Zeynep Tümer

Similar Splice-Site Mutations of the ATP7A Gene Lead to Different Phenotypes: Classical Menkes Disease or Occipital Horn Syndrome

More than 150 point mutations have now been identified in the ATP7A gene. Most of these mutations lead to the classic form of Menkes disease (MD), and a few lead to the milder occipital horn syndrome (OHS). To get a better understanding of molecular changes leading to classic MD and OHS, we took advantage of the unique finding of three patients with similar mutations but different phenotypes. Although all three patients had mutations located in the splice-donor site of intron 6, only two of the patients had the MD phenotype; the third had the OHS phenotype. Fibroblast cultures from the three patients were analyzed by reverse transcriptase (RT)-PCR to try to find an explanation of the different phenotypes. In all three patients, exon 6 was deleted in the majority of the ATP7A transcripts. However, by RT-PCR amplification with an exon 6-specific primer, we were able to amplify exon 6-containing mRNA products from all three patients, even though they were in low abundance. Sequencing of these products indicated that only the patient with OHS had correctly spliced exon 6-containing transcripts. We used two different methods of quantitative RT-PCR analysis and found that the level of correctly spliced mRNA in this patient was 2%-5% of the level found in unaffected individuals. These findings indicate that the presence of barely detectable amounts of correctly spliced ATP7A transcript is sufficient to permit the development of the milder OHS phenotype, as opposed to classic MD.

Pierre Robin sequence may be caused by dysregulation of SOX9 and KCNJ2

Background: The Pierre Robin sequence (PRS), consisting of cleft palate, micrognathia and glossoptosis, can be seen as part of the phenotype in other Mendelian syndromes—for instance, campomelic dysplasia (CD) which is caused by SOX9 mutations—but the aetiology of non-syndromic PRS has not yet been unravelled. Objective: To gain more insight into the aetiology of PRS by studying patients with PRS using genetic and cytogenetic methods. Methods: 10 unrelated patients with PRS were investigated by chromosome analyses and bacterial artificial chromosome arrays. A balanced translocation was found in one patient, and the breakpoints were mapped with fluorescence in situ hybridisation and Southern blot analysis. All patients were screened for SOX9 and KCNJ2 mutations, and in five of the patients expression analysis of SOX9 and KCNJ2 was carried out by quantitative real-time PCR. Results: An abnormal balanced karyotype 46,XX, t(2;17)(q23.3;q24.3) was identified in one patient with PRS and the 17q breakpoint was mapped to 1.13 Mb upstream of the transcription factor SOX9 and 800 kb downstream of the gene KCNJ2. Furthermore, a significantly reduced SOX9 and KCNJ2 mRNA expression was observed in patients with PRS. Conclusion: Our findings suggest that non-syndromic PRS may be caused by both SOX9 and KCNJ2 dysregulation.

Mapping of the Menkes locus to Xq13.3 distal to the X-inactivation center by an intrachromosomal insertion of the segment Xq13.3-q21.2

SummaryDuring a systematic chromosomal survey of 167 unrelated boys with the X-linked recessive Menkes disease (MIM 309400), a unique rearrangement of the X chromosome was detected, involving an insertion of the long arm segment Xq13.3-q21.2 into the short arm at band Xp11.4, giving the karyotype 46,XY,ins(X) (p11.4q13.3q21.2). The same rearranged X chromosome was present de novo in the subjects phenotypically normal mother, where it was preferentially inactivated. The restriction fragment length polymorphism and methylation patterns at DXS255 indicated that the rearrangement originated from the maternal grandfather. Together with a previously described X;autosomal translocation in a female Menkes patient, the present finding supports the localization of the Menkes locus (MNK) to Xq13, with a suggested fine mapping to sub-band Xq13.3. This localization is compatible with linkage data in both man and mouse. The chromosomal bend associated with the X-inactivation center (XIC) was present on the proximal long arm of the rearranged X chromosome, in line with a location of XIC proximal to MNK. Combined data suggest the following order: Xcen-XIST(XIC), DXS128-DXS171, DXS56-MNK-PGK1-Xqter.

First trimester prenatal diagnosis of Menkes disease by DNA analysis.

