@article {918, title = {De novo variants in SNAP25 cause an early-onset developmental and epileptic encephalopathy.}, journal = {Genet Med}, volume = {23}, year = {2021}, month = {2021 04}, pages = {653-660}, abstract = {

PURPOSE: This study aims to provide a comprehensive description of the phenotypic and genotypic spectrum of SNAP25 developmental and epileptic encephalopathy (SNAP25-DEE) by reviewing newly identified and previously reported individuals.

METHODS: Individuals harboring heterozygous missense or loss-of-function variants in SNAP25 were assembled through collaboration with international colleagues, matchmaking platforms, and literature review. For each individual, detailed phenotyping, classification, and structural modeling of the identified variant were performed.

RESULTS: The cohort comprises 23 individuals with pathogenic or likely pathogenic de novo variants in SNAP25. Intellectual disability and early-onset epilepsy were identified as the core symptoms of SNAP25-DEE, with recurrent findings of movement disorders, cerebral visual impairment, and brain atrophy. Structural modeling for all variants predicted possible functional defects concerning SNAP25 or impaired interaction with other components of the SNARE complex.

CONCLUSION: We provide a comprehensive description of SNAP25-DEE with intellectual disability and early-onset epilepsy mostly occurring before the age of two years. These core symptoms and additional recurrent phenotypes show an overlap to genes encoding other components or associated proteins of the SNARE complex such as STX1B, STXBP1, or VAMP2. Thus, these findings advance the concept of a group of neurodevelopmental disorders that may be termed "SNAREopathies."

}, keywords = {Brain Diseases, Child, Preschool, Epilepsy, Humans, Intellectual Disability, Neurodevelopmental Disorders, Phenotype, Synaptosomal-Associated Protein 25}, issn = {1530-0366}, doi = {10.1038/s41436-020-01020-w}, author = {Kl{\"o}ckner, Chiara and Sticht, Heinrich and Zacher, Pia and Popp, Bernt and Babcock, Holly E and Bakker, Dewi P and Barwick, Katy and Bonfert, Michaela V and B{\"o}nnemann, Carsten G and Brilstra, Eva H and Chung, Wendy K and Clarke, Angus J and Devine, Patrick and Donkervoort, Sandra and Fraser, Jamie L and Friedman, Jennifer and Gates, Alyssa and Ghoumid, Jamal and Hobson, Emma and Horvath, Gabriella and Keller-Ramey, Jennifer and Keren, Boris and Kurian, Manju A and Lee, Virgina and Leppig, Kathleen A and Lundgren, Johan and McDonald, Marie T and McLaughlin, Heather M and McTague, Amy and Mefford, Heather C and Mignot, Cyril and Mikati, Mohamad A and Nava, Caroline and Raymond, F Lucy and Sampson, Julian R and Sanchis-Juan, Alba and Shashi, Vandana and Shieh, Joseph T C and Shinawi, Marwan and Slavotinek, Anne and St{\"o}dberg, Tommy and Stong, Nicholas and Sullivan, Jennifer A and Taylor, Ashley C and Toler, Tomi L and van den Boogaard, Marie-Jos{\'e} and van der Crabben, Saskia N and van Gassen, Koen L I and van Jaarsveld, Richard H and Van Ziffle, Jessica and Wadley, Alexandrea F and Wagner, Matias and Wigby, Kristen and Wortmann, Saskia B and Zarate, Yuri A and M{\o}ller, Rikke S and Lemke, Johannes R and Platzer, Konrad} } @article {1001, title = {Loss of function mutations in GEMIN5 cause a neurodevelopmental disorder.}, journal = {Nat Commun}, volume = {12}, year = {2021}, month = {2021 05 07}, pages = {2558}, abstract = {

GEMIN5, an RNA-binding protein is essential for assembly of the survival motor neuron (SMN) protein complex and facilitates the formation of small nuclear ribonucleoproteins (snRNPs), the building blocks of spliceosomes. Here, we have identified 30 affected individuals from 22 unrelated families presenting with developmental delay, hypotonia, and cerebellar ataxia harboring biallelic variants in the GEMIN5 gene. Mutations in GEMIN5 perturb the subcellular distribution, stability, and expression of GEMIN5 protein and its interacting partners in patient iPSC-derived neurons, suggesting a potential loss-of-function mechanism. GEMIN5 mutations result in disruption of snRNP complex assembly formation in patient iPSC neurons. Furthermore, knock down of rigor mortis, the fly homolog of human GEMIN5, leads to developmental defects, motor dysfunction, and a reduced lifespan. Interestingly, we observed that GEMIN5 variants disrupt a distinct set of transcripts and pathways as compared to SMA patient neurons, suggesting different molecular pathomechanisms. These findings collectively provide evidence that pathogenic variants in GEMIN5 perturb physiological functions and result in a neurodevelopmental delay and ataxia syndrome.

