SP140 regulates the expression of immune-related genes associated with multiple sclerosis and other autoimmune diseases by NF-κB inhibition.

SP140 locus has been associated with multiple sclerosis (MS) as well as other autoimmune diseases by genome-wide association studies (GWAS). The causal variant of these associations (rs28445040-T) alters the splicing of the SP140 gene transcripts reducing the protein expression. We aimed to understand why the reduction of SP140 expression produced by the risk variant can increase the susceptibility to MS. To this end, we determined by RNA sequencing (RNA-seq) analysis the differentially expressed genes after SP140 silencing in lymphoblastoid cell lines (LCLs). We analyzed these genes by gene ontology (GO), comparative transcriptome profiles, enrichment of transcription factors (TFs) in the promoters of these genes and colocalization with GWAS risk variants. We also monitored the activity of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) in SP140-silenced cells by luciferase reporter system. We identified 100 genes that were up-regulated and 22 genes down-regulated in SP140-silenced LCLs. GO analysis revealed that genes affected by SP140 were involved in regulation of cytokine production, inflammatory response and cell-cell adhesion. We observed enrichment of NF-κB TF in the promoter of up-regulated genes and NF-κB-increased activity in SP140-silenced cell lines. We showed enrichment of genes regulated by SP140 in GWAS-detected risk loci for MS (14.63 folds), Crohn's disease (4.82 folds) and inflammatory bowel disease (4.47 folds), not observed in other unrelated immune diseases. Our findings showed that SP140 is an important repressor of genes implicated in inflammation, suggesting that decreased expression of SP140, promoted by the rs28445040-T risk variant, may lead to up-regulation of these genes by means of NF-κB inhibition in B cells.

Clinical and molecular characterization of steatotic liver disease in the setting of immune-mediated inflammatory diseases.

Background & Aims: Growing evidence suggests an increased prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) in the context of immune-mediated inflammatory diseases (IMIDs). We aimed to clinically and mechanistically characterize steatotic liver disease (SLD) in a prospective cohort of patients with IMID compared to controls. Methods: Cross-sectional, case-control study including a subset of patients with IMID. Controls from the general population were age-, sex-, type 2 diabetes-, and BMI-matched at a 1:2 ratio. SLD was established using controlled attenuation parameter. Liver biopsies were obtained when significant liver fibrosis was suspected. Total RNA was extracted from freshly frozen cases and analyzed by RNA-seq. Differential gene expression was performed with 'limma-voom'. Gene set-enrichment analysis was performed using the fgsea R package with a preranked "limma t-statistic" gene list. Results: A total of 1,456 patients with IMID and 2,945 controls were included. Advanced SLD (liver stiffness measurement ≥9.7 kPa) (13.46% vs. 3.79%; p <0.001) and advanced MASLD (12.8% vs. 2.8%; p <0.001) prevalence were significantly higher among patients with IMID than controls. In multivariate analysis, concomitant IMID was an independent, and the strongest, predictor of advanced SLD (adjusted odds ratio 3.318; 95% CI 2.225-4.947; p <0.001). Transcriptomic data was obtained in 109 patients and showed 87 significant genes differentially expressed between IMID-MASLD and control-MASLD. IMID-MASLD cases displayed an enriched expression of genes implicated in pro-tumoral activities or the control of the cell cycle concomitant with a negative expression of genes related to metabolism. Conclusions: The prevalence of advanced SLD and MASLD is disproportionately elevated in IMID cohorts. Our findings suggest that IMIDs may catalyze a distinct MASLD pathway, divergent from classical metabolic routes, highlighting the need for tailored clinical management strategies. Impact and implications: The prevalence of steatotic liver disease with advanced fibrosis is increased in patients with immune-mediated inflammatory diseases, independent of classic metabolic risk factors or high-risk alcohol consumption. Transcriptomic analysis revealed a unique gene expression signature associated with cellular activities that are compatible with a liver condition leading to an accelerated and aggressive form of steatotic liver disease. Our findings underscore the importance of heightened screening for advanced liver disease risk across various medical disciplines overseeing patients with immune-mediated inflammatory diseases.