Molecular cytogenetics in solid tumors: laboratorial tool for diagnosis, prognosis, and therapy.
ABSTRACT The remarkable progress in the understanding of leukemogenesis was soundly sustained by methodological developments in the cytogenetic field. Nonrandom chromosomal abnormalities frequently associated with specific types of hematological disease play a major role in their diagnosis and have been demonstrated as independent prognostic indicators. Molecular pathways altered by chimeric or deregulated proteins as a consequence of chromosomal abnormalities have also significantly contributed to the development of targeted therapies, and cytogenetic assays are valuable for selecting patients for treatment and monitoring outcome. In solid tumors, significantly high levels of chromosome abnormalities have been detected, but distinction between critical and irrelevant events has been a major challenge. Consequently, the application of cytogenetic technology as diagnostic, prognostic, or therapeutic tools for these malignancies remains largely under appreciated. The emergence of molecular-based techniques such as fluorescence in situ hybridization was particularly useful for solid malignancies, and the spectrum of their application is rapidly expanding to improve efficiency and sensitivity in cancer prevention, diagnosis, prognosis, and therapy selection, alone or in combination with other diagnostic methods. This overview illustrates current uses and outlines potential applications for molecular cytogenetics in clinical oncology.
Article: Alterations in genes of the EGFR signaling pathway and their relationship to EGFR tyrosine kinase inhibitor sensitivity in lung cancer cell lines.[show abstract] [hide abstract]
ABSTRACT: Deregulation of EGFR signaling is common in non-small cell lung cancers (NSCLC) and this finding led to the development of tyrosine kinase inhibitors (TKIs) that are highly effective in a subset of NSCLC. Mutations of EGFR (mEGFR) and copy number gains (CNGs) of EGFR (gEGFR) and HER2 (gHER2) have been reported to predict for TKI response. Mutations in KRAS (mKRAS) are associated with primary resistance to TKIs. We investigated the relationship between mutations, CNGs and response to TKIs in a large panel of NSCLC cell lines. Genes studied were EGFR, HER2, HER3 HER4, KRAS, BRAF and PIK3CA. Mutations were detected by sequencing, while CNGs were determined by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH). IC50 values for the TKIs gefitinib (Iressa) and erlotinib (Tarceva) were determined by MTS assay. For any of the seven genes tested, mutations (39/77, 50.6%), copy number gains (50/77, 64.9%) or either (65/77, 84.4%) were frequent in NSCLC lines. Mutations of EGFR (13%) and KRAS (24.7%) were frequent, while they were less frequent for the other genes. The three techniques for determining CNG were well correlated, and qPCR data were used for further analyses. CNGs were relatively frequent for EGFR and KRAS in adenocarcinomas. While mutations were largely mutually exclusive, CNGs were not. EGFR and KRAS mutant lines frequently demonstrated mutant allele specific imbalance i.e. the mutant form was usually in great excess compared to the wild type form. On a molar basis, sensitivity to gefitinib and erlotinib were highly correlated. Multivariate analyses led to the following results: 1. mEGFR and gEGFR and gHER2 were independent factors related to gefitinib sensitivity, in descending order of importance. 2. mKRAS was associated with increased in vitro resistance to gefitinib. Our in vitro studies confirm and extend clinical observations and demonstrate the relative importance of both EGFR mutations and CNGs and HER2 CNGs in the sensitivity to TKIs.PLoS ONE 02/2009; 4(2):e4576. · 4.09 Impact Factor
Chapter: Image Processing for Automated Analysis of the Fluorescence In-Situ Hybridization (FISH) Microscopic Images[show abstract] [hide abstract]
ABSTRACT: The paper describes automated segmentation and analysis of the microscopic images resulting from fluorescence in-situ hybridization (FISH) analysis. FISH is a popular molecular cytogenetic method. The output of a single FISH analysis is a set of several tens or hundreds microscopic images — a single evaluated sample is of roughly 20mm diameter. The goal of an automated evaluation is to replace the subjective evaluation of images by the laboratory technician to achieve higher uniformity of results. Following explanation of the principle of the method and the typical contents of images, the processing flow of image segmentation is outlined and the results are presented on several example images. With emphasis on a low-cost solution, the ITK library is used for implementation. Keywordsfluorescence in-situ hybridization (FISH)–image processing–image segmentation09/2011: pages 622-633;
[show abstract] [hide abstract]
ABSTRACT: Although presently known as an environmentally-related disease and appears mostly sporadic, cancer is regarded as a genetic disease based on the presence of gene mutation as a consistent factor. The "Philadelphia Chromosome" found consistently among chronic myeloid leukemia (CML) patients was the first significant finding of a chromosomal abnormality specifically related to a particular disease. Starting from this point, cytogenetics as the study of chromosomes has become a valuable tool in the assessment of cancer - as an aid in diagnosis, thus guiding therapy, and as a prognostic marker. As is the nature of the proliferating marrow, chromosomal abnormalities were found mostly in hematologic malignancies, and the findings more pathognomonic. The situation is different in solid tumors, which when visible to the naked eye already will have complex chromosomal changes and thus pose technical difficulties to the cytogeneticist. However, scientists believe that the shift in chromosomal studies from conventional cytogenetics to molecular cytogenetics will provide further information regarding solid tumors.Acta medica Indonesiana 01/2011; 43(1):68-73.