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Large-scale genetic analysis of gliomas: correlation with tumor cytogenetics and histopathology
Abstracts / Cancer Genetics and Cytogenetics 203 (2010) 66e99
85
LARGE-SCALE GENETIC ANALYSIS OF GLIOMAS: CORRELATION WITH TUMOR CYTOGENETICS AND HISTOPATHOLOGY
MOLECULAR GENETIC ALTERATIONS IN PROSTATE CANCER AND ITS MICROENVIRONMENT
Ana Luı´sa Vital1,2, Maria Dolores Tabernero3,4,5, Abel Castrillo6, Olinda Rebelo7, Hermı´nio Ta˜o8, Fernando Gomes8, Ctarina Resende de Oliveira2, Maria Celeste Lopes1,2, Alberto Orfao4
Tatiana Kekeeva1, Larisa Zavalishina1, Yulia Andreeva1, Georgy Frank1, Marina Nemtsova2, Dmitry Zaletaev2
1. Centre for Neurosciences and Cell Biology, University of Coimbra, Portugal 2. Faculty of Pharmacy, University of Coimbra, Portugal 3. Research Unit of the University Hospital of Salamanca, Spain 4. Centre for Cancer Research (CIC IBMCC-CSIC/USAL) Salamanca, Spain 5. Instituto de Estudios de Ciencias de la Salud de Castilla y Leo´n (IECSCYL), Spain 6. Mathematician-Neurosurgery Service of University Hospital of Salamanca, Spain 7. Neuropathology Laboratory, Neurology Service, University Hospital of Coimbra, Portugal 8. Neurosurgery Service, University Hospital of Coimbra, Portugal
Genetic alterations and molecular pathways involved in gliomas have been extensively studied. However, few studies have investigated the relationship of gene expression with cytogenetics. Our major goal was to recognize if the cytogenetic heterogeneity of human gliomas, particularly that of high-grade tumors, translates into different gene expression profiles, which may contribute to a better understanding of the behavior of the tumor and patient outcome. We assessed 40 gliomas to establish their gene expression profiles (GEP) using Affymetrix oligonucleotide arrays (U133Plus2.0 chip), correlating them with histopathology and patterns of genetic evolution as determined by fluorescence in situ hybridization (FISH). Data files containing the expression levels for the 40 tumors were analyzed using the R and Bioconductor software tools. Unsupervised and supervised analyses showed unique GEP for gliosarcomas versus all other glioma subtypes, with significantly different expression levels of genes coding for structural proteins, e.g., the KRT80, BAIP2L1 (over-expressed) and PTPRZ1 and GFAP (under-expressed) genes. Additionally, significantly different GEP were also found in low- versus highgrade gliomas, the 71 most discriminating genes being involved in the regulation of cell proliferation, apoptosis, DNA repair, and signal transduction: EXO1 (1q42-q43), CBX8 (17q25.3), NCOA4 (10q11.2), SGMS1 (10q11.2), ZYX (7q32), TK1 (17q23.2-q25), SCAPER (15q24), BLOC1S2 (10q24.31), DLG7 (14q22.3), AURKB (17p13.1), CHAF1A (19p13.3), RECQL4 (8q24.3), CCNA2 (4q25-q31), BIRC5 (17q25), and UBE2C (20q13.12). Finally, three subgroups of glioblastoma multiforme (GBM) were identified according to their GEP, which were closely associated with the cytogenetic profile of their ancestral tumor cell clones: (i) EGFR amplification, (ii) isolated trisomy 7, and (iii) more complex karyotypes. In summary, distinct glioma molecular subtypes according to GEP were identified that could be critical for the understanding of the biology and clinical behavior of the tumors. Our results show a clear association between the GEP of gliomas and tumor histopathology. Additionally, among grade IV astrocytomas, GEP are significantly associated with cell proliferation, apoptosis-mediated cell death, and other cellular functions, as also with ancestral tumor cell clone. These results could support the development of a new classification system for gliomas that could be of help in improving patient stratification for prognostic evaluation.