Menkes disease is an X linked recessive disorder of copper metabolism characterised by neurological symptoms and connective tissue manifestations. The defective gene in Menkes disease has recently been isolated and the gene product is predicted to be a copper transporting ATPase. The diagnosis of Menkes disease has hitherto been performed by biochemical analysis, based on intracellular accumulation of copper. Cloning the gene opened up the possibility of establishing precise and reliable carrier and prenatal diagnosis by defining the molecular defect. In this report we describe the partial deletion of the Menkes gene in a patient who had inherited the mutation from his phenotypically normal mother. This information enabled us to perform prenatal diagnosis by direct mutation analysis of the mothers sixth pregnancy and we detected the same deletion, indicating that the male fetus was affected. This first prenatal diagnosis of Menkes disease by direct mutation analysis shows some advantages of DNA analysis compared to biochemical diagnosis.

Assignment of the human gene for pregnancy-associated plasma protein A (PAPPA) to 9q33.1 by fluorescence in situ hybridization to mitotic and meiotic chromosomes

Low levels of pregnancy-associated plasma protein A (PAPPA) during the first trimester has been suggested as a biochemical indicator of pregnancies with aneuploid fetuses. Furthermore, the complete absence of PAPPA in pregnancies associated with Cornelia de Lange syndrome (CL) has suggested a causal connection between PAPPA and the development of CL. We have assigned the locus for PAPPA to chromosome region 9q33.1 on mitotic and meiotic chromosomes by fluorescence in situ hybridization, using a 3.7-kb partial PAPPA cDNA probe.

X-linked recessive Menkes disease: identification of partial gene deletions in affected males

Poulsen L, Horn N, Heilstrup H, Lund C, Tümer Z, Møller LB. X‐linked recessive Menkes disease: identification of partial gene deletions in affected males. 
Clin Genet 2002: 62: 449–457.

Early onset, non-progressive, mild cerebellar ataxia co-segregating with a familial balanced translocation t(8;20)(p22;q13)

Hereditary ataxia is a clinically and genetically heterogenous group of disorders. Most are progressive and associated with other neurological abnormalities. Early onset, non-progressive cerebellar ataxia (OMIM #117360) has been described as a dominantly inherited disorder associated with isolated vermal atrophy1–3 or generalised atrophy of the cerebellum.4,5 This is a rare entity compared with autosomal recessive early onset cerebellar ataxia with retained tendon reflexes (OMIM #212895).6 Various disease genes have been identified using rare disease associated balanced chromosomal rearrangements (DBCRs), for example, translocations or inversions that truncate, delete, or otherwise inactivate genes.7 DBCRs may occur in at least 1% of patients with autosomal dominant disorders caused by haploinsufficiency, and in many girls affected by X linked recessive disorders. During a systematic search for apparently balanced chromosomal rearrangements associated with abnormal phenotypes,7 we identified a four generation family in which a variable neurological phenotype including an early onset, non-progressive, and mild cerebellar ataxia segregates together with a balanced reciprocal translocation. ### Family history The study was approved by the local ethics committee (no. 1992–2489). The family consists of four generations as shown in fig 1. All family members, except II:2, were personally interviewed and underwent neurological examination by one of us (BS). The affected members in generations III, IV, and V have developed a phenotype of clumsiness starting in early childhood (1–7 years), including gait abnormalities with lurching and frequent falling, which increased upon physical activity. Objective findings included ataxia, dysmetria on finger to nose and/or heel to shin test, tremor, nystagmus, and retained reflexes in the lower limbs. Neurological symptoms and the phenotype of the affected members are presented in table 1. MRI of two of the patients (III:2 and III:4) performed at 49 and 43 years of age, respectively, gave inconclusive results. Anticipation was not observed …

Expression Profiling in Menkes Disease

The main focus in genomic research is starting to shift from structural genomics to functional genomics and proteomics, which deal with the function of genes and their products. Each cell expresses different sets of genes at different levels as the result of different situations such as development, environmental influences, and disease. Each physiological and pathological situation can thus be characterized by a specific set of gene transcripts (transcriptome) and protein products (proteome). To identify the transcriptomes in Menkes disease, we have employed differential display (DD) of mRNA, a technique which displays mRNA species expressed by a cell population and that is used to detect differences in gene expression between different cell types or under altered conditions (1). The primary defect in the Menkes disease is in the cellular export protein ATP7A, and several copper enzymes are affected secondarily (2). Alhough we can predict the role of some of the copper enzymes in the development of the multisystemic Menkes disease, it is likely that several other enzymes/proteins also contribute to disease progression.