}, keywords = {Alleles, Amino Acid Sequence, Animals, Child, Preschool, Developmental Disabilities, Drosophila, Female, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Gene Ontology, HEK293 Cells, Humans, Induced Pluripotent Stem Cells, Loss of Function Mutation, Male, Muscle Hypotonia, Myoclonic Cerebellar Dyssynergia, Neurodevelopmental Disorders, Neurons, Pedigree, Polymorphism, Single Nucleotide, Ribonucleoproteins, Small Nuclear, Rigor Mortis, RNA-Seq, SMN Complex Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-021-22627-w}, author = {Kour, Sukhleen and Rajan, Deepa S and Fortuna, Tyler R and Anderson, Eric N and Ward, Caroline and Lee, Youngha and Lee, Sangmoon and Shin, Yong Beom and Chae, Jong-Hee and Choi, Murim and Siquier, Karine and Cantagrel, Vincent and Amiel, Jeanne and Stolerman, Elliot S and Barnett, Sarah S and Cousin, Margot A and Castro, Diana and McDonald, Kimberly and Kirmse, Brian and Nemeth, Andrea H and Rajasundaram, Dhivyaa and Innes, A Micheil and Lynch, Danielle and Frosk, Patrick and Collins, Abigail and Gibbons, Melissa and Yang, Michele and Desguerre, Isabelle and Boddaert, Nathalie and Gitiaux, Cyril and Rydning, Siri Lynne and Selmer, Kaja K and Urreizti, Roser and Garcia-Oguiza, Alberto and Osorio, Andr{\'e}s Nascimento and Verdura, Edgard and Pujol, Aurora and McCurry, Hannah R and Landers, John E and Agnihotri, Sameer and Andriescu, E Corina and Moody, Shade B and Phornphutkul, Chanika and Sacoto, Maria J Guillen and Begtrup, Amber and Houlden, Henry and Kirschner, Janbernd and Schorling, David and Rudnik-Sch{\"o}neborn, Sabine and Strom, Tim M and Leiz, Steffen and Juliette, Kali and Richardson, Randal and Yang, Ying and Zhang, Yuehua and Wang, Minghui and Wang, Jia and Wang, Xiaodong and Platzer, Konrad and Donkervoort, Sandra and B{\"o}nnemann, Carsten G and Wagner, Matias and Issa, Mahmoud Y and Elbendary, Hasnaa M and Stanley, Valentina and Maroofian, Reza and Gleeson, Joseph G and Zaki, MAH S and Senderek, Jan and Pandey, Udai Bhan} } @article {806, title = {Biallelic loss of function variants in SYT2 cause a treatable congenital onset presynaptic myasthenic syndrome.}, journal = {Am J Med Genet A}, volume = {182}, year = {2020}, month = {2020 10}, pages = {2272-2283}, abstract = {

Synaptotagmins are integral synaptic vesicle membrane proteins that function as calcium sensors and regulate neurotransmitter release at the presynaptic nerve terminal. Synaptotagmin-2 (SYT2), is the major isoform expressed at the neuromuscular junction. Recently, dominant missense variants in SYT2 have been reported as a rare cause of distal motor neuropathy and myasthenic syndrome, manifesting with stable or slowly progressive distal weakness of variable severity along with presynaptic NMJ impairment. These variants are thought to have a dominant-negative effect on synaptic vesicle exocytosis, although the precise pathomechanism remains to be elucidated. Here we report seven patients of five families, with biallelic loss of function variants in SYT2, clinically manifesting with a remarkably consistent phenotype of severe congenital onset hypotonia and weakness, with variable degrees of respiratory involvement. Electrodiagnostic findings were consistent with a presynaptic congenital myasthenic syndrome (CMS) in some. Treatment with an acetylcholinesterase inhibitor pursued in three patients showed clinical improvement with increased strength and function. This series further establishes SYT2 as a CMS-disease gene and expands its clinical and genetic spectrum to include recessive loss-of-function variants, manifesting as a severe congenital onset presynaptic CMS with potential treatment implications.

}, keywords = {Adolescent, Child, Child, Preschool, Female, Genetic Predisposition to Disease, Humans, Male, Muscle Hypotonia, Muscle Weakness, Mutation, Missense, Myasthenic Syndromes, Congenital, Pedigree, Phenotype, Synaptic Transmission, Synaptotagmin II}, issn = {1552-4833}, doi = {10.1002/ajmg.a.61765}, author = {Donkervoort, Sandra and Mohassel, Payam and Laugwitz, Lucia and Zaki, MAH S and Kamsteeg, Erik-Jan and Maroofian, Reza and Chao, Katherine R and Verschuuren-Bemelmans, Corien C and Horber, Veronka and Fock, Annemarie J M and McCarty, Riley M and Jain, Minal S and Biancavilla, Victoria and McMacken, Grace and Nalls, Matthew and Voermans, Nicol C and Elbendary, Hasnaa M and Snyder, Molly and Cai, Chunyu and Lehky, Tanya J and Stanley, Valentina and Iannaccone, Susan T and Foley, A Reghan and Lochm{\"u}ller, Hanns and Gleeson, Joseph and Houlden, Henry and Haack, Tobias B and Horvath, Rita and B{\"o}nnemann, Carsten G} } @article {791, title = {Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content.}, journal = {Hum Mol Genet}, volume = {29}, year = {2020}, month = {2020 06 03}, pages = {1426-1439}, abstract = {

