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7 results on '"MESH: DNA, Neoplasm"'

1. Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics

Author

Caval, Mohamed S. Bouzidi, Jean-Pierre Vartanian, Michel Henry, Rodolphe Suspène, Simon Wain-Hobson, Rétrovirologie Moléculaire, Institut Pasteur [Paris] (IP), and This work was supported by grants from the Institut Pasteur, INCa and the CNRS. VC and MSB were supported by OSEO and the Ligue Nationale Contre le Cancer.

Subjects
MESH: Neoplasm Proteins, CD4-Positive T-Lymphocytes, Cancer Research, [SDV]Life Sciences [q-bio], MESH: beta Catenin, Cytidine, medicine.disease_cause, Nucleic Acid Denaturation, Genome, Polymerase Chain Reaction, law.invention, Cytosine Deaminase, chemistry.chemical_compound, MESH: Liver Neoplasms, law, APOBEC Deaminases, APOBEC3A, MESH: Carcinoma, Hepatocellular, Polymerase chain reaction, Cells, Cultured, beta Catenin, Genetics, Recombination, Genetic, Mutation, Liver Neoplasms, MESH: APOBEC Deaminases, Temperature, MESH: CD4-Positive T-Lymphocytes, APOBEC3, DNA, Neoplasm, MESH: Temperature, MESH: Hepatitis C, Chronic, Nuclear DNA, Neoplasm Proteins, Oncology, MESH: Recombination, Genetic, MESH: Interferon-alpha, MESH: Cytidine, MESH: Cells, Cultured, MESH: Mutation, Carcinoma, Hepatocellular, MESH: Hepatitis B, Chronic, MESH: DNA, Neoplasm, Context (language use), Genomics, MESH: Nucleic Acid Denaturation, Biology, MESH: Phytohemagglutinins, Hepatitis B, Chronic, Cytidine Deaminase, medicine, Humans, 3DPCR, Phytohemagglutinins, MESH: Cytidine Deaminase, cancer genomics, MESH: Humans, MESH: Cytosine Deaminase, hypermutation, Interferon-alpha, MESH: Interleukin-2, MESH: Polymerase Chain Reaction, Genetics and Genomics, Hepatitis C, Chronic, chemistry, Interleukin-2, DNA
Abstract

International audience; Background: The revolution in cancer genomics shows that the dominant mutations are CG->TA transitions. The sources of these mutations are probably two host cell cytidine deaminases APOBEC3A and APOBEC3B. The former in particular can access nuclear DNA and monotonously introduce phenomenal numbers of C->T mutations in the signature 5'TpC context. These can be copied as G->A transitions in the 5'GpA context.Methods: DNA hypermutated by an APOBEC3 enzyme can be recovered by a technique called 3DPCR, which stands for differential DNA denaturation PCR. This method exploits the fact that APOBEC3-edited DNA is richer in A+T compared with the reference. We explore explicitly 3DPCR error using cloned DNA.Results: Here we show that the technique has a higher error rate compared with standard PCR and can generate DNA strands containing both C->T and G->A mutations in a 5'GpCpR context. Sequences with similar traits have been recovered from human tumour DNA using 3DPCR.Conclusions: Differential DNA denaturation PCR cannot be used to identify fixed C->T transitions in cancer genomes. Presently, the overall mutation frequency is ∼10(4)-10(5) base substitutions per cancer genome, or 0.003-0.03 kb(-1). By contrast, the 3DPCR error rate is of the order of 4-20 kb(-1) owing to constant selection for AT DNA and PCR-mediated recombination. Accordingly, sequences recovered by 3DPCR harbouring mixed C->T and G->A mutations associated with the 5'GpC represent artefacts.

Published
2014
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2. Oncogene abnormalities in a series of primary melanomas of the sinonasal tract: NRAS mutations and cyclin D1 amplification are more frequent than KIT or BRAF mutations

Author

Nicolas Ortonne, Issam Abd Alsamad, Nicolas Dumaz, Meriem Chraybi, Maryse Baia, Christiane Copie-Bergman, Jocelyne André, Service d'anatomie et cytologie pathologiques, CHI Créteil, INSERM U955, équipe 9, Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Immunologie, dermatologie, oncologie, Oncodermatologie, immunologie et cellules souches cutanées (IDO (U976 / UMR_S 976)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, and Guellaen, Georges

