Determination of spontaneous loss of heterozygosity mutations in Aprt heterozygous mice.

A mouse model was generated to investigate loss of heterozygosity (LOH) events in somatic cells. The adenine phosphoribosyltransferase ( Aprt ) gene was disrupted in embryonic stem cells using a conventional gene targeting approach and subsequently Aprt hetero-zygous and homozygous mice were derived. Aprt homozygous deficient animals were viable though the mendelian inheritance pattern was skewed. On average these mice died at 6 months of age from severe renal failure. In T-lymphocytes of Aprt heterozygous mice the mean spontaneous mutant frequency at the Aprt locus was 8.7 x 10(-6) while the frequency was 0.8 x 10(-6) at the hypoxanthine phosphoribosyltransferase locus. In order to determine whether LOH events contribute to the high spontaneous mutant frequency at the Aprt locus, 140 Aprt mutant T-lymphocyte clones were expanded and analysed by allele-specific PCR. In 97 (69%) of these clones the wild-type allele had been lost. Nine of the mutant clones were characterized in more detail using dual-coloured fluorescence in situ hybridization analysis. Five out of six of the mutant clones which arose from an LOH event, based on the PCR assay, contained a duplication of the targeted allele. Therefore, mitotic recombination or chromosome loss followed by duplication of the remaining homologue appears to be the predominant mechanism for the in vivo generation of Aprt mutant T-lymphocytes.     

Hereditary conditions in which the loss of heterozygosity may be important.

Somatic mutations are a common event in multicellular organisms and, therefore, have a significant impact on health. They can lead to either heterozygosity or homozygosity. Since the multistep concept of carcinogenesis presupposes that mutations/deletions of several genes are acquired, the identification and location of the critical genes involved in this sequence is attempted either by the observation of cytogenetic or molecular abnormalities in tumorous tissue or by linkage analysis, or both. The retinoblastoma paradigm of loss of heterozygosity with respect to the loss of the only wild-type allele can be applied to familial neoplasias occurring in all organs as they are summarized in this review. The development of homozygosity in non-malignant tissue has not been extensively investigated. However, its study has contributed to the identification of new genetic phenomena such as parental unidisomy and genomic imprinting.     

Investigating loss of heterozygosity in a SCRaMbLEd yeast genome

Science China Life Sciences -     

Cytological evidence for assortment mitosis leading to loss of heterozygosity in rice.

In the root meristem cells of the rice line AMR, which causes loss of heterozygosity in its hybrids, both normal and assortment mitoses were observed. During normal mitosis, chromosomes did not form homologous pairs at metaphase; all chromosomes lined up at the equatorial plate and 2 chromatids of each chromosome disjoined at the centromere and moved toward opposite poles. During assortment mitosis, varying numbers of paired homologues were observed at mitotic metaphase. Two groups of 12 chromosomes separated and moved towards the opposite poles of daughter cells with few chromosomes having their chromatids separated at anaphase. These observations support the proposed mechanism that is responsible for early genotype fixation in rice hybrids involving AMR.     

Visualizing loss of heterozygosity in living mouse cells and tissues

Chronic exposure to oxidative stress especially to highly reactive hydroxyl radicals (HO*) could damage biomolecules, particularly DNA, that in turn would accelerate onset of degenerative diseases. In the present study a few standard phytochemicals (vitamin C, gallic acid, catechin, apigenin, naringenin and naringin) and plant extracts (Hippophae rhamnoides kernel (HRK), Syzygium cumini kernel (SCK) and Punica granatum pericarp (PGP)) were evaluated for their potential to protect/damage DNA in Fenton's system using in vitro models. The results indicated a significant DNA protective effect for naringin and PGP whereas other phytochemicals/extracts showed DNA damaging effect similar to or more than that of control value. The phytochemicals/extracts were also evaluated for their antioxidant and iron chelation properties. In general, the phytochemicals/extracts with high antioxidant activity but without iron chelation capacity failed to protect DNA in Fenton's system, suggesting that iron chelation was an essential requirement for the phytochemicals studied here to retard HO* generation by Fenton's reaction. This was demonstrated by the high iron chelation capacity of naringin and PGP (83.67% and 68.67% respectively) and their DNA protective effect. Commonly consumed phytochemicals such as vitamin C and gallic acid with their high reducing power and at higher physiological concentration, could regenerate free iron for Fenton's reaction leading to DNA damage as shown here.     

Development of a STS marker assay for detecting loss of heterozygosity in rice hybrids.