Defects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddaa051}, author = {Woldegebriel, Rosa and Kvist, Jouni and Andersson, Noora and {\~O}unap, Katrin and Reinson, Karit and Wojcik, Monica H and Bijlsma, Emilia K and Hoffer, Mariette J V and Ryan, Monique M and Stark, Zornitza and Walsh, Maie and Cuppen, Inge and van den Boogaard, Marie-Jose H and Bharucha-Goebel, Diana and Donkervoort, Sandra and Winchester, Sara and Zori, Roberto and B{\"o}nnemann, Carsten G and Maroofian, Reza and O{\textquoteright}Connor, Emer and Houlden, Henry and Zhao, Fang and Carp{\'e}n, Olli and White, Matthew and Sreedharan, Jemeen and Stewart, Murray and Ylikallio, Emil and Tyynismaa, Henna} } @article {713, title = {Recurrent TTN metatranscript-only c.39974-11T>G splice variant associated with autosomal recessive arthrogryposis multiplex congenita and myopathy.}, journal = {Hum Mutat}, volume = {41}, year = {2020}, month = {2020 02}, pages = {403-411}, abstract = {

We present eight families with arthrogryposis multiplex congenita and myopathy bearing a TTN intron 213 extended splice-site variant (NM_001267550.1:c.39974-11T>G), inherited in trans with a second pathogenic TTN variant. Muscle-derived RNA studies of three individuals confirmed mis-splicing induced by the c.39974-11T>G variant; in-frame exon 214 skipping or use of a cryptic 3{\textquoteright} splice-site effecting a frameshift. Confounding interpretation of pathogenicity is the absence of exons 213-217 within the described skeletal muscle TTN N2A isoform. However, RNA-sequencing from 365 adult human gastrocnemius samples revealed that 56\% specimens predominantly include exons 213-217 in TTN transcripts (inclusion rate >=66\%). Further, RNA-sequencing of five fetal muscle samples confirmed that 4/5 specimens predominantly include exons 213-217 (fifth sample inclusion rate 57\%). Contractures improved significantly with age for four individuals, which may be linked to decreased expression of pathogenic fetal transcripts. Our study extends emerging evidence supporting a vital developmental role for TTN isoforms containing metatranscript-only exons.

}, issn = {1098-1004}, doi = {10.1002/humu.23938}, author = {Bryen, Samantha J and Ewans, Lisa J and Pinner, Jason and MacLennan, Suzanna C and Donkervoort, Sandra and Castro, Diana and Topf, Ana and O{\textquoteright}Grady, Gina and Cummings, Beryl and Chao, Katherine R and Weisburd, Ben and Francioli, Laurent and Faiz, Fathimath and Bournazos, Adam M and Hu, Ying and Grosmann, Carla and Malicki, Denise M and Doyle, Helen and Witting, Nanna and Vissing, John and Claeys, Kristl G and Urankar, Kathryn and Beleza-Meireles, Ana and Baptista, Julia and Ellard, Sian and Savarese, Marco and Johari, Mridul and Vihola, Anna and Udd, Bjarne and Majumdar, Anirban and Straub, Volker and B{\"o}nnemann, Carsten G and MacArthur, Daniel G and Davis, Mark R and Cooper, Sandra T} } @article {567, title = {ACTN2 mutations cause "Multiple structured Core Disease" (MsCD).}, journal = {Acta Neuropathol}, volume = {137}, year = {2019}, month = {2019 03}, pages = {501-519}, abstract = {

The identification of genes implicated in myopathies is essential for diagnosis and for revealing novel therapeutic targets. Here we characterize a novel subclass of congenital myopathy at the morphological, molecular, and functional level. Through exome sequencing, we identified de novo ACTN2 mutations, a missense and a deletion, in two unrelated patients presenting with progressive early-onset muscle weakness and respiratory involvement. Morphological and ultrastructural analyses of muscle biopsies revealed a distinctive pattern with the presence of muscle fibers containing small structured cores and jagged Z-lines. Deeper analysis of the missense mutation revealed mutant alpha-actinin-2 properly localized to the Z-line in differentiating myotubes and its level was not altered in muscle biopsy. Modelling of the disease in zebrafish and mice by exogenous expression of mutated alpha-actinin-2 recapitulated the abnormal muscle function and structure seen in the patients. Motor deficits were noted in zebrafish, and muscle force was impaired in isolated muscles from AAV-transduced mice. In both models, sarcomeric disorganization was evident, while expression of wild-type alpha-actinin-2 did not result in muscle anomalies. The murine muscles injected with mutant ACTN2 displayed cores and Z-line defects. Dominant ACTN2 mutations were previously associated with cardiomyopathies, and our data demonstrate that specific mutations in the well-known Z-line regulator alpha-actinin-2 can cause a skeletal muscle disorder.

