Novel experimental strategies to characterize the genomic architecture of monogenic autoinflammatory diseases: from characterization of aberrant mRNA transcripts to elucidation of the role of post-zygotic variants in desease pathogenesis

Developments in sequencing technologies over the last decade have revolutionized the ability to identify the genetic mechanisms underlying rare autoinflammatory diseases (AIDs), enabling improved characterization and diagnosis. This PhD thesis combines the knowledge and application of the latest methodologies of genomic analyses to identify and characterize the genetic causes of different AIDs. The two main areas of interest of this work include the identification of transcript isoforms through mRNA sequencing and the evaluation of mosaicism in genetic diseases caused by somatic DNA variants. First, we demonstrated the impact of two novel variants in the IL1RN gene as the cause of DIRA in a family with two patients presenting with a severe, neonatal-onset and lethal undiagnosed inflammatory disease. Second, we conducted the most extensive longitudinal study in a cohort of CAPS patients with post-zygotic NLRP3 variants. Additionally, we characterized two transcript isoforms resulting from a novel somatic variant at a splice site of the UBA1 gene, which has been identified as causative of VEXAS syndrome. And finally, we implemented and validated innovative methodologies, including single-cell RNA sequencing, digital PCR, and adaptive sampling using Oxford Nanopore Technologies.