The RAPD (random amplified polymorphic DNA) markers OPE15750 and OPE15300 were affected by loss of heterozygosity (LOH) in rice hybrids AMR x 'M202' and AMR x 'L202'. The markers were mapped to the same locus at or near the centromere of rice chromosome 2. The two RAPD products were cloned, sequenced, and found to have lengths of 734 bp and 297 bp, respectively. The 297-bp sequence shares a 98% homology with one end of the 734-bp sequence, accounting for the cross-hybridization previously observed between the two clones. Based on the DNA sequence of the 734-bp fragment, a pair of STS (sequence-tagged site) primers was designed and tested. Rice plants homozygous for either OPE15734 or OPE15297 all produced PCR fragments of the same length, 482 bp. However, the two PCR products were discernible by digestion with the restriction enzyme XbaI prior to gel electrophoresis. The STS product from plants homozygous for OPE15734 was cut into two fragments of 239 and 240 bp, which appeared as one single band in an agarose gel; whereas the STS product from plants homozygous for OPE15297 was not cut by XbaI and was characterized by a 482-bp band in the agarose gel. These STS primers were tested in rice hybrids and F2 progenies derived from the hybrids of AMR x 'M202' and AMR x 'L202'. Homozygosity for OPE15297 was confirmed for all F2 panicle rows derived from AMR x 'M202'. In contrast, F2 panicle rows of AMR x 'L202' exhibited two different segregation patterns (genotypes), i.e., either uniformly homozygous for the 240-bp marker (OPE15734/OPE15734) or segregating for the 482- and 240-bp markers (OPE15734/OPE15297). This STS-marker system provides a robust assay for detecting the occurrence of LOH in rice hybrid progenies.     

Mitotic recombination is responsible for the loss of heterozygosity in cultured murine cell lines.

Heterozygous mammalian cell lines normally express both parental alleles at most autosomal loci. However, mutants can be isolated that fail to express one of the alleles. Using a murine pre-B cell line that is heterozygous for several loci on chromosome 12, including one encoding the cell surface antigen Ly-18, we found that one of the two Ly-18 antigenic forms was lost at a rate of 1.5 x 10(-5) per cell per generation. Molecular analysis revealed that a genetic marker distal to Ly-18 became homozygous. Analysis of the genotype of the mutants at the rDNA cluster, located close to the centromere, strongly suggests that the mutants arose by mitotic recombination within this multicopy locus.     

A genetic screen for increased loss of heterozygosity in Saccharomyces cerevisiae

Loss of heterozygosity (LOH) can be a driving force in the evolution of mitotic/somatic diploid cells, and cellular changes that increase the rate of LOH have been proposed to facilitate this process. In the yeast Saccharomyces cerevisiae, spontaneous LOH occurs by a number of mechanisms including chromosome loss and reciprocal and nonreciprocal recombination. We performed a screen in diploid yeast to identify mutants with increased rates of LOH using the collection of homozygous deletion alleles of nonessential genes. Increased LOH was quantified at three loci (MET15, SAM2, and MAT) on three different chromosomes, and the LOH events were analyzed as to whether they were reciprocal or nonreciprocal in nature. Nonreciprocal LOH was further characterized as chromosome loss or truncation, a local mutational event (gene conversion or point mutation), or break-induced replication (BIR). The 61 mutants identified could be divided into several groups, including ones that had locus-specific effects. Mutations in genes involved in DNA replication and chromatin assembly led to LOH predominantly via reciprocal recombination. In contrast, nonreciprocal LOH events with increased chromosome loss largely resulted from mutations in genes implicated in kinetochore function, sister chromatid cohesion, or relatively late steps of DNA recombination. Mutants of genes normally involved in early steps of DNA damage repair and signaling produced nonreciprocal LOH without an increased proportion of chromosome loss. Altogether, this study defines a genetic landscape for the basis of increased LOH and the processes by which it occurs.     

EXT-mutation analysis and loss of heterozygosity in sporadic and hereditary osteochondromas and secondary chondrosarcomas.

Osteochondromas occur as sporadic solitary lesions or as multiple lesions, characterizing the hereditary multiple exostoses syndrome (EXT). Approximately 15% of all chondrosarcomas arise within the cartilaginous cap of an osteochondroma. EXT is genetically heterogeneous, and two genes, EXT1 and EXT2, located on 8q24 and 11p11-p12, respectively, have been cloned. It is still unclear whether osteochondroma is a developmental disorder or a true neoplasm. Furthermore, it is unclear whether inactivation of both alleles of an EXT gene, according to the tumor-suppressor model, is required for osteochondroma development, or whether a single EXT germline mutation acts in a dominant negative way. We therefore studied loss of heterozygosity and DNA ploidy in eight sporadic and six hereditary osteochondromas. EXT1- and EXT2-mutation analysis was performed in a total of 34 sporadic and hereditary osteochondromas and secondary peripheral chondrosarcomas. We demonstrated osteochondroma to be a true neoplasm, since aneuploidy was found in 4 of 10 osteochondromas. Furthermore, LOH was almost exclusively found at the EXT1 locus in 5 of 14 osteochondromas. Four novel constitutional cDNA alterations were detected in exon 1 of EXT1. Two patients with multiple osteochondromas demonstrated a germline mutation combined with loss of the remaining wild-type allele in three osteochondromas, indicating that, in cartilaginous cells of the growth plate, inactivation of both copies of the EXT1 gene is required for osteochondroma formation in hereditary cases. In contrast, no somatic EXT1 cDNA alterations were found in sporadic osteochondromas. No mutations were found in the EXT2 gene.     

