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PubMed2003

Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation.

We examined the pattern of gene expression resulting from spontaneous differentiation of Caco-2 BBe cells to gain insight into the molecular changes necessary for enterocyte differentiation. RNA was prepared from cells harvested at three cell stages: proliferating (50% confluent, 2 days in culture), postproliferative nondifferentiated (8 days), and differentiated (15 days). Gene expression profiles were determined using Affymetrix Human Genome U95A GeneChips. Differentially expressed genes were identified following statistical analysis (i.e., ANOVA, bootstrapping adjustments to P values, false detection rate criterion). We identified 1,150 unique genes as differentially expressed; expression of 48.6% fell and 46% increased from 2 to 15 days, while 5.4% had expression that either peaked or dipped at 8 days. Genes expressed during differentiation included several small-intestine-specific genes involved in nutrient transport/metabolism, e.g., DCT1, hephaestin, folate receptor 1, sucrase-isomaltase, and apolipoproteins CI, CIII, B100, H, and M, indicating that this colonic adenocarcinoma cell line has a hybrid colonocyte/enterocyte phenotype. Patterns of gene expression based upon functional classification suggest a role for cell-cell/cell-matrix interactions, suppression of Wnt signaling, and activation of TGFbeta and phosphatidylinositol 3-kinase pathways during enterocyte differentiation.

Caco-2 Cells↗
PubMed2006

Comparative analysis of cancer genes in the human and chimpanzee genomes.

BACKGROUND: Cancer is a major medical problem in modern societies. However, the incidence of this disease in non-human primates is very low. To study whether genetic differences between human and chimpanzee could contribute to their distinct cancer susceptibility, we have examined in the chimpanzee genome the orthologous genes of a set of 333 human cancer genes. RESULTS: This analysis has revealed that all examined human cancer genes are present in chimpanzee, contain intact open reading frames and show a high degree of conservation between both species. However, detailed analysis of this set of genes has shown some differences in genes of special relevance for human cancer. Thus, the chimpanzee gene encoding p53 contains a Pro residue at codon 72, while this codon is polymorphic in humans and can code for Arg or Pro, generating isoforms with different ability to induce apoptosis or interact with p73. Moreover, sequencing of the BRCA1 gene has shown an 8 Kb deletion in the chimpanzee sequence that prematurely truncates the co-regulated NBR2 gene. CONCLUSION: These data suggest that small differences in cancer genes, as those found in tumor suppressor genes, might influence the differences in cancer susceptibility between human and chimpanzee. Nevertheless, further analysis will be required to determine the exact contribution of the genetic changes identified in this study to the different cancer incidence in non-human primates.

Animals↗
PubMed2006

Medulloblastoma outcome is adversely associated with overexpression of EEF1D, RPL30, and RPS20 on the long arm of chromosome 8.

BACKGROUND: Medulloblastoma is the most common malignant brain tumor of childhood. Improvements in clinical outcome require a better understanding of the genetic alterations to identify clinically significant biological factors and to stratify patients accordingly. In the present study, we applied cytogenetic characterization to guide the identification of biologically significant genes from gene expression microarray profiles of medulloblastoma. METHODS: We analyzed 71 primary medulloblastomas for chromosomal copy number aberrations (CNAs) using comparative genomic hybridization (CGH). Among 64 tumors that we previously analyzed by gene expression microarrays, 27 were included in our CGH series. We analyzed clinical outcome with respect to CNAs and microarray results. We filtered microarray data using specific CNAs to detect differentially expressed candidate genes associated with survival. RESULTS: The most frequent lesions detected in our series involved chromosome 17; loss of 16q, 10q, or 8p; and gain of 7q or 2p. Recurrent amplifications at 2p23-p24, 2q14, 7q34, and 12p13 were also observed. Gain of 8q is associated with worse overall survival (p = 0.0141), which is not entirely attributable to MYC amplification or overexpression. By applying CGH results to gene expression analysis of medulloblastoma, we identified three 8q-mapped genes that are associated with overall survival in the larger group of 64 patients (p < 0.05): eukaryotic translation elongation factor 1D (EEF1D), ribosomal protein L30 (RPL30), and ribosomal protein S20 (RPS20). CONCLUSION: The complementary use of CGH and expression profiles can facilitate the identification of clinically significant candidate genes involved in medulloblastoma growth. We demonstrate that gain of 8q and expression levels of three 8q-mapped candidate genes (EEF1D, RPL30, RPS20) are associated with adverse outcome in medulloblastoma.

