Comprehensive detection of genomic duplications and deletions in the DMD gene, by use of multiplex amplifiable probe hybridization

Duplications and deletions are known to cause a number of genetic disorders, yet technical difficulties and financial considerations mean that screening for these mutations, especially duplications, is often not performed. We have adapted multiplex amplifiable probe hybridization (MAPH) for the screening of the DMD gene, mutations in which cause Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy. MAPH involves the quantitative recovery of specifically designed probes following hybridization to immobilized genomic DNA. We have engineered probes for each of the 79 exons of the DMD gene, and we analyzed them by using a 96-capillary sequencer. We screened 24 control individuals, 102 patients, and 23 potential carriers and detected a large number of novel rearrangements, especially small, one- and two-exon duplications. A duplication of exon 2 alone was the most frequently occurring mutation identified. Our analysis indicates that duplications occur in 6% of patients with DMD. The MAPH technique as modified here is simple, quick, and accurate; furthermore, it is based on existing technology (i.e., hybridization, PCR, and electrophoresis) and should not require new equipment. Together, these features should allow easy implementation in routine diagnostic laboratories. Furthermore, the methodology should be applicable to any genetic disease, it should be easily expandable to cover >200 probes, and its characteristics should facilitate high-throughput screening.

Minimal residual disease quantification in patients with acute myeloid leukaemia and inv(16)/CBFB-MYH11 gene fusion

We have designed a real-time CBFB-MYH11 reverse transcription polymerase chain reaction (RT-PCR) assay to quantify minimal residual disease (MRD) in patients with inv(16)-positive acute myeloid leukaemia (AML). Six patients were followed for a median of 17.5 months after diagnosis during which 120 evaluable samples were analysed. The CBFB-MYH11 expression at diagnosis varied only fourfold between the six patients and was virtually identical to that observed in the CBFB-MYH11-positive cell line ME-1. For two cases, a patient-specific real-time PCR for CBFB-MYH11 quantification at genomic DNA level was designed. Similar disease levels were found at the RNA and genomic DNA level during and after treatment, indicating that CBFB-MYH11 gene expression was unaltered during treatment and that the percentage of malignant cells can be accurately quantified at the RNA level. Following successive courses of chemotherapy, the reduction of malignant cells was found to be significantly more pronounced (80-250-fold greater) in peripheral blood compared with bone marrow in five out of six cases tested. Treatment with gemtuzumab ozogamicin as sole agent at relapse did not result in a selective decrease of tumour cells in three cases analysed. We conclude that real-time PCR is a powerful method of monitoring MRD levels and quantifying the antileukaemic effect of separate (experimental) courses of chemotherapy.

Distinct subcellular expression of endogenous polycystin-2 in the plasma membrane and Golgi apparatus of MDCK cells

Polycystin-2 is a predicted integral membrane protein with non-selective cation channel activity. The protein is encoded by the PKD2 gene, which is mutated in approximately 15% of patients with autosomal dominant polycystic kidney disease (ADPKD). Polycystin-2 can interact with the transmembrane protein polycystin-1, the product of the PKD1 gene. However, endoplasmic reticulum (ER) localization was reported for (heterologously expressed) polycystin-2 in cultured cells and baso-lateral localization has been reported in renal tissues. Using two polyclonal antisera raised against polycystin-2 we demonstrated distinct expression of the endogenous protein in the Golgi apparatus and the plasma membrane of MDCK cells. In contrast, most of the heterologously expressed polycystin-2 (PC2-EGFP) remained in the ER, substantially overlapping with the staining pattern of protein-disulfide isomerase (PDI), a marker for the ER. Only in a small subset of these cells weak plasma membrane signals were observed. Membrane staining was also suggested by immunoelectron microscopy and was confirmed by subcellular fractionation on sucrose density gradients. The plasma membrane staining disappeared following extraction with a buffer containing Triton X-100, whereas signals for polycystin-1 and E-cadherin remained visible, suggesting that polycystin-2 is neither tightly bound to the Triton X-100 insoluble cytoskeleton, nor to these proteins. We conclude that endogenous polycystin-2 is transported via the Golgi apparatus to the plasma membrane and has a broader membrane localization than polycystin-1. These data suggest that polycystin-2 can move freely in certain regions of the membrane where it probably functions as a channel, activated by, or in complex with, polycystin-1.

