General Discussion
7.3. From mono to oligogenic and back?
A common synaptic link between NRXN1 and CNTNAP2 and possibly TCF4 might result in the implication of all three encoding genes in disorders across diagnostic boundaries, severe intellectual disability at one end of the spectrum184,247,248,285,308,340,341 and neuropsychiatric disorders with no or only mild cognitive impairment at the other end.266,272-278,280-283,299-307,342,343 Biallelic defects in NRXN1 or CNTNAP2 were observed in patients with severe cognitive disorders (chapter 4).184,285,340 Heterozygous copy number variants (CNVs) and single nucleotide changes in either gene at that time had been found in patients with neuropsychiatric disorders and no or only mild cognitive impairment.266,272-283,286,299-307 The apparent influence of gene-dosage on the phenotypic severity has been also perfectly mirrored in a published family. The index patient harboring a compound heterozygous deletion and splice site mutation in NRXN1 has severe ID with epilepsy and little social interaction, while some of his family members carrying only one of the NRXN1 aberrations have schizophrenia, psychotic disorders or sub-diagnostic autistic traits.344
The observation of heterozygous variants as risk factors for low penetrant neuropsychiatric disorders and of biallelic defects in the same gene as causative for fully penetrant severe ID has not been reported for other genes so far. Only recently, a
homozygous mutation in the ANK3 gene was reported in a consanguineous family with moderate ID and severe behavioral anomalies.345 De novo, heterozygous mutations in ANK3 had previously been implicated in ASD, and polymorphisms had been implicated as susceptibility factors for psychiatric disorders. However, in this study a correlation between severity and degree of inactivation due to the mutation was discussed rather than dosage sensitivity.345
We continued to screen NRXN1 and CNTNAP2 in a larger cohort of patients with Pitt- Hopkins like syndrome with severe ID and accepted samples from external patients with severe ID and a heterozygous CNV in NRXN1 or CNTNAP2 for mutational screening of the second allele. In this group we expected to identify more patients with biallelic defects in either gene and therefore to further delineate the associated clinical phenotype (chapter 5). However, surprisingly, in none of seven patients with severe ID and a heterozygous CNTNAP2 defect and in none of four patients with severe ID and a heterozygous NRXN1 defect we could identify a mutation on the respective second allele. In most of the patients, the heterozygous defect was inherited from a healthy parent, therefore a second defect on the other allele would have been expected in order to explain the severe phenotype. Prompted by the molecular link between NRXN1 and CNTNAP2/CASPR2 fly orthologs (chapter 4) and considering a possible digenic pathomechanism, screening of the respective other gene was performed in these patients but without resulting in the detection of mutations.
Of course the second mutation in either gene might have remained undetected due to localization in a non-coding regulatory element or in a non-tested alternative isoform, or the finding of the NRXN1 or CNTNAP2 defect might have been just coincidence without pathogenic relevance to the severe phenotype of these patients. This might be true for the patient with a splice site variant in CNTNAP2 and additionally a clearly pathogenic mutation in MEF2C.346 However, the large number of such severely affected patients, further raised by recent reports at least for NRXN1,347-349 might indicate the presence of a second and maybe third contributing factor somewhere else in the genome in terms of a digenic or oligogenic cause.
While mild forms of ID are assumed to represent the lower end of normal IQ distribution and to result from the interaction of various genetic and other factors, for severe ID mainly a single genetic cause is assumed.2 This is confirmed by recent exome sequencing studies identifying de novo mutations in a large proportion of patients with unspecific severe ID.34,35,42 For a small subset of developmental disorders that are frequently associated with mild cognitive impairment, such as autism or dyslexia, polygenic effects are discussed.314,350 However, in contrast to the multifactorial “common disease, common variant” model, suggesting many genetic and non-genetic factors (epigenetic and environmental) with small
effect in individual patients,351 the picture now rather points to single events of large effect. Recent studies on common neurodevelopmental disorders like autism spectrum disorders47,116,350,352,353 or schizophrenia354,355 revealed a large number of de novo mutations. One study on autism spectrum disorders estimated a 5- to 20-fold increased risk by spontaneous coding mutations in any of a large number of genes.350 The concurrent finding of de novo defects in SHANK2 with other inherited CNVs known to be risk factors for neuropsychiatric disorders would be in line with a multiple hit model for autism spectrum disorders.46 This is also supported by the finding of a de novo frameshift mutation in FOXP1 in combination with an inherited mutation in CNTNAP2 in a patient with severe language delay, moderate ID and regression.352 Before, FOXP1 defects were found in patients with mild to moderate ID and language defects.356,357 Therefore, a combination of FOXP1 haploinsufficiency with increased CNTNAP2 expression might contribute to the more severe phenotype in this patient.352 Interestingly, for FOXP2, another member of the forkhead transcription factor family and implicated in language disorders, a molecular link to CNTNAP2 had previously been shown.281
While monogenic or single chromosomal defects might still be responsible for the majority of severe ID, there are already a few examples for disorders with digenic inheritance or a two hit model. For some cases of Bardet-Biedl syndrome, a di- or even trigenic inheritance has been reported.48 Regarding a recurrent 16p12.1 microdeletion, second hits were shown to be necessary to evoke the full, severe phenotype.45
Only recently, two patients with heterozygous NRXN1 deletions and additionally a NRXN3 or a 16p11.2 deletion, respectively, were reported.349 As defects in NRXN3 as well the common 16p11.2 deletion have already been implicated in autism spectrum disorders,342,358,359 these findings support the presence and absence of additional genetic lesions as contributory to the variable expressivity and incomplete penetrance in carriers of a NRXN1 heterozygous exonic deletion.349 By comparing the de novo rate of mutations and the burden of “second hits” in individuals with NRXN1 deletions and carriers of known recurrent “susceptibility CNVs” the authors place NRXN1 exonic deletions somewhere in the spectrum between 15q13.3 and 16p12.1 deletions.349 In some of our patients with heterozygous CNTNAP2 or NRXN1 aberrations (chapter 5) additional unknown CNVs were observed by molecular karyotyping. However, an interpretation regarding a possible contributory effect of these CNVs is currently not yet possible.
The advances in NGS during the next years will hopefully help to understand how many cases of ID can indeed be explained by monogenic causes and how many will be due to a combination of multiple de novo and/or inherited defects.