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Biomedical subjects

D Labuda

Publications and source records attributed to D Labuda.

At least 37 records · Page 2Linked to original sources
PubMed1999

Risk of childhood leukemia associated with exposure to pesticides and with gene polymorphisms.

We conducted a population-based case-control study of childhood acute lymphoblastic leukemia (ALL) to evaluate the risk posed by reported exposure to pesticides used in and around the home. We compared 491 cases 0-9 years of age to as many controls. We also conducted a case-only study on a subsample of 123 cases to evaluate gene-environment interaction between child genotype and maternal exposure during pregnancy as well as child exposure after birth. We used the polymerase chain reaction (PCR) approach to analyze polymorphisms in CYP1A1, CYP2D6, GSTT1, and GSTM1 genes, which encode enzymes involved in carcinogen metabolism. Indoor use of some insecticides by the owners and pesticide use in the garden and on interior plants, in particular frequent prenatal use, was associated with increased risks up to severalfold in magnitude. Interaction odds ratios were increased among carriers of the CYP1A1m1 and CYP1a1m2 mutations when mother during pregnancy or the child had been exposed to certain indoor insecticides. No such effects were observed in the presence of other tested polymorphisms.

Case-Control Studies↗
PubMed1998

Distribution of the mammalian-wide interspersed repeats (MIRs) in the isochores of the human genome.

The distribution of MIRs (mammalian-wide interspersed repeats) was investigated in 164 human sequences (> or = 100 kb), which were assigned, according to their GC level, to isochore families L, H1, H2 and H3. MIR elements, whose total number in the genome was estimated to be about 3.3 x 10(5), were found to be unevenly distributed in human isochores. The majority of MIRs (55%) were found in the L isochore family. In contrast, MIR density was highest in H2, closely followed by H1, whereas densities in L and H3 were 2- and 3-fold lower than in H2, respectively. For this reason, the assessment of MIR distribution by inter-repeat PCR led to an overestimation of MIR numbers in H2 isochore and an underestimation in L isochores.

DNA↗
PubMed1998

High resolution deletion mapping reveals frequent allelic losses at the DNA mismatch repair loci hMLH1 and hMSH3 in non-small cell lung cancer.

To study the involvement of DNA mismatch repair genes in non-small cell lung cancer, matched normal and tumoral DNA samples from 31 patients were analyzed for both LOH and microsatellite instability with 34 markers at or linked to hMLH1 (3p21), hMSH2 (2p16), hMSH3 (5q11-q13), hMSH6 (2p16), hPMS1 (2q32), and hPMS2 (7p22) loci. Chromosomal regions 3p21 and 5q11-q13 were found to be hemizygously deleted in 55% and 42% of the patients, respectively. Sixty five percent of the patients deleted at hMLH1 were also deleted at hMSH3. The shortest regions of overlap for 3p21 and 5q11-q13 deletions delimited by D3S1561/D3S1612 and D5S2107/D5S624, respectively, were restricted to genetic distances of only 1 cM. Currently, the hMLH1 (3p21) and hMSH3 (5q11-q13) genes are the only known candidates located within these regions. The mutational analysis of hMLH1 and hMSH3 in hemizygously deleted patients led to the detection of 2 new polymorphisms in hMSH3. The consequence of these allelic losses remains unclear, but the lack of inactivating mutation might explain that replication error, the hallmark of mismatch repair genes inactivation in cancer cells, was quasi-absent in tumors. We suggest that hMLH1 and hMSH3 genes could be involved in lung tumorigenesis through dosage effect in cellular functions other than replication error correction.

Adaptor Proteins, Signal Transducing↗
PubMed1998

Genetic structure of the ancestral population of modern humans.

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n = 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The "age before fixation" of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n = 860 chromosomes in total). Seventeen polymorphisms older tan 100,000-200,000 years, which contributed approximately 90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000-200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period.

Alleles↗
PubMed1998

Monophyletic origin of Alu elements in primates.

To get insight into the early evolution of the primate Alu elements, we characterized sequences of these repeats from the Malagasy prosimians, lemurs (Lemuridae) and sifakas (Indriidae), as well as from galagos (Lorisidae). These sequences were compared with the oldest Alu species known from the human genome: dimeric Alu J and S and free Alu monomers. Our analysis indicates that about 60 Myr ago, before the prosimian divergence, free left and right monomers formed an Alu heterodimer connected by a 19-nucleotide-long A-rich linker. The resulting elements successfully propagated in diverging primate lineages until about approximately 20 Myr ago, conserving similar sequence features and essentially the same Alu RNA secondary structure. We suggest that until that time the same "retropositional niche", molecular machinery making possible the proliferation by retroposition, constrained the evolution of Alu elements in extant primate species. These constraints became subsequently relaxed. In the Malagasy prosimians the dimeric Alu continued to amplify after acquiring a 34- to 36-nucleotide extension of their linker segment, whereas in the galago genome the "retropositional niche" was occupied by novel short elements.