Mutation detection for exons 2 to 10 of the polycystic kidney disease 1 (PKD1)-gene by DGGE

The PKD1-gene encodes a 14 kb transcript spanning a 50 kb genomic interval. Two-thirds of the gene is reiterated at another locus on the same chromosome. Using Long Range PCR with primers in intron 1 and exon 11, 6.8 kb PKD1 specific fragments were generated on genomic DNA. These products were used as templates for nested PCR's to screen exons 2-10 by Denaturing Gradient Gel Electrophoresis (DGGE). Upon analysis of 36 patients, a total of 11 different sequence variants were observed: A nonsense mutation in exon 2, a frameshift mutation in exon 8 and furthermore, two amino acid changes, two silent polymorphisms and five intronic variants.

Autosomal dominant polycystic kidney disease: modification of disease progression

Autosomal dominant polycystic kidney disease is a common inherited disorder, which is characterised by the formation of fluid-filled cysts in both kidneys that leads to progressive renal failure. Mutations in two genes, PKD1 and PKD2, are associated with the disorder. We describe the various factors that cause variation in disease progression between patients. These include whether the patient has a germline mutation in the PKD1 or in the PKD2 gene, and the nature of the mutation. Detection of mutations in PKD1 is complicated, but the total number identified is rising and will enable genotype-to-phenotype studies. Another factor affecting disease progression is the occurrence of somatic mutations in PKD genes. Furthermore, modifying genes might directly affect the function of polycystins by affecting the rate of somatic mutations or the rate of protein interactions, or they might affect cystogenesis itself or clinical factors associated with disease progression. Finally, environmental factors that speed up or slow down progress towards chronic renal failure have been identified in rodents.

Cerebral microbleeds in CADASIL

BACKGROUND

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a hereditary arteriopathy leading to recurrent cerebral infarcts and dementia. Intracerebral hemorrhage (ICH) has been described sporadically in patients with CADASIL, suggesting that the affected arteries in CADASIL are not bleed-prone. However, the presence of cerebral microbleeds, which often remain undetected on conventional MRI, has not been determined in CADASIL.

OBJECTIVE

To determine whether cerebral vessels in patients with CADASIL are prone to microbleeding.

METHODS

T2*-weighted gradient echo MRI, which is highly sensitive for visualizing microbleeds, was performed in patients with CADASIL and their family members (n = 63). Known risk factors for ICH were determined for all individuals. On an exploratory basis, the presence of cerebral microbleeds was correlated with demographic variables, vascular risk factors, disease progression, ischemic MR lesions, and genotype.

RESULTS

Cerebral microbleeds were present in 31% of symptomatic CADASIL mutation carriers, predominantly in the thalamus. Vascular risk factors such as hypertension did not account for the microbleeds in these patients. Factors associated with microbleeds were age (p = 0.008), Rankin disability score (p = 0.017), antiplatelet use (p = 0.025), number of lacunae on MRI (p = 0.009), and the Arg153Cys Notch3 mutation (p = 0.017). After correction for age, only the Arg153Cys mutation remained significantly associated with the presence of microbleeds.

CONCLUSION

Patients with CADASIL have an age-related increased risk of intracerebral microbleeds. This implies that they may have an increased risk for ICH, which should be taken into account in CADASIL diagnosis and patient management.

A mutation in SLC11A3 is associated with autosomal dominant hemochromatosis

Hereditary hemochromatosis (HH) is a very common disorder characterized by iron overload and multi-organ damage. Several genes involved in iron metabolism have been implicated in the pathology of HH (refs. 1-4). We report that a mutation in the gene encoding Solute Carrier family 11, member A3 (SLC11A3), also known as ferroportin, is associated with autosomal dominant hemochromatosis.