High-resolution detection of loss of heterozygosity of dinucleotide microsatellite markers

Dinucleotide microsatellite markers are frequently investigated to study inheritance, genetic stability, and allele frequency distribution in a wide variety of genetic disorders. Previous studies have encountered significant problems regarding resolution and detection of dinucleotide, microsatellites. In this study, a useful method to investigate loss of heterozygosity (LOH) of dinucleotide microsatellite markers is described that involves the use of nondenaturing (Spreadex) submerged gel electrophoresis and SYBR Green I nucleic acid staining. This method omits the gel casting step and the use of hazardous radioactive materials frequently used in many microsatellite studies that employ polyacrylamide gel nucleic acid denaturation analysis. Using this method, 62 patients' paired tumor and normal samples were investigated to detect allele deletions in a region of chromosome 7q31.1, which is believed to harbor a tumor suppressor gene. Interpretable results were obtained in all cases. These results were compared to those attained using ABI Prism Genetic Analyzer 310 and Gene-Scan. There were no discrepancies in results obtained between the two assays. The Spreadex system is cheap, does not require larger equipment costs, and may prove to be a useful system for high-throughput investigation of microsatellites. It may have diagnostic significance and also prove useful if applied to population-based genomic screening and linkage analysis.     

Chromosome missegregation causes colon cancer by APC loss of heterozygosity

A longstanding hypothesis in the field of cancer biology is that aneuploidy causes cancer by promoting loss of chromosomes that contain tumor suppressor genes. By crossing aneuploidy-prone Bub1 hypomorphic mice onto a heterozygous null background for p53, we provided conclusive evidence for this idea.1 Surprisingly, the tumors that developed in this model had not just lost the chromosome 11 copy harboring wildtype p53, but had also gained an extra copy of chromosome 11 bearing the p53 null allele. Here we report that a similar chromosome-reshuffling blueprint drives colonic tumorigenesis in Bub1 hypomorphic mice that are heterozygous for ApcMin, but now involving chromosome 18. These extended studies highlight that in order for whole chromosome instability to drive tumorigenesis, it needs to establish tumor suppressor gene loss of heterozygosity while retaining two copies of the other genes on the chromosome. Additional restrictions seem to apply to whole chromosome instability as a cancer causing mechanism, which will be discussed in this paper.     

Differential loss of heterozygosity in familial, sporadic, and uremic hyperparathyroidism

Various genetic loci harboring oncogenes, tumor suppressor genes, and genes for calcium receptors have been implicated in the development of parathyroid tumors. We have carried out loss of heterozygosity (LOH) studies in chromosomes 1p, 1q, 3q, 6q, 11q, 13q, 15q, and X in a total of 89 benign parathyroid tumors. Of these, 28 were sporadic parathyroid adenomas from patients with no family history of the disease, 41 were secondary parathyroid tumors, 5 were from patients with a history of previous irradiation to the neck, 12 were from patients with a family history of hyperparathyroidism, and 3 were parathyroid tumors related to multiple endocrine neoplasia type 1 (MEN1). In addition, we determined the chromosomal localization of a second putative calcium-sensing receptor, CaS, for inclusion in the LOH studies. Based on analysis of somatic cell hybrids and fluorescent in situ hybridization to metaphase chromsomes, the gene for CaS was mapped to chromosomal region 2q21-q22. The following results were obtained from the LOH studies: (1) out of the 24 tumors that showed LOH, only 4 had more than one chromosomal region involved, (2) in the tumours from uremic patients, LOH of chromosome 3q was detected in a subset of the tumors, (3) LOH of the MEN1 region at 11q13 was the most common abnormality found in both MEN1-related and sporadic parathyroid tumours but was not a feature of the other forms of parathyroid tumors, (4) LOH in 1p and 6q was not as frequent as previously reported, and (5) tumor suppressor genes in 1q and X might have played a role, particularly on the X chromosome, in the case of familial parathyroid adenomas. We therefore conclude that the tumorigenesis of familial, sporadic, and uremic hyperparathyroidism involves different genetic triggers in a non-progressive pattern. Received: 28 October 1996 / Revised: 16 November 1996     

