Biomedical subjects

A de Klein

Publications and source records attributed to A de Klein.

At least 19 recordsLinked to original sources

PubMed2006

Congenital diaphragmatic hernia associated with duplication of 11q23-qter.

Congenital diaphragmatic hernia (CDH) is a relatively common birth defect with a high mortality. Although little is known about its etiology, there is increasing evidence for a strong genetic contribution. Both numerical and structural chromosomal abnormalities have been described in patients with CDH. Partial trisomy 11q and partial trisomy 22 associated with the common t(11;22) has been reported in several cases of CDH. It has been assumed that the diaphragmatic defect seen in these individuals was primarily due to duplication of material from chromosome 22q11. However, in this report we describe a family with a t(11;12) in which one of two brothers with partial trisomy 11q has a left sided posterolateral CDH. This is the second case of CDH in partial trisomy 11q due to an unbalanced translocation other than t(11;22). Using array-based comparative genomic hybridization and fluorescent in situ hybridization, we mapped the breakpoints in both brothers and their mother who is a balanced translocation carrier. Our results suggest that duplication of one or more genes on a approximately 19 Mb region of 11q23.3-qter predisposes to the development of CDH. These effects may be the primary cause of CDH in individuals t(11;22) or may be additive to effects from the duplication of chromosome 22 material. We also conclude that the partial trisomy 11q syndrome has a variable phenotype and that CDH should be added to the spectrum of anomalies that can be present in this syndrome.

Adult↗

PubMed2005

Early-onset parkinsonism associated with PINK1 mutations: frequency, genotypes, and phenotypes.

OBJECTIVE: To assess the prevalence, nature, and associated phenotypes of PINK1 gene mutations in a large series of patients with early-onset (<50 years) parkinsonism. METHODS: The authors studied 134 patients (116 sporadic and 18 familial; 77% Italian) and 90 Italian controls. The whole PINK1 coding region was sequenced from genomic DNA; cDNA was analyzed in selected cases. RESULTS: Homozygous pathogenic mutations were identified in 4 of 90 Italian sporadic cases, including the novel Gln456Stop mutation; single heterozygous truncating or missense mutations were found in another 4 Italian sporadic cases, including two novel mutations, Pro196Leu and Gln456Stop. Pathogenic mutations were not identified in the familial cases. Novel (Gln115Leu) and known polymorphisms were identified with similar frequency in cases and controls. In cases carrying single heterozygous mutation, cDNA analysis detected no additional mutations, and revealed a major pathogenic effect at mRNA level for the mutant C1366T/Gln456Stop allele. All patients with homozygous mutations had very early disease onset, slow progression, and excellent response to l-dopa, including, in some, symmetric onset, dystonia at onset, and sleep benefit, resembling parkin-related disease. Phenotype in patients with single heterozygous mutation was similar, but onset was later. CONCLUSIONS: PINK1 homozygous mutations are a relevant cause of disease among Italian sporadic patients with early-onset parkinsonism. The role of mutations found in single heterozygous state is difficult to interpret. Our study suggests that, at least in some patients, these mutations are disease causing, in combination with additional, still unknown factors.

Adolescent↗

PubMed2005

Congenital diaphragmatic hernia and chromosome 15q26: determination of a candidate region by use of fluorescent in situ hybridization and array-based comparative genomic hybridization.

Congenital diaphragmatic hernia (CDH) has an incidence of 1 in 3,000 births and a high mortality rate (33%-58%). Multifactorial inheritance, teratogenic agents, and genetic abnormalities have all been suggested as possible etiologic factors. To define candidate regions for CDH, we analyzed cytogenetic data collected on 200 CDH cases, of which 7% and 5% showed numerical and structural abnormalities, respectively. This study focused on the most frequent structural anomaly found: a deletion on chromosome 15q. We analyzed material from three of our patients and from four previously published patients with CDH and a 15q deletion. By using array-based comparative genomic hybridization and fluorescent in situ hybridization to determine the boundaries of the deletions and by including data from two individuals with terminal 15q deletions but without CDH, we were able to exclude a substantial portion of the telomeric region from the genetic etiology of this disorder. Moreover, one patient with CDH harbored a small interstitial deletion. Together, these findings allowed us to define a minimal deletion region of approximately 5 Mb at chromosome 15q26.1-26.2. The region contains four known genes, of which two--NR2F2 and CHD2--are particularly intriguing gene candidates for CDH.