Animals↗
PubMed1998

Chromosomal assignment of loci susceptible to replication errors by radiation hybrid mapping.

Genetic instability due to a DNA mismatch repair deficiency leads to the replication error (RER) phenotype in cancer cells. Certain loci are more susceptible to replication errors than the genomic average. The mapping of such loci is important, because it could indicate chromosomal domains preferentially affected by RER. Here, we report the radiation hybrid mapping of five markers known to be highly sensitive to RER in carcinomas. They were localized in chromosomes 2q34-q36.1, 6p24.3-25.2, 7q22.1-q13.2, 16q23.2-q23.3 and Xq13.1-q21.2 near genes that could be involved in oncogenesis.

Carcinoma↗
PubMed1998

Genomic loci susceptible to replication errors in cancer cells.

Microsatellite instability due to a deficiency in DNA mismatch repair is characteristic of a replication error (RER) phenotype. This widespread genomic instability is well documented in hereditary non-polyposis colon cancer (HNPCC) as well as subsets of sporadic carcinomas. Features of the RER phenotype such as the early appearance in tumour development and better prognosis of RER+ colorectal tumours render its examination important for cancer patients. Recently, we identified four loci that were shown to be highly susceptible to RER in cancer cells. Here, we used these loci to detect the RER phenotype in sporadic carcinomas of colon, breast, lung, endometrium and ovary. Replication errors revealed by these four markers followed the same tumour specificity as observed in HNPCC patients. In particular, 24% (6/25) of colorectal, 33% (4/12) of endometrial and 17% (2/12) of ovarian cancers displayed the RER phenotype characterized by an increased allelic mobility, whereas none of the breast (n = 22) and the lung (n = 27) carcinomas were found to be unstable. Assaying RERs sensitive loci provides us with a useful diagnostic tool for HNPCC-like sporadic tumours.

Colonic Neoplasms↗
PubMed1998

Allelic losses and DNA methylation at DNA mismatch repair loci in sporadic colorectal cancer.

Normal and tumor DNA samples of 35 patients with sporadic colorectal carcinoma were analyzed for microsatellite alterations at 12 markers linked to mismatch repair loci: hMLH1, hMSH2, hMSH3, hMSH6, hPMS1 and hPMS2. Remarkably, no correlation was observed between the replication error phenotype (RER+) and allelic losses at these loci. Hemizygous deletions, seen in 6/35 (17%) informative cases at hMLH1, 4/27 (15%) at hMSH2/hMSH6 and 6/34 (18%) at hMSH3, were rarely found in RER+ tumors. Since mismatch repair protein components act in molecular complexes of defined stoichiometry we propose that hemizygous deletion of the corresponding loci may be involved in colorectal tumorigenesis through defects in cellular functions other than replication error correction. The analysis of the methylation status of the promoter region of hMLH1 revealed that methylation might be an important mechanism of this locus inactivation in RER+ sporadic colorectal cancer.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Nuclear DNA diversity in worldwide distributed human populations.

Nucleotide variation was examined in an 8 kb intronic DNA bordering exon 44 of the human dystrophin gene on Xp21. Thirty-six polymorphisms (substitutions, small insertions/deletions and one (T)n microsatellite) were found using SSCP/heteroduplex analysis of DNA samples from mixed Europeans, Papua New Guineans as well as from six African, three Asian and two Amerindian populations. In this way the European bias in the nuclear polymorphism ascertainment has been avoided. In a maximum likelihood tree constructed from the frequency data, Africans clustered separately from the non-African populations. Fifteen polymorphisms were shared among most of the populations compared, whereas 13 sites were found to be endemic to Africans and four to non-Africans. The common sites contributed most to the average heterozygosity (Hn=0.101%+/-0.023), whereas the endemic ones, being rare, had little effect on this estimate. The F(ST) values were lower for Africans (0.072) than for non-Africans (0.158), suggesting a higher level of gene exchange within Africa, corroborating the observation of a greater number of segregating sites on this continent than elsewhere. The data suggest a recent common origin of the African and non-African populations, where a greater geographical isolation of the latter resulted in a smaller number of newly acquired polymorphisms.

Cell Nucleus↗
PubMed1996

Overall informativity, OI, in DNA polymorphisms revealed by inter-Alu PCR: detection of genomic rearrangements.

