Compound heterozygous POMGNT1 mutations leading to muscular dystrophy-dystroglycanopathy type A3: a case report

Saturation mutagenesis-reinforced functional assays for disease-related genes

Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods are obstacles for achieving genome-wide resolution of variants in disease-related genes. Our framework, saturation mutagenesis-reinforced functional assays (SMuRF), offers simple and cost-effective saturation mutagenesis paired with streamlined functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single-nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Overall, our approach enables variant-to-function insights for disease genes in a cost-effective manner that can be broadly implemented by standard research laboratories.

Deep Mutational Scanning in Disease-related Genes with Saturation Mutagenesis-Reinforced Functional Assays (SMuRF)

Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods hamper crowd-sourcing approaches toward genome-wide resolution of variants in disease-related genes. Our framework, Saturation Mutagenesis-Reinforced Functional assays (SMuRF), addresses these issues by offering simple and cost-effective saturation mutagenesis, as well as streamlining functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Our approach opens new directions for enabling variant-to-function insights for disease genes in a manner that is broadly useful for crowd-sourcing implementation across standard research laboratories.

Orthopedic manifestations of congenital muscular dystrophy subtypes in children: Emerging signatures need consolidation: a scoping review

Our objective was to screen the literature on congenital muscular dystrophy (CMD) children/adolescents regarding the extent/nature of reporting orthopedic manifestations/deformities and to assess its appropriateness in informing clinical practice/research. We searched PubMed for original research on orthopedic surgical/non-surgical manifestations of CMD. Eligible articles needed to focus on orthopedic manifestations/deformities as one of the study objectives with no restrictions on study designs/types or search period. Eight hundred and thirty articles were initially identified and screened. Following the exclusion of 501 articles for disagreeing titles/abstracts, 329 were available for eligibility assessment. Two hundred and fifty-five articles were excluded for reasons. Of one hundred articles, 15 were captured manually and 11 through pre-submission searches, with 1078 patients included in the final analysis. The most common subtype was Laminin alpha-2 (LAMA2)-relatedCMD. Orthopedic manifestations of CMD are generally underreported and insufficiently detailed. There is reliable evidence that accurate reporting of orthopedic manifestations can be a valuable clinical supplement to the complex differential diagnosis process in collagen VI-related CMD, LAMA2-related-CMD, LMNA-related-CMD, and SEPN1-related CMD (SELENON). For alpha dystroglycan-related CMD, there is insufficient information to delineate a subtype-specific pattern. There is emerging evidence that reporting spine surgery outcomes may facilitate orthopedic decision making. The greatest clinical/research utility was provided by articles with longitudinal, comprehensive, and correlative reporting of larger cohorts. Detailed reporting of the orthopedic phenotype of CMD in future research may further uncover its diagnostic potential.

Uniparental disomy for chromosome 1 with POMGNT1 splice-site variant causes muscle-eye-brain disease

POMGNT1, encoding protein O-mannose beta-1,2-N-acetylglucosaminyltransferase 1, is one of the genes responsible for dystroglycanopathy (DGP), which includes multiple phenotypes such as muscle-eye-brain disease (MEB), congenital muscular dystrophy with intellectual disability, and limb-girdle muscular dystrophy Here, we report a case of MEB that is the result of a homozygous variant of POMGNT1 that is revealed through uniparental disomy (UPD). An 8-month-old boy was admitted with mental and motor retardation, hypotonia, esotropia, early onset severe myopia, and structural brain abnormalities. A panel testing of genetic myopathy-related genes was used to identify a homozygous c.636C>T (p.Phe212Phe) variant in exon 7 of POMGNT1 in the patient, a heterozygous c.636C>T variant in the father, and the wild type in the mother. Quantitative polymerase chain reaction (q-PCR) revealed no abnormal copy numbers in exon 7. Trio-based whole-exome sequencing (trio-WES) revealed a possible paternal UPD on chromosome 1 of the patient. Chromosomal microarray analysis (CMA) revealed a 120,451 kb loss of heterozygosity (LOH) on 1p36.33-p11.2, encompassing POMGNT1, and a 99,319 kb loss of heterozygosity on 1q21.2-q44, which indicated UPD. Moreover, RNA sequencing (RNA-seq) verified that the c.636C>T variant was a splice-site variant, leading to skipping of exon 7 (p.Asp179Valfs*23). In conclusion, to the best of our knowledge, we present the first case of MEB caused by UPD, providing valuable insights into the genetic mechanisms underlying this condition.

Analysis of the expression and distribution of protein O-linked mannose β1,2-N-acetylglucosaminyltransferase 1 in the normal adult mouse brain

Introduction

Protein O-linked mannose β1,2-N-acetylglucosaminyltransferase 1 (POMGNT1) is crucial for the elongation of O-mannosyl glycans. Mutations in POMGNT1 cause muscle-eye-brain (MEB) disease, one of the main features of which is anatomical aberrations in the brain. A growing number of studies have shown that defects in POMGNT1 affect neuronal migration and distribution, disrupt basement membranes, and misalign Cajal-Retzius cells. Several studies have examined the distribution and expression of POMGNT1 in the fetal or neonatal brain for neurodevelopmental studies in the mouse or human brain. However, little is known about the neuroanatomical distribution and expression of POMGNT1 in the normal adult mouse brain.

