IFN signature in lupus endotypes may lead to ‘targeted and personalized’ treatments

Specific interferon signatures may influence the symptoms and severity of systemic lupus erythematosus, with various interferon types potentially “contributing to distinct pathogenic processes,” according to recent findings.

“These findings suggest that IFN-I blocking agents may be particularly effective in treating skin manifestations in patients with SLE,” Eduardo Gomez-Banuelos, MD, of the division of rheumatology at the Johns Hopkins School of Medicine, told Healio. “Rheumatologists can use this information to tailor their treatment plans for SLE patients, potentially improving outcomes and quality of life for those with skin involvement.

“Additionally, understanding the molecular pathways associated with IFN types may lead to more targeted and personalized treatment approaches in the future,” he added. “Clinicians should consider assessing interferon activity levels when managing patients with SLE to optimize treatment outcomes and improve patient care.”

In their study, Gomez-Banuelos and colleagues noted that despite the presence of a hallmark interferon (IFN) signature in SLE, clinical trials targeting type I IFN have yielded variable results. Meanwhile, type II IFN blockade also has failed to show efficacy in the disease.

In the current study, the researchers observed IFN-I, IFN-II and IFN-III fluctuate significantly over time in patients with SLE. Moreover, the IFN signature failed to predict elevations in IFN activity in these patients.

The researchers additionally observed that IFN types alone or in various combinations suggest that clinical or molecular subsets of SLE may exist. In addition, pathways that are dependent on or independent of interferons may define unique mechanistic endotypes of the disease.

“This study sheds light on mechanisms underlying SLE heterogeneity and the variable response to IFN-targeted therapies in clinical trials,” Gomez-Banuelos and colleagues wrote.

Healio sat down with Gomez-Banuelos to discuss all things pertaining to IFN in lupus and how these findings may further the understanding of this disease.

Healio: Why did you decide to investigate interferons in lupus in this way?

Gomez-Banuelos: We chose to look into interferons in SLE because we knew that blocking IFNs has had mixed results in SLE, even though it is well known that they play a part in the disease's development and activity. Because of this, we believe there are still a lot of unanswered questions regarding the relationship between the various IFN types, disease activity and particular SLE manifestations.

It was clear from the start of the project that the most important challenge in evaluating IFN in SLE was determining how to measure it.

Healio: Could you discuss the challenges in quantifying IFN levels in SLE?

Gomez-Banuelos: Interferon levels, particularly IFN-I, have long been difficult to measure in individuals with SLE for a variety of reasons. First, IFNs are present in serum and plasma at trace levels — femtograms to picograms per mL. As a result, any assay designed to assess them must be highly sensitive.

Second, the IFN family is made up of many different proteins that can be subclassified into three main groups: IFN-I, which has 12 different types of IFN-a, as well as IFN-, IFN-, IFN-, and IFN-; IFN-II, also called IFNg; and IFN-III, which has four different types. So, a second criteria for an assay for determining IFN levels is that it should encompass all forms of IFN-I and IFN-III.

Third, there is a significant overlap in the genes that all three IFN types can activate. Thus, the IFN signature cannot distinguish between the three IFN subsets. By using a commercially available reporter-cell assay consisting of cell lines bioengineered to specifically detect IFN-I, IFN-II or IFN-III, we could accurately measure the whole burden of active IFN-I or IFN-III in serum or plasma samples of SLE without leaving out any IFN subset.

Healio: What are the challenges of treating a disease like SLE, which has such heterogeneity in clinical presentation?

Gomez-Banuelos: The heterogeneity of SLE presents a multifaceted challenge in terms of diagnosis, treatment and management. In addition, recent studies have shown that, besides being clinically heterogeneous, SLE is a molecularly and immunologically diverse disease. This means that different immune cells and pathogenic mechanisms are at play in patients with SLE and diverse clinical manifestations. This variability makes it difficult to develop one-size-fits-all treatment strategies.

Our current data adds another layer of complexity to our understanding of the disease. In line with prior knowledge, we discovered that IFN-I is a key player in active SLE, but it does not control all clinical manifestations of active lupus. For instance, IFN-I was more important for active skin disease, while when combined with other IFN types, it was more relevant for renal involvement. This explains why IFN-I blocking therapies are more efficient to treat active skin disease in SLE.

Healio: To that point, you learned that IFN-1, 2 and 3 fluctuate over time. Why does this happen, and why is it important?

Gomez-Banuelos: Interferon levels fluctuate over time due to the dynamic nature of the immune response in SLE. Initially, we thought that a patient with SLE might present with the same IFN type elevated through their disease course. For instance, a patient who develops elevated IFN-I or IFN-II might develop it again later in their disease.

