Timeline of interferon, autoantibodies, and autoimmune disease development

[jnmaciuch]

Posting several links exploring temporal dynamics between interferon, autoantibodies, and autoimmune diseases (primarily lupus).

(Review) Emerging concepts of type I interferons in SLE pathogenesis and therapy
Note: SLE = systemic lupus erythematosus

The genetic susceptibility of SLE is complex, with >100 loci known at a genome-wide level that involve diverse immune pathways 20. Many newly identified loci are linked to activation of the interferon pathway 21. The importance of interferon regulatory factors such as IRF-5 was highlighted above, as the risk haplotype is associated with increased levels of serum IFNα and a risk of clinical progression to SLE in ANA-positive individuals 13. In particular, the IRF5 rs2004640-T allele enables expression of several distinct IRF-5 isoforms and conveys an important genetic risk for SLE 22. The IRF5 rs10488631 allele has an independent association with enhanced transcript and protein levels of IRF-5 in patients with SLE 23. Single-nucleotide polymorphisms (SNPs) in IRF7 loci also confer a strong genetic susceptibility to SLE 24. Additionally, genetic variations at the IRF7–PHRF1 locus are associated with high levels of serum IFNα and positivity for anti-Sm antibody in African American patients 25. Similarly, the IFIH1 rs1990760-T allele is associated with anti-dsDNA positivity as well as a high type I interferon gene signature (IFNGS) in peripheral blood mononuclear cells (PBMCs) of patients with SLE 26. SNPs in a STAT4 haplotype, such as the rs7574865 allele, are strongly linked to SLE, and homozygosity of this risk allele carries a more than doubled risk of developing the disease (compared with absence of the risk allele) 27. The STAT4 rs7574865-T allele is also linked to sensitivity to type I interferon signalling 28.

Notably, although there are many genetic associations involving components of the downstream signalling pathways of type I interferon, no polymorphisms within genes encoding most type I or II interferons are known to be linked to SLE susceptibility. An exception is the IFNK locus. As identified by a pooled genome-wide study, the rs1031154 SNP (which affects a site 25 kb upstream of the promoter for IFNK) is strongly associated with SLE susceptibility (rank number 51 of 116,204 SNPs) 29. SNPs at the IFNK locus are also associated with serum type I interferon activity as well as cutaneous lupus clinical phenotype. These results call into question whether IFNα has a particular importance in SLE pathogenesis compared with other type I interferon subtypes, such as IFNκ.

Genetic-transcriptomic studies can provide information on the tissues affected by pathogenic variants in SLE susceptibility genes. In a combined analysis of genotypic and transcriptomic data, susceptibility variants associated with SLE, including those in the type I interferon pathway, were shown to regulate gene expression across a range of blood and non-blood tissues 30.

Links to references are active in the quote. Being predisposed towards higher interferon levels confers causal risk for developing autoantibodies and lupus, though does not guarantee disease. Interestingly, this review also noted that mutations in most interferon or interferon receptor genes themselves are not associated with lupus--likely because individuals with those mutations simply develop severe "interferonopathies" first. I think it is an interesting concept that the degree and exact relationship to interferon regulation across various risk alleles can create different clinical outcomes in conjunction with environmental triggers.

Functionally impaired plasmacytoid dendritic cells and non-haematopoietic sources of type I interferon characterize human autoimmunity
Study followed SLE and primary Sjögren’s Syndrome (pSS), at-risk, and control populations. Individuals were classfied as "at risk" if they had positive anti-nuclear antibodies (ANAs) but did not meet clinical criteria for autoimmune disease. Higher interferon levels are seen in the blood, and much higher levels are seen in the skin, in both at-risk and autoimmune individuals compared to control. Although plasmacytoid dendritic cells (pDCs) are the main source of type I interferon in acute viral infection, they are not the source of high interferon levels seen in SLE and pSS. Interferon in the skin was determined to originate from keratinocytes (outermost layer skin cells).

Prediction of autoimmune connective tissue disease in an at-risk cohort: prognostic value of a novel two-score system for interferon status
Follow-up study of at-risk (ANA positive but not presenting with clinical disease) individuals. Interferon A and B scores (not to be confused with interferon-alpha and beta) were calculated using different subsets of genes stimulated by interferons. A contained genes stimulated by type I interferons, B contained genes stimulated by type I, II, and III. At-risk and SLE individuals both had higher interferon A scores than healthy controls. SLE individuals had higher interferon B scores compared to at-risk and HC (and at-risk/HC did not significantly differ from each other).

