Interferon beta corrects gene processing disrupted in MS: Study

Alternative splicing, a biological process that allows a single gene to code for multiple proteins, is extensively disrupted in immune cells isolated from untreated multiple sclerosis (MS) patients, and long-term treatment with interferon beta-based therapies largely corrects the defects, a study found.

“Alternative splicing is a potential biomarker warning of disease activity and for predicting therapeutic response to IFN-[beta] treatment,” the researchers wrote. “Alternative splicing in multiple sclerosis suggests new directions for investigation of disease mechanisms, therapeutic monitoring, and drug choices.”

The study, “Alternative Splicing of RNA Is Excessive in Multiple Sclerosis and Not Linked to Gene Expression Levels: Dysregulation Is Corrected by IFN-[beta],” was published in the Journal of Interferon & Cytokine Research.

The findings show that “measurement of alternatively spliced mRNA transcript levels in blood leukocytes from patients with multiple sclerosis may help to predict clinical responsiveness to IFN-[beta] therapy,” Raymond Donnelly, PhD, executive editor of the journal, said in a press release.

Alternative splicing has been implicated in MS, a disease caused by immune-mediated attacks on parts of the brain and spinal cord.

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Investigating alternative splicing

Genes that carry instructions for proteins contain alternating segments called exons and introns along the DNA chain. The DNA instructions are first copied into a messenger RNA (mRNA) molecule, which will serve as a template for protein production outside the nucleus.

But messenger RNA first needs to undergo a process of splicing, whereby introns are removed and exons, the segments that encode proteins, are stitched together. A single mRNA molecule can create different combinations of exons via alternative splicing, resulting in multiple different but related proteins. In fact, about 95% of genes with multiple exons undergo alternative splicing.

To further investigate alternative splicing in MS, scientists at the University of Chicago collected white blood cells (leukocytes) from 45 relapsing-remitting MS patients and eight healthy individuals who served as controls.

Among the patients, 26 received interferon beta-based disease-modifying therapies. Eleven of these were considered complete responders — meaning they experienced no relapses after starting treatment — and 15 were partial responders whose disease was stable but who had least one relapse over five years of follow-up. There were also 19 patients who were treatment-naïve, including 10 with stable MS and nine who experienced MS relapses.

Analysis of white blood cells from untreated MS patients revealed 4,605 alternatively spliced genes (ASGs) that differed from the healthy controls. At the same time, MS patients had 3,861 differentially expressed genes (DEGs), or genes whose activity was higher or lower than that of controls. Overall, however, these changes in ASGs were often independent of the DEGs.

Compared with MS patients treated with interferon beta, untreated patients had 10 times more alternatively spliced genes. Long-term interferon beta therapy nearly normalized the large number of alternatively spliced and differentially expressed genes in MS patients, to levels similar to controls.

Splicing differences between untreated, stable MS patients versus treated MS patients were mostly seen in genes associated with immune responses, interferon signaling, the splicing machinery itself, and the length of telomeres, the protective molecular caps on chromosomes. Shorter telomeres have been linked to extent of MS disability and progression.

Additional experiments showed that splicing events increased or decreased at hundreds of sites four hours after interferon beta treatment, returning to pre-treatment levels by 24 hours. This rapid change “suggests that there is a direct effect of IFN-[beta] on [alternative splicing],” the team wrote. Despite these short-term, treatment-related changes in alternative splicing, they were tenfold less than in long-term treated MS.

After interferon beta treatment was interrupted (washout), alternative splicing differed between stable patients with complete and partial responses. Even during therapy, patients with a partial response had more alternative splicing dysregulation, suggesting that “the level of [alternative splicing] after washout predicts future disease activity,” the researchers wrote.

Long-term interferon beta treatment was also found to regulate the alternative splicing of genes associated with immune-mediated attack in MS; these effects differed from the short-term effects of treatment.

“[Alternative splicing] is significantly increased in untreated MS, and long-term IFN-[beta] therapy corrects (i.e., decreases) [alternative splicing] to near healthy control levels,” the scientists wrote.