Localization of Human Cadherin Genes to Chromosome Regions Exhibiting Cancer-Related Loss of Heterozygosity

This report presents the chromosomal localization of cadherin genes. Cadherins are cellular adhesion molecules. Since disturbance of intracellular adhesion is important for invasion and metastasis of tumor cells, cadherins are considered prime candidates for tumor suppressor genes. A variety of solid tumors show loss of heterozygosity of the long arm of chromosome 16, which is indicative of the potential location of tumor suppressor genes. Refined and new localizations of six cadherin genes (CDH3, 5, 8, 11, 13, and 15) to the long arm of chromosome 16 are shown. CDH15 was localized to 16q24.3, in a region that exhibits loss of heterozygosity in a number of sporadic breast cancer tumors. Previous localization of CDH13 (H-cadherin) to 16q24 suggested this gene as a tumor suppressor candidate in the 16q24.3 loss of heterozygosity region; however, refined mapping presented in this report localizes CDH13 proximal to this region. A human EST homologous to the chicken cadherin-7 was partially sequenced and found to represent a new human cadherin. This cadherin mapped to chromosome 18q22–q23, a region that exhibits loss of heterozygosity in head and neck squamous cell carcinomas. CDH16 was localized to 8q22.1, a region exhibiting loss of heterozygosity in adult acute myeloid leukemia.     

Detection of differential gene flow from patterns of quantitative variation

A major goal in anthropological genetics is the assessment of the effects of different microevolutionary forces. Harpending and Ward (1982) developed a model that aids in this effort by comparing observed and expected heterozygosity within populations in a local region. The expected heterozygosity within a population is a function of the total heterozygosity of the entire region and the distance of the population from the regional mean centroid of allele frequencies. Greater than average gene flow from an external source will result in a population having greater heterozygosity than expected. Less than average gene flow from an external source will result in a population having less heterozygosity than expected. We extend the Harpending-Ward model to quantitative traits using an equal and additive effects model of inheritance. Here the additive genetic variance within a population is directly proportional to heterozygosity, and its expectation is directly proportional to the genetic distance from the centroid. Under certain assumptions the expectations for phenotypic variances are similar. Observed and expected genetic or phenotypic variance can then be compared to assess the effects of differential external gene flow. When the additive genetic covariance matrix or heritabilities are not known, the phenotypic covariance matrix can be used to provide a conservative application of the model. In addition, we develop new methods for estimation of the genetic relationship matrix (R) from quantitative traits. We apply these models to two data sets: (1) six principal components derived from twenty dermatoglyphic ridge count measures for nine villages in Nepal and (2) ten anthropometric measurements for seven isolated populations in western Ireland. In both cases both the univariate and multivariate analyses provide results that can be directly interpreted in terms of historically known patterns of gene flow.     

The Meiotic Effect of a Deficiency in DROSOPHILA MELANOGASTER with a Model for the Effects of Enzyme Deficiency on Recombination

The meiotic effects of heterozygosity for a deficiency of the zeste-white region of the X chromosome include reduced recombination and increased non-disjunction of the entire chromosome complement. Reduced dosage of a gene or genes in the zeste-white interval, rather than structural heterozygosity, is responsible for the meiotic effect. A model for the recombination effects of reduced enzyme concentration has been developed, and its consequences are comparable with the results obtained for deficiency heterozygosity. Thus, all of the observations can be accounted for by imagining a dosage-sensitive locus in the zeste-white region that codes for an enzyme involved in the recombination process. The interaction of the interchromosomal effect of heterozygous inversions with the deficiency has been examined, and the possibility of using the model for the analysis of other meiotic phenomena is considered.     

Dosage effects on morphological and quantitative traits in maize aneuploids.