Adolescent↗
PubMed2004

26th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 3-6 December 2003: update on preclinical and translational research.

The San Antonio Breast Cancer Symposium is the largest annual meeting devoted solely to breast cancer research. The late William L McGuire's vision for this meeting was to stimulate 'translational research', many years before this term became popular. In this way, the San Antonio Breast Cancer Symposium represents a forum in which basic and clinical researchers present their research side by side. Each year sees the continued evolution of our understanding of the basic mechanisms of breast cancer initiation and progression, and the clinical application of this knowledge. Major topics of discussion at the symposium this year were the cell cycle, new evolving concepts of estrogen receptor action, breast cancer stem cells, new predictive and prognostic markers (including microarray studies), and continued exploration of the mechanisms of drug resistance. This report will summarize preclinical and translational highlights from the meeting.

Breast Neoplasms↗
PubMed2005

Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories.

A major challenge in cancer diagnosis from microarray data is the need for robust, accurate, classification models which are independent of the analysis techniques used and can combine data from different laboratories. We propose such a classification scheme originally developed for phenotype identification from mass spectrometry data. The method uses a robust multivariate gene selection procedure and combines the results of several machine learning tools trained on raw and pattern data to produce an accurate meta-classifier. We illustrate and validate our method by applying it to gene expression datasets: the oligonucleotide HuGeneFL microarray dataset of Shipp et al. (www.genome.wi.mit.du/MPR/lymphoma) and the Hu95Av2 Affymetrix dataset (DallaFavera's laboratory, Columbia University). Our pattern-based meta-classification technique achieves higher predictive accuracies than each of the individual classifiers , is robust against data perturbations and provides subsets of related predictive genes. Our techniques predict that combinations of some genes in the p53 pathway are highly predictive of phenotype. In particular, we find that in 80% of DLBCL cases the mRNA level of at least one of the three genes p53, PLK1 and CDK2 is elevated, while in 80% of FL cases, the mRNA level of at most one of them is elevated.

Biomarkers, Tumor↗
PubMed1994

Spatial and structural segregation of the transcribed and nontranscribed alleles of c-myc in Namalva-S cells.

By using various approaches we received evidence that, in Namalva-S cells carrying a t(8;14) translocation and highly expressing c-myc, the two alleles of the gene are spatially and structurally segregated. Spatial segregation of the alleles was observed in all nuclei analyzed by in situ hybridization technique. Their structural segregation, i.e., association with different intranuclear structures, was confirmed in a number of experiments. When high-salt extracted nuclei were digested with EcoRI, which is known to produce fragments containing the entire c-myc locus, the sequences of the gene were found separated between the pellet, containing sequences firmly associated with the heavier matrix structures, and the supernatant, containing sequences from the free length of the DNA loops. Southern hybridization performed with a probe representative for the constant region of the human IgH locus revealed that this fractionation in fact segregates the reorganized from the normal allele of c-myc. Run-on experiments carried out with two fractions, topologically equivalent to the above P and S but isolated as intact chromatin structures, indicated that the allele associated with nuclear matrix is actively transcribed, while that located in the free length of the chromatin loops is practically nontranscribed. Studies on the chromatin organization of transcribed and nontranscribed alleles revealed the existence in them of two alternative chromatin structures. Control experiments with beta-globin gene, performed with cells constitutively nontranscribing or actively transcribing this gene, confirmed our conclusions about the spatial segregation of the two alleles and clarified that their structural segregation occurs when the gene is activated for transcription.

Alleles↗
PubMed1997

Detection of chromosomal aberrations in seminomatous germ cell tumours using comparative genomic hybridization.

Comparative genomic hybridization (CGH) was used to evaluate tissue specimens from 16 seminomas in order to elucidate the pathogenesis of germ cell tumours in males. A characteristic pattern of losses and gains within the entire genomes was detected in 94% of the seminomas by comparing the ratio profiles of the tumours with a standard of cytogenetically normal genomic DNA. Losses represented 43% of the total number of alterations often affecting chromosomes and chromosome arms 4, 5, 11, 13q, and 18q. Gains amounted to 57% and were often observed on 1q, 7, 8, 12, 14q, 15q, 21q, and 22q. Aberrations of 12p and 21q appeared most consistently. Results from CGH analysis displayed no relationship to the clinical stages of the malignancy. Some rare aberrations appeared, however, only in clinical stage II and in tumours showing relapse in the contralateral testis following orchiectomy, although the alterations were not present in all of the tumours in question. Losses of 16q13-21 and gains of 9q22.1-22.2 were demonstrated in both groups, while loss of 16p12 and gains of 6p21 and 6q23.3-24 were detected in the latter group as well. In conclusion, a specific pattern of chromosomal alterations was demonstrated in the seminomas by improved detection criteria, which increased specificity and sensitivity. The rare aberrations, which appeared only in tumours in improved detection criteria, which increased specificity and sensitivity. The rare aberrations, which appeared only in tumours in clinical stage II and relapsed tumours, may be linked to tumour progression, invasiveness, and bilateral disease.

