorok, M. G. Dozmorov, K. A. Koelsch, J. D. Wren, J. T. Merrill, W. J. McCune, A. H. Sawalha, Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naive CD4+ T cells from lupus patients, J Autoimmun 43 (2013) 78–84.
[9] E. L. Lim, K. Okkenhaug, PI3Kdelta is a Treg target in cancer immunotherapy, Immunology (2019).
[10] H. R. Ali, E. Provenzano, S. J. Dawson, F. M. Blows, B. Liu, M. Shah, H. M. Earl, C. J. Poole, L. Hiller, J. A. Dunn, S. J. Bowden, C. Twelves, J. M. Bartlett, S. M. Mahmoud, E. Rakha, I. O. Ellis, S. Liu, D. Gao, T. O. Nielsen, P. D. Pharoah, C. Caldas, Association between CD8+ T-cell infiltration and breast cancer survival in 12,439 patients, Ann Oncol 25(8) (2014) 1536–43.
[11] B. Chen, M. S. Khodadoust, C. L. Liu, A.M. Newman, A. A. Alizadeh, Profiling Tumor Infiltrating Immune Cells with CIBERSORT, Methods Mol Biol 1711 (2018) 243–259.
[12] A.M. Newman, C. L. Liu, M. R. Green, A. J. Gentles, W. Feng, Y. Xu, C. D. Hoang, M. Diehn, A. A. Alizadeh, Robust enumeration of cell subsets from tissue expression profiles, Nat Methods 12(5) (2015) 453–7.
[13] H. R. Ali, L. Chlon, P. D. Pharoah, F. Markowetz, C. Caldas, Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study, PLoS Med 13(12) (2016) e1002194.
[14] N. Rohr-Udilova, F. Klinglmuller, R. Schulte-Hermann, J. Stift, M. Herac, M. Salzmann, F. Finotello, G. Timelthaler, G. Oberhuber, M. Pinter, T. Reiberger, E. Jensen-Jarolim, R. Eferl, M. Trauner, Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma, Sci Rep 8(1) (2018) 6220.
[15] Y. Xiong, K. Wang, H. Zhou, L. Peng, W. You, Z. Fu, Profiles of immune infiltration in colorectal cancer and their clinical significant: A gene expression-based study, Cancer Med 7(9) (2018) 4496–4508.
[16] V. R. Moulton, G. C. Tsokos, T cell signaling abnormalities contribute to aberrant immune cell function and autoimmunity, J Clin Invest 125(6) (2015) 2220–7.
[17] S. Q. Khan, I. Khan, V. Gupta, CD11b Activity Modulates Pathogenesis of Lupus Nephritis, Front Med (Lausanne) 5 (2018) 52.
[18] A. S. Bomback, G. B. Appel, Updates on the treatment of lupus nephritis, J Am Soc Nephrol 21(12) (2010) 2028–35.
[19] S. Hirose, Q. Lin, M. Ohtsuji, H. Nishimura, J. S. Verbeek, Monocyte subsets involved in the development of systemic lupus erythematosus and rheumatoid arthritis, Int Immunol (2019).
[20] M. L. Santiago-Raber, H. Amano, E. Amano, L. Baudino, M. Otani, Q. Lin, F. Nimmerjahn, J. S. Verbeek, J. V. Ravetch, Y. Takasaki, S. Hirose, S. Izui, Fcgamma receptor-dependent expansion of a hyperactive monocyte subset in lupus-prone mice, Arthritis Rheum 60(8) (2009) 2408–17.
[21] Y. W. Park, S. J. Kee, Y. N. Cho, E. H. Lee, H. Y. Lee, E. M. Kim, M. H. Shin, J. J. Park, T. J. Kim, S. S. Lee, D. H. Yoo, H. S. Kang, Impaired differentiation and cytotoxicity of natural killer cells in systemic lupus erythematosus, Arthritis Rheum 60(6) (2009) 1753–63.
[22] R. Spada, J. M. Rojas, D. F. Barber, Recent findings on the role of natural killer cells in the pathogenesis of systemic lupus erythematosus, J Leukoc Biol 98(4) (2015) 479–87.
[23] N. Schleinitz, F. Vely, J. R. Harle, E. Vivier, Natural killer cells in human autoimmune diseases, Immunology 131(4) (2010) 451–8.
[24] P. Blanco, H. Ueno, N. Schmitt, T follicular helper (Tfh) cells in lupus: Activation and involvement in SLE pathogenesis, Eur J Immunol 46(2) (2016) 281–90.
[25] Y. T. S Iwata, B-cell subsets, signaling and their roles in secretion of autoantibodies, Lupus 25 (2016) 850–856.
[26] S. J. Kim, K. Lee, B. Diamond, Follicular Helper T Cells in Systemic Lupus Erythematosus, Front Immunol 9 (2018) 1793.
[27] Y. L. Zhao, P. X. Tian, F. Han, J. Zheng, X. X. Xia, W. J. Xue, X. M. Ding, C. G. Ding, Comparison of the characteristics of macrophages derived from murine spleen, peritoneal cavity, and bone marrow, J Zhejiang Univ Sci B 18(12) (2017) 1055–1063.
