Severe Expressive Language Delay Research Articles

Deep computational phenotyping of genomic variants impacting the SET domain of KMT2C reveal molecular mechanisms for their dysfunction.

Introduction: Kleefstra Syndrome type 2 (KLEFS-2) is a genetic, neurodevelopmental disorder characterized by intellectual disability, infantile hypotonia, severe expressive language delay, and characteristic facial appearance, with a spectrum of other distinct clinical manifestations. Pathogenic mutations in the epigenetic modifier type 2 lysine methyltransferase KMT2C have been identified to be causative in KLEFS-2 individuals. Methods: This work reports a translational genomic study that applies a multidimensional computational approach for deep variant phenotyping, combining conventional genomic analyses, advanced protein bioinformatics, computational biophysics, biochemistry, and biostatistics-based modeling. We use standard variant annotation, paralog annotation analyses, molecular mechanics, and molecular dynamics simulations to evaluate damaging scores and provide potential mechanisms underlying KMT2C variant dysfunction. Results: We integrated data derived from the structure and dynamics of KMT2C to classify variants into SV (Structural Variant), DV (Dynamic Variant), SDV (Structural and Dynamic Variant), and VUS (Variant of Uncertain Significance). When compared with controls, these variants show values reflecting alterations in molecular fitness in both structure and dynamics. Discussion: We demonstrate that our 3D models for KMT2C variants suggest distinct mechanisms that lead to their imbalance and are not predictable from sequence alone. Thus, the missense variants studied here cause destabilizing effects on KMT2C function by different biophysical and biochemical mechanisms which we adeptly describe. This new knowledge extends our understanding of how variations in the KMT2C gene cause the dysfunction of its methyltransferase enzyme product, thereby bearing significant biomedical relevance for carriers of KLEFS2-associated genomic mutations.

Integrative Modeling, Molecular Mechanics, and Molecular Dynamics Evaluation of Genomics Variants in KMT2C (MLL3), a Gene Involved in Kleefstra Syndrome Type 2

Kleefstra Syndrome (KS) is a genetic, neurodevelopmental disorder characterized by intellectual disability, infantile hypotonia, severe expressive language delay, and characteristic facial appearance, with a spectrum of other distinct clinical manifestations. Pathogenic mutations in the epigenetic modifier, type 2 lysine methyltransferase (KMT2C), are attributed to cause KS core features in individuals who are Euchromatic Histone Lysine Methyltransferase 1, EHMT1, mutation negative. These individuals are designated as having KS type 2. In this study, we made use of multidimensional approaches, including conventional genomic bioinformatics, molecular modeling, molecular mechanics, and molecular dynamics simulations, to understand and enhance the annotation and potential mechanisms by which disease‐associated missense variants affect KMT2C function. In addition, we report a scoring system based on statistical integration and modeling of data derived from the structure and dynamics of KMT2C, which allows us to classify germline variants into SV (Structural Variants), DV (Dynamic Variants), SDV (Structural and Dynamic Variant), and VUS (Variant of Uncertain Significance). Moreover, these scores of disease‐associated variants reflect alterations in molecular fitness when compared with tolerated, benign variants, used as controls. Thus, these studies provide data that is more refined, both structurally and functionally for each variant, compared to current annotation tools used in human genomics databases and reveal mechanisms for their dysfunction not predictable from clinical genomic methods alone. This new knowledge extends our understanding of molecular mechanisms underlying the dysfunction of KS type 2‐associated genomic mutations. Lastly, by identifying KMT2C mutation‐specific druggable conformations, this study builds the trajectory toward the future development of small molecules to ameliorate the symptoms of this disease.

The Road to Personalized Therapies: Lessons Learned From Angelman Syndrome.

Angelman syndrome (AS) is a neurogenetic disorder characterized by delays including a severe expressive language delay, motor concerns, ataxia, epilepsy, sleep disturbances, gastrointestinal problems, and characteristic behaviors, including a happy demeanor, hyperactivity, and excitability. The syndrome is one of the first neurodevelopmental disorders with a clear trajectory towards meaningful treatment with approximately 20 companies actively developing targeted therapeutics for AS. Herein, we highlight the historical context of the road to therapeutics and some of the challenges in the field with the potential to impact the success of clinical trials for Angelman syndrome and also have relevance of other neurogenetic developmental disabilities.

MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis.

MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.

