Short communication: Mapping of two tumor suppressor genes in the pig

Abstract

Mutations in the breast cancer 1, early onset (BRCA1) gene confer an increased risk of breast and ovarian cancer in humans. The human MAD (mothers against decapentaplegic, Drosophila) homolog 4 (MADH4) locus is a target for deletion in pancreatic and other cancers. Given the role of the pig in biomedical studies, pig orthologs of BRCAl and MADH4 were identified and localized in the porcine genome.     

Population genetics of tumor suppressor genes

Cancer emerges when a single cell receives multiple mutations. For example, the inactivation of both alleles of a tumor suppressor gene (TSG) can imply a net reproductive advantage of the cell and might lead to clonal expansion. In this paper, we calculate the probability as a function of time that a population of cells has generated at least one cell with two inactivated alleles of a TSG. Different kinetic laws hold for small and large populations. The inactivation of the first allele can either be neutral or lead to a selective advantage or disadvantage. The inactivation of the first and of the second allele can occur at equal or different rates. Our calculations provide insights into basic aspects of population genetics determining cancer initiation and progression.     

Mapping and association studies of diabetes related genes in the pig

The mitogen-activated protein kinase 8 (MAPK8), resistin (RETN), 11 beta hydroxysteroid dehydrogenase isoform 1 (HSD11B1) and protein kinase B Akt2 (AKT2) genes are all genes known to affect insulin signalling and have been implicated in the progression of obesity and type 2 diabetes in humans. In this study, polymorphisms in the porcine diabetes related MAPK8, RETN, HSD11B1 and AKT2 genes were identified, mapped and their associations with phenotypic measurements in swine were analysed. Polymorphisms detected in the MAPK8, RETN and HSD11B1 loci were used to genotype a Berkshire-Yorkshire pig breed reference family. Using linkage analysis, RETN, HSD11B1 and MAPK8 genes were mapped to pig chromosomes 2, 9 and 14, respectively, while the AKT2 gene was physically mapped to pig chromosome 6q21. Results presented here suggest associations between the polymorphisms in the MAPK8, RETN and HSD11B1 genes with several phenotypic measurements, including fat deposition traits in the pig. Because these genes have been implicated in obesity and diabetes in humans, and this study suggests associations with fat related traits, further research on these genes in swine may provide useful information on genetic factors underlying lean pork production.     

DNA damage tumor suppressor genes and genomic instability

Disruption of the mechanisms that regulate cell-cycle checkpoints, DNA repair, and apoptosis results in genomic instability and the development of cancer in multicellular organisms. The protein kinases ATM and ATR, as well as their downstream substrates Chk1 and Chk2, are central players in checkpoint activation in response to DNA damage. Histone H2AX, ATRIP, as well as the BRCT-motif-containing molecules 53BP1, MDC1, and BRCA1 function as molecular adapters or mediators in the recruitment of ATM or ATR and their targets to sites of DNA damage. The increased chromosomal instability and tumor susceptibility apparent in mutant mice deficient in both p53 and either histone H2AX or proteins that contribute to the nonhomologous end-joining mechanism of DNA repair indicate that DNA damage checkpoints play a pivotal role in tumor suppression.     

Mapping two genes in the purine metabolism pathway of soybean.

Mapping genes in biochemical pathways allow study of the genomic organization of pathways and geneic relationships within these pathways. Additionally, molecular markers located within the boundaries of a specific gene sequence represent important marker assisted selection resources. We report map locations of two geneic markers from the purine synthesis pathway in soybean (Glycine max (L. merr.)), utilizing a 90 plant F(2) population created from the cross of "DT97-4290" x "DS97-84-1". Primers were designed based on sequences from annotated soybean complimentary DNA. A polymorphic, co-dominant, sequence-characterized amplified region marker was created for hypoxanthine phosphoribosyl transferase (EC 2.4.2.8). Linkage analysis placed this gene on linkage group (LG) O. In addition, a single-nucleotide polymorphism (SNP) marker was developed for a urate oxidase gene (EC 1.7.3.3). Linkage analysis of the SNP placed the urate oxidase gene on LG I. For both genes, amplicon sequence data confirmed the identification of the respective gene. Mapping these genes represents the first step in understanding the genomic organization of the purine biochemical pathway in soybean.     

Discovering tumor suppressor genes through genome-wide copy number analysis

Classical tumor suppressor gene discovery has largely involved linkage analysis and loss-of-heterozygosity (LOH) screens, followed by detailed mapping of relatively large chromosomal regions. Subsequent efforts made use of genome-wide PCR-based methods to detect rare homozygous deletions. More recently, high-resolution genomic arrays have been applied to cancer gene discovery. However, accurate characterization of regions of genomic loss is particularly challenging due to sample heterogeneity, the small size of deleted regions and the high frequency of germline copy number polymorphisms. Here, we review the application of genome-wide copy number analysis to the specific problem of identifying tumor suppressor genes.     