}, issn = {1432-0533}, doi = {10.1007/s00401-019-01963-8}, author = {Lornage, Xavi{\`e}re and Romero, Norma B and Grosgogeat, Claire A and Malfatti, Edoardo and Donkervoort, Sandra and Marchetti, Michael M and Neuhaus, Sarah B and Foley, A Reghan and Labasse, Cl{\'e}mence and Schneider, Rapha{\"e}l and Carlier, Robert Y and Chao, Katherine R and Medne, Livija and Deleuze, Jean-Fran{\c c}ois and Orlikowski, David and B{\"o}nnemann, Carsten G and Gupta, Vandana A and Fardeau, Michel and B{\"o}hm, Johann and Laporte, Jocelyn} } @article {648, title = {Clinical, genetic, and pathologic characterization of Mexican founder mutation c.1387A>G.}, journal = {Neurol Genet}, volume = {5}, year = {2019}, month = {2019 Apr}, pages = {e315}, abstract = {

Objective: To characterize the clinical phenotype, genetic origin, and muscle pathology of patients with the c.1387A>G mutation.

Methods: Standardized clinical data were collected for all patients known to the authors with c.1387A>G mutations in . Muscle biopsies were reviewed and used for histopathology, immunostaining, Western blotting, and DNA extraction. Genetic analysis was performed on extracted DNA.

Results: We report the clinical phenotypes of 6 patients homozygous for the c.1387A>G mutation in . Onset of symptoms was <2 years, and 5 of the 6 patients never learned to walk. Brain MRIs were normal. Cognition was normal to mildly impaired. Microarray analysis of 5 homozygous c.1387A>G patients revealed a 500-kb region of shared homozygosity at 19q13.32, including . All 4 muscle biopsies available for review showed end-stage dystrophic pathology, near absence of glycosylated α-dystroglycan (α-DG) by immunofluorescence, and reduced molecular weight of α-DG compared with controls and patients with homozygous c.826C>A limb-girdle muscular dystrophy.

Conclusions: The clinical features and muscle pathology in these newly reported patients homozygous for c.1387A>G confirm that this mutation causes congenital muscular dystrophy. The clinical severity might be explained by the greater reduction in α-DG glycosylation compared with that seen with the c.826C>A mutation. The shared region of homozygosity at 19q13.32 indicates that c.1387A>G is a founder mutation with an estimated age of 60 generations (\~{}1,200-1,500 years).

}, issn = {2376-7839}, doi = {10.1212/NXG.0000000000000315}, author = {Lee, Angela J and Jones, Karra A and Butterfield, Russell J and Cox, Mary O and Konersman, Chamindra G and Grosmann, Carla and Abdenur, Jose E and Boyer, Monica and Beson, Brent and Wang, Ching and Dowling, James J and Gibbons, Melissa A and Ballard, Alison and Janas, Joanne S and Leshner, Robert T and Donkervoort, Sandra and B{\"o}nnemann, Carsten G and Malicki, Denise M and Weiss, Robert B and Moore, Steven A and Mathews, Katherine D} } @article {706, title = {Genetic regulatory variation in populations informs transcriptome analysis in rare disease.}, journal = {Science}, volume = {366}, year = {2019}, month = {2019 10 18}, pages = {351-356}, abstract = {

Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application of ANEVA to the Genotype-Tissues Expression (GTEx) data showed that this variance estimate is robust and correlated with selective constraint in a gene. Using these variance estimates in a dosage outlier test (ANEVA-DOT) applied to AE data from 70 Mendelian muscular disease patients showed accuracy in detecting genes with pathogenic variants in previously resolved cases and led to one confirmed and several potential new diagnoses. Using our reference estimates from GTEx data, ANEVA-DOT can be incorporated in rare disease diagnostic pipelines to use RNA-sequencing data more effectively.

}, issn = {1095-9203}, doi = {10.1126/science.aay0256}, author = {Mohammadi, Pejman and Castel, Stephane E and Cummings, Beryl B and Einson, Jonah and Sousa, Christina and Hoffman, Paul and Donkervoort, Sandra and Jiang, Zhuoxun and Mohassel, Payam and Foley, A Reghan and Wheeler, Heather E and Im, Hae Kyung and B{\"o}nnemann, Carsten G and MacArthur, Daniel G and Lappalainen, Tuuli} } @article {561, title = {Novel SPEG mutations in congenital myopathies: Genotype-phenotype correlations.}, journal = {Muscle Nerve}, volume = {59}, year = {2019}, month = {2019 03}, pages = {357-362}, abstract = {

INTRODUCTION: Centronuclear myopathies (CNMs) are a subtype of congenital myopathies (CMs) characterized by muscle weakness, predominant type 1 fibers, and increased central nuclei. SPEG (striated preferentially expressed protein kinase) mutations have recently been identified in 7 CM patients (6 with CNMs). We report 2 additional patients with SPEG mutations expanding the phenotype and evaluate genotype-phenotype correlations associated with SPEG mutations.

METHODS: Using whole exome/genome sequencing in CM families, we identified novel recessive SPEG mutations in 2 patients.