Chromosome Aberrations↗
PubMed1995

Abnormal expression of the retinoblastoma gene in ovarian neoplasms and correlation to p53 and K-ras mutations.

We analyzed the expression of the retinoblastoma (Rb) gene in a group of ovarian neoplasms previously characterized for mutations in the p53 suppressor gene and the Ki-ras oncogene. Using immunohistochemical techniques, a total of 59 ovarian neoplasms spanning the histiologic spectrum from benign to malignant were examined for the expression of the Rb protein. All benign cystic adenomas and low malignant potential tumors exhibited normal expression of the Rb protein. Abnormalities in Rb protein staining were noted in 3 of 22 (14%) ovarian carcinomas. The staining patterns included tumors that were totally or focally negative for Rb protein. One tumor focally expressed Rb. This tumor demonstrated a direct juxtaposition of sections of Rb expressing and nonexpressing malignant epithelial cells. Two of the three tumors with abnormal Rb expression also had p53 mutations and staining on serial sections demonstrated that selected ovarian cancer cells possessed mutations in both oncogenes. These data suggest that the loss of Rb gene expression may play a role in the pathogenesis of a small number of invasive ovarian malignancies, but not in noninvasive ovarian neoplasms.

Female↗
PubMed1995

Rearranged NFKB-2 genes in lymphoid neoplasms code for constitutively active nuclear transactivators.

The NFKB-2 gene codes for an NF-kappa B-related transcription factor containing rel-polyG-ankyrin domains. Chromosomal rearrangements of the NFKB-2 locus have been found in various types of lymphoid neoplasms, suggesting that they may contribute to lymphomagenesis. Rearrangements cluster within the 3'-terminal ankyrin-encoding domain of the NFKB-2 gene and lead to the production of C-terminally truncated proteins which, in some cases, are fused to heterologous protein domains. In order to determine the functional consequences of these alterations, we have analyzed the subcellular localization, DNA binding, and transcriptional activity of two representative tumor-associated mutants in which the ankyrin domain is either terminally truncated (NFKB-2p85) or truncated and joined to an out-of-frame immunoglobulin C alpha domain (lyt-10C alpha). Immunofluorescence studies performed on cells transfected with p85 or lyt-10C alpha expression vectors showed that both the abnormal proteins were constitutively localized in the nucleus. Immunoprecipitation analysis of UV-cross-linked DNA-protein adducts showed that p85 can bind kappa B sites in its unprocessed form. Cotransfection of p85 or lyt-10C alpha expression vectors with kappa B-driven reporter plasmids showed that both p85 and lyt-10C alpha have retained the ability to mediate transcriptional activation via heterodimerization with Rel-Ap65 but have lost the transrepression activity associated with homodimeric DNA binding. Furthermore, both p85 and lyt-10C alpha were capable of independent transactivation of kappa B-reporter genes and this activity could not be further stimulated by Bcl-3. These abnormal proteins may contribute to lumphomagenesis by determining a constitutive activation of the NF-kappa B system and, in particular, of NFKB-2 target genes.

Ankyrins↗
PubMed1983

Immunoglobulin-gene rearrangements as unique clonal markers in human lymphoid neoplasms.

Immunoglobulin genes in their germ-line form are separated DNA subsegments that must be joined by means of recombinations during B-cell development. Individual immunoglobulin-gene rearrangements are specific for a given B cell and its progeny. We show that the detection of such gene rearrangements by Southern hybridization provides a sensitive marker for both clonality and B-cell lineage within lymphoid tissues lacking expression of definitive surface phenotypes. We have used these genetic markers in three ways: to establish a diagnosis of lymphoma in a neoplastic disorder of uncertain cell type, to show that some lymphomas that were previously classified as being of T-cell type in fact contain monoclonal B cells, and to detect clonal B-cell populations within lymphomatous tissues of uncertain immunotype and within an atypical lymphofollicular hyperplasia having no other clonal surface markers. These sensitive and unique indicators of clonality located directly at the DNA level are capable of providing insights into the cellular origin, early detection, and natural history of neoplasia.