Atypical HNPCC owing to MSH6 germline mutations: analysis of a large Dutch pedigree

Hereditary non-polyposis colorectal cancer (HNPCC) is the most common genetic susceptibility syndrome for colorectal cancer. HNPCC is most frequently caused by germline mutations in the DNA mismatch repair (MMR) genes MSH2 and MLH1. Recently, mutations in another MMR gene, MSH6 (also known as GTBP), have also been shown to result in HNPCC. Preliminary data indicate that the phenotype related to MSH6 mutations may differ from the classical HNPCC caused by defects in MSH2 and MLH1. Here, we describe an extended Dutch HNPCC family not fulfilling the Amsterdam criteria II and resulting from a MSH6 mutation. Overall, the penetrance of colorectal cancer appears to be significantly decreased (p<0.001) among the MSH6 mutation carriers in this family when compared with MSH2 and MLH1 carriers (32% by the age of 80 v >80%). Endometrial cancer is a frequent manifestation among female carriers (six out of 13 malignant tumours). Transitional cell carcinoma of the urinary tract is also relatively common in both male and female carriers (10% of the carriers). Moreover, the mean age of onset of both colorectal cancer (MSH6 v MSH2/MLH1 = 55 years v 44/41 years) and endometrial carcinomas (MSH6 v MSH2/MLH1 = 55 years v 49/48 years) is delayed. As previously reported, we confirm that the pattern of microsatellite instability, in combination with immunohistochemical analysis, can predict the presence of a MSH6 germline defect. The detailed characterisation of the clinical phenotype of this kindred contributes to the establishment of genotype-phenotype correlations in HNPCC owing to mutations in specific mismatch repair genes.

New mutations in the neuronal ceroid lipofuscinosis genes

Thirty-eight mutations and seven polymorphisms have recently been reported in the genes underlying the neuronal ceroid lipofuscinoses (NCLs) including 11 new mutations described here. A total of 114 mutations and 28 polymorphisms have now been described in the five human genes identified which cause NCL. Thirty-eight mutations are recorded for CLN1/PPT; 40 for CLN2/TTP-1, 31 for CLN3, four for CLN5, one for CLN8. Two mutations have been described in animal genes (cln8/mnd, CTSD). All mutations in NCL genes are contained in the NCL Mutation Database (http://www.ucl.ac.uk/NCL).

Polycystin-1, the product of the polycystic kidney disease 1 gene, co-localizes with desmosomes in MDCK cells

Polycystin-1 is a novel protein predicted to be a large membrane-spanning glycoprotein with an extracellular N-terminus and an intracellular C-terminus, harboring several structural motifs. To study the subcellular localization, antibodies raised against various domains of polycystin-1 and against specific adhesion complex proteins were used for two-color immunofluorescence staining. In Madine Darby canine kidney (MDCK) cells, polycystin-1 was detected in the cytoplasm as well as co-localizing with desmosomes, but not with tight or adherens junctions. Using confocal laser scanning and immunoelectron microscopy we confirmed the desmosomal localization. By performing a calcium switch experiment, we demonstrated the sequential reassembly of tight junctions, subsequently adherens junctions and finally desmosomes. Polycystin-1 only stained the membrane after incorporation of desmoplakin into the desmosomes, suggesting that membrane-bound polycystin-1 may be important for cellular signaling or cell adhesion, but not for the assembly of adhesion complexes.

CBFB/MYH11 fusion in a patient with AML-M4Eo and cytogenetically normal chromosomes 16

We present a unique case of acute myeloid leukemia M4Eo (AML-M4Eo) with a CBFB/MYH11 fusion transcript and a trisomy 22, but in whom cytogenetic analyses did not disclose an inv(16). Fluorescence in situ hybridization (FISH) analysis with chromosome arm-specific painting probes as well as with the c40 and c36 cosmids also revealed no evidence for an inv(16), whereas the application of locus-specific probes confirmed the presence of a masked inv(16). The results of our comprehensive FISH investigations indicate that the events leading to this masked inv(16) were complex and concurred with deletions on both the long and short arms. The most likely explanation for the formation of the relevant CBFB/MYH11 fusion is an insertion of parts of the MYH11 into the CBFB gene, although it is also possible that it was formed by a double inversion.