Subjects
Male, Neuroblastoma RAS viral oncogene homolog, MESH: Cyclin D1, DNA Mutational Analysis, cyclin D1, sinonasal melanoma, medicine.disease_cause, MESH: Gene Amplification, GTP Phosphohydrolases, MESH: Aged, 80 and over, 0302 clinical medicine, Epidermal growth factor receptor, MESH: DNA Mutational Analysis, Melanoma, Aged, 80 and over, MESH: Aged, 0303 health sciences, Mutation, MESH: Middle Aged, medicine.diagnostic_test, biology, KIT, DNA, Neoplasm, Middle Aged, CCND1 amplification, 3. Good health, MESH: Proto-Oncogene Proteins c-kit, Proto-Oncogene Proteins c-kit, Real-time polymerase chain reaction, 030220 oncology & carcinogenesis, Female, MESH: Membrane Proteins, Paranasal Sinus Neoplasms, Proto-Oncogene Proteins B-raf, MESH: Mutation, MESH: GTP Phosphohydrolases, MESH: Melanoma, MESH: DNA, Neoplasm, NRAS, Article, Pathology and Forensic Medicine, 03 medical and health sciences, Cyclin D1, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, neoplasms, Aged, Retrospective Studies, 030304 developmental biology, MESH: Paranasal Sinus Neoplasms, MESH: Proto-Oncogene Proteins B-raf, MESH: Humans, Gene Amplification, Membrane Proteins, MESH: Retrospective Studies, Sinonasal Tract, medicine.disease, MESH: Male, BRAF mutation, Primary malignant melanoma of sinonasal tract, Cancer research, biology.protein, MESH: Female, Fluorescence in situ hybridization
Abstract

International audience; Primary malignant melanoma of sinonasal tract is a rare but severe form of melanoma. We retrospectively analyzed 17 cases and focused on the histologic presentation and the expression of c-Kit, epidermal growth factor receptor (EGFR), cyclin D1/Bcl-1, PS100, and HMB45 and searched for BRAF, NRAS, and KIT mutations that are known to be associated with melanoma subtypes, together with amplifications of KIT, cyclin D1, cyclin-dependent kinase 4, MDM2, and microphthalmia-associated transcription factor using quantitative polymerase chain reaction. In most cases (78%), an in situ component was evidenced. Invasive components were composed of diffuse areas of rhabdoid, epithelioid, or spindle cells and, in most cases, lacked inflammatory reaction, suggesting that an immune escape phenomenon probably develops when the disease progresses. EGFR was rarely and weakly expressed in the in situ component of 2 cases. None of the investigated case showed BRAF V600E, but 1 had a D594G mutation. NRAS mutations in exon 2 (G12D or G12A) were found in 3 cases (18%), and a KIT mutation in exon 11 (L576P), in 1, whereas c-Kit was expressed at the protein level in half of the cases. Amplifications of cyclin D1 were evidenced in 5 cases, confirmed in 3 by fluorescence in situ hybridization, but this was not always correlated with protein expression, found in 8 patients (62.5%), 3 having no significant amplification. In conclusion, primary malignant melanoma of sinonasal tract is not associated with BRAF V600E mutations. Instead, NRAS or KIT mutations and cyclin D1 amplification can be found in a proportion of cases, suggesting that primary malignant melanoma of sinonasal tract is heterogeneous at the molecular level and should not be sensitive to therapeutic approaches aiming at BRAF.

Published
2013
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3. Aberrant DNA methylation distinguishes hepatocellular carcinoma associated with HBV and HCV infection and alcohol intake

