Microsatellite Expansions Selectively Trigger Intron Retention

Published on Tue, 05/08/2018

Microsatellite expansions triggering a variety of neurological disorders occur in both coding and non-coding regions. Trinucleotide CNG expansions (e.g., DM1) predominate in exonic and UTR regions, while intronic expansions can vary from tri- to hexanucleotide repeats and are associated with eight diseases that include DM2, C9orf72 ALS/FTD, and Fuchs endothelial corneal dystrophy. How the sequence and differential localization of microsatellite expansions impacts disease mechanisms is not fully known.

Dr. Maury Swanson (University of Florida), Łukasz Sznjader, a 2016-2017 MDF Fellow, and researchers from the University of Rochester, Houston Methodist Hospital, and Adam Mickiewicz University in Poland, have recently evaluated the concept that intronic microsatellite expansions themselves act as a trigger to host gene intron retention and thereby to the pathogenesis of disease. In this study, they assessed a variety of neurological diseases linked to GC- and A/AT-rich intronic expansions.

The presence of microsatellites in introns alone conveys very low risk of expansion and triggering of inherited diseases—of 80,000 intronic microsatellites with expansion potential, only 0.01% are actually known to expand and cause disease. The research team mapped the intronic localization of both pathogenic expanded microsatellites and unexpanded repeats and demonstrated a bias of disease-causing microsatellites toward splice sites and thereby represent potential triggers for splicing alterations and intron inclusion. CNBP intron 1 inclusion as determined from a DM muscle RNA-seq database and patient biopsy samples was substantially elevated in contrast to intron inclusion across a broad range of neuromuscular disease controls. Notably, only CNBP intron 1 (the site of the microsatellite expansion) was spliced in, while other downstream CNBP introns were not. Further studies showed that intron 1 retention was not a developmentally regulated event.

Dr. Swanson and colleagues then tested the hypothesis that CNBP intron 1 inclusion in DM2 patient peripheral blood could be used as a disease biomarker. These studies confirmed intron inclusion in DM2, but not in controls, in a repeat length-dependent fashion. At this point it was as yet unclear whether the expanded CCUG repeat itself was mechanistic in altering CNBP splicing to include intron 1. A mouse reporter gene model was used to confirm that intron inclusion was driven by CCUGexp in a repeat length-dependent manner. Finally, the research team showed that intronic retention occurred only for GC- (e.g., DM2), but not A/AT-rich (e.g., Friedrich’s ataxia), microsatellite expansion diseases.

Taken together, this report identifies the molecular mechanisms underlying intronic retention in DM2 and emphasizes its value as a putative biomarker, particularly since intronic retention is so easily assessed in peripheral blood using routine RT-PCR assays. Such an approach to disease detection is much more efficient than conventional genetic strategies as a means of mapping heritable microsatellite expansion disorders and can be broadly used in discovery of the genetic basis of currently undiagnosed diseases.

Intron retention induced by microsatellite expansions as a disease biomarker.
Sznajder ŁJ, Thomas JD, Carrell EM, Reid T, McFarland KN, Cleary JD, Oliveira R, Nutter CA, Bhatt K, Sobczak K, Ashizawa T, Thornton CA, Ranum LPW, Swanson MS.
Proc Natl Acad Sci U S A. 2018 Apr 2. pii: 201716617. doi: 10.1073/pnas.1716617115. [Epub ahead of print]