B-Lymphocytes↗
PubMed1996

Silencing of the mammary-derived growth inhibitor (MDGI) gene in breast neoplasms is associated with epigenetic changes.

Recently, we reported that breast cancer cell lines fail to express the gene encoding the fatty acid binding protein mammary derived growth inhibitor (MDGI) and that transfection with an MDGI expression vector results in suppression of the malignant phenotype, suggesting that MDGI is a tumor suppressor gene. We also demonstrated that homozygous deletion and point mutation are not common mechanisms for silencing of the MDGI gene in human breast neoplasms. We now report that hypermethylation of HpaII and HhaI sites upstream of the first exon of the MDGI gene, and a SacII site in the first intron, occurs frequently in human breast cancer cell lines. This distinct methylation pattern is associated with loss of transcription and is reversible by treatment with 5-aza-deoxycytidine. Primary breast tumors also exhibited methylation of the SacII site (19 of 35, 54.3%) and the HpaII and HhaI sites (21 of 35, 66%). Hypermethylation of these sites was correlated with the absence of MDGI mRNA in these tumors. Our results suggest that epimutation of the MDGI gene leads to silencing, which, in turn, may initiate or contribute to progression of breast cancer.

Azacitidine↗
PubMed2006

Diagnostic and prognostic value of cell-cycle regulatory genes in malignant thyroid neoplasms.

BACKGROUND: Approximately 30% of patients with thyroid nodules have indeterminate or suspicious fine-needle aspiration (FNA) biopsy results. Because their risk of cancer is approximately 20%, these patients undergo thyroidectomy. We hypothesized that genes that regulate cell-cycle progression would be differentially expressed in malignant versus benign thyroid nodules and could serve as diagnostic markers and markers of disease aggressiveness. METHODS: We used a cDNA array with 96 cell-cycle regulatory genes to identify differentially expressed genes in pooled benign versus malignant thyroid neoplasms. Genes up- or down-regulated by more than 2-fold in malignant thyroid neoplasms were further evaluated by real-time quantitative polymerase chain reaction (PCR) in 95 patients with hyperplastic nodules (n = 19), follicular adenoma (n = 19), follicular thyroid cancer (n = 19), the follicular variant of papillary thyroid cancer (n = 19), and papillary thyroid cancer (n = 19). RESULTS: cDNA array analysis showed that cyclin B1, MCM5, MCM7, RAD9, ubiquitin C, CDK6, SKP2, and APAF1 were up-regulated in malignant thyroid neoplasms. Real-time quantitative PCR showed that MCM5, MCM7, and RAD9 mRNA expression were significantly higher in malignant than in benign thyroid neoplasms (< or = 0.0012). The combined use of MCM5, MCM7, and RAD9 mRNA expression had a sensitivity of 98.2% and a specificity of 65.7%. The level of MCM7 mRNA expression was higher in T4 than in T1, T2, and T3 differentiated thyroid cancers (P < 0.0127). CONCLUSIONS: MCM5, MCM7, and RAD9 are overexpressed in malignant thyroid neoplasms of follicular cell origin. These genes may be useful markers of malignant thyroid neoplasms as an adjunct to FNA biopsy. MCM7 mRNA expression is higher in locally invasive differentiated thyroid cancer.

Adenocarcinoma, Follicular↗
PubMed2002

Gene therapy for lung neoplasms.

The field of gene therapy is still in its infancy, but significant accomplishments have been achieved. The ability to transfer genes safely and successfully into animals and patients clearly has been established. It is highly likely that in the near future, gene therapy will be shown to have clear therapeutic efficacy in diseases such as the treatment of hemophilia (using adeno-associated virus vectors) and the stimulation of angiogenesis in peripheral vascular disease and myocardial ischemia. Although only Phase 1 cancer gene therapy trials for thoracic malignancy have been conducted (usually in patients with large tumor burdens and at submaximal doses), there are some hints of efficacy at higher doses of vector in trials for localized malignancy. The studies reviewed in this article demonstrate the first attempts to use gene therapy vectors for lung cancer and mesothelioma. Although none of the diseases studied was "cured," valuable lessons have been learned from these trials, especially in defining the challenges of relatively inefficient and transient delivery of transgene in vivo. Using this knowledge, the second phase of gene therapy research has begun, with a strong focus on developing improved vector technology. Given the progress so far, there is little doubt that gene therapy will become a key approach for the treatment of thoracic malignancies in the near future.

