Loss of MBNL1 induces RNA misprocessing in the thymus and peripheral blood

Łukasz J Sznajder,Laura P W Ranum,Franjo Ivankovic,Maurice S Swanson,S H Subramony,Curtis A Nutter,Faaiq N Aslam,Marina M Scotti,Katarzyna Taylor,Jihae Shin

doi:10.1038/s41467-020-15962-x

Abstract

The thymus is a primary lymphoid organ that plays an essential role in T lymphocyte maturation and selection during development of one arm of the mammalian adaptive immune response. Although transcriptional mechanisms have been well documented in thymocyte development, co-/post-transcriptional modifications are also important but have received less attention. Here we demonstrate that the RNA alternative splicing factor MBNL1, which is sequestered in nuclear RNA foci by C(C)UG microsatellite expansions in myotonic dystrophy (DM), is essential for normal thymus development and function. Mbnl1 129S1 knockout mice develop postnatal thymic hyperplasia with thymocyte accumulation. Transcriptome analysis indicates numerous gene expression and RNA mis-splicing events, including transcription factors from the TCF/LEF family. CNBP, the gene containing an intronic CCTG microsatellite expansion in DM type 2 (DM2), is coordinately expressed with MBNL1 in the developing thymus and DM2 CCTG expansions induce similar transcriptome alterations in DM2 blood, which thus serve as disease-specific biomarkers.

Highlights

The thymus is a primary lymphoid organ that plays an essential role in T lymphocyte maturation and selection during development of one arm of the mammalian adaptive immune response
We report that loss of MBNL1 expression in 129S1-Mbnl1ΔE3/ΔE3 knockout (KO) mice results in postnatal thymic hyperplasia and thymocyte accumulation and we identify misprocessing of developmental splicing events critical for T lymphocyte maturation
2 out of 3 129-Mbnl[1] KO thymi showed altered clonotype frequencies for both Tcrb and Tcra transcripts suggesting clonal expansion of thymocytes (Fig. 1e–g and Supplementary Fig. 1h). Since these results demonstrated that MBNL1 loss led to aberrant thymic gene expression and T-Cell Receptor (TCR) alterations, we investigated potential effects of these changes on thymus and thymocyte development

Summary

Introduction

The thymus is a primary lymphoid organ that plays an essential role in T lymphocyte maturation and selection during development of one arm of the mammalian adaptive immune response. DM1 and DM2 are autosomal dominant disorders caused by microsatellite, or short tandem repeat (STR), CTG and CCTG expansions (exp) encoded in either the 3′ untranslated region (UTR) of DMPK (DM1) or the first intron of CNBP (DM2), respectively In both DM types, transcription of these mutant STRs results in the expression of C(C)UGexp RNAs that are retained in the nucleus as RNA foci together with MBNL proteins[14]. We report that loss of MBNL1 expression in 129S1-Mbnl1ΔE3/ΔE3 knockout (KO) mice results in postnatal thymic hyperplasia and thymocyte accumulation and we identify misprocessing of developmental splicing events critical for T lymphocyte maturation. These splicing changes are detectable in DM2, but not DM1, peripheral blood. We provide evidence that the degree of splicing dysregulation is proportional to DM2 CCTG STR length and CNBP intron 1 retention level

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Conclusion