Abnormalities, Multiple↗

PubMed2005

Large deletion at the TSC1 locus in a family with tuberous sclerosis complex.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by seizures, mental retardation and the development of hamartomas in a variety of organs and tissues. The disease is caused by mutations in either the TSC1 gene on chromosome 9q34, or the TSC2 gene on chromosome 16p13.3. Here we describe a deletion encompassing the TSC1 gene and two neighboring transcripts on chromosome 9q34 in six affected individuals from a family with TSC. To our knowledge, this is the first report of such a large deletion at the TSC1 locus and indicates that screening for similar mutations at the TSC1 locus is warranted in individuals with TSC.

Base Sequence↗

PubMed2004

New approach for the identification of folate-related pathways in human embryogenesis.

The role of natural folate intake and synthetic folic acid supplementation in the prevention of some congenital malformations is known, but on a molecular biological level poorly understood. In a first approach to identify folate-regulated pathways in human embryogenesis, tryptic digests of Epstein Barr Virus-immortalized B-lymphoblasts proteins from 6 cleft lip and/or palate patients and 2 controls were compared using matrix assisted laser desorption ionisation--time of flight (MALDI-TOF) mass spectrometry. After immortalisation, the lymphoblasts were cultured for 22 days in folate-rich, i.e. 5-methyltetrahydrofolate (5-mTHF), or folate-free medium. On day 22, 5-mTHF was added to the folate-free cultures and the profiles on day 22 and 23 were compared. After background correction for the peptide profiles of the folate-rich cultures, we found in the folate-free mediaseveral differentially expressed peptide peaks upon addition of 5-mTHF. These peptide peaks were mass annotated and matched withthe MSDB human database. The results suggest some folate-regulated protein candidates as Frizzled and the Rho GTP-ases WRCH and Chp that are known in human embryogenesis. Differential folate expressed proteins in patients and controls, however, have to be further investigated.

B-Lymphocytes↗

PubMed2001

Fusion of the homeobox gene HLXB9 and the ETV6 gene in infant acute myeloid leukemias with the t(7;12)(q36;p13).

Recently, we and others reported a recurrent t(7;12)(q36;p13) found in myeloid malignancies in children < or =18 months of age and associated with a poor prognosis. Fluorescence in situ hybridization studies mapped the 12p13 breakpoint to the first intron of ETV6 and narrowed down the region of 7q36 involved. By using the sequences made public recently by the Human Genome Project, two candidate genes in 7q36 were identified: the homeobox gene HLXB9 and c7orf3, a gene with unknown function. Reverse transcription-PCR of two cases with t(7;12), using primers for c7orf3 and ETV6, was negative. However, reverse transcription-PCR for HLXB9-ETV6 demonstrated alternative splicing; the two major bands corresponded to fusion of exon 1 of HLXB9 to exons 2 and 3, respectively, of ETV6. The reciprocal ETV6-HLXB9 transcript was not detected. It remains to be elucidated if the leukemic phenotype is attributable to the formation of the HLXB9-ETV6 fusion protein, which includes the helix-loop-helix and E26 transformation-specific DNA binding domains of ETV6 or to the disruption of the normal ETV6 protein.

Acute Disease↗

PubMed2001

Characterization of complex chromosomal abnormalities in uveal melanoma by fluorescence in situ hybridization, spectral karyotyping, and comparative genomic hybridization.

