Femke Hannes

Recurrent reciprocal deletions and duplications of 16p13.11: The deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant

Background: Genomic disorders are often caused by non-allelic homologous recombination between segmental duplications. Chromosome 16 is especially rich in a chromosome-specific low copy repeat, termed LCR16. Methods and Results: A bacterial artificial chromosome (BAC) array comparative genome hybridisation (CGH) screen of 1027 patients with mental retardation and/or multiple congenital anomalies (MR/MCA) was performed. The BAC array CGH screen identified five patients with deletions and five with apparently reciprocal duplications of 16p13 covering 1.65 Mb, including 15 RefSeq genes. In addition, three atypical rearrangements overlapping or flanking this region were found. Fine mapping by high-resolution oligonucleotide arrays suggests that these deletions and duplications result from non-allelic homologous recombination (NAHR) between distinct LCR16 subunits with >99% sequence identity. Deletions and duplications were either de novo or inherited from unaffected parents. To determine whether these imbalances are associated with the MR/MCA phenotype or whether they might be benign variants, a population of 2014 normal controls was screened. The absence of deletions in the control population showed that 16p13.11 deletions are significantly associated with MR/MCA (p = 0.0048). Despite phenotypic variability, common features were identified: three patients with deletions presented with MR, microcephaly and epilepsy (two of these had also short stature), and two other deletion carriers ascertained prenatally presented with cleft lip and midline defects. In contrast to its previous association with autism, the duplication seems to be a common variant in the population (5/1682, 0.29%). Conclusion: These findings indicate that deletions inherited from clinically normal parents are likely to be causal for the patients’ phenotype whereas the role of duplications (de novo or inherited) in the phenotype remains uncertain. This difference in knowledge regarding the clinical relevance of the deletion and the duplication causes a paradigm shift in (cyto)genetic counselling.

Nuclear speckles and nucleoli targeting by PIP2–PDZ domain interactions

PDZ (Postsynaptic density protein, Disc large, Zona occludens) domains are protein–protein interaction modules that predominate in submembranous scaffolding proteins. Recently, we showed that the PDZ domains of syntenin‐1 also interact with phosphatidylinositol 4,5‐bisphosphate (PIP2) and that this interaction controls the recruitment of the protein to the plasma membrane. Here we evaluate the general importance of PIP2–PDZ domain interactions. We report that most PDZ proteins bind weakly to PIP2, but that syntenin‐2, the closest homolog of syntenin‐1, binds with high affinity to PIP2 via its PDZ domains. Surprisingly, these domains target syntenin‐2 to nuclear PIP2 pools, in nuclear speckles and nucleoli. Targeting to these sites is abolished by treatments known to affect these PIP2 pools. Mutational and domain‐swapping experiments indicate that high‐affinity binding to PIP2 requires both PDZ domains of syntenin‐2, but that its first PDZ domain contains the nuclear PIP2 targeting determinants. Depletion of syntenin‐2 disrupts the nuclear speckles–PIP2 pattern and affects cell survival and cell division. These findings show that PIP2–PDZ domain interactions can directly contribute to subnuclear assembly processes.

Fine-grained facial phenotype-genotype analysis in Wolf-Hirschhorn syndrome.

Wolf–Hirschhorn syndrome is caused by anomalies of the short arm of chromosome 4. About 55% of cases are due to de novo terminal deletions, 40% from unbalanced translocations and 5% from other abnormalities. The facial phenotype is characterized by hypertelorism, protruding eyes, prominent glabella, broad nasal bridge and short philtrum. We used dense surface modelling and pattern recognition techniques to delineate the milder facial phenotype of individuals with a small terminal deletion (breakpoint within 4p16.3) compared to those with a large deletion (breakpoint more proximal than 4p16.3). Further, fine-grained facial analysis of several individuals with an atypical genotype and/or phenotype suggests that multiple genes contiguously contribute to the characteristic Wolf–Hirschhorn syndrome facial phenotype.

Molecular karyotyping of patients with MCA/MR: the blurred boundary between normal and pathogenic variation

Molecular karyotyping has revealed that microdeletions/duplications in the human genome are a major cause of multiple congenital anomalies associated with mental retardation (MCA/MR). The identification of a de novo chromosomal imbalance in a patient with MCA/MR is usually considered causal for the phenotype while a chromosomal imbalance inherited from a phenotypically normal parent is considered as a benign variation and not related to the disorder. Around 40% of imbalances in patients with MCA/MR in this series is inherited from a healthy parent and the majority of these appear to be (extremely) rare variants. As some of these contain known disease-causing genes and have also been found to be de novo in MCA/MR patients, this challenges the general view that such familial variants are innocent and of no major phenotypic consequence. Rather, we argue, that human genomes can be tolerant of genomic copy number variations depending on the genetic and environmental background and that different mechanisms play a role in determining whether these chromosomal imbalances manifest themselves.