Dosage effects generated by either loss or gain of a chromosome segment were used to identify chromosome regions associated with morphological and quantitative characters in maize (Zea mays L.). Using B-A translocation stocks introgressed into a B73Ht background, a chromosome arm dosage series in a Mo17Ht x B73Ht F1 hybrid background was created for 18 of the 20 chromosome arms. The dosage series was then evaluated for 12 quantitatively inherited characters to associate specific phenotypic changes in a trait with a specific chromosome arm. Not only did our results show the familiar aneuploid syndrome phenomenon, but differential dosage effects among particular chromosome arms were demonstrated. All the quantitative traits measured and all the chromosome arms examined in this study were responsive to changes in chromosome arm dosage. The possible bases behind those differences and their utility in identifying quantitative trait loci, as well as the genetic relationships among the group of quantitatively inherited characters studied, are considered. Key words : corn, chromosome arm, B-A translocations, dosage analysis.     

Overproduction of human Cu/Zn-superoxide dismutase in transfected cells: extenuation of paraquat-mediated cytotoxicity and enhancement of lipid peroxidation.

The 'housekeeping' enzyme Cu/Zn-superoxide dismutase (SOD-1) is encoded by a gene residing on human chromosome 21, at the region 21q22 known to be involved in Down's syndrome. The SOD-1 gene and the SOD-1 cDNA were introduced into mouse L-cells and human HeLa cells, respectively as part of recombinant plasmids containing the neoR selectable marker. Human and mouse transformants were obtained that expressed elevated levels (up to 6-fold) of authentic, enzymatically active human SOD-1. This enabled us to examine the consequences of hSOD-1 gene dosage, apart from gene dosage effects contributed by other genes residing on chromosome 21. Human and mouse cell clones that overproduce the hSOD-1 had altered properties; they were more resistant to paraquat than the parental cells and showed an increase in lipid peroxidation. The data are consistent with the possibility that gene dosage of hSOD-1 contributes to some of the clinical symptoms associated with Down's syndrome.     

The genes for the highly homologous Ca(2+)-binding proteins oncomodulin and parvalbumin are not linked in the human genome.

The chromosomal loci of the human parvalbumin and oncomodulin single-copy genes that encode structurally and evolutionarily closely related Ca(2+)-binding proteins were determined by somatic cell hybrid analysis. Southern blot analysis of genomic DNA from 25 human-hamster somatic cell hybrids showed that the human gene for oncomodulin resides on chromosome 7. Analysis of human-mouse hybrids selectively retaining human chromosome 7 or a portion of it allowed specific assignment of the gene locus to the p11-p13 region of chromosome 7 known to be mutated or deleted in patients with the Greig cephalopolysyndactyly syndrome. By gene dosage analysis on Southern blots, we showed that the gene for human parvalbumin maps distally to the cat eye syndrome marker D22S9 on chromosome 22q. Using somatic cell hybrids containing parts of human chromosome 22, the parvalbumin gene was sublocalized to the region 22q12-q13.1. This region contains a linkage group that maps to mouse chromosome 15, region E, and includes the SIS, ARSA, and DIA 1 genes. Our findings are consistent with the recent localization of the mouse parvalbumin gene to this region by two independent methods (C. H. Zühlke et al., 1989, Genet. Res. 54:37-43; S. Adolph et al., 1989, Cytogenet. Cell Genet. 52:177-179).     

Ultrastructure of sheep metaphase chromosomes identified by study of total preparations of metaphase plates]

The data obtained suggest wide possibilities of using the elaborated method of the whole metaphase plates investigation under the electron microscope to disclose the specific characters of the structure of individual chromosomes. Each chromosome has a definite number of bands of condensed DNP material. The number and disposition of bands are essentially the same in homologous chromosomes. The Giemsa-positive disks which could be seen after differential chromosome staining correspond to the bands of condensed material.     

Linkage mapping of highly informative DNA polymorphisms within the human interferon-alpha receptor gene on chromosome 21.