Several nonrandom recurrent chromosomal changes are observed in uveal melanoma. Some of these abnormalities, e.g., loss of chromosome 3, gain of the q arm of chromosome 8, and chromosome 6 abnormalities, are of prognostic value. Cytogenetic analysis and/or fluorescence in situ hybridization (FISH) are used to detect these changes. In some cases, however, detailed cytogenetic analysis is not possible due to the presence of complex abnormalities. To define more accurately these cytogenetic changes, we have applied comparative genomic hybridization (CGH) and/or spectral karyotyping (SKY) to two uveal melanoma cell lines and five primary uveal melanomas, with partially defined and/or complex abnormalities. SKY provided additional information on 34/39 partially defined aberrant chromosomes and revealed a new abnormality, a der(17)t(7;17)(?;q?), that had not been recognized by conventional cytogenetics. Additionally, using SKY, abnormalities involving chromosome 6 or 8 were found to be twice as common as observed with cytogenetic analysis. CGH was especially useful in assigning the abnormalities identified by SKY to specific chromosomal regions and, in addition, resulted in the detection of a small deletion of chromosome region 3q13 approximately 21. We conclude that SKY and CGH, as methods complementary to cytogenetic and FISH analysis, provide more complete information on the chromosomal abnormalities occurring in uveal melanoma.

Adult↗

PubMed2000

Targeted disruption of the cell-cycle checkpoint gene ATR leads to early embryonic lethality in mice.

Checkpoints of DNA integrity are conserved throughout evolution, as are the kinases ATM (Ataxia Telangiectasia mutated) and ATR (Ataxia- and Rad-related), which are related to phosphatidylinositol (PI) 3-kinase [1] [2] [3]. The ATM gene is not essential, but mutations lead to ataxia telangiectasia (AT), a pleiotropic disorder characterised by radiation sensitivity and cellular checkpoint defects in response to ionising radiation [4] [5] [6]. The ATR gene has not been associated with human syndromes and, structurally, is more closely related to the canonical yeast checkpoint genes rad3(Sp) and MEC1(Sc) [7] [8]. ATR has been implicated in the response to ultraviolet (UV) radiation and blocks to DNA synthesis [8] [9] [10] [11], and may phosphorylate p53 [12] [13], suggesting that ATM and ATR may have similar and, perhaps, complementary roles in cell-cycle control after DNA damage. Here, we report that targeted inactivation of ATR in mice by disruption of the kinase domain leads to early embryonic lethality before embryonic day 8.5 (E8.5). Heterozygous mice were fertile and had no aberrant phenotype, despite a lower ATR mRNA level. No increase was observed in the sensitivity of ATR(+/-) embryonic stem (ES) cells to a variety of DNA-damaging agents. Attempts to target the remaining wild-type ATR allele in heterozygous ATR(+/-) ES cells failed, supporting the idea that loss of both alleles of the ATR gene, even at the ES-cell level, is lethal. Thus, in contrast to the closely related checkpoint gene ATM, ATR has an essential function in early mammalian development.

Alleles↗

PubMed1999

Human and mouse homologs of the Schizosaccharomyces pombe rad17+ cell cycle checkpoint control gene.

The Schizosaccharomyces pombe rad17+ cell cycle checkpoint control gene is required for S-phase and G2/M arrest in response to both DNA damage and incomplete DNA replication. We isolated and characterized the putative human (RAD17Sp) and mouse (mRAD17Sp) homologs of the S. pombe Rad17 (Rad17Sp) protein. The human RAD17Sp open reading frame (ORF) encodes a protein of 681 amino acids; the mRAD17Sp ORF codes for a protein of 688 amino acids. The mRAD17Sp messenger is highly expressed in the testis as a single 3-kb mRNA species. The human RAD17Sp and mRAD17Sp proteins are 24% identical and 46% similar to the S.pombe Rad17Sp protein. Sequence homology was also noted with the Saccharomyces cerevisiae Rad24Sc (which is the structural counterpart of S.pombe Rad17Sp) and structurally related polypeptides from Caenorhabditis elegans, Arabidopsis thaliana, Pyrococcus horikoshii, and Drosophila melanogaster. The degree of conservation between the mammalian RAD17Sp proteins and those of the other species is consistent with the evolutionary distance between the species, indicating that these proteins are most likely true counterparts. In addition, homology was found between the Rad17Sp homologs and proteins identified as components of mammalian replication factor C (RF-C)/activator 1, especially in several highly conserved RF-C-like domains including a "Walker A" motif. Using FISH and analysis of a panel of rodent-human cell hybrids, the human RAD17Sp gene (HGMW-approved symbol RAD17 could be localized on human chromosome 5q13-q14, a region implicated in the etiology of small cell lung carcinoma, non-small-cell lung carcinoma, duodenal adenocarcinoma, and head and neck squamous cell carcinoma. Our results suggest that the structure and function of the checkpoint "rad" genes in the G2/M checkpoint pathway are evolutionary conserved between yeast and higher eukaryotes.

