A genome-wide analysis in consanguineous families reveals new chromosomal loci in specific language impairment (SLI)

Interactions between ABC gene polymorphisms and processing speed in predicting depression severity

BACKGROUND

ABC family genes encode ATP-binding cassette proteins, which are involved in the transport of various substances and are associated with major depressive disorder (MDD); however, their clinical significance in MDD remains unclear. Therefore, this study aimed to investigate whether ABC family genes are associated with cognitive function, and the combined effects of genes and cognitive function on the severity of depression.

METHOD

Linear models or logistic regression models were used to investigate the associations of ABC family gene variants with clinical symptoms and cognitive function in 805 MDD patients (12-65 years old) and 1493 age-matched healthy controls (HCs). Seven single nucleotide polymorphisms (rs28401781, rs4148739, rs3747802, rs1109866, rs1109867, rs3731885, and rs3755047) of ABCB1 and ABCB6 were selected. The cognitive function was assessed by the Wisconsin Card Sorting Test (WCST), Tower of Hanoi Test (TOH), Trail Making Test (TMT), and Verbal Fluency Test (VF).

RESULTS

Significant differences in gene frequency and genotype frequency were observed at the rs1109866 (X2 = 8.22, p = 0.004; X2 = 9.82, p = 0.007) and rs1109867 (X2 = 7.35, p = 0.007; X2 = 9.15, p = 0.010) between MDD patients and HCs, even after correction. While rs28401781 (t = 2.78, p = 0.006) and rs4148739 (t = 3.08, p = 0.003) were associated with the TOH test. And both rs1109866 and rs1109867 interacted with TMT results to influence depression severity in MDD patients.

CONCLUSION

The results suggest that ABC family genes influence the severity of depression through cognitive functioning, providing possible evidence for genetic markers in MDD patients.

Whole exome sequencing identifies ABHD14A and MRNIP as novel candidate genes for developmental language disorder

Developmental language disorder (DLD) is a neurodevelopmental disorder involving impaired language abilities. Its genetic etiology is heterogeneous, involving rare variations in multiple susceptibility loci. However, family-based studies on gene mutations are scarce. We performed whole-exome sequencing (WES) of a first-time-described Tunisian-family with DLD. Analyses of segregation patterns with stringent filtering of the exome data identified disease-causing compound heterozygous variants. In the MRNIP gene, two variants were detected including a synonymous low-frequency variant c.345G > C and a nonsense rare variant c.112G > A predicted pathogenic. In the ABHD14A gene, four variants were identified including a rare missense variant c.689T > G and three splice-site variants c.70-8C > T, c.282-25A > T and c.282-10G > C with low-frequency MAF < 5%. Complementary analyses showed that these variants are predicted pathogenic and the missense variant Leu230Arg significantly affects the stability and structure modelling of the ABHD14A protein. Biological functions and interconnections analyses predicted the potential roles of ABHD14A and MRNIP in neuronal development pathways. These results suggest ABHD14A and MRNIP, as putative candidate genes for DLD susceptibility. Our findings reveal the involvement of novel candidate genes in the genetic etiology of DLD and explore the potential future utility of WES in the diagnosis of such complex disorders.

Genome-Wide Mapping of Consanguineous Families Confirms Previously Implicated Gene Loci and Suggests New Loci in Specific Language Impairment (SLI)

Specific language impairment (SLI) is a developmental disorder with substantial genetic contributions. A genome-wide linkage analysis and homozygosity mapping were performed in five consanguineous families from Pakistan. The highest LOD scores of 2.49 at 12p11.22-q11.21 in family PKSLI-31 and 1.92 at 6p in family PKSLI-20 were observed. Homozygosity mapping showed a loss of heterozygosity on 1q25.3-q32.2 and 2q36.3-q37.3 in PKSLI-20. A loss of heterozygosity mapped, in PKSLI-31 and PKSLI-34 flanks, NFXL1 and CNTNAP2, which are genes previously identified in SLI. Our findings report novel SLI loci and corroborate previously reported SLI loci, indicating the utility of a family-based approach.

Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD)

Speech is the most common means of communication in humans. Any defect in accurate speech production ability results in the development of speech sound disorder (SSD), a condition that can significantly impair an individual's academic performance, social interactions, and relationships with peers and adults. This study investigated the genetic basis of SSD in three Pakistani families. We performed family-based genome-wide parametric linkage analysis and homozygosity mapping in three consanguineous families with SSD from the Punjab province of Pakistan. The Test for Assessment of Articulation and Phonology in Urdu (TAAPU) was used to analyze the speech articulation data and determine the Percentage Correct Consonants (PCC) score. The PCC score defined the affected and unaffected individuals in each family. Parametric linkage analysis revealed a linkage to chromosome 5 (5q21.3-5q23.1) with a significant logarithm of the odds (LOD) score of 3.13 in a Pakistani family with specific language impairment-97 (PKSLI-97) under an autosomal recessive mode of inheritance. The other two families showed a suggestive linkage at 6p22.1, 14q12, and 16q12.1 under the recessive mode of inheritance. Interestingly, homozygosity mapping showed a loss of heterozygosity in the linkage region at 5q15-5q23.1, shared among seven affected (mostly in the younger generation) and one unaffected individual of PKSLI-97. Our analysis identified the 6p22 locus previously implicated in dyslexia, childhood apraxia of speech (CAS), and language impairment, confirming the role of KIAA0319 and DCDC2 in this locus. These findings provide statistical evidence for the genomic regions associated with articulation disorder and offer future opportunities to further the role of genes in speech production.

Receptive vocabulary, memory span, and speech articulation in Pakistani children with developmental language disorders

This study aimed to find the association of receptive vocabulary in the development of speech and language among school-going children (4-13 years) with language disorders. On the basis of non-verbal receptive vocabulary and percentage correct consonants (PCC) scores, children from public schools in Punjab, Pakistan with speech and language issues were separated into three groups; Speech sound disordered (SSD, N = 15), Language Impaired (LI) comorbid with SSD (N = 42) and typically developed (TD, N = 15). Urdu version of Peabody picture vocabulary test, fourth edition (U-PPVT-4), Digit memory test (DMT), and Test for assessment of articulation and phonology in Urdu (TAAPU) were used to assess non-verbal receptive vocabulary, Short-term memory (STM), Working memory (WM), and SSD. Correlation and regression analyses were performed to find the association of receptive vocabulary with other measures used. Receptive vocabulary, STM, WM, omission, substitution, and PCC scores were significantly different (p < 0.01) when compared among LI+SSD, SSD, and TD groups. Regression analysis showed that receptive vocabulary was significantly associated with STM and WM in the LI+SSD group. A positive correlation was found between the U-PPVT-4 standard score with STM and WM for LI+SSD and SSD groups. Our findings in Urdu-speaking children suggested that STM and WM were less developed in children with speech and language impairments. Moreover, children with speech and language deficits not only had weaker receptive vocabulary but also attention should be given to improving STM and WM that contribute to LI.

Genome-wide analysis of runs of homozygosity in Pakistani controls with no history of speech or language-related developmental phenotypes

BACKGROUND

Runs of homozygosity (ROHs) analysis of controls provide a convenient resource to minimize the association of false positive results of disease-associated ROHs and genetic variants for simple and complex disorders in individuals from the same population. Evidence for the value of ROHs to speech or language-related traits is restricted due to the absence of population-matched behaviourally defined controls and limited family-based studies.

AIM

This study aims to identify common ROHs in the Pakistani population, focussing on the total length and frequency of ROHs of variable sizes, shared ROHs, and their genomic distribution.

SUBJECTS AND METHODS

We performed homozygosity analysis (in PLINK) of 86 individuals (39 males, 47 females) with no history of speech or language-related phenotypes (controls) who had been genotyped with the Illumina Infinium QC Array-24.