Two polymorphic loci within the interferon-alpha receptor (IFNAR) gene on human chromosome 21 have been identified and mapped by linkage analysis in 40 CEPH families. These markers are (1) a multiallelic RFLP with an observed heterozygosity of 0.72 and (2) a variable (AT3)n short sequence repeat at the poly(A) tail of an Alu sequence (AluVpA) with an observed heterozygosity of 0.83. This locus is close to D21S58 (theta = 0.02, zeta = 36.76) and D21S17 (theta = 0.02, Zeta = 21.76) with chromosomal band 21q22.1. Multipoint linkage analysis suggests the most likely locus order to be 21cen-D21S58-IFNAR-D21S17-21qter. Given its high heterozygosity, the IFNAR gene can be used as an index marker on human chromosome 21.     

Chromosome 7 suppresses indefinite division of nontumorigenic immortalized human fibroblast cell lines KMST-6 and SUSM-1.

Using nontumorigenic immortalized human cell lines KMST-6 (KMST) and SUSM-1 (SUSM), we attempted to identify the chromosome that carries a putative senescence-related gene(s). These cell lines are the only ones that have been established independently from normal human diploid fibroblasts following in vitro mutagenesis. We first examined restriction fragment length polymorphisms on each chromosome of these immortalized cell lines and their parental cell lines and found specific chromosomal alterations common to these cell lines (a loss of heterozygosity in KMST and a deletion in SUSM) on the long arm of chromosome 7. In addition to these, we also found that introduction of chromosome 7 into these cell lines by means of microcell fusion resulted in the cessation of cell division, giving rise to cells resembling cells in senescence. Introduction of other chromosomes, such as chromosomes 1 and 11, on which losses of heterozygosity were also detected in one of the cell lines (KMST), to either KMST or SUSM cells or of chromosome 7 to several tumor-derived cell lines had no effect on their division potential. These results strongly suggest that a gene(s) affecting limited-division potential or senescence of normal human fibroblasts is located on chromosome 7, probably at the long arm of the chromosome, representing the first case in which a specific chromosome reverses the immortal phenotype of otherwise normal human cell lines.     

A novel mouse model for Down syndrome that harbor a single copy of human artificial chromosome (HAC) carrying a limited number of genes from human chromosome 21

Down syndrome (DS), also known as Trisomy 21, is the most common chromosome aneuploidy in live-born children and displays a complicated symptom. To date, several kinds of mouse models have been generated to understand the molecular pathology of DS, yet the gene dosage effects and gene(s)-phenotype(s) correlation are not well understood. In this study, we established a novel method to generate a partial trisomy mice using the mouse ES cells that harbor a single copy of human artificial chromosome (HAC), into which a small human DNA segment containing human chromosome 21 genes cloned in a bacterial artificial chromosome (BAC) was recombined. The produced mice were found to maintain the HAC carrying human genes as a mini-chromosome, hence termed as a Trans-Mini-Chromosomal (TMC) mouse, and HAC was transmitted for more than twenty generations independent from endogenous mouse chromosomes. The three human transgenes including cystathionine β-synthase, U2 auxiliary factor and crystalline alpha A were expressed in several mouse tissues with various expression levels relative to mouse endogenous genes. The novel system is applicable to any of human and/or mouse BAC clones. Thus, the TMC mouse carrying a HAC with a limited number of genes would provide a novel tool for studying gene dosage effects involved in the DS molecular pathogenesis and the gene(s)-phenotype(s) correlation.     

Dynamics of correlated genetic systems. II. Simulation studies of chromosomal segments under selection

The dynamics of chromosomal segments under selection are investigated by comparing experimental data to simulations of simple models of selection. The simulations assume 93 loci distributed evenly along an entire chromosome. The two issues addressed in this paper concern rates of decay of linkage disequilibria for chromosomes under selection and rates of gene frequency change after perturbation of gametic frequencies to states near the edge of the gametic frequency simplex. The findings are: (1) If reasonable values of inbreeding depression are assumed, linkage disequilibria decays to zero but at a rate nearly twice that expected from neutral theory. Experimental results also show accelerated decay rates. The acceleration of decay seems to be a simple consequence of the increased heterozygosity produced by selection. It is, therefore, argued that massive linkage disequilibria, of the kind found by Franklin and Lewontin (1970) in their simulations, are unlikely to characterize the genetic structure of natural populations of random mating organisms. (2) It is possible to distinguish between two time-honored models of multilocus selection, known as the symmetric overdominant and classical models, on the basis of gene frequency change near the edge of the gametic frequency simplex assuming linkage disequilibria is intense. (3) Examination of experimental data from perturbation experiments shows that neither of these elementary models adequately account for observed rates of gene frequency change, although the symmetric overdominant model does provide the better fit. Instead the experimental data suggest a markedly nonuniform distribution of selective effects along the chromosome. The data also suggest that these selective effects combine in markedly nonadditive ways in determining joint fitness.     