Amino Acid Sequence↗

PubMed1999

Orbital chondrosarcoma developing in a patient with Paget disease.

PURPOSE: To describe the radiologic, histopathologic, and cytogenetic features of an orbital chondrosarcoma developing in a patient with Paget disease. METHODS: A 64-year-old woman presented with rapidly progressive proptosis of her right eye. Computed tomographic scans, histopathologic examination, and cytogenetic analysis were performed. RESULTS: Computed tomographic scans disclosed osseous changes of the temporal and frontal bones, with areas of high density consistent with Paget disease. A soft-tissue tumor in the right lateral orbital wall was consistent with Paget sarcoma. On histology, a chondrosarcoma was diagnosed, which was confirmed by fluorescent in situ hybridization. CONCLUSION: This is a unique case of orbital chondrosarcoma developing in a patient with Paget disease.

Chondrosarcoma↗

PubMed1998

A human and mouse homolog of the Schizosaccharomyces pombe rad1+ cell cycle checkpoint control gene.

The Schizosaccharomyces pombe rad1+ cell cycle checkpoint control gene is required for S-phase and G2/M arrest in response to both DNA damage and incomplete DNA replication. We isolated and characterized the putative human RAD1 (hRAD1) and mouse RAD1 (mRAD1) homologs of the S. pombe Rad1 (Rad1) protein. The human RAD1 open reading frame (ORF) encodes a protein of 282 amino acids; the mRAD1 ORF codes for a protein of 280 amino acids. The human RAD1 and mRAD1 messengers are highly expressed in the testis as different mRNA species (varying from 1.0, 1.4, 1.5, to 3.0 kb). The hRAD1 and mRAD1 proteins are 30% identical and 56% similar to the S. pombe Rad1 protein. Sequence homology was also noted with the Saccharomyces cerevisiae Rad17p, the putative 3'-5' exonuclease Rec1 from Ustilago maydis, and the structurally related polypeptides from Arabidopsis thaliana and Caenorhabditis elegans. The degree of conservation between the mammalian RAD1 proteins and those of the other species is consistent with the evolutionary distance between the species, implicating that these proteins are most likely true counterparts. Together, this suggests that the structure and function of the checkpoint "rad" genes in the G2/M checkpoint pathway are evolutionarily conserved between yeasts and higher eukaryotes. The human RAD1 gene could be localized on human chromosome 5p13, a region that has been implicated in the etiology of small cell lung carcinomas, squamous cell carcinomas, adenocarcinomas, and bladder cancer.

Amino Acid Sequence↗

PubMed1998

ATM germline mutations in classical ataxia-telangiectasia patients in the Dutch population.

Germline mutations in the ATM gene are responsible for the autosomal recessive disorder ataxia-telangiectasia (A-T). In our study, we have determined the ATM mutation spectrum in 19 classical A-T patients, including some immigrant populations, as well as 12 of Dutch ethnic origin. Both the protein truncation test (PTT) and the restriction endonuclease fingerprinting (REF) method were used and compared for their detection efficiency, identifying 76% and 60% of the mutations, respectively. Most patients were found to be compound heterozygote. Seventeen mutations were distinct, of which 10 were not reported previously. Mutations are small deletions or point mutations frequently affecting splice sites. Moreover, a 16.7-kb genomic deletion of the 3' end of the gene, most likely a result of recombination between two LINE elements, was identified. The most frequently found mutation, identified in three unrelated Turkish A-T individuals, was previously described to be a Turkish A-T founder mutation. The presence of a founder mutation among relatively small ethnic population groups in Western Europe could indicate a high carrier frequency in such communities. In patients of Dutch ethnic origin, however, no significant founder effect could be identified. The observed genetic heterogeneity including the relative high percentage of splice-site mutations had no reflection on the phenotype. All patients manifested classical A-T and increased cellular radioresistant DNA synthesis.