RESULTS

ROHs of 1-<4 megabases (Mb) were frequent in unrelated individuals. We observed ROHs over 20 Mb among six individuals. Over 30 percent of the identified ROHs were shared among several individuals, indicating consanguinity's effect on the Pakistani population.

CONCLUSION

Our findings serve as a foundation for family-based genetic studies of consanguineous families with speech or language-related disorders to ultimately narrow the homozygosity regions of interest to identify pathogenic variants.

Working memory span and receptive vocabulary assessment in Urdu speaking children with speech sound disorder

Emerging evidence suggests that impaired speech may be related to reduced working memory (WM). The current study aimed to validate and compare the influence of articulation, short-term memory (STM), WM, and receptive vocabulary abilities of Pakistani children with speech sound disorder (SSD; N = 50) versus typically developing (TD; N = 30) children aged 7-13 years. Assessments included the Test for Assessment of Articulation and Phonology in Urdu (TAAPU), Peabody Picture Vocabulary Test-4, translated to Urdu (U-PPVT-4), and Digit Memory Test (DMT) used to determine speech articulation, receptive vocabulary, and memory abilities respectively. The percentage correct consonants (PCC) score was used to divide the SSD group further into SSD severity groups. The TD and SSD groups significantly differed in performance on all tasks (p < 0.05). Moreover, the SSD severity groups showed significant differences (p < 0.0001) in performance on different components of TAAPU (total errors and substitution errors) and DMT tasks. However, the SSD severity groups did not show significant differences in performance on the U-PPVT-4. Correlational analyses indicate statistically significant correlations of PCC with STM, WM, and receptive vocabulary. Regression analyses suggested that both WM and STM contribute to speech intelligibility in children with SSD. Our findings in Urdu-speaking children support previous results in English-speaking children suggesting the articulation skills, receptive vocabulary, STM, and WM were less developed in children with SSD than in TD children.

The Genetic and Molecular Basis of Developmental Language Disorder: A Review

Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.

Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm

BACKGROUND

Although survival rates for infants born extremely preterm (gestation < 28 weeks) have improved significantly in recent decades, neurodevelopmental impairment remains a major concern. Children born extremely preterm remain at high risk for cognitive impairment from early childhood to adulthood. However, there is limited evidence on genetic factors associated with cognitive impairment in this population.

METHODS

First, we used a latent profile analysis (LPA) approach to characterize neurocognitive function at age 10 for children born extremely preterm. Children were classified into two groups: (1) no or low cognitive impairment, and (2) moderate-to-severe cognitive impairment. Second, we performed TOPMed-based genotype imputation on samples with genotype array data (n = 528). Third, we then conducted a genome-wide association study (GWAS) for LPA-inferred cognitive impairment. Finally, computational analysis was conducted to explore potential mechanisms underlying the variant x LPA association.

RESULTS

We identified two loci reaching genome-wide significance (p value < 5e-8): TEA domain transcription factor 4 (TEAD4 at rs11829294, p value = 2.40e-8) and syntaxin 18 (STX18 at rs79453226, p value = 1.91e-8). Integrative analysis with brain expression quantitative trait loci (eQTL), chromatin conformation, and epigenomic annotations suggests tetraspanin 9 (TSPAN9) and protein arginine methyltransferase 8 (PRMT8) as potential functional genes underlying the GWAS signal at the TEAD4 locus.

CONCLUSIONS

We conducted a novel computational analysis by utilizing an LPA-inferred phenotype with genetics data for the first time. This study suggests that rs11829294 and its LD buddies have potential regulatory roles on genes that could impact neurocognitive impairment for extreme preterm born children.

Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex

Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.