Human elastin gene: new evidence for localization to the long arm of chromosome 7.

In this study we have utilized human elastin cDNAs in molecular hybridizations to establish the chromosomal location of the human elastin gene. First, in situ hybridizations were performed with metaphase chromosomes from phytohemagglutinin-stimulated human peripheral blood lymphocytes. In three separate experiments using two different regions of human elastin cDNAs, the distribution of grains was found to be concentrated on the long arm of chromosome 7 within the [q11.1-21.1] region, and the peak number of grains coincided with the locus 7q11.2. Second, hybridizations with a panel of human-rodent cell hybrids showed concordance with human chromosome 7. Third, PCR analyses with elastin-specific primers of DNA from a hybrid cell line containing chromosome 7 as the only human chromosome yielded a product of the expected size, while DNA containing human chromosome 2, but not chromosome 7, did not result in a product. The results indicate that the human elastin gene is located in the proximal region of the long arm of chromosome 7. The precise localization of the elastin gene in the human genome is useful in establishing genetic linkage between inheritance of an allele with a mutated elastin gene and a heritable disorder.     

Genetic linkage studies of chromosome 17 RFLPs in von Recklinghausen neurofibromatosis (NF1)

Recent localization of the gene for von Recklinghausen neurofibromatosis (NF1) to chromosome 17 has led to studies to identify additional tightly linked probes that can be used in defining the primary genetic defect in NF1. We have examined and obtained blood for DNA linkage studies on over 250 individuals from 10 multigeneration neurofibromatosis families. We have analyzed 130 members in 7 families with the available chromosome 17 NF1 linked probes, pE51, D17S71, and D17Z1, as well as two probes generated from our own chromosome 17/19 enriched library (LDR92, LDR152A). Tight linkage was found between NF1 and the centromeric probe D17Z1 (theta = 0.04) and between NF1 and D17S71 (theta = 0.08). A definite recombinant was seen for the D17Z1 marker, which previously had not exhibited crossingover. Chromosome 17 DNA markers pE51, LDR92, and LDR152A gave slightly positive scores, which were not statistically significant.     

Molecular genetic investigations of the mechanism of tumourigenesis in von Hippel-Lindau disease: analysis of allele loss in VHL tumours

Von Hippel-Lindau (VHL) disease is a dominantly inherited familial cancer syndrome characterised by the development of retinal and central nervous system haemangioblastomas, renal cell carcinoma (RCC), phaeochromocytoma and pancreatic tumours. The VHL disease gene maps to chromosome 3p25-p26. To investigate the mechanism of tumourigenesis in VHL disease, we analysed 24 paired blood/tumour DNA samples from 20 VHL patients for allele loss on chromosome 3p and in the region of tumour suppressor genes on chromosomes 5, 11, 13, 17 and 22. Nine out of 24 tumours showed loss of heterozygosity (LOH) at at least one locus on chromosome 3p and in each case the LOH included the region to which the VHL gene has been mapped. Chromosome 3p allele loss was found in four tumour types (RCC, haemangioblastoma, phaeochromocytoma and pancreatic tumour) suggesting a common mechanism of tumourigenesis in all types of tumour in VHL disease. The smallest region of overlap was between D3S1038 and D3S18, a region that corresponds to the target region for the VHL gene from genetic linkage studies. The parental origin of the chromosome 3p25-p26 allele loss could be determined in seven tumours from seven familial cases; in each tumour, the allele lost had been inherited from the unaffected parent. Our results suggest that the VHL disease gene functions as a recessive tumour suppressor gene and that inactivation of both alleles of the VHL gene is the critical event in the pathogenesis of VHL neoplasms. Four VHL tumours showed LOH on other chromosomes (5q21, 13q, 17q) indicating that homozygous VHL gene mutations may be required but may not be sufficient for tumourigenesis in VHL disease.     

