Common variation within the SETBP1 gene is associated with reading-related skills and patterns of functional neural activation

Genetic architecture of childhood speech disorder: a review

Severe speech disorders lead to poor literacy, reduced academic attainment and negative psychosocial outcomes. As early as the 1950s, the familial nature of speech disorders was recognized, implying a genetic basis; but the molecular genetic basis remained unknown. In 2001, investigation of a large three generational family with severe speech disorder, known as childhood apraxia of speech (CAS), revealed the first causative gene; FOXP2. A long hiatus then followed for CAS candidate genes, but in the past three years, genetic analysis of cohorts ascertained for CAS have revealed over 30 causative genes. A total of 36 pathogenic variants have been identified from 122 cases across 3 cohorts in this nascent field. All genes identified have been in coding regions to date, with no apparent benefit at this stage for WGS over WES in identifying monogenic conditions associated with CAS. Hence current findings suggest a remarkable one in three children have a genetic variant that explains their CAS, with significant genetic heterogeneity emerging. Around half of the candidate genes identified are currently supported by medium (6 genes) to strong (9 genes) evidence supporting the association between the gene and CAS. Despite genetic heterogeneity; many implicated proteins functionally converge on pathways involved in chromatin modification or transcriptional regulation, opening the door to precision diagnosis and therapies. Most of the new candidate genes for CAS are associated with previously described neurodevelopmental conditions that include intellectual disability, autism and epilepsy; broadening the phenotypic spectrum to a distinctly milder presentation defined by primary speech disorder in the setting of normal intellect. Insights into the genetic bases of CAS, a severe, rare speech disorder, are yet to translate to understanding the heritability of more common, typically milder forms of speech or language impairment such as stuttering or phonological disorder. These disorders likely follow complex inheritance with polygenic contributions in many cases, rather than the monogenic patterns that underly one-third of patients with CAS. Clinical genetic testing for should now be implemented for individuals with CAS, given its high diagnostic rate, which parallels many other neurodevelopmental disorders where this testing is already standard of care. The shared mechanisms implicated by gene discovery for CAS highlight potential new targets for future precision therapies.

Precision Medicine as a New Frontier in Speech-Language Pathology: How Applying Insights From Behavior Genomics Can Improve Outcomes in Communication Disorders

PURPOSE

Precision medicine is an emerging intervention paradigm that leverages knowledge of risk factors such as genotypes, lifestyle, and environment toward proactive and personalized interventions. Regarding genetic risk factors, examples of interventions informed by the field of medical genomics are pharmacological interventions tailored to an individual's genotype and anticipatory guidance for children whose hearing impairment is predicted to be progressive. Here, we show how principles of precision medicine and insights from behavior genomics have relevance for novel management strategies of behaviorally expressed disorders, especially disorders of spoken language.

METHOD

This tutorial presents an overview of precision medicine, medical genomics, and behavior genomics; case examples of improved outcomes; and strategic goals toward enhancing clinical practice.

RESULTS

Speech-language pathologists (SLPs) see individuals with various communication disorders due to genetic variants. Ways of using insights from behavior genomics and implementing principles of precision medicine include recognizing early signs of undiagnosed genetic disorders in an individual's communication patterns, making appropriate referrals to genetics professionals, and incorporating genetic findings into management plans. Patients benefit from a genetics diagnosis by gaining a deeper and more prognostic understanding of their condition, obtaining more precisely targeted interventions, and learning about their recurrence risks.

CONCLUSIONS

SLPs can achieve improved outcomes by expanding their purview to include genetics. To drive this new interdisciplinary framework forward, goals should include systematic training in clinical genetics for SLPs, enhanced understanding of genotype-phenotype associations, leveraging insights from animal models, optimizing interprofessional team efforts, and developing novel proactive and personalized interventions.

A systematic review and meta-analysis of imaging genetics studies of specific reading disorder

The imaging genetics of specific reading disabilities (SRD) is an emerging field that aims to characterize the disabilities' neurobiological causes, including atypical brain structure and function and distinct genetic architecture. The present review aimed to summarize current imaging genetics studies of SRD, characterize the effect sizes of reported results by calculating Cohen's d, complete a Fisher's Combined Probability Test for genes featured in multiple studies, and determine areas for future research. Results demonstrate associations between SRD risk genes and reading network brain phenotypes. The Fisher's test revealed promising results for the genes DCDC2, KIAA0319, FOXP2, SLC2A3, and ROBO1. Future research should focus on exploratory approaches to identify previously undiscovered genes. Using comprehensive neuroimaging (e.g., functional and effective connectivity) and genetic (e.g., sequencing and epigenetic) techniques, and using larger samples, diverse stages of development, and longitudinal investigations, would help researchers understand the neurobiological correlates of SRD to improve early identification.

Speech and language deficits are central to SETBP1 haploinsufficiency disorder

Expressive communication impairment is associated with haploinsufficiency of SETBP1, as reported in small case series. Heterozygous pathogenic loss-of-function (LoF) variants in SETBP1 have also been identified in independent cohorts ascertained for childhood apraxia of speech (CAS), warranting further investigation of the roles of this gene in speech development. Thirty-one participants (12 males, aged 0; 8-23; 2 years, 28 with pathogenic SETBP1 LoF variants, 3 with 18q12.3 deletions) were assessed for speech, language and literacy abilities. Broader development was examined with standardised motor, social and daily life skills assessments. Gross and fine motor deficits (94%) and intellectual impairments (68%) were common. Protracted and aberrant speech development was consistently seen, regardless of motor or intellectual ability. We expand the linguistic phenotype associated with SETBP1 LoF syndrome (SETBP1 haploinsufficiency disorder), revealing a striking speech presentation that implicates both motor (CAS, dysarthria) and language (phonological errors) systems, with CAS (80%) being the most common diagnosis. In contrast to past reports, the understanding of language was rarely better preserved than language expression (29%). Language was typically low, to moderately impaired, with commensurate expression and comprehension ability. Children were sociable with a strong desire to communicate. Minimally verbal children (32%) augmented speech with sign language, gestures or digital devices. Overall, relative to general development, spoken language and literacy were poorer than social, daily living, motor and adaptive behaviour skills. Our findings show that poor communication is a central feature of SETBP1 haploinsufficiency disorder, confirming this gene as a strong candidate for speech and language disorders.