Radiation specific patterns of loss of heterozygosity on chromosome 17q

We and others have previously reported that the percentage of ionizing radiation-induced TK(-) mutants exhibiting loss of heterozygosity (LOH) is not significantly different from those occurring spontaneously. In order to search further for a distinguishing feature of the X-ray-induced spectrum, and to characterize mechanisms of chromosomal scale mutagenesis, we used detailed mapping information to analyze the extent of LOH along chromosome 17q. Significant differences were observed when the extent of LOH tracts was considered. The representation of very long LOH tracts (>/=41 cM) was significantly (p=0.004) more common among spontaneous mutants, while relatively local LOH events, involving only markers in a 1-10 cM region surrounding the tk locus, are significantly (p=0.018) more prevalent among X-ray-induced mutants. Our data suggests that, although large deletions are recoverable, X-ray-induced autosomal deletions are not evenly distributed over the available size range. This indicates a mechanistic rather than biological restriction to the size of radiation-induced deletions, and demonstrates that the pattern of LOH may also be useful as a distinguishing component of the mutational spectrum.     

Mechanisms for the control of respiratory evaporative heat loss in panting animals.

Panting is a controlled increase in respiratory frequency accompanied by a decrease in tidal volume, the purpose of which is to increase ventilation of the upper respiratory tract, preserve alveolar ventilation, and thereby elevate evaporative heat loss. The increased energy cost of panting is offset by reducing the metabolism of nonrespiratory muscles. The panting mechanism tends to be important in smaller mammalian species and in larger species is supplemented by sweating. At elevated respiratory frequencies and body temperatures alveolar hyperventilation begins to develop but is accompanied by a decline in the control of carbon dioxide partial pressure in arterial blood, probably through central chemoreceptors. Most heat exchange takes place at the nasal epithelial lining, and venous drainage can be directed to a special network of arteries at the base of the brain whereby countercurrent heat transfer can occur, which results in selective brain cooling. Such a phenomenon has also been suggested in nonpanting species, including humans, and although originally thought to be a mechanism for protecting the thermally vulnerable brain is now considered to be one of the thermoregulatory reflexes whereby respiratory evaporation can be closely controlled in the interests of thermal homeostasis.     

Age-associated loss of heterozygosity of tumor suppressor genes in the gastric mucosa of humans

The current study is based on the hypothesis that aging predisposes gastric mucosa to carcinogenesis through altered expression and/or mutations of genes involved in cell growth. To test this hypothesis, we investigated the age-associated changes in mutation of adenomatous polyposis coli (APC), deleted in colorectal cancer (DCC), p53, and K-ras genes in the gastric mucosa of 19 healthy subjects of varying ages (25-91 yr). Specifically, we studied the loss of heterozygosity (LOH) of these genes in cardia, body, and antrum of the stomach. We observed that 3 of 19 subjects (16%) over 60 yr of age show LOH of at least one of the tumor suppressor genes. Among the subjects over 60 yr of age, the incidence of LOH is 38% (3/8). Two of three subjects had mutations in more than one tumor suppressor gene. In all three affected subjects, mutation in APC, DCC, or p53 was located mainly in the body of the stomach, suggesting increased susceptibility of this region to neoplastic changes. However, no LOH of K-ras was observed in these subjects. Our observation that subjects over 60 yr of age show mutation in one or more of the tumor suppressor genes suggests an age-related increase in predisposition of the stomach to neoplasia.     

Extensive loss of heterozygosity is suppressed during homologous repair of chromosomal breaks

Loss of heterozygosity (LOH) is a common genetic alteration in tumors and often extends several megabases to encompass multiple genetic loci or even whole chromosome arms. Based on marker and karyotype analysis of tumor samples, a significant fraction of LOH events appears to arise from mitotic recombination between homologous chromosomes, reminiscent of recombination during meiosis. As DNA double-strand breaks (DSBs) initiate meiotic recombination, a potential mechanism leading to LOH in mitotically dividing cells is DSB repair involving homologous chromosomes. We therefore sought to characterize the extent of LOH arising from DSB-induced recombination between homologous chromosomes in mammalian cells. To this end, a recombination reporter was introduced into a mouse embryonic stem cell line that has nonisogenic maternal and paternal chromosomes, as is the case in human populations, and then a DSB was introduced into one of the chromosomes. Recombinants involving alleles on homologous chromosomes were readily obtained at a frequency of 4.6 x 10(-5); however, this frequency was substantially lower than that of DSB repair by nonhomologous end joining or the inferred frequency of homologous repair involving sister chromatids. Strikingly, the majority of recombinants had LOH restricted to the site of the DSB, with a minor class of recombinants having LOH that extended to markers 6 kb from the DSB. Furthermore, we found no evidence of LOH extending to markers 1 centimorgan or more from the DSB. In addition, crossing over, which can lead to LOH of a whole chromosome arm, was not observed, implying that there are key differences between mitotic and meiotic recombination mechanisms. These results indicate that extensive LOH is normally suppressed during DSB-induced allelic recombination in dividing mammalian cells.