Prospective investigation of FOXP1 syndrome

Abstract

Background: Haploinsufficiency of the forkhead-box protein P1 (FOXP1) gene leads to a neurodevelopmental disorder termed FOXP1 syndrome. Previous studies in individuals carrying FOXP1 mutations and deletions have described the presence of autism spectrum disorder (ASD) traits, intellectual disability, language impairment, and psychiatric features. The goal of the present study was to comprehensively characterize the genetic and clinical spectrum of FOXP1 syndrome. This is the first study to prospectively examine the genotype-phenotype relationship in multiple individuals with FOXP1 syndrome, using a battery of standardized clinical assessments.

Methods: Genetic and clinical data was obtained and analyzed from nine children and adolescents between the ages of 5-17 with mutations in FOXP1. Phenotypic characterization included gold standard ASD testing and norm-referenced measures of cognition, adaptive behavior, language, motor, and visual-motor integration skills. In addition, psychiatric, medical, neurological, and dysmorphology examinations were completed by a multidisciplinary team of clinicians. A comprehensive review of reported cases was also performed. All missense and in-frame mutations were mapped onto the three-dimensional structure of DNA-bound FOXP1.

Results: We have identified nine de novo mutations, including three frameshift, one nonsense, one mutation in an essential splice site resulting in frameshift and insertion of a premature stop codon, three missense, and one in-frame deletion. Reviewing prior literature, we found seven instances of recurrent mutations and another 34 private mutations. The majority of pathogenic missense and in-frame mutations, including all four missense mutations in our cohort, lie in the DNA-binding domain. Through structural analyses, we show that the mutations perturb amino acids necessary for binding to the DNA or interfere with the domain swapping that mediates FOXP1 dimerization. Individuals with FOXP1 syndrome presented with delays in early motor and language milestones, language impairment (expressive language > receptive language), ASD symptoms, visual-motor integration deficits, and complex psychiatric presentations characterized by anxiety, obsessive-compulsive traits, attention deficits, and externalizing symptoms. Medical features included non-specific structural brain abnormalities and dysmorphic features, endocrine and gastrointestinal problems, sleep disturbances, and sinopulmonary infections.

Conclusions: This study identifies novel FOXP1 mutations associated with FOXP1 syndrome, identifies recurrent mutations, and demonstrates significant clustering of missense mutations in the DNA-binding domain. Clinical findings confirm the role FOXP1 plays in development across multiple domains of functioning. The genetic findings can be incorporated into clinical genetics practice to improve accurate genetic diagnosis of FOXP1 syndrome and the clinical findings can inform monitoring and treatment of individuals with FOXP1 syndrome.

Fig. 1

FOXP1 mutations. The mutations described in this study and those described in the literature are shown in the upper and lower panels, respectively. FOXP1 domains are reported as described for Q9H334–1 in Uniprot. The two nuclear localization signals (NLS) are indicated as previously reported [68]. Missense and in-frame mutations are indicated in blue, while loss-of-function (LoF) mutations are indicated in black. Recurrent mutations are indicated in bold. The position of c.975-2A > C reflects the Lys325Asnfs*12 mutation. The positions of the other splice-site mutations reflect the first residue of the exon downstream of the intron

Fig. 2

Exon skipping caused by the c.975-2A > C mutation. a RT-PCR results for exons 6–9 of FOXP1 mRNA for blood-derived RNA for individual S1 and her parents. The upper band is the PCR amplicon resulting from the mRNA with exons 7 (blue), 8 (black), and 9 (purple); the lower band results from skipping of exon 8. b Sanger sequencing results of the PCR amplicons obtained in a. The nucleotide of the splice site mutated is indicated on the pre-mRNA in red

Fig. 3

Pathogenic missense mutations in the FOXP1 DNA-binding domain. a Primary sequence and topological representation of the DNA-binding domain (as reported in PDB 2KIU). The five helices (H1-H5), the three β sheet (β1-β3) and the two wings regions (W1, W2) are shown. Residues mutated in the cohort described in this study are in red, while those affected by mutations described in literature are in blue. b Ribbon representation of the DNA binding domain of the FOXP1 monomer interacting with one double-stranded DNA molecule. The surface for the interaction with the DNA and the region involved in domain swapping are indicated by dashed lines. c Ribbon representation of the unbound FOXP1 DNA binding domain showing the missense mutations reported in the literature in blue (Additional file 2: Table S1). d Ribbon representation of the unbound FOXP1 DNA binding domain showing the missense and in-frame mutations reported in our cohort in red (Table 1)

Fig. 4

Dysmorphisms in individuals with FOXP1 mutations. Most common features include prominent forehead (evident in a, b, c, d, g, and h), bulbous nose (evident in a, c, e, f, g, and h), broad nasal bridge (evident in a, b, c, e, and h), hypertelorism (evident in a, c, and h), thick vermillion (evident in e, f, and h), and long philtrum (evident in c and g)