Diego Arenas

A molecular analysis by gene expression profiling reveals Bik/NBK overexpression in sporadic breast tumor samples of Mexican females

BackgroundBreast cancer is one of the most frequent causes of death in Mexican women over 35 years of age. At molecular level, changes in many genetic networks have been reported as associated with this neoplasia. To analyze these changes, we determined gene expression profiles of tumors from Mexican women with breast cancer at different stages and compared these with those of normal breast tissue samples.Methods32P-radiolabeled cDNA was synthesized by reverse transcription of mRNA from fresh sporadic breast tumor biopsies, as well as normal breast tissue. cDNA probes were hybridized to microarrays and expression levels registered using a phosphorimager. Expression levels of some genes were validated by real time RT-PCR and immunohistochemical assays.ResultsWe identified two subgroups of tumors according to their expression profiles, probably related with cancer progression. Ten genes, unexpressed in normal tissue, were turned on in some tumors. We found consistent high expression of Bik gene in 14/15 tumors with predominant cytoplasmic distribution.ConclusionRecently, the product of the Bik gene has been associated with tumoral reversion in different neoplasic cell lines, and was proposed as therapy to induce apoptosis in cancers, including breast tumors. Even though a relationship among genes, for example those from a particular pathway, can be observed through microarrays, this relationship might not be sufficient to assign a definitive role to Bik in development and progression of the neoplasia. The findings herein reported deserve further investigation.

Multiple copies of RUNX1: description of 14 new patients, follow-up, and a review of the literature

RUNX1 over-representation is present in children with acute lymphoblastic leukemia. Although these cases have been related with poor outcome, not all reports describe patient follow-up. To understand its associated clinical features and prognosis, we report on 14 children with ALL and RUNX1 over-representation with laboratory data and outcomes compared to previous reports. Eighty-six children with RUNX1 over-representation have been described, including the 14 patients of this study. Most of them are between 6 and 15 years of age, have low leukocyte counts, pre-B immunophenotype, and three to eight RUNX1 copies. Of the 69 patients with follow-up data, 21 of them relapsed or died, suggesting that RUNX1 over-representation is associated to a poor outcome.

Identification of novel mutations in the RB1 gene in Mexican patients with retinoblastoma

Retinoblastoma (RB) is a childhood tumor of the eye with an average incidence of one case in every 15,000-20,000 live births and occurs in sporadic or hereditary form. This cancer results from loss or inactivation of the RB1 gene located at 13q14.1. This gene encodes for a 110 Kd nuclear phosphoprotein (pRB) that plays a major role in cell proliferation control. Different types of mutations in the RB1 gene have been reported, but point mutations are the most common. There are no molecular studies on RB1 gene mutation in Mexican patients. In this study, 19 patients with bilateral or unilateral RB were analyzed. Genetic and cytogenetic studies were carried out. Detection of RB1 gene mutations was done using single-strand conformational polymorphism (SSCP). Five conformational polymorphisms were identified in different exons. In all cases, SSCP sequence showed new non-described mutations that produced a frameshift on the open reading frame. The identification of mutations in the RB1 gene contributes to basic knowledge of this neoplasia and permits the possibility to offer adequate genetic counseling to relatives at risk.

Using linear-bilinear models for studying gene expression × treatment interaction in microarray experiments

In microarray experiments, the global and the specific gene expression in the two-way table of gene x treatments (or tissues) can be studied using linear-bilinear models that incorporate the main effects of genes (G), treatment (T), and gene x treatment interaction (G x T). The plot of the first two axes obtained from the singular value decomposition of the bilinear (multiplicative) term of these models (biplot) facilitates the interpretation of the gene expression patterns. In this study, two microarray datasets were used to illustrate how two linear-bilinear models, the additive main effect and multiplicative interaction (AMMI) and the treatment regression model (TREG) and their biplots can be used to determine the overall gene expression pattern across treatments (or tissues) and for specific treatments. Dataset 1 had 5,339 genes and the objective was to identify genes with modified expression during maize (Zea mays) seed development in response to different parental ploidy levels. In Dataset 2, the aim was to study gene expression in 15 tissue samples with different levels of development of breast cancer when compared with the expression of the genes in noninfected tissues. The results from the analyses of Dataset 1 showed that the biplots of the AMMI and TREG models allow identification of subsets of genes and treatments with noncrossover G x T interaction or with important levels of crossover G x T. Results from Dataset 2 showed that the TREG model and its biplot facilitates the identification of genes with high expression in all tumor cells. Also, the TREG biplots allowed identification of subsets of genes with a low level of gene x tissue crossover interaction.

