Lupus is an autoimmune disease that is estimated to affect nearly 1 million Americans, primarily women between the ages of 20-40. Lupus involves antibodies that attack connective tissue. The principal form of lupus is a systemic one (systemic lupus erythematosus; SLE). SLE is a chronic autoimmune disease with strong genetic as well as environmental components (See, e.g., Hochberg M C, Dubois' Lupus Erythematosus. 5th ed., Wallace D J, Hahn B H, eds. Baltimore: Williams and Wilkins (1997); Wakeland E K, et al., Immunity 2001; 15(3):397-408; Nath S K, et al., Curr. Opin. Immunol. 2004; 16(6):794-800; D'Cruz et al., Lancet (2007), 369:587-596). Various additional forms of lupus are known, including, but not limited to, cutaneous lupus erythematosus (CLE), lupus nephritis (LN), and neonatal lupus.
Untreated lupus can be fatal as it progresses from attack of skin and joints to internal organs, including lung, heart, and kidneys (with renal disease being the primary concern), thus making early and accurate diagnosis of and/or assessment of risk of developing lupus particularly critical. Lupus mainly appears as a series of flare-ups, with intervening periods of little or no disease manifestation. Kidney damage, measured by the amount of proteinuria in the urine, is one of the most acute areas of damage associated with pathogenicity in SLE, and accounts for at least 50% of the mortality and morbidity of the disease.
Clinically, SLE is a heterogeneous disorder characterized by high-affinity autoantibodies (autoAbs). AutoAbs play an important role in the pathogenesis of SLE, and the diverse clinical manifestations of the disease are due to the deposition of antibody-containing immune complexes in blood vessels leading to inflammation in the kidney, brain and skin. AutoAbs also have direct pathogenic effects contributing to hemolytic anemia and thrombocytopenia. SLE is associated with the production of antinuclear antibodies, circulating immune complexes, and activation of the complement system. SLE has an incidence of about 1 in 700 women between the ages of 20 and 60. SLE can affect any organ system and can cause severe tissue damage. Numerous autoAbs of differing specificity are present in SLE. SLE patients often produce autoAbs having anti-DNA, anti-Ro, and anti-platelet specificity and that are capable of initiating clinical features of the disease, such as glomerulonephritis, arthritis, serositis, complete heart block in newborns, and hematologic abnormalities. These autoAbs are also possibly related to central nervous system disturbances. Arbuckle et al. described the development of autoAbs before the clinical onset of SLE (Arbuckle et al, N. Engl. J. Med. 349(16): 1526-1533 (2003)). Definitive diagnosis of lupus, including SLE, is not easy, resulting in clinicians resorting to a multi-factorial signs and symptoms-based classification approach (Gill et al., American Family Physician 68(11): 2179-2186(2003)).
One of the most difficult challenges in clinical management of complex autoimmune diseases such as lupus is the accurate and early identification of the disease in a patient. Over the years, many linkage and candidate gene studies have been performed to identify genetic factors contributing to SLE susceptibility. Haplotypes carrying the HLA Class II alleles DRB1*0301 and DRB1*1501 are clearly associated with disease as well as the presence of antibodies to nuclear autoantigens. See, e.g., Goldberg M A, et al., Arthritis Rheum. 19(2):129-32 (1976); Graham R R, et al., Am J Hum Genet. 71(3):543-53 (2002); and Graham R R, et al., Eur J Hum Genet. 15(8):823-30 (2007). More recently, variants of Interferon Regulatory Factor 5 (IRF5) and Signal Transducer and Activator of Transcription 4 (STAT4) were discovered to be significant risk factors for SLE. See, e.g., Sigurdsson S, et al., Am J Hum Genet. 76(3):528-37 (2005); Graham R R, et al., Nat Genet. 38(5):550-55 (2006); Graham R R, et al., Proc Natl Acad Sci USA 104(16):6758-63 (2007); and Remmers E F, et al., N Engl J Med. 357(10):977-86 (2007). The identification of IRF5 and STAT4 as SLE risk genes provides support for the concept that, in certain instances, the type I interferon (IFN) pathway plays an important role in SLE disease pathogenesis. Type I IFN is present in serum of SLE cases, and production of IFN is linked to the presence of Ab and nucleic acid containing immune complexes reviewed in Ronnblom et al., J Exp Med 194:F59 (2001); see also Baechler E C, et al., Curr Opin Immunol. 16(6):801-07 (2004); Banchereau J, et al., Immunity 25(3):383-92 (2006); Miyagi et al., J Exp Med 204(10):2383-96 (2007)). The majority of SLE cases exhibit a prominent type I IFN gene expression ‘signature’ in blood cells (Baechler et al., Proc Natl Acad Sci USA 100:2610 (2003); Bennett et al., J Exp Med 197:711 (2003)) and have elevated levels of IFN-inducible cytokines and chemokines in serum (Bauer et al., PLoS Med 3:e491 (2006)). Immune complexes containing native DNA and RNA stimulate toll-like receptors (TLRs) 7 and 9 expressed by dendritic cells and B cells to produce type interferon which further stimulates immune complex formation (reviewed in (Marshak-Rothstein et al., Annu Rev Immunol 25, 419 (2007)).