Author

Fabien Zoulim, Marie-Pierre Lambert, Massimo Tommasino, Zdenko Herceg, Jörg Tost, Jean-Yves Scoazec, Anupam Paliwal, Pierre Hainaut, Thomas Vaissière, Bakary S. Sylla, Isabelle Chemin, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Interactions Bactéries-Cellules (UIBC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), International Agency for Cancer Research (IACR), Equipe 16, Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Service d'hépatologie et de gastroentérologie, Hospices Civils de Lyon (HCL)-Hôtel-Dieu-Hospices Civils de Lyon (HCL)-Hôtel-Dieu-Centre de Recherche en Cancérologie de Lyon (CRCL), Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Sect Mech Carcinogenesis, equipe 4, Laboratoire Central d'Anatomie et de Cytologie Pathologiques [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Centre de Recherche en Cancérologie de Lyon (CRCL), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Interactions Bactéries-Cellules ( UIBC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), International Agency for Cancer Research ( IACR ), International Agency for Cancer Research, Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Hospices Civils de Lyon ( HCL ) -Hôtel-Dieu-Hospices Civils de Lyon ( HCL ) -Hôtel-Dieu-Centre de Recherche en Cancérologie de Lyon ( CRCL ), Centre International de Recherche contre le Cancer - International Agency for Research on Cancer ( CIRC - IARC ), Organisation mondiale de la santé (OMS/WHO), international Agency for Research on Cancer - IARC, Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ) -Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ) -Centre de Recherche en Cancérologie de Lyon ( CRCL ), Centre National de Génotypage ( CNG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Hospices Civils de Lyon (HCL)-Hôtel-Dieu-Hospices Civils de Lyon (HCL)-Hôtel-Dieu-Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), and Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Male, MESH : Liver Neoplasms, MESH : Aged, Receptors, Nicotinic, MESH: Base Sequence, medicine.disease_cause, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH: DNA Methylation, 0302 clinical medicine, Risk Factors, MESH: Liver Neoplasms, MESH: Risk Factors, MESH : Female, MESH: Gene Silencing, MESH: Carcinoma, Hepatocellular, MESH: Glutathione S-Transferase pi, MESH: Aged, 0303 health sciences, MESH: Middle Aged, MESH : Tumor Suppressor Proteins, Liver Neoplasms, RNA-Binding Proteins, DNA, Neoplasm, Hepatitis C, Methylation, Middle Aged, MESH : Adult, Hepatitis B, MESH : Risk Factors, 3. Good health, DNA-Binding Proteins, 030220 oncology & carcinogenesis, Hepatocellular carcinoma, DNA methylation, MESH: Receptors, Nicotinic, Female, MESH : DNA Primers, MESH : DNA, Neoplasm, MESH : DNA-Binding Proteins, Adult, MESH : Carcinoma, Hepatocellular, MESH: DNA Primers, Carcinoma, Hepatocellular, Alcohol Drinking, MESH : Male, Hepatitis C virus, MESH : RNA-Binding Proteins, MESH: DNA, Neoplasm, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, MESH: Phosphoproteins, 03 medical and health sciences, MESH : Gene Silencing, medicine, Humans, MESH : Middle Aged, MESH: Tumor Suppressor Proteins, Gene Silencing, neoplasms, Aged, DNA Primers, 030304 developmental biology, MESH: Hepatitis C, Hepatitis B virus, MESH: Humans, Base Sequence, MESH : Receptors, Nicotinic, MESH: Hepatitis B, Hepatology, Tumor Suppressor Proteins, MESH : Humans, MESH : Hepatitis B, Cancer, MESH: Adult, DNA Methylation, MESH : Hepatitis C, Phosphoproteins, medicine.disease, MESH: Male, digestive system diseases, MESH : Alcohol Drinking, MESH: RNA-Binding Proteins, Glutathione S-Transferase pi, MESH : Glutathione S-Transferase pi, Immunology, MESH : Base Sequence, MESH : Phosphoproteins, MESH : DNA Methylation, MESH: Female, MESH: Alcohol Drinking, MESH: DNA-Binding Proteins
Abstract

International audience; BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) is one of the most frequent human cancers and a major cause of cancer-related death worldwide. The major risk factors for developing HCC are infection by hepatitis B virus (HBV) and hepatitis C virus (HCV), chronic alcoholism, and aflatoxins; however, critical gene targets remain largely unknown. Herein, we sought to establish DNA methylation patterns in HCC and corresponding cirrhotic tissues and to identify DNA methylation changes associated with major risk factors. METHODS: We have established assays for quantitative analysis of DNA methylation levels in a panel of seven cancer-associated genes and repetitive elements, and combined these assays with a series of HCC tumors, associated with major risk factors, collected from two different geographical areas. RESULTS: We found a high frequency of aberrant hypermethylation of specific genes (RASSF1A, GSTP1, CHRNA3, and DOK1) in HCC tumors as compared to control cirrhotic or normal liver tissues, suggesting that aberrant hypermethylation exhibits non-random and tumor-specific patterns in HCC. Importantly, our analysis revealed an association between alcohol intake and the hypomethylation of MGMT and between hypermethylation of GSTP1 and HBV infection, indicating that hypermethylation of the genes analyzed in HCC tumors exhibits remarkably distinct patterns depending on associated risk factors. CONCLUSIONS: This study identifies aberrant DNA methylation of specific cellular genes in HCC and the major risk factors associated with these changes, providing information that could be exploited for biomarker discovery in clinics and molecular epidemiology.