Characterizing the functional consequences of haploinsufficiency of NELF-A (WHSC2) and SLBP identifies novel cellular phenotypes in Wolf–Hirschhorn syndrome

Wolf-Hirschhorn syndrome (WHS) is a contiguous gene deletion disorder associated with the distal part of the short arm of chromosome 4 (4p16.3). Employing a unique panel of patient-derived cell lines with differing-sized 4p deletions, we provide evidence that haploinsufficiency of SLBP and/or WHSC2 (NELF-A) contributes to several novel cellular phenotypes of WHS, including delayed progression from S-phase into M-phase, reduced DNA replication in asynchronous culture and altered higher order chromatin assembly. The latter is evidenced by reduced histone-chromatin association, elevated levels of soluble chaperone-bound histone H3 and increased sensitivity to micrococcal nuclease digestion in WHS patient-derived cells. We also observed increased camptothecin-induced inhibition of DNA replication and hypersensitivity to killing. Our work provides a novel pathogenomic insight into the aetiology of WHS by describing it, for the first time, as a disorder of impaired chromatin reorganization. Delayed cell-cycle progression and impaired DNA replication likely underlie or contribute to microcephaly, pre- and postnatal growth retardation, which constitute the core clinical features of WHS.

Pathogenic significance of deletions distal to the currently described Wolf-Hirschhorn syndrome critical regions on 4p16.3.

Within recent years, numerous individuals have been identified with terminal 4p microdeletions distal to the currently described critical regions for the Wolf–Hirschhorn syndrome (WHS). Some of these individuals do not display features consistent with WHS whereas others have a clinical phenotype with some overlap to the WHS phenotype. In this review we discuss the genetic and clinical presentation of these cases in an attempt to understand the consequence of monosomy of the genes distal to the proposed critical regions and identify the distal boundary for pathogenic genes involved in components of the WHS phenotype.

Duplication of the Wolf-Hirschhorn syndrome critical region causes neurodevelopmental delay

Wolf-Hirschhorn Syndrome (WHS) is caused by deletions on chromosome 4p and is clinically well defined. Genotype-phenotype correlations of patients with WHS point to a critical locus to be responsible for the main characteristics of this disorder. Submicroscopic duplications of this region, however, are not known. Here we report a patient with an interstitial 560 kb duplication overlapping this critical locus. The present case shows that not only deletions but also duplications of the Wolf-Hirshhorn critical region cause mental retardation and multiple congenital anomalies. Interestingly, the duplication phenotype overlaps partially with the deletion phenotype. However, his facial phenotype differs from the typical WHS gestalt.

A microdeletion proximal of the critical deletion region is associated with mild Wolf-Hirschhorn syndrome.

It is generally accepted that the facial phenotype of Wolf–Hirschhorn syndrome is caused by deletions of either Wolf–Hirschhorn critical regions 1 or 2 (WHSCR 1–2). Here, we identify a 432 kb deletion located 600 kb proximal to both WHSCR1–2 in a patient with a WHS facial phenotype. Seven genes are underlying this deletion region including FAM193a, ADD1, NOP14, GRK4, MFSD10, SH3BP2, TNIP2. The clinical diagnosis of WHS facial phenotype was confirmed by 3D facial analysis using dense surface modeling. Our results suggest that the WHSCR1–2 flanking sequence contributes directly or indirectly to the severity of WHS. Sequencing the Wolf–Hirschhorn syndrome candidate 1 and 2 genes did not reveal any mutations. Long range position effects of the deletion that could influence gene expression within the WHSCR were excluded in EBV cell lines derived from patient lymphoblasts. We hypothesize that either (1) this locus harbors regulatory sequences which affect gene expression in the WHSCR1–2 in a defined temporal and spatial developmental window or (2) that this locus is additive to deletions of WHSCR1–2 increasing the phenotypic expression.

Benign and pathogenic copy number variation on the short arm of chromosome 4.

The terminal deletion of the short arm of chromosome 4 causing the Wolf-Hirschhorn syndrome is one of the first pathogenic copy number variations (CNVs) ever described. Since this first discovery, a large number of 4p CNVs causing variable phenotypes have been described. Here, we present an overview on those benign and pathogenic visible and submicroscopic 4p imbalances. Interestingly, some CNVs can be, dependent on their copy number state, both benign and pathogenic. In addition, we show how the collection of both phenotypes and genotypes of 4p terminal deletions is leading towards the genetic dissection of the Wolf-Hirschhorn syndrome.