RESULTS: Patient 1, with severe muscle weakness requiring respiratory support, dilated cardiomyopathy, ophthalmoplegia, and findings of nonspecific CM on muscle biopsy carried a homozygous SPEG mutation (p.Val3062del). Patient 2, with milder muscle weakness, ophthalmoplegia, and CNM carried compound heterozygous mutations (p.Leu728Argfs*82) and (p.Val2997Glyfs*52).

CONCLUSIONS: The 2 patients add insight into genotype-phenotype correlations of SPEG-associated CMs. Clinicians should consider evaluating a CM patient for SPEG mutations even in the absence of CNM features. Muscle Nerve 59:357-362, 2019.

}, keywords = {Biopsy, Child, Child, Preschool, Consanguinity, Exome, Female, Genetic Association Studies, Humans, Infant, Male, Muscle Proteins, Muscle Weakness, Muscle, Skeletal, Mutation, Myopathies, Structural, Congenital, Protein-Serine-Threonine Kinases, Sequence Analysis}, issn = {1097-4598}, doi = {10.1002/mus.26378}, author = {Qualls, Anita E and Donkervoort, Sandra and Herkert, Johanna C and D{\textquoteright}Gama, Alissa M and Bharucha-Goebel, Diana and Collins, James and Chao, Katherine R and Foley, A Reghan and Schoots, Mirthe H and Jongbloed, Jan D H and B{\"o}nnemann, Carsten G and Agrawal, Pankaj B} } @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 {451, title = {Congenital Titinopathy: Comprehensive characterization and pathogenic insights.}, journal = {Ann Neurol}, volume = {83}, year = {2018}, month = {2018 Jun}, pages = {1105-1124}, abstract = {

OBJECTIVE: Comprehensive clinical characterization of congenital titinopathy to facilitate diagnosis and management of this important emerging disorder.

METHODS: Using massively parallel sequencing we identified 30 patients from 27 families with 2 pathogenic nonsense, frameshift and/or splice site TTN mutations in trans. We then undertook a detailed analysis of the clinical, histopathological and imaging features of these patients.

RESULTS: All patients had prenatal or early onset hypotonia and/or congenital contractures. None had ophthalmoplegia. Scoliosis and respiratory insufficiency typically developed early and progressed rapidly, whereas limb weakness was often slowly progressive, and usually did not prevent independent walking. Cardiac involvement was present in 46\% of patients. Relatives of 2 patients had dilated cardiomyopathy. Creatine kinase levels were normal to moderately elevated. Increased fiber size variation, internalized nuclei and cores were common histopathological abnormalities. Cap-like regions, whorled or ring fibers, and mitochondrial accumulations were also observed. Muscle magnetic resonance imaging showed gluteal, hamstring and calf muscle involvement. Western blot analysis showed a near-normal sized titin protein in all samples. The presence of 2 mutations predicted to impact both N2BA and N2B cardiac isoforms appeared to be associated with greatest risk of cardiac involvement. One-third of patients had 1 mutation predicted to impact exons present in fetal skeletal muscle, but not included within the mature skeletal muscle isoform transcript. This strongly suggests developmental isoforms are involved in the pathogenesis of this congenital/early onset disorder.

INTERPRETATION: This detailed clinical reference dataset will greatly facilitate diagnostic confirmation and management of patients, and has provided important insights into disease pathogenesis. Ann Neurol 2018;83:1105-1124.

}, issn = {1531-8249}, doi = {10.1002/ana.25241}, author = {Oates, Emily C and Jones, Kristi J and Donkervoort, Sandra and Charlton, Amanda and Brammah, Susan and Smith, John E and Ware, James S and Yau, Kyle S and Swanson, Lindsay C and Whiffin, Nicola and Peduto, Anthony J and Bournazos, Adam and Waddell, Leigh B and Farrar, Michelle A and Sampaio, Hugo A and Teoh, Hooi Ling and Lamont, Phillipa J and Mowat, David and Fitzsimons, Robin B and Corbett, Alastair J and Ryan, Monique M and O{\textquoteright}Grady, Gina L and Sandaradura, Sarah A and Ghaoui, Roula and Joshi, Himanshu and Marshall, Jamie L and Nolan, Melinda A and Kaur, Simranpreet and Punetha, Jaya and Topf, Ana and Harris, Elizabeth and Bakshi, Madhura and Genetti, Casie A and Marttila, Minttu and Werlauff, Ulla and Streichenberger, Nathalie and Pestronk, Alan and Mazanti, Ingrid and Pinner, Jason R and Vuillerot, Carole and Grosmann, Carla and Camacho, Ana and Mohassel, Payam and Leach, Meganne E and Foley, A Reghan and Bharucha-Goebel, Diana and Collins, James and Connolly, Anne M and Gilbreath, Heather R and Iannaccone, Susan T and Castro, Diana and Cummings, Beryl B and Webster, Richard I and Lazaro, Le{\"\i}la and Vissing, John and Coppens, Sandra and Deconinck, Nicolas and Luk, Ho-Ming and Thomas, Neil H and Foulds, Nicola C and Illingworth, Marjorie A and Ellard, Sian and McLean, Catriona A and Phadke, Rahul and Ravenscroft, Gianina and Witting, Nanna and Hackman, Peter and Richard, Isabelle and Cooper, Sandra T and Kamsteeg, Erik-Jan and Hoffman, Eric P and Bushby, Kate and Straub, Volker and Udd, Bjarne and Ferreiro, Ana and North, Kathryn N and Clarke, Nigel F and Lek, Monkol and Beggs, Alan H and B{\"o}nnemann, Carsten G and MacArthur, Daniel G and Granzier, Henk and Davis, Mark R and Laing, Nigel G} } @article {560, title = {Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration.}, journal = {EMBO J}, volume = {37}, year = {2018}, month = {2018 Dec 03}, abstract = {