Published
2011
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4. A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours

Author

Fabienne Escande, Jean Michel Coindre, Silvana Pilotti, Sébastien Forget, Paolo Dei Tos, Pierre Paul Bringuier, Maria Debiec-Rychter, Elena Tamborini, David Gonzalez, Nicolas Faur, L Morzuch, Isabelle Hostein, Louisa Toffolati, Sylvianne Olschwang, Jean-François Emile, Département de pathologie, Institut Bergonié - CRLCC Bordeaux, university of leuven, Department of Human Genetics, Centre de Recherche en Cancérologie de Marseille ( CRCM ), Aix Marseille Université ( AMU ) -Institut Paoli-Calmettes-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), CA foncello Hospital, Department of pathology, Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Laboratoire de Physique des Lasers ( LPL ), Université Paris 13 ( UP13 ) -Université Sorbonne Paris Cité ( USPC ) -Institut Galilée-Centre National de la Recherche Scientifique ( CNRS ), biology and pathological laboratory, Laboratoire épidémiologie et oncogénèse des tumeurs digestives, Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ), Service de Pathologie, Institut Bergonié, Institut Bergonié [Bordeaux], UNICANCER-UNICANCER, UNICANCER, Radboud University Medical Center [Nijmegen], Centre de Recherche en Cancérologie de Marseille (CRCM / U891 Inserm), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique des Lasers (LPL), Université Paris 13 (UP13)-Centre National de la Recherche Scientifique (CNRS), Medical University of Gdańsk, Fondazione IRCCS Istituto Nazionale Tumori - National Cancer Institute [Milan], Biomarqueurs et essais cliniques en Cancérologie et Onco-Hématologie (BECCOH), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay

Subjects
Oncology, Receptor, Platelet-Derived Growth Factor alpha, MESH : Polymorphism, Genetic, MESH: Receptor, Platelet-Derived Growth Factor alpha, DNA Mutational Analysis, MESH: Quality Control, MESH : Genotype, medicine.disease_cause, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH: Genotype, MESH : Exons, 0302 clinical medicine, Surgical oncology, Genotype, MESH: DNA Mutational Analysis, 0303 health sciences, Mutation, MESH : Gastrointestinal Stromal Tumors, GiST, Gastroenterology, MESH : Quality Control, DNA, Neoplasm, Exons, 3. Good health, MESH: Proto-Oncogene Proteins c-kit, Proto-Oncogene Proteins c-kit, 030220 oncology & carcinogenesis, MESH: Laboratories, MESH : DNA, Neoplasm, MESH : Mutation, MESH: Gastrointestinal Stromal Tumors, Quality Control, medicine.medical_specialty, MESH: Mutation, Gastrointestinal Stromal Tumors, MESH: DNA, Neoplasm, [SDV.CAN]Life Sciences [q-bio]/Cancer, MESH : DNA Mutational Analysis, PDGFRA, Biology, MESH : Laboratories, MESH : Proto-Oncogene Proteins c-kit, 03 medical and health sciences, Internal medicine, MESH: Polymorphism, Genetic, medicine, Humans, Genotyping, 030304 developmental biology, MESH: Humans, Polymorphism, Genetic, MESH : Humans, Hepatology, digestive system diseases, Immunology, MESH : Receptor, Platelet-Derived Growth Factor alpha, MESH: Exons, Laboratories
Abstract

International audience; BACKGROUND: Although most gastrointestinal stromal tumours (GIST) carry oncogenic mutations in KIT exons 9, 11, 13 and 17, or in platelet-derived growth factor receptor alpha (PDGFRA) exons 12, 14 and 18, around 10% of GIST are free of these mutations. Genotyping and accurate detection of KIT/PDGFRA mutations in GIST are becoming increasingly useful for clinicians in the management of the disease. METHOD: To evaluate and improve laboratory practice in GIST mutation detection, we developed a mutational screening quality control program. Eleven laboratories were enrolled in this program and 50 DNA samples were analysed, each of them by four different laboratories, giving 200 mutational reports. RESULTS: In total, eight mutations were not detected by at least one laboratory. One false positive result was reported in one sample. Thus, the mean global rate of error with clinical implication based on 200 reports was 4.5%. Concerning specific polymorphisms detection, the rate varied from 0 to 100%, depending on the laboratory. The way mutations were reported was very heterogeneous, and some errors were detected. CONCLUSION: This study demonstrated that such a program was necessary for laboratories to improve the quality of the analysis, because an error rate of 4.5% may have clinical consequences for the patient.