1. Herzen Moscow Oncological Research Institute, Russia 2. Sechenov Moscow Medical Academy, Russia
Due to intensive investigations during the last ten years it has become increasingly clear that the tumor microenvironment plays a critical role in prostate carcinogenesis. The tumor microenvironment undergoes significant modifications, such as protein expression alterations and various genetic changes of stromal cells. Accumulation of multiple genetic alterations, such as tumor suppressor hypermethylation, allelic imbalance, loss of heterozygosity, and mutations, is typical not only for epithelial cancer cells but also for tumor-associated fibroblasts and endothelial cells. We have investigated epigenetic changes, allelic imbalance (LOH/AI), and TMPRSS2/ERG fusion gene expression in prostate cancers and their microenvironment. Tumor epithelia, tumor-associated stroma, and prostate intraepithelial neoplasia (PIN) in 51 prostatectomy specimens from patients with pT1eT4 stage prostate cancer were isolated using laser capture micro-dissection. Microsatellite allelotyping was evaluated using 4 highly polymorphic markers for chromosomal regions 8p22, 16q23-24, and 13q14. The methylation status of the p16, HIC1, N33, and GSTP1 genes and mRNA expression level of TMPRSS2/ERG, significant in prostate carcinogenesis, were investigated using methylationsensitive PCR and RT-PCR, respectively. Our results show that genetic and epigenetic aberrations of stromal cells are frequent events present at all stages of prostate cancer development. First, frequencies of genetic aberrations are as high in stromal cells as in tumor cells. Second, the molecular aberration spectra in stroma and tumor tissue are discordant. Third, stromal AI frequencies for initial prostate cancer stages demonstrate an at least 2-fold excess over epithelial ones. Fourth, some methylation in both hyperplastic epithelium and stromal cells was observed in normal-appearing tissues located adjacent to tumors. In contrast, we found TMPRSS2/ERG expression only in tumor epithelium samples (8/10) and not in the adjacent tumor stroma or PIN specimens. This could be an unique tumor epithelial cell alteration distinct from nonspecific allelic imbalance or gene methylation. Thus, numerous stroma investigations testify that cancer is not an epithelium cell disease but includes the tumor microenvironment. Although some molecular alterations are common for prostate cancer cells and their tumor microenvironment, TMPRSS2/ ERG gene fusions are restricted to the tumor only. Which genetic alterations are primary is a question that remains to be elucidated.
85
LARGE-SCALE GENETIC ANALYSIS OF GLIOMAS: CORRELATION WITH TUMOR CYTOGENETICS AND HISTOPATHOLOGY
MOLECULAR GENETIC ALTERATIONS IN PROSTATE CANCER AND ITS MICROENVIRONMENT
Ana Luı´sa Vital1,2, Maria Dolores Tabernero3,4,5, Abel Castrillo6, Olinda Rebelo7, Hermı´nio Ta˜o8, Fernando Gomes8, Ctarina Resende de Oliveira2, Maria Celeste Lopes1,2, Alberto Orfao4
Tatiana Kekeeva1, Larisa Zavalishina1, Yulia Andreeva1, Georgy Frank1, Marina Nemtsova2, Dmitry Zaletaev2
1. Centre for Neurosciences and Cell Biology, University of Coimbra, Portugal 2. Faculty of Pharmacy, University of Coimbra, Portugal 3. Research Unit of the University Hospital of Salamanca, Spain 4. Centre for Cancer Research (CIC IBMCC-CSIC/USAL) Salamanca, Spain 5. Instituto de Estudios de Ciencias de la Salud de Castilla y Leo´n (IECSCYL), Spain 6. Mathematician-Neurosurgery Service of University Hospital of Salamanca, Spain 7. Neuropathology Laboratory, Neurology Service, University Hospital of Coimbra, Portugal 8. Neurosurgery Service, University Hospital of Coimbra, Portugal
Genetic alterations and molecular pathways involved in gliomas have been extensively studied. However, few studies have investigated the relationship of gene expression with cytogenetics. Our major goal was to recognize if the cytogenetic heterogeneity of human gliomas, particularly that of high-grade tumors, translates into different gene expression profiles, which may contribute to a better understanding of the behavior of the tumor and patient outcome. We assessed 40 gliomas to establish their gene expression profiles (GEP) using Affymetrix oligonucleotide arrays (U133Plus2.0 chip), correlating them with histopathology and patterns of genetic evolution as determined by fluorescence in situ hybridization (FISH). Data files