The neurofibromin 1 type I isoform predominance characterises female population affected by sporadic breast cancer: preliminary data

Aims Neurofibromin 1 (NF1) as a tumour suppressor gene can give rise to several transcripts by an alternative splicing event, generated at least for CELF cofactors. At present, the NF1 isoforms and CELF splicing transcripts in sporadic breast cancer are unknown. The aim of the authors was to detect NF1 gene expression, the NF1 isoform ratio and the CELF transcripts present in sporadic breast cancer. Methods Neurofibromin and RAS expression were analysed on tissue microarrays containing sporadic breast cancer (n=22), benign lesions (n=18, including six fibroadenomas, six fibrocystic changes and six ductal hyperplasias) and normal breast tissue (n=6) by immunohistochemistry assay. NF1 and CELF 3–6 RNA expression was performed by end point reverse transcription-PCR in the breast samples. Results NF1 and RAS expression in breast tissues showed no differential expression by immunohistochemistry results. Interestingly, the authors observed a shift transition in the isoform transcripts, from type II in normal breast tissue to type I isoform in breast carcinomas. CELF cofactor expression failed to be related with the shift transition of NF1 in breast tissues. Conclusions These data suggest that there is a tendency for an NF1 expression shift transition from type II to type I isoform, which could comprise a significant event in the development and progression of sporadic breast cancer. This shift transition may not be related with CELF cofactors.

Biomarker analysis by tissue microarray technology of Bik, Bcl-2, Bax, ER-α, ER-β, Her2/neu, PCNA, P53, pRB proteins and apoptotic index (by TUNEL) in breast cancer Mexican biopsies.

CTRC-AACR San Antonio Breast Cancer Symposium: 2008 Abstracts Abstract #4043 Background: The development and progression of epithelial cancers are the results of changes in many genetic networks. Through massive analysis techniques various prognostic factors have been studied to determine proteins implicated in cancer. A new technology used is tissue microarray (TMAs), which allows the assessment of several patients at different stages in a single slide. Methods: TMA blocks with up to 128 cylinders were made by using 1.5-mm diameter tissue cores from each paraffin block. In a series of 70 formalin-fixed carcinomas, we analyzed the immuno-expression of Bik, Bcl-2, Bax, ER-α, ER-β, Her2, PCNA, P53 and RB proteins. For apoptosis detection the TUNEL technique was used. Expression profiles for these tumors were generated with an unsupervised clustering and a T Test analysis. Results: We developed TMAs with samples from Mexican women with breast cancer at different stages (type I, II and III) and compared these with those of non affected breast tissue of the same womens samples. Through a hierarchical cluster we found three subgroups of tumors according to protein expression behavior. The apoptotic process was found in low grade 4.28%; moderate grade 90% and high grade 5.71% of samples. Statistical analysis revealed that Bax gene ( p=0.000 ) expression was significantly increased in samples stage I and underexpressed in samples stage IIIA. The Bcl-2 gene was under-expressed in the majority of samples of the stage II. Even when the Bik gene was detected the protein level was over-expressed in 44.29% of the cases with noa significant correlation with apoptosis (TUNEL) ( p=0.006) . The samples where there were more alterations of the studied proteins were understood in the stages IIA (T2N0M0) and IIB (T2N1M0). ![][1] Conclusions: The analysis of specimens of several patients in different stages of the disease turns out to be useful to establish a better diagnosis and prognosis. Differential regulation of these genes, especially Bik and Bax, may contribute to the biological nature of a clinically more aggressive and highly proliferative breast cancers. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4043. [1]: /embed/graphic-1.gif

Proteomic analysis for NBK, Bcl-2, Bax genes and apoptosis (TUNEL) in breast cancer biopsies (stage II/III) by tissue microarray technology.

22194 Background: Breast cancer is the second leading cause of cancer deaths in Mexican females. Various prognostic factors have been studied to determine proteins from genes implicated in cancer d...