TSGDB: a database system for tumor suppressor genes

A Web-based database system was constructed and implemented that contains 174 tumor suppressor genes. The database homepage was created to accommodate these genes in a pull-down window so that each gene can be viewed individually in a separate Web page. Information displayed on each page includes gene name, aliases, source organism, chromosome location, expression cells/tissues, gene structure, protein size, gene functions and major reference sources. Queries to the database can be conducted through a user-friendly interface, and query results are returned in the HTML format on dynamically generated web pages. AVAILABILITY: The database is available at http://www.cise.ufl.edu/~yy1/HTML-TSGDB/Homepage.html (data files also at http://www.patcar.org/Databases/Tumor_Suppressor_Genes)     

两例新的稀毛小鼠突变基因的染色体定位

用连锁分析法对乙烷基亚硝基脲(ENU) 诱变获得的两例被毛突变小鼠(snthr 1Bao及snthr 2Bao) 的突变基因进行定位。选择平均分布于小鼠基因组且在C57BL/6J和DBA/2 间有差异的39 个微卫星对B6D2F1 互交得到的稀毛F2 进行全基因组扫描。扫描了9个微卫星后发现snthr 1Bao突变基因与D9Mit243 的LOD值为7 73。突变基因被定位于9号染色体。在此基础上又选择了D9Mit355 和D9Mit18 两个微卫星进行检测, 并扩大F2 的数量至145只。结果发现, snthr 1Bao与D9Mit18间无1 例重组, 稀毛突变基因与该微卫星紧密连锁, 距着丝点71cM。同理, 将snthr 2Bao突变基因也定位在与snthr 1Bao相近的区域。检索发现snthr 1Bao是一尚未克隆的新基因。     

An ANN model for the identification of deleterious nsSNPs in tumor suppressor genes

Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occurs approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs), lead to amino acid changes in the protein product may account for nearly half of the known genetic variations linked to inherited human diseases and cancer. One of the main problems of medical genetics today is to identify nsSNPs that underlie disease-related phenotypes in humans. An attempt was made to develop a new approach to predict such nsSNPs. This would enhance our understanding of genetic diseases and helps to predict the disease. We detect nsSNPs and all possible and reliable alleles by ANN, a soft computing model using potential SNP information. Reliable nsSNPs are identified, based on the reconstructed alleles and on sequence redundancy. The model gives good results with mean specificity (95.85&), sensitivity (97.40&) and accuracy (96.25&). Our results indicate that ANNs can serve as a useful method to analyze quantitative effect of nsSNPs on protein function and would be useful for large-scale analysis of genomic nsSNP data. AVAILABILITY: The database is available for free at http://www.snp.mirworks.in.     

Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma

Background

Uterine leiomyomas, or fibroids, represent the most common benign tumor of the female reproductive tract. Fibroids become symptomatic in 30% of all women and up to 70% of African American women of reproductive age. Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown.

Principal Findings

We characterized and compared genome-wide DNA methylation and mRNA expression profiles in uterine leiomyoma and matched adjacent normal myometrial tissues from 18 African American women. We found 55 genes with differential promoter methylation and concominant differences in mRNA expression in uterine leiomyoma versus normal myometrium. Eighty percent of the identified genes showed an inverse relationship between DNA methylation status and mRNA expression in uterine leiomyoma tissues, and the majority of genes (62%) displayed hypermethylation associated with gene silencing. We selected three genes, the known tumor suppressors KLF11, DLEC1, and KRT19 and verified promoter hypermethylation, mRNA repression and protein expression using bisulfite sequencing, real-time PCR and western blot. Incubation of primary leiomyoma smooth muscle cells with a DNA methyltransferase inhibitor restored KLF11, DLEC1 and KRT19 mRNA levels.

Conclusions

These results suggest a possible functional role of promoter DNA methylation-mediated gene silencing in the pathogenesis of uterine leiomyoma in African American women.     

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.     

Analysis of p53 tumor suppressor pathway genes in chronic lymphocytic leukemia

The p53 tumor suppressor gene plays an important role in preventing tumor development. The p53 protein interacts with other p53 signal pathway members to control cell proliferation. In this study, expression of the p53, Human homolog of murine Double Minute 2 (HDM2), p14Alternating Reading Frame (ARF), Zinc Finger and BTB domain containing 7A (ZBTB7A), and B-Cell Lymphoma 6 (BCL6) genes was quantitatively investigated by real-time polymerase chain reaction (PCR) in the peripheral blood of patients with chronic lymphocytic leukemia (CLL) and healthy controls. Plasma fibronectin levels were determined by enzyme-linked immunosorbent assay. Expression of the p53, p14, and HDM2 genes were significantly higher in the patients. However, ZBTB7A and BCL6 gene expression was not detectable in both groups. A positive correlation between p14ARF and HDM2 expression and a negative correlation between p53 and p14ARF expression was observed. Expression of the p14ARF and HDM2 genes were inversely correlated in the control group. Neither HDM2 nor p14ARF gene expression was correlated with p53 expression. The p53 gene was also analyzed for the presence of mutations. A splice-site mutation was found in a single patient. Our findings indicate that expression of the p53, p14ARF, and HDM2 genes are associated with CLL. Elucidation of the mutual interactions at the protein level warrants further studies.