High-resolution chromosomal microarray analysis of early-stage human embryonic stem cells reveals an association between X chromosome instability and skewed X inactivation

X chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell via a random process. Skewed XCI is relevant to many diseases, but the mechanism leading to it remains unclear. Human embryonic stem cells (hESCs) derived from the inner cell mass (ICM) of blastocyst-stage embryos have provided an excellent model system for understanding XCI initiation and maintenance. Here, we derived hESC lines with random or skewed XCI patterns from poor-quality embryos and investigated the genome-wide copy number variation (CNV) and loss of heterozygosity (LOH) patterns at the early passages of these two groups of hESC lines. It was found that the average size of CNVs on the X chromosomes in the skewed group is twice as much as that in the random group. Moreover, the LOH regions of the skewed group covered the gene locus of either XIST or XACT, which are master long non-coding RNA (lncRNA) effectors of XCI in human pluripotent stem cells. In conclusion, our work has established an experimentally tractable hESC model for study of skewed XCI and revealed an association between X chromosome instability and skewed XCI.     

Interferon induction of (2′–5′) oligoisoadenylate synthetase in diploid and trisomy 21 human fibroblasts: Relation to dosage of the interferon receptor gene (IRFC)

Trisomy 21 human fibroblasts are more sensitive to human interferon-alpha (IFN-alpha) than are diploid controls, consistent with the location of the gene (IFRC) which codes for the IFN-alpha receptor on chromosome 21. When compared in the antiviral assay, the difference in sensitivity is five- to tenfold, much greater than the 50% difference in IFRC gene dosage. An understanding of the mechanism by which this amplification of gene dosage occurs is relevant to the specific pathology of Down's syndrome and as a model system for studying the pathogenic effects of chromosomal aneuploidy. The enzyme (2'-5') oligoisoadenylate synthetase (2-5A synthetase), which is believed to be central to the interferon-induced antiviral response, is induced 50% more in trisomy 21 fibroblasts than in diploid controls. Thus the amplification in response occurs subsequent to the binding of IFN-alpha to its receptor and the triggering of the first set of intracellular events, the latter exemplified by the induction of 2-5A synthetase. Similar results were obtained with IFN-gamma, consistent with other evidence which indicates that a gene coding for a separate IFN-gamma receptor is also located on chromosome 21.     

Localization of human cardiac beta-myosin heavy chain gene (MYH7) to chromosome 14q12 by in situ hybridization

The genes coding for each human cardiac myosin heavy chain (alpha-MHC and beta-MHC, MYH6 and MYH7, respectively) are tightly linked and the alpha-MHC gene has been assigned to chromosome 14. In order to provide a more precise regional localization, in situ hybridization experiments were carried out using a 3H-labeled probe derived from a beta-MHC genomic clone. The results demonstrated that the human cardiac MHC genes are located within the q12 band of chromosome 14.     

Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

Aneuploidy has profound effects on an organism,typically more so than polyploidy,and the basis of this contrast is not fully understood.A dosage series of the maize long arm of chromosome 1(1L)was used to compa re relative global gene expression in diffe rent types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene expression.While previously available methods require a selective examination of specific genes,RNA sequencing provides a whole-genome view of gene expression in aneuploids.Most studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic organisms.The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms.Thus,a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible,in both hypoploids and hyperploids,compared with euploid controls.Previous studies observed the inverse trans effect,in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal region.This response was also the major type of changes found globally in this study.Many genes varied in dosage showed proportional expression changes,though some were seen to be partly or fully dosage compensated.It was also found that the effects of aneuploidy were progressive,with more severe aneuploids producing effects of greater magnitude.