@article {571, title = {Recessive mutations in muscle-specific isoforms of FXR1 cause congenital multi-minicore myopathy.}, journal = {Nat Commun}, volume = {10}, year = {2019}, month = {2019 02 15}, pages = {797}, abstract = {

FXR1 is an alternatively spliced gene that encodes RNA binding proteins (FXR1P) involved in muscle development. In contrast to other tissues, cardiac and skeletal muscle express two FXR1P isoforms that incorporate an additional exon-15. We report that recessive mutations in this particular exon of FXR1 cause congenital multi-minicore myopathy in humans and mice. Additionally, we show that while Myf5-dependent depletion of all FXR1P isoforms is neonatal lethal, mice carrying mutations in exon-15 display non-lethal myopathies which vary in severity depending on the specific effect of each mutation on the protein.

}, keywords = {Animals, Cells, Cultured, Exons, Gene Expression, Genes, Recessive, Genetic Predisposition to Disease, HEK293 Cells, HeLa Cells, Humans, Mice, Transgenic, Muscle, Skeletal, Mutation, Myopathies, Structural, Congenital, Ophthalmoplegia, RNA-Binding Proteins, Ryanodine Receptor Calcium Release Channel}, issn = {2041-1723}, doi = {10.1038/s41467-019-08548-9}, author = {Esta{\~n}, Mar{\'\i}a Cristina and Fern{\'a}ndez-N{\'u}{\~n}ez, Elisa and Zaki, Maha S and Esteban, Mar{\'\i}a Isabel and Donkervoort, Sandra and Hawkins, Cynthia and Caparros-Martin, Jos{\'e} A and Saade, Dimah and Hu, Ying and Bolduc, Veronique and Chao, Katherine Ru-Yui and Nevado, Juli{\'a}n and Lamuedra, Ana and Largo, Raquel and Herrero-Beaumont, Gabriel and Regadera, Javier and Hernandez-Chico, Concepci{\'o}n and Tizzano, Eduardo F and Martinez-Glez, Victor and Carvajal, Jaime J and Zong, Ruiting and Nelson, David L and Otaify, Ghada A and Temtamy, Samia and Aglan, Mona and Issa, Mahmoud and B{\"o}nnemann, Carsten G and Lapunzina, Pablo and Yoon, Grace and Ruiz-Perez, Victor L} } @article {655, title = {A recurrent COL6A1 pseudoexon insertion causes muscular dystrophy and is effectively targeted by splice-correction therapies.}, journal = {JCI Insight}, volume = {4}, year = {2019}, month = {2019 Mar 21}, abstract = {

The clinical application of advanced next-generation sequencing technologies is increasingly uncovering novel classes of mutations that may serve as potential targets for precision medicine therapeutics. Here, we show that a deep intronic splice defect in the COL6A1 gene, originally discovered by applying muscle RNA sequencing in patients with clinical findings of collagen VI-related dystrophy (COL6-RD), inserts an in-frame pseudoexon into COL6A1 mRNA, encodes a mutant collagen α1(VI) protein that exerts a dominant-negative effect on collagen VI matrix assembly, and provides a unique opportunity for splice-correction approaches aimed at restoring normal gene expression. Using splice-modulating antisense oligomers, we efficiently skipped the pseudoexon in patient-derived fibroblast cultures and restored a wild-type matrix. Similarly, we used CRISPR/Cas9 to precisely delete an intronic sequence containing the pseudoexon and efficiently abolish its inclusion while preserving wild-type splicing. Considering that this splice defect is emerging as one of the single most frequent mutations in COL6-RD, the design of specific and effective splice-correction therapies offers a promising path for clinical translation.

}, issn = {2379-3708}, doi = {10.1172/jci.insight.124403}, author = {Bolduc, Veronique and Foley, A Reghan and Solomon-Degefa, Herimela and Sarathy, Apurva and Donkervoort, Sandra and Hu, Ying and Chen, Grace S and Sizov, Katherine and Nalls, Matthew and Zhou, Haiyan and Aguti, Sara and Cummings, Beryl B and Lek, Monkol and Tukiainen, Taru and Marshall, Jamie L and Regev, Oded and Marek-Yagel, Dina and Sarkozy, Anna and Butterfield, Russell J and Jou, Cristina and Jimenez-Mallebrera, Cecilia and Li, Yan and Gartioux, Corine and Mamchaoui, Kamel and Allamand, Val{\'e}rie and Gualandi, Francesca and Ferlini, Alessandra and Hanssen, Eric and Wilton, Steve D and Lamand{\'e}, Shireen R and MacArthur, Daniel G and Wagener, Raimund and Muntoni, Francesco and B{\"o}nnemann, Carsten G} } @article {364, title = {Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.}, journal = {Sci Transl Med}, volume = {9}, year = {2017}, month = {2017 04 19}, abstract = {

Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50\%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35\%. We also report the discovery of a highly recurrent de novo intronic mutation in that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25\% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.

}, keywords = {Collagen Type VI, High-Throughput Nucleotide Sequencing, Humans, Muscular Diseases, Mutation, Transcriptome}, issn = {1946-6242}, doi = {10.1126/scitranslmed.aal5209}, author = {Cummings, Beryl B and Marshall, Jamie L and Tukiainen, Taru and Lek, Monkol and Donkervoort, Sandra and Foley, A Reghan and Bolduc, Veronique and Waddell, Leigh B and Sandaradura, Sarah A and O{\textquoteright}Grady, Gina L and Estrella, Elicia and Reddy, Hemakumar M and Zhao, Fengmei and Weisburd, Ben and Karczewski, Konrad J and O{\textquoteright}Donnell-Luria, Anne H and Birnbaum, Daniel and Sarkozy, Anna and Hu, Ying and Gonorazky, Hernan and Claeys, Kristl and Joshi, Himanshu and Bournazos, Adam and Oates, Emily C and Ghaoui, Roula and Davis, Mark R and Laing, Nigel G and Topf, Ana and Kang, Peter B and Beggs, Alan H and North, Kathryn N and Straub, Volker and Dowling, James J and Muntoni, Francesco and Clarke, Nigel F and Cooper, Sandra T and B{\"o}nnemann, Carsten G and MacArthur, Daniel G} }