To our surprise, we found that levels of IFN are highly dynamic during the disease course, which means that a given patient can develop elevations of different IFN types, either alone or combined, during their disease course.

However, what was more interesting is that these elevations or combinations of IFN levels do not occur randomly. For instance, in the case of IFN-I, elevations occur during active disease, while IFN-II seems to be more frequently elevated in patients with a longer disease duration. Importantly, these elevations in the IFN types were associated with an increased probability of particular disease manifestations.

Single IFN-I was associated with increased probabilities of skin activity and anti-dsDNA antibodies. There was a link between a mix of IFN-I, IFN-II and III and anti-dsDNA, low complement, higher SLEDAI scores, and more likely active renal disease. Combined IFN-II and IFN-III were associated with milder disease activity. And, importantly, when all three IFN types were normal, the probability of active disease was lower.
Healio: You also learned that the IFN signature does not predict IFN activity levels. Why not?

Gomez-Banuelos: One of our first questions during this project was: How well does the IFN signature predict elevated IFN activity in SLE? To answer this, we classified patients with SLE as having an elevated or normal IFN signature, using the same method that is often used in clinical trials of IFN-I blocking agents to classify patients with high IFN-I activity.

We averaged the expression of four genes commonly associated with IFN-I — IFI27, IFI44, IFI44L and RSAD2. We observed that, indeed, the IFN signature was significantly correlated with the activity levels of IFN-I, but this correlation was small (r2 = 0.168). This is because only 36% of the patients with an elevated IFN signature had elevated levels of IFN-I. Indeed, an elevated IFN signature had a 38% sensitivity to detect patients with elevated IFN-I activity.

In addition, the IFN signature was not associated with elevated IFN-II and III. This suggests that the IFN signature is not predictive of the IFN activity of plasma. Additionally, the signature may reflect downstream effects of interferon signaling rather than direct interferon activity. This discrepancy highlights the complexity of SLE pathogenesis and the need for comprehensive assessments of disease activity.

Healio: What SLE clinical endotypes were associated with IFN-1? And IFN-2? And IFN-3?

Gomez-Banuelos: We mostly saw that IFN-I, especially when it was present by itself, was linked to skin involvement. On the other hand, systemic features of the disease like nephritis, arthritis and complement deposition were linked to elevated levels of all three IFN types together.

We observed that the different IFN types were associated with distinct molecular signatures in SLE. IFN-I was associated with signatures commonly associated with active SLE — expression of interferon induced genes, plasmablasts and granulopoiesis signatures.

Meanwhile, IFN-II was associated with the expression of mitochondrial genes, genes involved in T-cell signaling, and a transcriptional signature related to CD8+ GZMH+ T cells, a cytotoxic cell type that is expanded in SLE. This suggests a role for IFN-II in the cytotoxic immune response seen in SLE.

These findings highlight the complexity of the IFN response in SLE and suggest that different IFN types may contribute to distinct pathogenic processes in the disease. Further research is needed to fully understand the implications of these findings for the development of targeted therapies for SLE.

Healio: What is the difference between IFN dependent and independent pathways in SLE, and why is it important that you observe this?

Gomez-Banuelos: IFN-dependent pathways in SLE are those controlled by interferons and their direct effects on immune cells and tissues. On the other hand, other cytokines or immune dysregulation mechanisms may start IFN-independent pathways. This is relevant because we observed that not every SLE clinical manifestation was associated with the different IFN types.

As an example, SLE symptoms like mucosal ulcers, thrombocytopenia, leukopenia, serositis and vasculitis are not linked to IFNs. Instead, other pathways or cytokines different from IFN may be more important in the pathogenesis of these clinical endotypes. Recognizing the distinction between these pathways is important for understanding the underlying mechanisms of disease and developing targeted therapies.
Healio: How can your findings inform treatment paradigms in SLE?

Gomez-Banuelos: Our findings can inform treatment paradigms in SLE by highlighting the importance of considering individual interferon activity levels and clinical endotypes when selecting therapeutic interventions. We consider that our data is particularly relevant to selecting the patients that would benefit the most from IFN-I blocking therapies.

The findings also offer a rational explanation for the results of IFN-I blocking clinical trials. Patients with active skin manifestations are the most responsive to IFN-I blocking agents.

Healio: What are the next steps for research?

Gomez-Banuelos: The next steps in research might include learning more about the relevance of molecular pathways associated with the interaction of the three IFN types to sustain the ongoing immune response in SLE. Also, we are interested in investigating the utility of IFN activity in plasma to select patients who will benefit the most from IFN-I blocking therapies.

References:

Gomez-Banuelos E, et al. Cell Rep Med. 2024; doi:10.1016/j.xcrm.2024.101569.