Methods

We analyzed the expression of POMGNT1 mRNA and protein in the brains of various neuroanatomical regions and spinal cords by western blotting and RT-qPCR. We also detected the distribution profile of POMGnT1 in normal adult mouse brains by immunohistochemistry and double-immunofluorescence.

Results

In the present study, we found that POMGNT1-positive cells were widely distributed in various regions of the brain, with high levels of expression in the cerebral cortex and hippocampus. In terms of cell type, POMGNT1 was predominantly expressed in neurons and was mainly enriched in glutamatergic neurons; to a lesser extent, it was expressed in glial cells. At the subcellular level, POMGNT1 was mainly co-localized with the Golgi apparatus, but expression in the endoplasmic reticulum and mitochondria could not be excluded.

Discussion

The present study suggests that POMGNT1, although widely expressed in various brain regions, may has some regional and cellular specificity, and the outcomes of this study provide a new laboratory basis for revealing the possible involvement of POMGNT1 in normal physiological functions of the brain from a morphological perspective.

Clinical and Molecular Spectrum of Muscular Dystrophies (MDs) with Intellectual Disability (ID): a Comprehensive Overview

Muscular dystrophies encompass a wide and heterogeneous subset of hereditary myopathies that manifest by the structural or functional abnormalities in the skeletal muscle. Some pathogenic mutations induce a dysfunction or loss of proteins that are critical for the stability of muscle cells, leading to progressive muscle degradation and weakening. Several studies have well-established cognitive deficits in muscular dystrophies which are mainly due to the disruption of brain-specific expression of affected muscle proteins. We provide a comprehensive overview of the types of muscular dystrophies that are accompanied by intellectual disability by detailed consulting of the main libraries. The current paper focuses on the clinical and molecular evidence about Duchenne, congenital, limb-girdle, and facioscapulohumeral muscular dystrophies as well as myotonic dystrophies. Because these syndromes impose a heavy burden of psychological and financial problems on patients, their families, and the health care community, a thorough examination is necessary to perform timely psychological and medical interventions and thus improve the quality of life.

Unravelling the genetic causes of multiple malformation syndromes: A whole exome sequencing study of the Cypriot population

Multiple malformation syndromes (MMS) belong to a group of genetic disorders characterised by neurodevelopmental anomalies and congenital malformations. Here we explore for the first time the genetic aetiology of MMS using whole-exome sequencing (WES) in undiagnosed patients from the Greek-Cypriot population after prior extensive diagnostics workup including karyotype and array-CGH. A total of 100 individuals (37 affected), from 32 families were recruited and family-based WES was applied to detect causative single-nucleotide variants (SNVs) and indels. A genetic diagnosis was reported for 16 MMS patients (43.2%), with 10/17 (58.8%) of the findings being novel. All autosomal dominant findings occurred de novo. Functional studies were also performed to elucidate the molecular mechanism relevant to the abnormal phenotypes, in cases where the clinical significance of the findings was unclear. The 17 variants identified in our cohort were located in 14 genes (PCNT, UBE3A, KAT6A, SPR, POMGNT1, PIEZO2, PXDN, KDM6A, PHIP, HECW2, TFAP2A, CNOT3, AGTPBP1 and GAMT). This study has highlighted the efficacy of WES through the high detection rate (43.2%) achieved for a challenging category of undiagnosed patients with MMS compared to other conventional diagnostic testing methods (10-20% for array-CGH and ~3% for G-banding karyotype analysis). As a result, family-based WES could potentially be considered as a first-tier cost effective diagnostic test for patients with MMS that facilitates better patient management, prognosis and offer accurate recurrence risks to the families.

Identification of a novel missense c.386G > A variant in a boy with the POMGNT1-related muscular dystrophy-dystroglycanopathy

Muscular dystrophy-dystroglycanopathies are autosomal recessive neurologic disorders, caused by homozygous or compound heterozygous mutations in the POMGNT1 gene-encoding protein O-mannose beta-1,2-N-acetylglucosaminyl transferase. This type of muscular dystrophy is characterized by early-onset muscle weakness, gait ataxia, microcephaly, and developmental delay.We performed whole-exome sequencing to detect the disease-causing variants in a 4 year-old boy. Afterwards, Sanger sequencing was performed to confirm the detected variant in the patient and his family. We evaluated a 4 year-old Iranian boy presented with delayed speech and language development, gait ataxia, global developmental delay, motor delay, neurodevelopmental delay, postnatal microcephaly and strabismus. His parents were first cousins, and the mother had a history of spontaneous abortion. In this study, we report a novel missense c.386G > A; p.(Arg129Gln) variant in the POMGNT1 gene which was confirmed by Sanger sequencing in the patient and segregated with the disease in the family.

Two middle-aged women with the Finnish variant of muscle-eye-brain disease (MEB)

Muscle-eye-brain disease (MEB) is a recessively inherited rare disease. Sixteen different gene mutations are known, with the most common mutations in the POMGNT1 gene. The disease is now called congenital muscular dystrophy-dystroglycanopathy type A3 (MDDGA3). It manifests itself as muscular dystrophy with eye and brain anomalies and intellectual disability. Previous clinical reports describe young patients. We have been able to follow two patients for almost 40 years. Their clinical picture has remained quite stable since adolescence, appearing as severe intellectual and motor disability, extremely limited communication skills, visual impairment, epilepsy, joint contractures, repeated bowel obstructions, teeth abrasion due to bruxism, an irregular sleep pattern and as a previously unreported feature hypothermic periods manifesting as excessive sleepiness.