We studied two systems of multilocus markers revealed by PCR using primers directing amplification between Alu repeats in a tail-to-tail orientation. Genomic polymorphisms were detected as the presence or absence of the electrophoretic bands representing DNA fragments of a given length. A total of 104 such fragments segregating as Mendelian markers in a panel of eight CEPH families were analyzed by two-point linkage analysis. Fifty-one of these fragments were localized with respect to CEPH markers; they represented 33 loci, 7 of which were multiallelic. Locus-specific oligonucleotides were developed and used as hybridization probes to identify the mapped loci within a complex pattern of inter-Alu PCR products. A great proportion of inter-Alu PCR polymorphisms represented length variants within amplified DNA segments, while others were presumably due to mutations within the priming sites. To describe the expected number of informative loci per typing experiment we introduced a parameter called overall informativity (OI), which provides a single measure of the multiplex ratio and the informativity of markers contributing to a multilocus system (OI of a single locus is equivalent to its heterozygosity and cannot exceed 0.5 for a biallelic codominant marker). High OI values (5.8 and 11.5) of the two presented systems of inter-Alu PCR markers of random chromosomal distribution render them suitable for mapping genomic rearrangements such as genomic deletions in tumoral tissues. This was illustrated by the detection of loss of heterozygosity in the 9q22-qter region in sporadic colon cancer.

Animals↗
PubMed1996

Detection of a mutator phenotype in cancer cells by inter-Alu polymerase chain reaction.

A mutator phenotype due to a DNA mismatch repair deficiency is usually detected by typing a number of microsatellite markets. Here, eight hereditary nonpolyposis colon cancer patients with microsatellite instability were investigated by inter-Alu PCR, known to amplify DNA segments that may represent preferential targets of replication errors. Among 40-60 bands revealed in a single PCR experiment, more than 20% were found altered in tumoral DNA samples compared to matched normal samples from the same patient. Shifts and changes in signal intensity accounted for most of the alterations, whereas gains or losses of bands were rare. Certain bands were affected only in a single patient, whereas the instabilities in others were common. These results suggest that some genomic regions are more susceptible than others to the expression of a mutator phenotype. Four such bands altered in at least five patients were characterized further and shown to be unstable because of contractions of the Alu poly(A) tails. Interestingly, none of the bands representing loci shown previously to be polymorphic in the population displayed instability in the tumoral samples. Inter-Alu PCR appears to be a robust, cost-effective, and sensitive technique for revealing the mutator phenotype in cancer cells.

Base Sequence↗
PubMed1996

Mosaic evolution of rodent B1 elements.

We have determined sequences of PCR-amplified B1 elements from hamster and rat (Myomorpha), chipmunk (Sciuromorpha), and guinea pig (Caviomorpha). Between three and six B1 subfamilies were found in these species. In the phylogenetic analysis B1 sequences of hamster, mouse, and rat clustered separately from those of chipmunk and those of guinea pig. This is consistent with an independent evolution of B1 elements in separate rodent lineages. We exclude the possibility of convergent mutations to explain certain diagnostic characters within the modern B1 quasi-dimers and view these elements as mosaic structures assembling preexisting mutations. Furthermore, the presence of Alu-like structural motifs supports the hypothesis of the monophyletic origin of Alu and B1 repeats, i.e., from a common 7SL RNA-derived retroposing monomeric element.

Animals↗
PubMed1996

Lipid processing and lipoprotein synthesis by the developing human fetal colon.

Despite significant progress in the elucidation of the ontogeny of gastrointestinal function, little attention has been given to colonic lipid processing during development. The major purpose of this study was to explore the intracellular phase of fat absorption, lipid synthesis, and secretion in the human fetal colon compared with the jejunum originating from the same fetuses. The synthesis of lipids and major apolipoproteins was examined using cultured fetal colonic explants incubated with [14C]oleic acid and [36S]methionine, respectively. Fetal colonic explants demonstrated substantial ability to incorporate [14C]oleic acid (dpm/mg protein) into phospholipids (48,743 +/- 4,783), triglycerides (25,687 +/- 2,469), and cholesteryl esters (6,751 +/- 1,227). The total amount of radiolabeled lipids was much higher within the tissue (87,472 +/- 9,142) than in the medium (51,916 +/- 4,970), indicating a limited capacity of the fetal colon to export newly synthesized lipids. The limited colonic lipid secretory process was even more evident when compared with homologous fetal jejunal de novo synthesized lipids in tissue (133,975 +/- 13,836) and medium (279,858 +/- 1,610), respectively. Similar to the jejunum, the colon was able to elaborate all the phospholipid classes, with phosphatidylcholine accounting for > 70% of tissue phospholipids. However, their individual levels were present in lesser amounts in the colon (P < 0.001). Colonic explants elaborated most of the major lipoprotein classes but were less efficient than jejunal explants in exporting chylomicrons (33-fold), very low density lipoprotein (1.5-fold), and high-density lipoprotein (9-fold) into the medium. Apolipoprotein (apo) B synthesis and apo B mRNA editing were comparable in colonic and jejunal explants; thus they are not responsible for the defective lipoprotein secretion in the fetal large bowel. These results establish for the first time te capability of the human fetal colon to form, but not to efficiently transport, lipids, lipoproteins, and apoproteins.

Apolipoproteins B↗