Ataxia Telangiectasia↗

PubMed1998

Development of an interphase fluorescent in situ hybridization (FISH) test to detect t(8;21) in AML patients.

The translocation (8;21) is a chromosome abnormality associated with acute myeloid leukemia (AML). As a consequence of the translocation the AML1 (CBFA2) gene in the 21q22 region is fused to the ETO(CDR,MTG8) gene in the 8q22 region, resulting in one transcriptionally active gene on the 8q- derivative chromosome. In this report we demonstrate the use of a highly specific dual-colour FISH method for the detection of t(8;21) on interphase cells. Genomic probes able to detect the chimeric AML1/ETO gene on the 8q- derivative chromosome were assayed on both normal and leukemic bone marrow and peripheral blood samples. Cut-off values were established by independent analysis of 15 bone marrow specimens negative for the translocation. The cut-off value of positive nuclei was determined to be 2% and the cut-off value for both positive nuclei and nuclei of uncertain classification, 4%. Persistence of cells above these cut-off values was interpreted as persistence of the mutated clone. A total of 36 samples at different disease stages were tested. Interphase cytogenetics detected the translocation at the onset and relapse in the BM or the PB of 14 AML patients with t(8;21). The technique appears to be an alternative tool to both conventional cytogenetics and reverse transcription polymerase chain reaction (RT-PCR) for the monitoring of disease during patients' follow-up. By enabling the analysis of individual cells, interphase FISH is ideal for clonality studies both for clinical and experimental applications.

Acute Disease↗

PubMed1996

Disturbed interaction of p21-rac with mutated p67-phox causes chronic granulomatous disease.

Chronic granulomatous disease (CGD) is characterized by the failure of phagocytic leukocytes to generate superoxide, needed for the intracellular killing of microorganisms. This is caused by mutations in any one of the four subunits of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. In a rare, autosomal recessive form of CGD, a 67-kD cytosolic component of this enzyme (p67-phox) is missing. We here report on a patient with a mutation in the p67-phox gene that leads to expression of a nonfunctional p67-phox protein. The purified granulocytes of this patient failed to produce superoxide and contained about half of the normal amount of p67-phox. Analysis of the cDNA and genomic DNA of this patient showed that the patient is a compound heterozygote for a triplet nucleotide deletion in the p67-phox gene, predicting an in-frame deletion of lysine 58 in the p67-phox protein and a larger deletion of 11-13 kb in the other allele. Interestingly, the 58Lys deletion in p67-phox disrupts the interaction with p21-rac1, a ras-related protein involved in the activation of the NADPH oxidase. In contrast to normal neutrophils, in which p47-phox and p67-phox translocate to the plasma membrane upon cell activation, the cells of the patient did not show this translocation, indicating that an interaction between p67-phox and p21-rac1 is essential for translocation of these cytosolic proteins and activation of the NADPH oxidase. Moreover, this CGD patient represents the first case of disease caused by a disturbed binding of a ras-related protein to its target protein.

Biological Transport↗

PubMed1996

Effect of interferon-gamma, in vitro and in vivo, on mRNA levels of phagocyte oxidase components.

During the international placebo-controlled trial on the efficacy of interferon-gamma (IFN-gamma) in chronic granulomatous disease (CGD), 19 patients entered the study via our Institute. One patient stopped treatment shortly thereafter. RNA was purified from the mononuclear cells of the remaining 18 CGD patients before and during this placebo-controlled trial. The mRNA levels for the NADPH oxidase components were subsequently analyzed. Compared with the placebo-treated CGD patients, the mRNA levels for p47-phox were significantly increased in the IFN-gamma-treated CGD patients (P < 0.002). No significant changes were observed in the mRNA levels of the other oxidase components. These findings are in agreement with observations in vitro and indicate that IFN-gamma is active on the NADPH oxidase in vivo as well. However, it remains questionable whether these effects in vivo can explain the observed reduction of infections in these patients.