Severe Expressive-Language Delay and Congenital Malformations in a Boy with Microduplication 7q11.23 Diagnosed by Molecular Cytogenetic Analysis

We report a patient with speech delay and hydronephrosis ascertained with array-CGH screening of patients with abnormal neuronal migration and intellectual disability, having a 7q11.23 duplication reciprocal to the Williams-Beuren critical region (WBCR) deletion. Similarly to the reported patients, he showed serious difficulties in expressive language in the absence of severe intellectual disability and marked dysmorphic features. In addition to the abnormal development of the cerebral cortex with simplified gyral pattern and hydronephrosis. Chromosomal analysis showed normal karytoptype, so Micro-array comparative genomic hybridization was used to search for a possible cryptic anomaly. An interstitial duplication of 1.46 Mb was detected in 7q11.23. Fluorescence in situ hybridization confirmed the diagnosis, revealing a tandem duplication of the Williams-Beuren critical region. Our study provides an additional case for better understanding and delineating the duplication 7q11.23. We thus performed a genotype-phenotype correlation analysis to ascertain the contribution of 7q11.23 to the clinical features of our patient.

Guanidinoacetate methyltransferase (GAMT) deficiency: late onset of movement disorder and preserved expressive language

Guanidinoacetate methyltransferase (GAMT) deficiency is a disorder of creatine biosynthesis, characterized by early-onset learning disability and epilepsy in most affected children. Severe expressive language delay is a constant feature even in the mildest clinical phenotypes.We report the clinical, biochemical, imaging, and treatment data of two female siblings (18y and 13y) with an unusual phenotype of GAMT deficiency. The oldest sibling had subacute onset of a movement disorder at age 17 years, later than has been previously reported. The younger sibling had better language skills than previously described in this disorder. After treatment with creatine, arginine restriction and ornithine-supplemented diet, seizure severity and movement disorder were reduced but cognition did not improve. This report confirms that GAMT deficiency, a heterogeneous, potentially treatable disorder, detected by increased levels of guanidinoacetate in body fluids (e.g. plasma or urine) or by an abnormal creatine peak on magnetic resonance spectroscopy, should be considered in patients of any age with unexplained, apparently static learning disability and epilepsy.

Duplication of 17(p11.2p11.2) in a male child with autism and severe language delay

Duplications of 17(p11.2p11.2) have been associated with various behavioral manifestations including attention deficits, obsessive-compulsive symptoms, autistic traits, and language delay. We are conducting a genetic study of autism and are screening all cases for submicroscopic chromosomal abnormalities, in addition to standard karyotyping, and fragile X testing. Using array-based comparative genomic hybridization analysis of data from the Affymetrix GeneChip(R) Human Mapping Array set, we detected a duplication of approximately 3.3 Mb on chromosome 17p11.2 in a male child with autism and severe expressive language delay. The duplication was confirmed by measuring the copy number of genomic DNA using quantitative polymerase chain reaction. Gene expression analyses revealed increased expression of three candidate genes for the Smith-Magenis neurobehavioral phenotype, RAI1, DRG2, and RASD1, in transformed lymphocytes from Case 81A, suggesting gene dosage effects. Our results add to a growing body of evidence suggesting that duplications of 17(p11.2p11.2) result in language delay as well as autism and related phenotypes. As Smith-Magenis syndrome is also associated with language delay, a gene involved in acquisition of language may lie within this interval. Whether a parent of origin effect, gender of the case, the presence of allelic variation, or changes in expression of genes outside the breakpoints influence the resultant phenotype remains to be determined.

Cortical dysplasia of the left temporal lobe might explain severe expressive-language delay in patients with duplication of the Williams–Beuren locus

We report on a new duplication case of 7q11.23, reciprocal of the Williams-Beuren (WB) deletion. The patient, a 13-year-old girl, was ascertained within an array-CGH screening of patients with epilepsy and neuronal migration defects. Similarly to the first reported patient, she showed serious difficulties in expressive language in the absence of severe mental retardation and marked dysmorphic features. Magnetic resonance imaging (MRI) of the brain revealed an abnormal development of the cerebral cortex in the left temporal lobe, which showed a simplified gyral pattern, and increased cortical thickness. This finding, which might explain poor language development, suggests that the WB critical region might harbour a dosage-sensitive gene controlling the molecular machinery of neuronal migration, with regional specificity and lateralization. It will be important to confirm our findings in newly diagnosed patients with dup(7)(q11.23). We expect to detect many more patients with the same duplication using widespread clinical implementation of high-resolution genome analysis.

ProSAP/Shank proteins - a family of higher order organizing molecules of the postsynaptic density with an emerging role in human neurological disease.