In addition, a number of studies have been performed to identify reliable biomarkers for diagnostic and prognostic purposes. No clinically validated diagnostic markers, however, e.g., biomarkers, have been identified that enable clinicians or others to accurately define pathophysiological aspects of SLE, clinical activity, response to therapy, prognosis, or risk of developing the disease, although a number of candidate genes and alleles (variants) have been identified that are thought to contribute to SLE susceptibility. For example, at least 13 common alleles that contribute risk for SLE in individuals of European ancestry have been reported (Kyogoku et al., Am J Hum Genet 75(3):504-7 (2004); Sigurdsson et al., Am J Hum Genet 76(3):528-37 (2005); Graham et al., Nat Genet 38(5):550-55 (2006); Graham et al., Proc Natl Acad Sci USA 104(16):6758-63 (2007); Remmers et al., N Engl J Med 357(10):977-86 (2007); Cunninghame Graham et al., Nat Genet 40(1):83-89 (2008); Harley et al., Nat Genet 40(2):204-10 (2008); Horn et al., N Engl J Med 358(9):900-9 (2008); Kozyrev et al., Nat Genet 40(2):211-6 (2008); Nath et al., Nat Genet 40(2):152-4 (2008); Sawalha et al., PLoS ONE 3(3):e1727 (2008)). The putative causal alleles are known for HLA-DR3, HLA-DR2, FCGR2A, PTPN22, ITGAM and BANK1 (Kyogoku et al., Am J Hum Genet 75(3):504-7 (2004); Kozyrev et al., Nat Genet 40(2):211-6 (2008); Nath et al., Nat Genet 40(2):152-4 (2008)), white the risk haplotypes for IRF5, TATSF 4 and BLK likely contribute to SLE by influencing mRNA and protein expression levels (Sigurdsson et al., Am J Hum Genet 76(3):528-37 (2005); Graham et al., Nat Genet 38(5):550-55 (2006); Graham et al., Proc Natl Acad Sci USA 104(16):6758-63 (2007); Cunninghame Graham et al., Nat Genet 40(1):83-89 (2008); Horn et al., N Engl J Med 358(9):900-9 (2008)). The causal alleles for STAT4, KIAA1542, IRAK1, PXK and other genes, such as BLK, have not been determined (Remmers et al., N Engl J Med 357(10):977-86 (2007); Harley et al., Nat Genet 40(2):204-1.0 (2008); Hom et al., N Engl J Med 358(9000-9 (2008); Sawalha et al., PLoS ONE 3(3):e1727 (2008)). These and other genetic variations associated with lupus are also described in Int'l Pat. Appl. No. PCT/US2008/064430 (Int'l Pub. No. WO 2008/144761). While the contribution of such genetic variation to various aspects of SLE risk and disease that has been described to date has been important, more information about the contribution of genetic variation to, for example, the significant clinical heterogeneity of SLE remains to be determined.
It would therefore be highly advantageous to have additional molecular-based diagnostic methods that can be used to objectively identify the presence of and/or classify the disease in a patient, define pathophysiologic aspects of lupus, clinical activity, response to therapy, prognosis, and/or risk of developing lupus. In addition, it would be advantageous to have molecular-based diagnostic markers associated with various clinical and/or pathophysiological and/or other biological indicators of disease. Thus, there is a continuing need to identify new risk loci and polymorphisms associated with lupus as well as other autoimmune disorders. Such associations would greatly benefit the identification of the presence of lupus in patients or the determination of susceptibility to develop the disease. Such associations would also benefit the identification of pathophysiologic aspects of lupus, clinical activity, response to therapy, or prognosis. In addition, statistically and biologically significant and reproducible information regarding such associations could be utilized as an integral component in efforts to identify specific subsets of patients who would be expected to significantly benefit from treatment with a particular therapeutic agent, for example where the therapeutic agent is or has been shown in clinical studies to be of therapeutic benefit in such specific lupus patient subpopulation.
The invention described herein meets above-described needs and provides other benefits.
All references cited herein, including patent applications and publications, are incorporated by reference in their entirety for any purpose.