Gene Expression Regulation, Enzymologic↗

PubMed1995

Breakpoint heterogeneity in t(10;11) translocation in AML-M4/M5 resulting in fusion of AF10 and MLL is resolved by fluorescent in situ hybridization analysis.

Ten AML-M4/M5 patients' samples containing a t(10;11) translocation, but with different cytogenetic breakpoints on chromosome 11q (11q13-23), were studied by G- and R-banding and fluorescent in situ hybridization. Southern blotting analysis, studied in five patients, revealed a rearranged MLL gene. Reverse transcription-PCR analysis carried out in six patients showed a 5' MLL-3' AF-10 fusion transcript. Fluorescent in situ hybridization studies suggested that in 8 of 10 patients, the rearrangement/fusion transcript resulted from an inversion of a part of 11q (q13q23) translocated to 10p12. In the other two patients, it is assumed that an inversion/translocation has occurred of a part of 10p to the der(11). The results suggest that the orientation of the AF-10 gene on 10p is 5' telomeric and 3' centromeric. This is the first example of opposite-oriented genes being involved in translocation to yield fusion transcripts.

Adult↗

PubMed1995

Association between RB-1 gene alterations and factors of favourable prognosis in human breast cancer, without effect on survival.

The retinoblastoma (RB) tumour suppressor gene has been associated not only with retinoblastoma but also with several other tumours like osteosarcoma, small cell lung carcinoma and prostate and breast cancer. We have studied the incidence of RB gene alterations in 96 primary breast tumours using Southern blotting techniques. The outcome has been related with patient and tumour characteristics, oncogene amplifications, p53 mutations and prognosis. RB gene alterations were found to occur more frequently in estrogen receptor (ER)-positive than in ER-negative tumours and less frequently in tumours with oncogene amplification than in tumours without oncogene amplification of HER2/neu, c-myc or 11q13. RB gene alteration was observed in tumours both with and without a p53 gene mutation. Data on 87 patients (mean age, 59.6 years; median follow-up, 108 months) and RB gene alterations revealed a significant association between the frequency of RB gene alterations and node-negative patients (p < 0.01) or smaller (< 2 cm) tumours (p < 0.01), but no relation with age, differentiation grade or (relapse-free) survival. Patients with and without RB gene alterations showed the same relapse-free and overall survival.

Adult↗

PubMed1993

Somatostatin receptor-positive primary breast tumors: genetic, patient and tumor characteristics.

In a series of 87 primary breast tumors, somatostatin receptor (SSR) expression was detected by in vitro autoradiography in 58 tumors. In 41 tumors the SSR expression was homogeneous and in 17 it was heterogeneous. Although the tumors were not selected by the investigators upon entry in the study, examination of the tumor and patient characteristics showed that a pre-selection had taken place for small tumors. Eighty percent of the tumors were classified as stage pT1 or pT2 tumors. This small tumor size and the large size of the tumor sections used for autoradiography can explain the high incidence of somatostatin expression in our series. Forty-three of these tumors, 30 SSR-positive and 13 SSR-negative, were tested for morphological and (immuno)histochemical markers of neuroendocrine differentiation. Three SSR-positive tumors were also positive for 2 or more other markers of neuroendocrine differentiation, suggesting that neuroendocrine breast tumors and SSR-positive breast tumors are overlapping, but independent, subgroups of tumors. To test whether specific genetic alterations are associated with SSR-positive or SSR-negative breast tumors, we examined in a selected series of 47 SSR-positive and 32 SSR-negative breast tumors a number of known genetic markers by Southern blotting. Deletions or rearrangements of the retinoblastoma (RB) tumor-suppressor gene were observed in 5 SSR-positive and 5 SSR-negative tumors. In 4 SSR-positive and also in 4 SSR-negative tumors an amplification of the neu oncogene was observed. Amplifications of the int-2 oncogene were found in 2 SSR-positive and 1 SSR-negative breast tumor. In one SSR-positive tumor an amplification of the c-myc oncogene was observed and in another SSR-positive tumor a rearrangement of the L-myc oncogene was found.

Autoradiography↗