Background/Purpose: Vitamin D modulates the immune response. Exposing normal PBMCs to activating SLE sera induces an interferon signature which can be inhibited by preexposure of the PBMCs to1,25 OH vitamin D . We explored effects of vitamin D supplementation on gene expression in whole blood in SLE using a modular microarray analysis.  In addition to examining expression of IFN inducible genes, modular microarray analysis allows a comprehensive study of genes associated with inflammation, B cells, myeloid cells and others.

Methods: RNA was prepared from 40 stable,  inactive, anti-DNA+ SLE patients with vitamin D deficiency and an IFN signature who were participating in a 12 week double-blind placebo controlled trial of daily vitamin D3 supplementation (0, 2000 or 4000 IU) at baseline and week 12, and 23 normal controls. A IFN signature was defined to be present if expression of 1 of 3 IFN responsive genes (Mx1, Ifit1, or Ifi44) determined using RT-PCR from whole blood RNA, was expressed at a level ≥ 4 SD, or if 2 of the 3 genes were expressed > 2 SD above the mean of normal controls. The Illumina HT12v4 platform was used for microarray analyses. Gene expression data were grouped using a modular framework for blood genomic analysis developed by Chaussabel et al. (Immunity 2008). Statistical significance for microarray modules was evaluated using a hypergeometric test.  The 28 modules evaluated included modules for IFN as well as plasma cell, myeloid lineage and inflammation modules.

Results: Baseline characteristics of the three treatment groups were similar.  Ten subjects had persistently low vitamin D levels (≤ 20 ng/ml) while 13 subjects achieved repletion (25 OH D ≥ 30ng/ml). Significant overexpression of IFN inducible genes and genes within the inflammation and myeloid modules was noted in all SLE subjects compared to controls at baseline and week 12.  Expression of the T cell and other “undetermined” modules was decreased in the SLE group compared to controls .  No significant changes in the IFN inducible module between baseline and week 12 were found within any treatment group. Examination of module 2_11 (an indeterminate group containing genes for kinases and RAS family members) was significantly decreased at week 12 compared to baseline in the high dose group only.  When comparing the week 12 gene expression data from vitamin D repleted subjects to persistently deficient subjects, no significant differences in module expression (including the IFN module) other than a decrease in module 2_11 were noted.

Conclusion:

There are highly significant differences in gene expression between lupus patients and controls with overexpression of IFN, inflammation and myeloid related modules.  Vitamin D supplementation for 12 weeks failed to diminish expression of IFN inducible genes and with the possible exception of an indeterminate module (2_11), no major differences in modular expression was observed.  Overall, module expression at week 12 between treatment groups was minimally different in this controlled clinical trial, with no significant biological changes distinguishing vitamin D repleted and deficient patients.

Sponsored by NIAID Autoimmunity Centers of Excellence: NCT00710021

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/modular-microarray-analysis-fails-to-reveal-a-significant-biological-effect-of-vitamin-d3-treatment-in-patients-participating-in-a-double-blind-randomized-placebo-controlled-trial-of-the-effect-o/