[28] Z. M. Cristina pamfil, Aurélie de Groof, Gaëlle tilman,Sepideh Babaei, Christine Galant, pauline Montigny, nathalie demoulin, Michel Jadoul,Selda Aydin, ralf Lesche, Fiona Mcdonald, Frédéric A Houssiau, Bernard r Lauwerys, Intrarenal activation of adaptive immune effectors is associated with tubular damage and impaired renal function in lupus nephritis, Annals of the Rheumatic Diseases 77 (2018) 1782–1789.
[29] A. A. Herrada, N. Escobedo, M. Iruretagoyena, R. A. Valenzuela, P. I. Burgos, L. Cuitino, C. Llanos, Innate Immune Cells’ Contribution to Systemic Lupus Erythematosus, Front Immunol 10 (2019) 772.
[30] E. Muso, D. Okuzaki, S. Kobayashi, Y. Iwasaki, M. A. Sakurai, A. Ito, H. Nojima, Ficolin–1 is up-regulated in leukocytes and glomeruli from microscopic polyangiitis patients, Autoimmunity 46(8) (2013) 513–24.
[31] M. Feng, J. Y. Chen, R. Weissman-Tsukamoto, J. P. Volkmer, P. Y. Ho, K. M. McKenna, S. Cheshier, M. Zhang, N. Guo, P. Gip, S. S. Mitra, I. L. Weissman, Macrophages eat cancer cells using their own calreticulin as a guide: roles of TLR and Btk, Proc Natl Acad Sci U S A 112(7) (2015) 2145–50.
[32] A. T. Bender, A. Pereira, K. Fu, E. Samy, Y. Wu, L. Liu-Bujalski, R. Caldwell, Y. Y. Chen, H. Tian, F. Morandi, J. Head, U. Koehler, M. Genest, S. L. Okitsu, D. Xu, R. Grenningloh, Btk inhibition treats TLR7/IFN driven murine lupus, Clin Immunol 164 (2016) 65–77.
[33] S. A. Chalmers, E. Glynn, S. J. Garcia, M. Panzenbeck, J. Pelletier, J. Dimock, E. Seccareccia, T. Bosanac, S. Khalil, C. Harcken, D. Webb, G. Nabozny, J. S. Fine, D. Souza, E. Klein, L. Herlitz, M. Ramanujam, C. Putterman, BTK inhibition ameliorates kidney disease in spontaneous lupus nephritis, Clin Immunol 197 (2018) 205–218.
[34] R. A. Sweet, K. M. Nickerson, J. L. Cullen, Y. Wang, M. J. Shlomchik, B Cell-Extrinsic Myd88 and Fcer1g Negatively Regulate Autoreactive and Normal B Cell Immune Responses, J Immunol 199(3) (2017) 885–893.
[35] C. Salazar-Aldrete, M. Galan-Diez, E. Fernandez-Ruiz, P. Nino-Moreno, L. Estrada-Capetillo, C. Abud-Mendoza, E. Layseca-Espinosa, L. Baranda, R. Gonzalez-Amaro, Expression and function of dectin–1 is defective in monocytes from patients with systemic lupus erythematosus and rheumatoid arthritis, J Clin Immunol 33(2) (2013) 368–77.
[36] Y. S. Xiao-wei Chen, Chuan-yin Sun, Feng-xia Wu, Yi Chen, Cheng-de Yang, Anti-class a scavenger receptor autoantibodies from systemic lupus erythematosus patients impair phagocytic clearance of apoptotic cells by macrophages in vitro, Arthritis Research & Therapy 13(1) (2011).
[37] K. Nakamura, M. Jinnin, H. Kudo, K. Inoue, W. Nakayama, N. Honda, I. Kajihara, S. Masuguchi, S. Fukushima, H. Ihn, The role of PSMB9 upregulated by interferon signature in the pathophysiology of cutaneous lesions of dermatomyositis and systemic lupus erythematosus, Br J Dermatol 174(5) (2016) 1030–41.
[38] P. Renauer, P. Coit, M. A. Jeffries, J. T. Merrill, W. J. McCune, K. Maksimowicz-McKinnon, A. H. Sawalha, DNA methylation patterns in naive CD4+ T cells identify epigenetic susceptibility loci for malar rash and discoid rash in systemic lupus erythematosus, Lupus Sci Med 2(1) (2015) e000101.
[39] K. Moorthy, A. N. Jaber, M. A. Ismail, F. Ernawan, M. S. Mohamad, S. Deris, Missing-Values Imputation Algorithms for Microarray Gene Expression Data, Methods Mol Biol 1986 (2019) 255–266.
[40] I. Diboun, L. Wernisch, C. A. Orengo, M. Koltzenburg, Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma, BMC Genomics 7 (2006) 252.
[41] G. Yu, L. G. Wang, Y. Han, Q. Y. He, clusterProfiler: an R package for comparing biological themes among gene clusters, OMICS 16(5) (2012) 284–7.