[From gene to disease; from hemoglobin genes to thalassemia and sickle cell anemia]

Haemoglobinopathies are the commonest autosomal recessive diseases in men. Mutations on the alpha and beta genes clusters, located on chromosome 16 and 11 respectively, have been strongly selected in many populations by the increased chance of survival of carriers in areas infested with malaria tropica. Unfortunately many of these mutations in homozygous or compound heterozygous forms generate severe phenotypes such as sickle cell disease and beta-thalassaemia major. The population at risk for haemoglobinopathies is increasing in the industrialized areas of northern Europe. Without preventive measures a cumulative number of 1,000 severely affected patients can be expected in the Netherlands if information and carrier diagnostics are not efficiently offered at the GP level. A specialized laboratory for postnatal and prenatal diagnosis has been available in Leiden for more than 10 years now; however, couples at risk are only sporadically referred for counselling and/or prenatal diagnosis.

Recurrent digital fibroma, focal dermal hypoplasia, and limb malformations

Recurrent digital fibroma of infancy generally is considered a sporadic tumor of childhood. We describe the case of a mother with recurrent digital fibroma at a young age who gave birth to a daughter with focal dermal hypoplasia, coloboma of the iris and eyelids, anal atresia, and extensive limb malformations. When the infant was 3 months old, fibromas started to appear at the fingertips. The cases of three additional patients are described, with a similar combination of multiple digital fibromas, pigmented marks on the temporal region, and limb malformations. One of these patients has consanguineous parents. The clinical findings overlap partially with Gorlin-Goltz syndrome, which has been renamed by some authors "microphthalmia with linear skin defects" (MLS). Since the skin signs are clearly different, however-more like those of Setleis syndrome ("forceps mark" temporal dysplasia)-the patients described here seem to have a new combination of congenital malformations. Deletion of distal Xp, known to occur in some MLS patients, was not detected using cosmids in fluorescence in situ hybridization. This pattern of digital fibroma with congenital malformations seems to represent a new syndrome.

[From gene to disease; marenostrine and familial Mediterranean fever]

Familial mediterranean fever (FMF) is an autosomal recessive hereditary disorder associated with mutations in the gene on chromosome 16 encoding the protein pyrine (marenostrine). Marenostrine is thought to stimulate the production of an inactivator of a chemotactic factor (possibly C5a). The mutations result in ongoing inflammation, a hallmark of FMF. DNA diagnosis of FMF is operational in Leiden University, the Netherlands, for one year now.

[From gene to disease: introduction]

The knowledge of the molecular basis of many diseases is expanding rapidly. Consequently, molecular pathophysiology is becoming an integral part of all medical specialisms. In the evaluation of the relation between genes and diseases many aspects have to be considered: clinical manifestations of disease, gene structure, structure and function of the molecule encoded by the gene and molecular epidemiology in order to dissect the impact of molecular alterations in the population. In the series 'From gene to disease' these clinical, molecular and epidemiological aspects will be described for a number of diseases.

[From gene to disease; basic concepts]

The twenty-three pairs of chromosomes in the nuclei of human cells consist of four different components: the nucleotides adenosine, cytidine, guanosine and thymidine. Of this chromosomal DNA, 5% of the nucleotides owing to their sequence code for proteins. This involves first transcription of DNA to messenger RNA (mRNA) following which the coding part is spliced and transported from the nucleus. Translation of mRNA to amino acids takes place in the endoplasmatic reticulum. Mutations in the nucleotide sequence (deletion, insertion, duplication or substitution) lead to a change in the reading of the sequence resulting in the production of no or of different proteins (gain of function and loss of function, respectively) with possibly a disease as the consequence.

