Biomarker discovery in systemic lupus erythematosus: genome-methylation approaches : Research report

Abstract

Discovery of novel biomarkers in lupus nephritis Biomarkers are needed for making diagnosis and prognosis. In lupus nephritis, conventional tests like urinalysis or serum creatinine remain inadequate for patient care. In this proposal, we focused on non-invasive tools like blood and urine mRNAs or proteins. We chose candidate genes involving regulatory T-cell, B-lymphocyte signatures or vascular protective factors. Expression of regulatory cell signature (FOXP3) in peripheral blood mononuclear cells is associated with activity of lupus nephritis. We found FOXP3 mRNA levels in PBMCs from patients with active lupus nephritis were significantly lower than inactive lupus nephritis. Expression levels of FOXP3 mRNA were associated with pathological activity index, cellular crescent and fibrinoid necrosis. BLyS and APRIL are B-lymphocyte related cytokines that play an important role in generating and maintaining the mature B-cell pool. In this study, we found blood APRIL correlated with activity of lupus nephritis. Blood APRIL levels could precisely predict failure of standard treatment treatment. APRIL is a potential biomarker for predicting treatment failure. Lastly, we found an expression of VEGF in renal tissue may serve as a molecular marker of renal damage from LN and may be a predictive factor for short-term loss of kidney function in lupus nephritis patients. We proposed that reduction of intra-renal VEGF level caused by losses of podocyte cells. Genetic polymorphism of drug toxicity or pharmacokinetics in SLE patients We began to explore the pharmacokinetics and pharmacogenomics of two important immunosuppressants, azathioprine and mycophenolate. In this study, we report TPMT polymorphisms and TPMT enzyme activity were important predictors of AZA-induced myelosuppression. The tests are available for routine care. Mycophenolic acid (MPA) is active metabolite of mycophenalate. We found MPA levels is important predictor of therapeutic response. The therapeutic drug monitoring is now an important issue of patient care. We found UGT1A9 polymorphism may play a pivotal role in drug metabolisms. Methylation study We examined and compared the methylation levels of long terminal repeats (LTRs) and non-LTR retroelements in normal and SLE CD4+ T lymphocytes, CD8+ T lymphocytes and B lymphocytes. Hypomethylation of LINE-1 but not Alu was found in CD4+ T lymphocytes, CD8+ T lymphocytes, and B lymphocytes of SLE patient. Moreover, when the SLE patients were divided into active and inactive groups, LINE-1 hypomethylation was more significantly distinguished in both CD4+ and CD8+ T lymphocytes of patients from the active SLE group when compared to the controls. Genome-wide scanning using SNP microarrays In this study, we applied case-control association study including pooling genome wide association (GWA) and candidate gene association studies to search for SNPs associated with SLE susceptibility and/or severity. We could not identify any SNPs with distinct p-value or odds ratio from our pooling GWA result due to limited power. We selected IFIX for further study in candidate gene’s part. Besides IFIX, we also focus on MNDA, IFI16 and AIM2 genes which located in the same region and are all IFN-inducible genes. They are important SLE susceptibility genes due to several reasons including 1) genetic mapping from lupus murine model and 2) an upregulated IFN-inducible genes in patients with SLE from microarray studies and 3) IFI16 was identified as new autoantigen for patients with SLE. We genotyped 10 SNPs from these 4 genes and found that SNP within IFIX and IFI16 are independently important.