Study of rare genetic variants in TM4SF20, NFXL1, CNTNAP2, and ATP2C2 in Pakistani probands and families with language impairment

Language impairment (LI) is highly heritable and aggregates in families. Genetic investigation of LI has revealed many chromosomal regions and genes of interest, though very few studies have focused on rare variant analysis in non-English speaking or non-European samples. We selected four candidate genes (TM4SF20, NFXL1, CNTNAP2 and ATP2C2) strongly suggested for specific language impairment (SLI), a subtype of LI, and investigated rare protein coding variants through Sanger sequencing of probands with LI ascertained from Pakistan. The probands and their family members completed a speech and language family history questionnaire and a vocabulary measure, the Peabody Picture Vocabulary Test-fourth edition (PPVT-4), translated to Urdu, the national language of Pakistan. Our study aimed to determine the significance of rare variants in these SLI candidate genes through segregation analysis in a novel population with a high rate of consanguinity. In total, we identified 16 rare variants (according to the rare MAF in the global population in gnomAD v2.1.1 database exomes), including eight variants with a MAF <0.5 % in the South Asian population. Most of the identified rare variants aggregated in proband's families, one rare variant (c.*9T>C in CNTNAP2) co-segregated in a small family (PKSLI-64) and another (c.2465C>T in ATP2C2) co-segregated in the proband branch (PKSLI-27). The lack of complete co-segregation of most of the identified rare variants indicates that while these genes could be involved in overall risk for LI, other genes are likely involved in LI in this population. Future investigation of these consanguineous families has the potential to expand our understanding of gene function related to language acquisition and impairment.

[Behavioral disorders in children with specific language impairment]

OBJECTIVE

To study emotional and behavioral disorders in children with specific language impairment (SLI).

MATERIAL AND METHODS

The study group included 60 children with a diagnosis of specific expressive language impairment at the age of 4-6 years. The following methods were used to assess emotional and behavioral disorders: the Strengths and Difficulties Questionnaire, the SNAP-IV scale, and the Questionnaire created by G.P. Lavrentieva and T.M. Titarenko. To objectify the severity of speech disorders, 10-point scales were used, assessing the level of comprehension of the addressed speech, the volume of the active vocabulary and the lexico-grammatical structure of speech. The control group consisted of 30 children of the same age without psycho-neurological disorders.

RESULTS AND CONCLUSION

Speech disorders in children are often combined with behavioral disorders (61.7%). Children with SLI have significant attention disorders, hyperactivity and difficulties in relationships with peers compared with the control group. A comparative study shows that combined SLI and behavioral disorders lead to a more severe course of speech impairment.

Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment

Purpose Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions These results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material https://doi.org/10.23641/asha.13203218.

Clinical Lessons From Studies of Children With Specific Language Impairment

Purpose

This clinical focus article addresses a current debate contrasting the long-standing label of “specific language impairment” (SLI) with a recent alternative, “developmental language disorders” (DLDs); the criteria for SLI yields a subset of children defined as DLD. Recent social media advocacy for DLD asserts that the two categories of children are clinically equivalent, and therefore, DLD can be used as a label for which SLI criteria would hold. Coupled with DLD advocacy is the assumption that research on SLI has not yielded clinically relevant outcomes. This clinical focus article challenges those assumptions. The clinical focus article is framed as parallels between precision medicine and evidence-based practice. The purposes of this clinical focus article are as follows: (a) revisit the legacy of research on SLI; (b) describe language development in children with SLI into adulthood; (c) address widespread but erroneous assumptions about relationships between speech impairments and language impairments, and relationships between nonverbal IQ and language impairments; (d) briefly review evidence for causal pathways; and (e) present clinical lessons from research on children with SLI.

Method

Narrative review is the method used in the study.

Conclusions

The purposes of the clinical focus article were met by reviews, commentary, and supporting arguments in each section. The conclusions are that the research and clinical category of SLI is needed for accurate and precise clinical practice, including diagnosis, prognosis, clinical goals, sequencing of tasks for success, and consideration of language disorders in the context of a broad thicket of related consequences.