Forecasting↗
PubMed1999

Quantitative study on expression of p16 multiple tumor suppressor gene in salivary gland neoplasm.

The expression of p16 gene in normal salivary acini, benign tumors and carcinomas were microscopically and quantitatively observed by using immunohistochemical method LSAB and CMIASWIN methods. The expression of p16 gene were found in all 3 groups. The positive unit (PU) was higher in tumor group and cancer group than that in normal group (P < 0.01). Furthermore, the PU of p16 was stronger in cytoplasm than in nucleus. Malignant tumors and acini surrounding the tumor revealed strong positives and weak positives respectively. The PU of p16 gene was higher in deep lobe of recurrent parotid neoplasm with incomplete capsule than that in shallow lobe of primary parotid neoplasm with complete capsule. The findings suggests that p16 gene plays an equally important role in the salivary gland tumors and tumors in other part of the body.

Adenoma, Pleomorphic↗
PubMed2003

Genetic alterations in the Catnb gene but not the H-ras gene in hepatocellular neoplasms and hepatoblastomas of B6C3F(1) mice following exposure to diethanolamine for 2 years.

The present study characterized the immunohistochemical localization of beta-catenin protein in hepatocellular neoplasms and hepatoblastomas in B6C3F(1) mice exposed to diethanolamine (DEA) for 2 years and evaluated genetic alterations in the Catnb and H-ras genes which are known to play important roles in the pathogenesis of liver malignancies. Genomic DNA was isolated from paraffin sections of each liver tumor. Catnb exon 2 (corresponds to exon 3 in human) genetic alterations were identified in 18/18 (100%) hepatoblastomas from DEA exposed mice. Deletion mutations (15/18, 83%) were identified more frequently than point mutations (6/18, 33%) in hepatoblastomas. Eleven of 34 (32%) hepatocellular adenomas and carcinomas from DEA treated mice had mutations in exon 2 of the beta-catenin gene, while only 1 of 10 spontaneous neoplasms had a deletion mutation of codon 5-6. Common to all liver neoplasms (hepatocellular adenomas, carcinomas and hepatoblastomas) was membrane staining for the beta-catenin protein, while cytoplasmic and nuclear staining was observed only in hepatoblastomas. The lack of H-ras mutations in hepatocellular neoplasms and hepatoblastomas suggests that the ras signal transduction pathway is not involved in the development of liver tumors following DEA exposure which is different from that of spontaneous liver tumors that often contain H-ras mutations.

Adenoma, Liver Cell↗
PubMed2001

Absence of mutation of the p73 gene in astrocytic neoplasms.

In subgroups of astrocytic neoplasms, including glioblastoma (GBM), mutations of the p53 tumour suppressor gene lead to loss of growth-suppressive properties. A p53-related gene termed p73 has recently been identified; its gene product shows structural and functional similarities to p53. After being mapped to chromosome region 1p36, p73 was proposed to act as a tumour suppressor gene, as this region is frequently deleted in a variety of human cancers, including astrocytic tumours. To determine whether p73 is involved in astrocytoma/GBM development, we analysed 10 pilocytic astrocytomas, 15 WHO grade II astrocytomas, 15 WHO grade III anaplastic astrocytomas, and 20 GBM for p73 gene alterations. In parallel, we used six polymorphic markers to determine the allelic status of region 1p36 in this tumour series. Although loss of heterozygosity was evidenced in 12 of 60 cases (20% of samples), PCR-SSCP and direct sequencing failed to detect any gene mutation in the entire coding region and intronic sequences of p73. Eight tumours displayed five distinct polymorphic nucleotide changes, also present in the corresponding normal DNA. These variations consisted of T-->C variation, with no change in Thr173; C-->T transition, with no change in His197; exon 9 simultaneous double change C-->T and T-->C , with no variations in Ala336 and His349, respectively, and C-->T change at exon 9/-24 position of intron 8. These results suggest that, in astrocytic gliomas, p73 may not play a major role as a tumour suppressor, but the relatively high incidence of LOH confirms the presence at 1p36 of an as yet unidentified gene of this category, with a key function in astrocytoma/GBM progression.

Astrocytoma↗