A set of glutamylases and deglutamylases controls levels of tubulin polyglutamylation, a prominent post-translational modification of neuronal microtubules. Defective tubulin polyglutamylation was first linked to neurodegeneration in the () mouse, which lacks deglutamylase CCP1, displays massive cerebellar atrophy, and accumulates abnormally glutamylated tubulin in degenerating neurons. We found biallelic rare and damaging variants in the gene encoding CCP1 in 13 individuals with infantile-onset neurodegeneration and confirmed the absence of functional CCP1 along with dysregulated tubulin polyglutamylation. The human disease mainly affected the cerebellum, spinal motor neurons, and peripheral nerves. We also demonstrate previously unrecognized peripheral nerve and spinal motor neuron degeneration in mice, which thus recapitulated key features of the human disease. Our findings link human neurodegeneration to tubulin polyglutamylation, entailing this post-translational modification as a potential target for drug development for neurodegenerative disorders.

}, issn = {1460-2075}, doi = {10.15252/embj.2018100540}, author = {Shashi, Vandana and Magiera, Maria M and Klein, Dennis and Zaki, Maha and Schoch, Kelly and Rudnik-Sch{\"o}neborn, Sabine and Norman, Andrew and Lopes Abath Neto, Osorio and Dusl, Marina and Yuan, Xidi and Bartesaghi, Luca and De Marco, Patrizia and Alfares, Ahmed A and Marom, Ronit and Arold, Stefan T and Guzm{\'a}n-Vega, Francisco J and Pena, Loren Dm and Smith, Edward C and Steinlin, Maja and Babiker, Mohamed Oe and Mohassel, Payam and Foley, A Reghan and Donkervoort, Sandra and Kaur, Rupleen and Ghosh, Partha S and Stanley, Valentina and Musaev, Damir and Nava, Caroline and Mignot, Cyril and Keren, Boris and Scala, Marcello and Tassano, Elisa and Picco, Paolo and Doneda, Paola and Fiorillo, Chiara and Issa, Mahmoud Y and Alassiri, Ali and Alahmad, Ahmed and Gerard, Amanda and Liu, Pengfei and Yang, Yaping and Ertl-Wagner, Birgit and Kranz, Peter G and Wentzensen, Ingrid M and Stucka, Rolf and Stong, Nicholas and Allen, Andrew S and Goldstein, David B and Schoser, Benedikt and R{\"o}sler, Kai M and Alfadhel, Majid and Capra, Valeria and Chrast, Roman and Strom, Tim M and Kamsteeg, Erik-Jan and B{\"o}nnemann, Carsten G and Gleeson, Joseph G and Martini, Rudolf and Janke, Carsten and Senderek, Jan} } @article {490, title = {Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy.}, journal = {Am J Hum Genet}, volume = {102}, year = {2018}, month = {2018 05 03}, pages = {858-873}, abstract = {

The exosome is a conserved multi-protein complex that is essential for correct RNA processing. Recessive variants in exosome components EXOSC3, EXOSC8, and RBM7 cause various constellations of pontocerebellar hypoplasia (PCH), spinal muscular atrophy (SMA), and central nervous system demyelination. Here, we report on four unrelated affected individuals with recessive variants in EXOSC9 and the effect of the variants on the function of the RNA exosome in~vitro in affected individuals{\textquoteright} fibroblasts and skeletal muscle and in~vivo in zebrafish. The clinical presentation was severe, early-onset, progressive SMA-like motor neuronopathy, cerebellar atrophy, and in one affected individual, congenital fractures of the long bones. Three affected individuals of different ethnicity carried the homozygous c.41T>C (p.Leu14Pro) variant, whereas one affected individual was compound heterozygous for c.41T>C (p.Leu14Pro) and c.481C>T (p.Arg161). We detected reduced EXOSC9 in fibroblasts and skeletal muscle and observed a reduction of the whole multi-subunit exosome complex on blue-native polyacrylamide gel electrophoresis. RNA sequencing of fibroblasts and skeletal muscle detected significant >2-fold changes in genes involved in neuronal development and cerebellar and motor neuron degeneration, demonstrating the widespread effect of the variants. Morpholino oligonucleotide knockdown and CRISPR/Cas9-mediated mutagenesis of exosc9 in zebrafish recapitulated aspects of the human phenotype, as they have in other zebrafish models of exosomal disease. Specifically, portions of the cerebellum and hindbrain were absent, and motor neurons failed to develop and migrate properly. In summary, we show that variants in EXOSC9 result in a neurological syndrome combining cerebellar atrophy and spinal motoneuronopathy, thus expanding the list of human exosomopathies.