(Abstract/Poster) Prediction of response to rituximab in SLE using a validated two-score system for interferon status
Using same interferon-stimulated gene scores from above. High interferon A and B scores predicted non-responsiveness to rituximab (though only B score was p < 0.05).

Altered Type II Interferon Precedes Autoantibody Accrual and Elevated Type I Interferon Activity Prior to Systemic Lupus Erythematosus Classification
Longitudinal data for individuals who eventually developed lupus and age-and-sex-matched controls. Autoantibodies and elevated type II interferon could be seen several years (up to ~8) prior to clinical disease, and in healthy controls that never progressed to disease. Type I interferon levels peaked 1-2 years before clinical disease onset, but were not detected as elevated in the serum prior to detection of autoantibodies. This suggests that development of lupus is a combined effect of autoantibodies and elevated type I interferon over time. A caveat is that pre-autoantibody measurements were taken at random, and therefore cannot exclude the possibility of a precipitating event involving high interferon (e.g. viral infection) triggering autoantibody formation (which did not result in permanently elevated type I interferon prior to autoantibodies).

Induction of Dendritic Cell Differentiation by IFN-a in Systemic Lupus Erythematosus
Circulating monocytes from SLE participants were found to present antigen more than controls, and serum from SLE induced monocytes to differentiate into dendritic cells (which have higher expression of MHCI/II and induce higher T-cell responses). This differentiation effect was recapitulated only with interferon-alpha. The authors speculate that type I interferon priming may explain increased likelihood to develop autoantibodies.
https://pmc.ncbi.nlm.nih.gov/articles/PMC3694565/#S5
(Review) The innate immune system in SLE: type I interferons and dendritic cells

Through their direct effect on B cells, type I IFNs enhance primary antibody responses to soluble proteins and induce the production of all subclasses of IgG in mice.33 IFN-α upregulates CD38, a germinal centre B-cell and plasma cell marker, on B lymphocytes and BAFF (B cell–activating factor) on monocytes and mDCs. BAFF in turn contributes to the survival of autoreactive B lymphocytes.34 In addition, IFN-α promotes the differentiation of activated B lymphocytes into plasmablasts. pDCs activated with viruses secrete IFN-α and IL-6, which permits plasmablasts to become antibody-secreting plasma cells.35 The same effect is observed when pDCs are activated with SLE ICs containing nucleic acids that bind TLRs.36, 37 This could contribute to amplify the production of type I IFN and subsequently the differentiation of autoreactive plasma cells that would further secrete autoantibodies, thus, perpetuating this pathogenic loop.

Auto-antibody production induced by type I interferon has not been directly observed, though there is evidence that type I interferon may create optimal conditions for auto-antibody generation. Selected quote is only for effect of type I interferon on B-cells, there are other potentially salient effects on other cell types as well outlined in the linked review.

Inactive disease in patients with lupus is linked to autoantibodies to type I interferons that normalize blood IFNa and B cell subsets
Just an interesting tidbit--turns out that some lupus patients naturally develop auto-antibodies against type I interferon, and this ends up having a protective effect reducing disease severity.

Low-titre auto-antibodies predict autoimmune disease during interferon-α treatment of chronic hepatitis C
Patients with pre-existing anti-nuclear antibodies were more likely to develop autoimmune disease during interferon alpha therapy, although there were a few de-novo cases as well.

Summary:

Genetic studies indicate that higher levels of type I interferons predispose the development of lupus, though congenitally high type I interferon levels do not guarantee autoimmunity and are not present in all cases of autoimmunity. Anti-nuclear antibodies themselves do not create disease either since they are observed in the absence of disease. The combination of auto-antibodies and induced high levels of type I interferon are both necessary to manifest tissue damage associated with auto-immune disease, and auto-antibodies may be drivers of later type I interferon production ultimately leading to disease.

One additional caveat is that serum levels are not reflective of tissue-specific levels, and none of these studies explore parenchymal interferon production beyond the skin. Therefore, it is possible that any disease manifestations dependent on type I interferon are actually dependent on tissue-specific presence of interferon, rather than just in the blood.