The postsynaptic density (PSD) is a specialized electron-dense structure underneath the postsynaptic plasmamembrane of excitatory synapses. It is thought to anchor and cluster glutamate receptors exactly opposite to the presynaptic neurotransmitter release site. Various efforts to study the molecular structure of the PSD identified several new proteins including membrane receptors, cell adhesion molecules, components of signalling cascades, cytoskeletal elements and adaptor proteins with scaffolding functions to interconnect these PSD components. The characterization of a novel adaptor protein family, the ProSAPs or Shanks, sheds new light on the basic structural organization of the PSD. ProSAPs/Shanks are multidomain proteins that interact directly or indirectly with receptors of the postsynaptic membrane including NMDA-type and metabotropic glutamate receptors, and the actin-based cytoskeleton. These interactions suggest that ProSAP/Shanks may be important scaffolding molecules of the PSD with a crucial role in the assembly of the PSD during synaptogenesis, in synaptic plasticity and in the regulation of dendritic spine morphology. Moreover the analysis of a patient with 22q13.3 distal deletion syndrome revealed a balanced translocation with a breakpoint in the human ProSAP2/Shank3 gene. This ProSAP2/Shank3 haploinsufficiency may cause a syndrome that is characterized by severe expressive language delay, mild mental retardation and minor facial dysmorphisms.

No evidence for submicroscopic 22qter deletions in patients with features suggestive for Angelman syndrome.

Patients with monosomy 22q13.3 --> qter have, in addition to (usually severe) developmental delay, hypotonia, severe expressive language delay leading to absence of speech, pervasive developmental abnormalities, and subtle facial anomalies. Thus far, it has been one of the more common submicroscopic telomere deletions seen in patients with mental retardation. Due to the phenotypic overlap between monosomy 22q13.3 and Angelman syndrome (AS), 44 patients with AS features but without one of the characteristic molecular 15q abnormalities were tested for 22qter deletions. In the study group, 31/44 (70%) were heterozygous for locus D22S163 with probe cMS607 (distance 0.125 Mb from telomere). The remaining 13/44 (30%) patients were heterozygous for one or more of four microsatellite markers centromeric from D22S163 in the 22qter region (distances 1.5-4.3 Mb from telomere). Based on the present study, there is no evidence that patients with an "Angelman-like" phenotype are more likely to have a 22qter deletion than other individuals with mental retardation.

Disruption of the ProSAP2 Gene in a t(12;22)(q24.1;q13.3) Is Associated with the 22q13.3 Deletion Syndrome

The terminal 22q13.3 deletion syndrome is characterized by severe expressive-language delay, mild mental retardation, hypotonia, joint laxity, dolichocephaly, and minor facial dysmorphisms. We identified a child with all the features of 22q13.3 deletion syndrome. The patient's karyotype showed a de novo balanced translocation between chromosomes 12 and 22, with the breakpoint in the 22q13.3 critical region of the 22q distal deletion syndrome [46, XY, t(12;22)(q24.1;q13.3)]. FISH investigations revealed that the translocation was reciprocal, with the chromosome 22 breakpoint within the 22q subtelomeric cosmid 106G1220 and the chromosome 12q breakpoint near STS D12S317. Using Southern blot analysis and inverse PCR, we located the chromosome 12 breakpoint in an intron of the FLJ10659 gene and located the chromosome 22 breakpoint within exon 21 of the human homologue of the ProSAP2 gene. Short homologous sequences (5-bp, CTG[C/A]C) were found at the breakpoint on both derivative chromosomes. The translocation does not lead to the loss of any portion of DNA. Northern blot analysis of human tissues, using the rat ProSAP2 cDNA, showed that full-length transcripts were found only in the cerebral cortex and the cerebellum. The FLJ10659 gene is expressed in various tissues and does not show tissue-specific isoforms. The finding that ProSAP2 is included in the critical region of the 22q deletion syndrome and that our proband displays all signs and symptoms of the syndrome suggests that ProSAP2 haploinsufficiency is the cause of the 22q13.3 deletion syndrome. ProSAP2 is a good candidate for this syndrome, because it is preferentially expressed in the cerebral cortex and the cerebellum and encodes a scaffold protein involved in the postsynaptic density of excitatory synapses.

症状分類Ｂ群（音声発信困難）の１類型 発信行動習得モデルによる分析の試み

症状分類Ｂ群（音声発信困難）の１類型 発信行動習得モデルによる分析の試み