}, keywords = {Amino Acid Sequence, Animals, Atrophy, Base Sequence, Cerebellum, Child, Preschool, Exosome Multienzyme Ribonuclease Complex, Exosomes, Female, Fibroblasts, Gene Knockdown Techniques, Genetic Variation, Haplotypes, Humans, Infant, Male, Motor Neurons, Muscle, Skeletal, Pedigree, RNA-Binding Proteins, Spinal Cord, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2018.03.011}, author = {Burns, David T and Donkervoort, Sandra and M{\"u}ller, Juliane S and Knierim, Ellen and Bharucha-Goebel, Diana and Faqeih, Eissa Ali and Bell, Stephanie K and AlFaifi, Abdullah Y and Monies, Dorota and Millan, Francisca and Retterer, Kyle and Dyack, Sarah and MacKay, Sara and Morales-Gonzalez, Susanne and Giunta, Michele and Munro, Benjamin and Hudson, Gavin and Scavina, Mena and Baker, Laura and Massini, Tara C and Lek, Monkol and Hu, Ying and Ezzo, Daniel and Alkuraya, Fowzan S and Kang, Peter B and Griffin, Helen and Foley, A Reghan and Schuelke, Markus and Horvath, Rita and B{\"o}nnemann, Carsten G} } @article {638, title = {A defect in myoblast fusion underlies Carey-Fineman-Ziter syndrome.}, journal = {Nat Commun}, volume = {8}, year = {2017}, month = {2017 07 06}, pages = {16077}, abstract = {

Multinucleate cellular syncytial formation is a hallmark of skeletal muscle differentiation. Myomaker, encoded by Mymk (Tmem8c), is a well-conserved plasma membrane protein required for myoblast fusion to form multinucleated myotubes in mouse, chick, and zebrafish. Here, we report that autosomal recessive mutations in MYMK (OMIM 615345) cause Carey-Fineman-Ziter syndrome in humans (CFZS; OMIM 254940) by reducing but not eliminating MYMK function. We characterize MYMK-CFZS as a congenital myopathy with marked facial weakness and additional clinical and pathologic features that distinguish it from other congenital neuromuscular syndromes. We show that a heterologous cell fusion assay in vitro and allelic complementation experiments in mymk knockdown and mymk zebrafish in vivo can differentiate between MYMK wild type, hypomorphic and null alleles. Collectively, these data establish that MYMK activity is necessary for normal muscle development and maintenance in humans, and expand the spectrum of congenital myopathies to include cell-cell fusion deficits.

}, keywords = {Adult, Amino Acid Sequence, Animals, Cell Fusion, Child, Disease Models, Animal, Embryo, Nonmammalian, Female, Gene Expression, Genes, Recessive, Genetic Complementation Test, Humans, Infant, Male, Membrane Proteins, Mobius Syndrome, Morphogenesis, Muscle Proteins, Muscle, Skeletal, Muscular Diseases, Mutation, Myoblasts, Pedigree, Pierre Robin Syndrome, Sequence Alignment, Sequence Homology, Amino Acid, Zebrafish, Zebrafish Proteins}, issn = {2041-1723}, doi = {10.1038/ncomms16077}, author = {Di Gioia, Silvio Alessandro and Connors, Samantha and Matsunami, Norisada and Cannavino, Jessica and Rose, Matthew F and Gilette, Nicole M and Artoni, Pietro and de Macena Sobreira, Nara Lygia and Chan, Wai-Man and Webb, Bryn D and Robson, Caroline D and Cheng, Long and Van Ryzin, Carol and Ramirez-Martinez, Andres and Mohassel, Payam and Leppert, Mark and Scholand, Mary Beth and Grunseich, Christopher and Ferreira, Carlos R and Hartman, Tyler and Hayes, Ian M and Morgan, Tim and Markie, David M and Fagiolini, Michela and Swift, Amy and Chines, Peter S and Speck-Martins, Carlos E and Collins, Francis S and Jabs, Ethylin Wang and B{\"o}nnemann, Carsten G and Olson, Eric N and Carey, John C and Robertson, Stephen P and Manoli, Irini and Engle, Elizabeth C} } @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} } @article {454, title = {P4HA1 mutations cause a unique congenital disorder of connective tissue involving tendon, bone, muscle and the eye.}, journal = {Hum Mol Genet}, volume = {26}, year = {2017}, month = {2017 06 15}, pages = {2207-2217}, abstract = {

Collagen prolyl 4-hydroxylases (C-P4Hs) play a central role in the formation and stabilization of the triple helical domain of collagens. P4HA1 encodes the catalytic α(I) subunit of the main C-P4H isoenzyme (C-P4H-I). We now report human bi-allelic P4HA1 mutations in a family with a congenital-onset disorder of connective tissue, manifesting as early-onset joint hypermobility, joint contractures, muscle weakness and bone dysplasia as well as high myopia, with evidence of clinical improvement of motor function over time in the surviving patient. Similar to P4ha1 null mice, which die prenatally, the muscle tissue from P1 and P2 was found to have reduced collagen IV immunoreactivity at the muscle basement membrane. Patients were compound heterozygous for frameshift and splice site mutations leading to reduced, but not absent, P4HA1 protein level and C-P4H activity in dermal fibroblasts compared to age-matched control samples. Differential scanning calorimetry revealed reduced thermal stability of collagen in patient-derived dermal fibroblasts versus age-matched control samples. Mutations affecting the family of C-P4Hs, and in particular C-P4H-I, should be considered in patients presenting with congenital connective tissue/myopathy overlap disorders with joint hypermobility, contractures, mild skeletal dysplasia and high myopia.