containing the expression levels for the 40 tumors were analyzed using the R and Bioconductor software tools. Unsupervised and supervised analyses showed unique GEP for gliosarcomas versus all other glioma subtypes, with significantly different expression levels of genes coding for structural proteins, e.g., the KRT80, BAIP2L1 (over-expressed) and PTPRZ1 and GFAP (under-expressed) genes. Additionally, significantly different GEP were also found in low- versus highgrade gliomas, the 71 most discriminating genes being involved in the regulation of cell proliferation, apoptosis, DNA repair, and signal transduction: EXO1 (1q42-q43), CBX8 (17q25.3), NCOA4 (10q11.2), SGMS1 (10q11.2), ZYX (7q32), TK1 (17q23.2-q25), SCAPER (15q24), BLOC1S2 (10q24.31), DLG7 (14q22.3), AURKB (17p13.1), CHAF1A (19p13.3), RECQL4 (8q24.3), CCNA2 (4q25-q31), BIRC5 (17q25), and UBE2C (20q13.12). Finally, three subgroups of glioblastoma multiforme (GBM) were identified according to their GEP, which were closely associated with the cytogenetic profile of their ancestral tumor cell clones: (i) EGFR amplification, (ii) isolated trisomy 7, and (iii) more complex karyotypes. In summary, distinct glioma molecular subtypes according to GEP were identified that could be critical for the understanding of the biology and clinical behavior of the tumors. Our results show a clear association between the GEP of gliomas and tumor histopathology. Additionally, among grade IV astrocytomas, GEP are significantly associated with cell proliferation, apoptosis-mediated cell death, and other cellular functions, as also with ancestral tumor cell clone. These results could support the development of a new classification system for gliomas that could be of help in improving patient stratification for prognostic evaluation.
1. Herzen Moscow Oncological Research Institute, Russia 2. Sechenov Moscow Medical Academy, Russia
Due to intensive investigations during the last ten years it has become increasingly clear that the tumor microenvironment plays a critical role in prostate carcinogenesis. The tumor microenvironment undergoes significant modifications, such as protein expression alterations and various genetic changes of stromal cells. Accumulation of multiple genetic alterations, such as tumor suppressor hypermethylation, allelic imbalance, loss of heterozygosity, and mutations, is typical not only for epithelial cancer cells but also for tumor-associated fibroblasts and endothelial cells. We have investigated epigenetic changes, allelic imbalance (LOH/AI), and TMPRSS2/ERG fusion gene expression in prostate cancers and their microenvironment. Tumor epithelia, tumor-associated stroma, and prostate intraepithelial neoplasia (PIN) in 51 prostatectomy specimens from patients with pT1eT4 stage prostate cancer were isolated using laser capture micro-dissection. Microsatellite allelotyping was evaluated using 4 highly polymorphic markers for chromosomal regions 8p22, 16q23-24, and 13q14. The methylation status of the p16, HIC1, N33, and GSTP1 genes and mRNA expression level of TMPRSS2/ERG, significant in prostate carcinogenesis, were investigated using methylationsensitive PCR and RT-PCR, respectively. Our results show that genetic and epigenetic aberrations of stromal cells are frequent events present at all stages of prostate cancer development. First, frequencies of genetic aberrations are as high in stromal cells as in tumor cells. Second, the molecular aberration spectra in stroma and tumor tissue are discordant. Third, stromal AI frequencies for initial prostate cancer stages demonstrate an at least 2-fold excess over epithelial ones. Fourth, some methylation in both hyperplastic epithelium and stromal cells was observed in normal-appearing tissues located adjacent to tumors. In contrast, we found TMPRSS2/ERG expression only in tumor epithelium samples (8/10) and not in the adjacent tumor stroma or PIN specimens. This could be an unique tumor epithelial cell alteration distinct from nonspecific allelic imbalance or gene methylation. Thus, numerous stroma investigations testify that cancer is not an epithelium cell disease but includes the tumor microenvironment. Although some molecular alterations are common for prostate cancer cells and their tumor microenvironment, TMPRSS2/ ERG gene fusions are restricted to the tumor only. Which genetic alterations are primary is a question that remains to be elucidated.