[Intracranial aneurysms and autosomal dominant polycystic kidney disease]

Three women aged 55, 47 and 40 years with polycystic kidney disease had several relatives with cystic kidneys, some of whom had died or been crippled after (presumably) a subarachnoid haemorrhage. Two of these patients had a haemorrhage from an aneurysm of a cerebral artery; after clipping of the vessel they recovered without sequelae. The third patient had magnetic resonance (MR) angiography performed, which revealed no aneurysm. The prevalence of intracranial, saccular aneurysms in patients with autosomal dominant polycystic kidney disease (ADPKD) is about 10%. ADPKD patients with questions about the risk of a subarachnoid haemorrhage should be informed about the need of blood pressure control and the possibility of screening by MR angiography. Diagnosed aneurysms can be treated neurosurgically or endovascularly. Since aneurysms develop in the course of life, screening as a rule is only necessary from the age of 20 years, and its repetition every 5 years should be considered.

Deletions spanning the neurofibromatosis type 1 gene: implications for genotype-phenotype correlations in neurofibromatosis type 1?

Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder characterized by abnormalities of tissues predominantly derived from the neural crest. Symptoms are highly variable and severity cannot be predicted, even within families. DNA of 84 unrelated patients with NF1, unselected for clinical features or severity, were screened with intragenic polymorphic repeat markers and by Southern analysis with cDNA probes. Deletions of the entire gene were detected in five patients from four unrelated families. Their phenotype resembled that of five previously reported patients with deletions, including intellectual impairment and dysmorphic features, but without an excessive number of dermal neurofibromas. This report supports the hypothesis that large deletions spanning the entire NF1 gene may lead to a specific phenotype.

The ACE insertion/deletion polymorphism has no influence on progression of renal function loss in autosomal dominant polycystic kidney disease

BACKGROUND

Autosomal dominant polycystic kidney disease (ADPKD) shows a variable clinical course that is not fully explained by the genetic heterogeneity of this disease. We looked for a possible genetic modifier, the ACE I/D polymorphism, and its influence on progression towards end-stage renal failure (ESRF).

METHODS

Forty-nine ADPKD patients who reached ESRF <40 years, and 21 PKD1 patients who reached ESRF > 60 years or were not on dialysis at 60 years of age were recruited. Clinical data were provided by questionnaires. Blood was collected for the determination of the ACE insertion/deletion (I/D) polymorphism genotype. The ACE genotype was also determined in a general, control PKD1 group (n=59).

RESULTS

Patients who reached ESRF <40 years had significantly more early onset hypertension than patients reaching ESRF >60 years (80% vs 21%; P<0.001). The ACE genotype distribution showed no differences between the groups of the rapid progressors (DD 20%, ID 56%, II 24%), the slow progressors (DD 29%, ID 52%, II 19%) and the general PKD1 control population (DD 31%, ID 47%, II 22%).

CONCLUSION

There is no relationship between progression towards ESRD and the ACE I/D polymorphism in ADPKD patients.

Rubinstein-Taybi syndrome caused by a De Novo reciprocal translocation t(2;16)(q36.3;p13.3)

Rubinstein-Taybi syndrome (RTS) is a multiple congenital anomalies and mental retardation syndrome characterized by facial abnormalities, broad thumbs, and broad big toes. We have shown previously that disruption of the human CREB-binding protein (CBP) gene, either by gross chromosomal rearrangements or by point mutations, leads to RTS. Translocations and inversions involving chromosome band 16p13.3 form the minority of CBP mutations, whereas microdeletions occur more frequently (approximately 10%). Breakpoints of six translocations and inversions in RTS patients described thus far were found clustered in a 13-kb intronic region at the 5' end of the CBP gene and could theoretically only result in proteins containing the extreme N-terminal region of CBP. In contrast, in one patient with a translocation t(2;16)(q36.3;p13.3) we show by using fiber FISH and Southern blot analysis that the chromosome 16 breakpoint lies about 100 kb downstream of this breakpoint cluster. In this patient, Western blot analysis of extracts prepared from lymphoblasts showed both a normal and an abnormal shorter protein lacking the C-terminal domain, indicating expression of both the normal and the mutant allele. The results suggest that the loss of C-terminal domains of CBP is sufficient to cause RTS. Furthermore, these data indicate the potential utility of Western blot analysis as an inexpensive and fast approach for screening RTS mutations.