Published
2011
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5. Integrative genome-wide analysis reveals a robust genomic glioblastoma signature associated with copy number driving changes in gene expression

Author

André Le Treut, Stephan Saikali, Véronique Quillien, Marc Aubry, Marie-Dominique Galibert, Amandine Etcheverry, Abderrahmane Hamlat, Marie de Tayrac, Jean Mosser, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Service de néphrologie [Rennes], CHU Pontchaillou [Rennes]-Hôpital Pontchaillou-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Plate-forme transcriptome, Service d'anatomie et cytologie pathologiques [Rennes] = Anatomy and Cytopathology [Rennes], CHU Pontchaillou [Rennes], Centre de ressources biologiques de Rennes, Service de neurochirurgie [Rennes] = Neurosurgery [Rennes], Service de Biologie, CRLCC Eugène Marquis (CRLCC), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Université de Rennes (UR), and De Villemeur, Hervé

Subjects
Cancer Research, Gene Dosage, MESH: Genes, erbB-1, Genome, MESH: Cadherins, MESH: Gene Dosage, 0302 clinical medicine, Gene expression, Oligonucleotide Array Sequence Analysis, Regulation of gene expression, Genetics, 0303 health sciences, MESH: Glioblastoma, GTPase-Activating Proteins, Chromosome Mapping, DNA, Neoplasm, MESH: Gene Expression Regulation, Neoplastic, Cadherins, Gene Expression Regulation, Neoplastic, 030220 oncology & carcinogenesis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Metabolic Networks and Pathways, MESH: DNA, Neoplasm, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Gene dosage, MESH: Gene Expression Profiling, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, MESH: Chromosome Aberrations, MESH: Tumor Suppressor Proteins, Gene, MESH: Genome, Human, 030304 developmental biology, Chromosome Aberrations, MESH: Humans, Genome, Human, Microarray analysis techniques, Gene Expression Profiling, Tumor Suppressor Proteins, Genes, erbB-1, Protocadherins, Gene expression profiling, MESH: Metabolic Networks and Pathways, MESH: Oligonucleotide Array Sequence Analysis, Human genome, Glioblastoma, MESH: Chromosome Mapping
Abstract

International audience; Glioblastoma multiforme shows multiple chromosomal aberrations, the impact of which on gene expression remains unclear. To investigate this relationship and to identify putative initiating genomic events, we integrated a paired copy number and gene expression survey in glioblastoma using whole human genome arrays. Loci of recurrent copy number alterations were combined with gene expression profiles obtained on the same tumor samples. We identified a set of 406 "cis-acting DNA targeted genes" corresponding to genomic aberrations with direct copy-number-driving changes in gene expression, defined as genes with either significantly concordant or correlated changes in DNA copy number and expression. Functional annotation revealed that these genes participate in key processes of cancer cell biology, providing insights into the genetic mechanisms driving glioblastoma. The robustness of the gene selection was validated on an external microarray data set including 81 glioblastomas and 23 non-neoplastic brain samples. The integration of array CGH and gene expression data highlights a robust cis-acting DNA targeted genes signature that may be critical for glioblastoma progression, with two tumor suppressor genes PCDH9 and STARD13 that could be involved in tumor invasiveness and resistance to etoposide.

Published
2009
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6. Fourth Updated ESACP Consensus Report on Diagnostic DNA Image Cytometry

Author

Albrecht Reith, Alfred Böcking, Gunter Haroske, Håvard E. Danielsen, Françoise Giroud, P. Spieler, Martin Oberholzer, A. Gschwendtner, Jan P. A. Baak, RFMQ, Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), and Usson, Yves

