Background/Purpose:

All lymphocyte populations contribute to SLE pathogenesis, but little is known of the specific gene transcripts particularly involved in each cell type. Activation of the type I interferon (IFN-I) pathway is observed in most lupus patients and is associated with more severe disease. To gain insight into the contribution of major lymphocyte subsets to autoimmune disease we studied gene expression and directed analysis to components of the IFN-I pathway.

Methods:

PBMC were isolated from 15 SLE patients and 10 matched healthy controls. Participating patients met ACR criteria for SLE and were adult females of different ages, racial backgrounds and disease manifestations. Patients had received stable doses of steroids and/or plaquenil but had not received biologics. CD4⁺T, CD8⁺T, CD56⁺NK and CD19⁺B cell fractions were isolated using magnetic beads, purity was assessed by flow cytometry, and RNA was extracted. Transcriptional profiles were obtained using Affymetrix U133Plus 2.0 microarray chips, and transcripts differentially expressed between SLE and control cell preparations were identified using the limma package. Weighted gene co-expression network analysis was performed using the WGCNA package. A difference in expression was considered statistically significant when p<0.05 and absolute fold change was more than two.

Results:

A linear blocking model identified differentially expressed genes in each of the studied fractions (PBMC 122; CD4⁺T 107; CD8⁺T 124; CD56⁺NK 506; and CD19⁺B 112 genes). A similar list was obtained using gene co-expression network analysis. All cell fractions and the unfractionated PBMC from SLE patients demonstrated the IFN-I signature, with 27 IFN-I-induced gene transcripts common to all fractions. The IFN-I signature correlated with a lower proportion of CD3⁺CD4⁺T (R=

-0.3, p<0.01) and CD56⁺NK (R= -0.6, p<0.01) cells and an increase in monocytes (R = +0.6, p<0.01) in PBMC as measured by flow cytometry. Other SLE-associated transcripts were independent of the IFN-I signature but were cell-type specific and potentially affect immune functions. IRF7, IRF9, STAT1 and STAT2 were increased in all fractions, but IRF5 showed significant upregulation only in the CD56 cell fraction. Among Toll-like receptors, TLR5 was significantly higher in CD4⁺T cells while TLR7 was significantly higher in B cells. Expression of IFN-I receptor genes was comparable in all fractions, and IFN-I transcripts were generally undetectable in lymphocytes.

Conclusion:

The IFN-I signature reflects an important pathophysiologic pathway in autoimmune conditions, particularly in SLE. Our data demonstrate that the IFN-I signature is ubiquitous among lymphocyte populations and includes common transcript components. Other pathway transcripts, including IRF5 and TLR7, point to distinct and significant roles of lymphocyte subsets in disease.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/major-lymphocyte-populations-share-a-common-interferon-signature-but-express-cell-type-specific-interferon-pathway-genes-in-sle/