Localization of the oncogene c-erbA2 to human chromosome 3

Identification of a novel subgroup of endometrial cancer patients with loss of thyroid hormone receptor beta expression and improved survival

BACKGROUND

Endometrial cancer (EC) is the most common gynecologic cancer in women, and the incidence of EC has increased by about 1% per year in the U. S over the last 10 years. Although 5-year survival rates for early-stage EC are around 80%, certain subtypes of EC that lose nuclear hormone receptor (NHR) expression are associated with poor survival rates. For example, estrogen receptor (ER)-negative EC typically harbors a worse prognosis compared to ER-positive EC. The molecular basis for the loss of NHR expression in endometrial tumors and its contribution to poor survival is largely unknown. Furthermore, there are no tools to systematically identify tumors that lose NHR mRNA expression relative to normal tissue. The development of such an approach could identify sets of NHR-based biomarkers for classifying patients into subgroups with poor survival outcomes.

METHODS

Here, a new computational method, termed receptLoss, was developed for identifying NHR expression loss in endometrial cancer relative to adjacent normal tissue. When applied to gene expression data from The Cancer Genome Atlas (TCGA), receptLoss identified 6 NHRs that were highly expressed in normal tissue and exhibited expression loss in a subset of endometrial tumors.

RESULTS

Three of the six identified NHRs - estrogen, progesterone, and androgen receptors - that are known to lose expression in ECs were correctly identified by receptLoss. Additionally, a novel association was found between thyroid hormone receptor beta (THRB) expression loss, increased expression of miRNA-146a, and increased rates of 5-year survival in the EC TCGA patient cohort. THRB expression loss occurs independently of estrogen and progesterone expression loss, suggesting the discovery of a distinct, clinically-relevant molecular subgroup.

CONCLUSION

ReceptLoss is a novel, open-source software tool to systematically identify NHR expression loss in cancer. The application of receptLoss to endometrial cancer gene expression data identified THRB, a previously undescribed biomarker of survival in endometrial cancer. Applying receptLoss to expression data from additional cancer types could lead to the development of biomarkers of disease progression for patients with any other tumor type. ReceptLoss can be applied to expression data from additional cancer types with the goal of identifying biomarkers of differential survival.

Genomic Alterations in Human Breast Cancer: A Review

We review and discuss data on the genetic alterations documented in human breast carcinomas at the molecular level. These alterations may result in: 1) deletion of genetic material (chromosome 11p, 13q, 3p, 1q, 17p); 2) amplification of genes or entire chromosomal segments (c-myc, c-erb-B2, locus DF3/PUM, loci on 11q13); 3) rearrangements (c-myc); 4) point mutations (c-ras). Presently available informations do not allow the development of cohesive pathogenetic models but indicate that the molecular basis of human breast cancer is heterogeneous.

Cytogenetic study of a nodular hyperplasia of the thyroid after irradiation for Hodgkin's disease

We describe cytogenetics of a case of nodular hyperplasia of the thyroid with papillary microcarcinoma following radiotherapy for Hodgkin's disease. The chromosomal pattern found was very heterogeneous with a clonal abnormality of chromosome 10, among others. Together with some recent data from the literature, this finding may point to an important role of chromosome 10 abnormalities in the pathogenesis of benign and malignant thyroid neoplasms.

Cytogenetic and molecular observations in human and experimental salivary gland tumors

The chromosomal banding patterns in 189 benign and malignant salivary gland tumors are reviewed. For comparison, karyotypic data from a recent series of polyoma virus-induced salivary gland tumors in the mouse are discussed. Special interest is focused on the relationships between the highly specific patterns of translocations and deletions in these tumors and different genes involved in neoplasia, in particular oncogenes, and tumor suppressor genes.

Molecular mapping of deletion sites in the short arm of chromosome 3 in human lung cancer

We used 10 restriction fragment length polymorphism (RFLP) probes spanning the length of the short arm of chromosome 3 (3p) to map deletion sites in human lung cancer. Two approaches were used. 1) When a patient's tumor and normal tissue were available, loci with allelic heterozygosity in the normal tissue were tested for loss of alleles at 3p. 2) When the corresponding normal tissue was not available, the frequency of heterozygosity at each locus in a panel of tumors was compared to the corresponding published frequencies in nontumor tissue of healthy individuals or patients with lung cancer. In 14 small cell lung carcinomas (SCLC) with normal DNA for comparison, allele loss was found at all heterozygous loci, with one exception at a locus near the 3p centromere (D3S4). In the total of 53 SCLCs, which included tumors without paired normal tissue, frequency of heterozygosity was significantly reduced in all 10 3p loci. Three loci, DNF 15S2, RAF1, and D3S18, were homozygous in all tumors in the SCLC panel. These loci, which are in regions 3p21 and 3p25, may thus be involved in the origin or evolution of SCLC. We also investigated 24 non-SCLC tumors. In this panel, frequency of heterozygosity was significantly reduced at seven of the 10 loci tested. Comparison of the results shows that the pattern of allele loss on 3p is different in SCLC and non-SCLC, suggesting a difference in pathogenesis at the genetic level.