Subjects
medicine.medical_specialty, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, MEDLINE, MESH: DNA, Neoplasm, MESH: Algorithms, computer.software_genre, lcsh:RC254-282, 03 medical and health sciences, 0302 clinical medicine, Neoplasms, International congress, medicine, Humans, Medical physics, MESH: Neoplasms, lcsh:QH573-671, DNA Image Cytometry, Image Cytometry, 030304 developmental biology, 0303 health sciences, MESH: Humans, Task force, business.industry, lcsh:Cytology, MESH: DNA, DNA, DNA, Neoplasm, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, 3. Good health, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, 030220 oncology & carcinogenesis, Other, Data mining, business, computer, Algorithms, MESH: Image Cytometry
Abstract

A task force of experts in the field of diagnostic DNA image cytometry, invited by the ESACP, and further scientists or physicians revealing experience in that diagnostic procedure (names are given in Addendum A), agreed upon the following 4th updated Consensus Report on Standardised Diagnostic DNA Image Cytometry during the 7th International Congress of that society in Caen, 2001. This report is based on the three preceding ones [6,14,17]. It deals with the following items: – Critical review and update of the definitions given in the 1997 Consensus Update; – Review and detailed description of basic terms, principles and algorithms for diagnostic interpretation; – Recommendations concerning diagnostic or prognostic applications in specific fields of tumour pathology. This update is not aimed to substitute the 1997 consensus, but to make necessary addenda and give more detailed descriptions of those items not unequivocally to interpret by potential users of the methodology.

Published
2001

7. Comprehensive allelotyping of human hepatocellular carcinoma

Author

Hisaki Nagai, Anne Dejean, Pascal Pineau, Marie Annick Buendia, Pierre Tiollais, Cheriet Rauline, Samia, Recombinaison et Expression Génétique, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported in part by grants from the Ligue Nationale contre le Cancer and the Association pour la Recherche sur le Cancer. HN was supported by a grant from the Ligue Nationale contre le Cancer. PP was supported by grants from the Fondation pour la Recherche Médicale and the Institut Electricité-Santé., and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Cancer Research, [SDV]Life Sciences [q-bio], Polymerase Chain Reaction, Loss of heterozygosity, 0302 clinical medicine, MESH: Liver Neoplasms, Chromosomes, Human, hepatitis, tumor suppressor gene, MESH: Carcinoma, Hepatocellular, MESH: Heterozygote, Genetics, 0303 health sciences, Liver cell, Liver Neoplasms, hepatocellular carcinoma, DNA, Neoplasm, MESH: DNA, Satellite, 3. Good health, [SDV] Life Sciences [q-bio], 030220 oncology & carcinogenesis, Hepatocellular carcinoma, loss of heterozygosity, Liver cancer, Heterozygote, Carcinoma, Hepatocellular, Tumor suppressor gene, MESH: DNA, Neoplasm, Locus (genetics), Biology, DNA, Satellite, MESH: Chromosomes, Human, 03 medical and health sciences, Gene mapping, MESH: Polymorphism, Genetic, Carcinoma, medicine, Humans, Molecular Biology, neoplasms, MESH: Genome, Human, Alleles, 030304 developmental biology, MESH: Humans, Polymorphism, Genetic, Genome, Human, MESH: Alleles, MESH: Polymerase Chain Reaction, microsatellite markers, medicine.disease, digestive system diseases, MESH: Gene Deletion, Cancer research, Gene Deletion
Abstract

International audience; Hepatocellular carcinoma (HCC) is one of the most common cancers in many parts of the world, however the molecular mechanisms underlying liver cell transformation remain obscure. A genome-wide scan of loss of heterozygosity (LOH) in tumors provides a powerful tool to search for genes involved in neoplastic processes. To identify recurrent genetic alterations in liver tumors, we examined DNAs isolated from 120 HCCs and their adjacent non tumorous parts for LOH using a collection of 195 microsatellite markers located roughly every 20 cM throughout 39 autosomal arms. The mean heterozygosity was 73%. Our findings provide additional support that LOH for loci on chromosomal arms 1p, 4q, 6q, 8p, 13q and 16p is significantly elevated in HCC. The highest percentage of LOH is found for a locus in 8p23 (42% of informative csaes). This corresponds to one of the most common genetic abnormalities reported to date in these tumors. In addition, high ratio of LOH (> or = 35%) is observed on chromosome arms which had not been implicated in previous studies, notably on 1q, 2q and 9q. No correlation was found between LOH of specific chromosomal regions and etiologic factors such as chronic infections with hepatitis B or C viruses. This first report of an extensive allelotypic analysis of HCC should help in identifying new genes whose loss of function contributes to the development of liver cancer.

Published
1997
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