The Mediation Role of Dynamic Multisensory Processing Using Molecular Genetic Data in Dyslexia

Although substantial heritability has been reported and candidate genes have been identified, we are far from understanding the etiopathogenetic pathways underlying developmental dyslexia (DD). Reading-related endophenotypes (EPs) have been established. Until now it was unknown whether they mediated the pathway from gene to reading (dis)ability. Thus, in a sample of 223 siblings from nuclear families with DD and 79 unrelated typical readers, we tested four EPs (i.e., rapid auditory processing, rapid automatized naming, multisensory nonspatial attention and visual motion processing) and 20 markers spanning five DD-candidate genes (i.e., DYX1C1, DCDC2, KIAA0319, ROBO1 and GRIN2B) using a multiple-predictor/multiple-mediator framework. Our results show that rapid auditory and visual motion processing are mediators in the pathway from ROBO1-rs9853895 to reading. Specifically, the T/T genotype group predicts impairments in rapid auditory and visual motion processing which, in turn, predict poorer reading skills. Our results suggest that ROBO1 is related to reading via multisensory temporal processing. These findings support the use of EPs as an effective approach to disentangling the complex pathways between candidate genes and behavior.

A Novel SETBP1 Gene Disruption by a De Novo Balanced Translocation in a Patient with Speech Impairment, Intellectual, and Behavioral Disorder

Balanced chromosomal abnormalities (BCAs) can disrupt gene function resulting in disease. To date, BCA disrupting the SET binding protein 1 (SETBP1) gene has not been reported. On the other hand, de novo heterozygous variants in the highly conserved 11-bp region in SETBP1 can result in the Schinzel–Giedion syndrome. This condition is characterized by severe intellectual disability, a characteristic face, and multiple-system anomalies. Further other types of mutations involving SETBP1 are associated with a different phenotype, mental retardation, autosomal dominant 29 (MRD29), which has mild dysmorphic features, developmental delay, and behavioral disorders. Here we report a male patient who has moderate intellectual disability, mild behavioral difficulties, and severe expressive speech impairment resulting from a de novo balanced chromosome translocation, t(12;18)(q22;q12.3). By whole genome sequencing, we determined the breakpoints at the nucleotide level. The 18q12.3 breakpoint was located between exons 2 and 3 of SETBP1. Phenotypic features of our patient are compatible with those with MRD29. This is the first reported BCA disrupting SETBP1.

From BDNF to reading: Neural activation and phonological processing as multiple mediators

The BDNF gene is a prominent promoter of neuronal development, maturation and plasticity. Its Val⁶⁶Met polymorphism affects brain morphology and function within several areas and is associated with several cognitive functions and neurodevelopmental disorder susceptibility. Recently, it has been associated with reading, reading-related traits and altered neural activation in reading-related brain regions. However, it remains unknown if the intermediate phenotypes (IPs, such as brain activation and phonological skills) mediate the pathway from gene to reading or reading disability. By conducting a serial multiple mediation model in a sample of 94 children (age 5-13), our findings revealed no direct effects of genotype on reading. Instead, we found that genotype is associated with brain activation in reading-related and more domain general regions which in turn is associated with phonological processing which is associated with reading. These findings suggest that the BDNF-Val⁶⁶Met polymorphism is related to reading via phonological processing and functional activation. These results support brain imaging data and neurocognitive traits as viable IPs for complex behaviors.

Neuroimaging genetics studies of specific reading disability and developmental language disorder: A review

Developmental disorders of spoken and written language are heterogeneous in nature with impairments observed across various linguistic, cognitive, and sensorimotor domains. These disorders are also associated with characteristic patterns of atypical neural structure and function that are observable early in development, often before formal schooling begins. Established patterns of heritability point toward genetic contributions, and molecular genetics approaches have identified genes that play a role in these disorders. Still, identified genes account for only a limited portion of phenotypic variance in complex developmental disorders, described as the problem of "missing heritability." The characterization of intermediate phenotypes at the neural level may fill gaps in our understanding of heritability patterns in complex disorders, and the emerging field of neuroimaging genetics offers a promising approach to accomplish this goal. The neuroimaging genetics approach is gaining prevalence in language- and reading-related research as it is well-suited to incorporate behavior, genetics, and neurobiology into coherent etiological models of complex developmental disorders. Here, we review research applying the neuroimaging genetics approach to the study of specific reading disability (SRD) and developmental language disorder (DLD), much of which links genes with known neurodevelopmental function to functional and structural abnormalities in the brain.

Williams Syndrome, Human Self-Domestication, and Language Evolution

Language evolution resulted from changes in our biology, behavior, and culture. One source of these changes might be human self-domestication. Williams syndrome (WS) is a clinical condition with a clearly defined genetic basis which results in a distinctive behavioral and cognitive profile, including enhanced sociability. In this paper we show evidence that the WS phenotype can be satisfactorily construed as a hyper-domesticated human phenotype, plausibly resulting from the effect of the WS hemideletion on selected candidates for domestication and neural crest (NC) function. Specifically, we show that genes involved in animal domestication and NC development and function are significantly dysregulated in the blood of subjects with WS. We also discuss the consequences of this link between domestication and WS for our current understanding of language evolution.