Frequency and extent of allelic loss in the short arm of chromosome 3 in nonsmall-cell lung cancer

DNA was prepared from tumour and normal tissue from 48 patients representing all common histological types of nonsmall-cell lung cancer. Using eight DNA probes, which detect nine restriction enzyme fragment length polymorphisms (RFLP) on chromosome 3, we established that among the 44 informative patients 32 had lost alleles on the short arm of one of their copies of chromosome 3. Of these 32, at least 13 had also lost alleles on the long arm of chromosome 3, suggesting that the whole chromosome might be lost. For one patient, cytogenetic analysis indicated that the mechanism of allelic loss was reciprocal translocation followed by chromosomal loss of one of the reciprocal products. Two patients with allelic loss distal to the D3S3 locus (which maps to 3p13-14) retained heterozygosity at that locus. These results indicate that loss of alleles on the short arm of chromosome 3 is a common event in lung tumours of the nonsmall-cell type, that this loss occurs by a variety of chromosomal mechanisms, and that the minimally deleted region is 3p13-14----3pter.

Localization of polymorphic DNA probes frequently deleted in lung carcinoma

Five polymorphic DNA segments from human chromosome 3, that are frequently deleted in lung carcinoma were mapped by non-isotopic in situ hybridization to metaphase chromosomes. The DNA segment D3S3 mapped to 3p13-p14.2, D3S6 to 3p14.3-p14.5, D3S48 to distal 3p21-p22, ERBA beta to 3p24.3 and ERBA2 to 3p24.3. The map location of ERBA beta and ERBA2 was confirmed by re-mapping each probe in combination with D3S6 as a marker for 3p14.

Genetic alterations in primary breast cancer

A serious effort has been made to identify and characterize mutations that frequently occur during the evolution of primary human breast cancer. Some of these mutations involve amplification of protooncogenes (c-myc, c-erbB-2, and int-2) that have been shown to contribute to experimentally induced breast cancer in mouse model systems. Tumor development in mice containing the c-myc or c-erbB-2 transgene suggests that the cellular and developmental contexts in which the genes are expressed define their relative contribution to tumorigenesis. Homozygous deletions or loss of heterozygosity (LOH) represent another type of mutation that has been frequently observed on four chromosomes (1q, 3p, 11p, and 13q) in tumor DNA. They are thought to unmask recessive mutations (LOH) that inactivate or remove (homozygous deletion) suppressor genes that regulate normal cell proliferation. Attempts to determine whether specific mutations are associated with certain clinical parameters have led to the controversial hypothesis that some mutations may be useful prognostic indicators of the post-surgical course of the disease. The current results underscore the necessity for much larger, better control studies to unambiguously define the potential of such mutations as clinical markers.

Cytogenetic studies of Hodgkin's disease. Analysis of involved lymph nodes from 12 patients

Cytogenetic studies were performed on 12 involved lymph nodes from Hodgkin's disease patients utilizing conditioned medium from 12-O-tetradecanoylphorbol-13-acetate-staphylococcus enterotoxin A induced mononuclear cells. The majority of cells analyzed had a normal karyotype. An unusually high rate of nonclonal karyotypic abnormalities was noted in most cultures. Clonal abnormalities involving chromosomes 3 and 21 were noted in two patients. Cytogenetic analysis of cultures stimulated with conditioned medium or specific growth factors may lead to a better understanding of the genetic mechanisms involved in Hodgkin's disease.

Applications of coding theory to the design of somatic cell hybrid panels

The somatic cell hybridization technique for gene mapping depends on assembling panels of rodent-human hybrid clones containing random subsets of the human chromosomes. Such panels should be as informative as possible and permit error detection and error correction for assays of the human gene in the various clones. We derive estimates of the number of randomly generated clones required to be reasonably confident of accurately and unambiguously assigning a gene to a particular human chromosome. The collection of clones in such a random panel is contrasted with minimal panels suggested by algebraic coding theory. To approximate minimal panels we suggest the method of simulated annealing for selecting small, informative panels from larger existing collections of clones. These theoretical insights emphasize the need for more collaboration and coordination among gene mapping groups so that optimal clone panels can be assembled, stored, and distributed.

Assignment of complement components C4 binding protein (C4BP) and factor H (FH) to human chromosome 1q, using cDNA probes

Using cDNA probes for Factor H (FH) and C4 binding protein (C4BP) on a panel of somatic cell hybrids, we show that both of these genes map to the long arm of chromosome 1.

Regional localization of CD18, the beta-subunit of the cell surface adhesion molecule LFA-1, on human chromosome 21 by in situ hybridization

The gene coding for the beta-subunit of the cell surface adhesion glycoprotein LFA-1 has been localized to the tip of the long arm of chromosome 21 at 21q22.1-qter.