}, keywords = {Animals, Basement Membrane, Bone and Bones, Child, Collagen Type IV, Connective Tissue, Humans, Male, Mice, Mice, Knockout, Muscles, Mutation, Osteochondrodysplasias, Procollagen-Proline Dioxygenase, Prolyl Hydroxylases, Tendons}, issn = {1460-2083}, doi = {10.1093/hmg/ddx110}, author = {Zou, Yaqun and Donkervoort, Sandra and Salo, Antti M and Foley, A Reghan and Barnes, Aileen M and Hu, Ying and Makareeva, Elena and Leach, Meganne E and Mohassel, Payam and Dastgir, Jahannaz and Deardorff, Matthew A and Cohn, Ronald D and DiNonno, Wendy O and Malfait, Fransiska and Lek, Monkol and Leikin, Sergey and Marini, Joan C and Myllyharju, Johanna and B{\"o}nnemann, Carsten G} } @article {455, title = {Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization.}, journal = {Am J Hum Genet}, volume = {99}, year = {2016}, month = {2016 Nov 03}, pages = {1086-1105}, abstract = {

This study establishes PYROXD1 variants as a cause of early-onset myopathy and uses biospecimens and cell lines, yeast, and zebrafish models to elucidate the fundamental role of PYROXD1 in skeletal muscle. Exome sequencing identified recessive variants in PYROXD1 in nine probands from five families. Affected individuals presented in infancy or childhood with slowly progressive proximal and distal weakness, facial weakness, nasal speech, swallowing difficulties, and normal to moderately elevated creatine kinase. Distinctive histopathology showed abundant internalized nuclei, myofibrillar disorganization, desmin-positive inclusions, and thickened Z-bands. PYROXD1 is a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins (FAD-binding) and catalyze pyridine-nucleotide-dependent (NAD/NADH) reduction of thiol residues in other proteins. Complementation experiments in yeast lacking glutathione reductase glr1 show that human PYROXD1 has reductase activity that is strongly impaired by the disease-associated missense mutations. Immunolocalization studies in human muscle and zebrafish myofibers demonstrate that PYROXD1 localizes to the nucleus and to striated sarcomeric compartments. Zebrafish with ryroxD1 knock-down recapitulate features of PYROXD1 myopathy with sarcomeric disorganization, myofibrillar aggregates, and marked swimming defect. We characterize variants in the oxidoreductase PYROXD1 as a cause of early-onset myopathy with distinctive histopathology and introduce altered redox regulation as a primary cause of congenital muscle disease.

}, keywords = {Amino Acid Sequence, Animals, Cell Nucleus, Cercopithecus aethiops, Cohort Studies, COS Cells, Creatine Kinase, Cytoplasm, Distal Myopathies, ELAV-Like Protein 4, Female, Flavoproteins, Gene Deletion, Genetic Variation, Genome-Wide Association Study, Glutathione Reductase, HEK293 Cells, Humans, Male, Muscle, Skeletal, Mutation, Missense, Myopathies, Structural, Congenital, Oxidoreductases, Pedigree, Protein Conformation, Saccharomyces cerevisiae Proteins, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.09.005}, author = {O{\textquoteright}Grady, Gina L and Best, Heather A and Sztal, Tamar E and Schartner, Vanessa and Sanjuan-Vazquez, Myriam and Donkervoort, Sandra and Abath Neto, Osorio and Sutton, Roger Bryan and Ilkovski, Biljana and Romero, Norma Beatriz and Stojkovic, Tanya and Dastgir, Jahannaz and Waddell, Leigh B and Boland, Anne and Hu, Ying and Williams, Caitlin and Ruparelia, Avnika A and Maisonobe, Thierry and Peduto, Anthony J and Reddel, Stephen W and Lek, Monkol and Tukiainen, Taru and Cummings, Beryl B and Joshi, Himanshu and Nectoux, Juliette and Brammah, Susan and Deleuze, Jean-Fran{\c c}ois and Ing, Viola Oorschot and Ramm, Georg and Ardicli, Didem and Nowak, Kristen J and Talim, Beril and Topaloglu, Haluk and Laing, Nigel G and North, Kathryn N and MacArthur, Daniel G and Friant, Sylvie and Clarke, Nigel F and Bryson-Richardson, Robert J and B{\"o}nnemann, Carsten G and Laporte, Jocelyn and Cooper, Sandra T} }