Patterns of chromosomal copy-number alterations in intrahepatic cholangiocarcinoma

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• 作者：Cyril Dalmasso (1)
  Wassila Carpentier (2)
  Catherine Guettier (3) (4)
  Sophie Camilleri-Bro毛t (5)
  Wyllians Vendramini Borelli (4) (6)
  Ced谩lia Rosane Campos dos Santos (4) (6)
  Denis Castaing (3) (4)
  Jean-Charles Duclos-Vall茅e (3) (4)
  Philippe Bro毛t (4) (7) (8)
  
  1. Laboratoire de Math茅matiques et Mod茅lisation d鈥橢vry (LaMME) ; Universit茅 d鈥橢vry Val d鈥橢ssonne ; UMR CNRS 8071 ; USC INRA ; Evry ; France
  2. Plate-forme Post-G茅nomique P3S ; UPMC ; Facult茅 de M茅decine ; Paris ; France
  3. DHU Hepatinov ; Centre H茅pato-Biliaire ; H么pital Paul Brousse ; AP-HP ; Villejuif ; France
  4. Facult茅 de M茅decine ; Univ. Paris-Sud ; Kremlin-Bic锚tre ; France
  5. Department of Pathology ; McGill University ; Montreal ; Canada
  6. Faculdade de Medicina ; Hospital S茫o Lucas da Pontif铆cia Universidade Cat贸lica do Rio Grande do Sul ; Porto Alegre ; Brazil
  7. DHU Hepatinov ; UF Biostatistiques ; H么pital Paul Brousse ; AP-HP ; Villejuif ; France
  8. INSERM UMR-669 ; Villejuif ; France
  
• 关键词：Cholangiocarcinoma ; DNA copy ; number ; Genomic
• 刊名：BMC Cancer
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：15
• 期：1
• 全文大小：1,741 KB
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• 刊物主题：Cancer Research; Oncology; Stem Cells; Animal Models; Internal Medicine;
• 出版者：BioMed Central
• ISSN：1471-2407

文摘

Background Intrahepatic cholangiocarcinomas (ICC) are relatively rare malignant tumors associated with a poor prognosis. Recent studies using genome-wide sequencing technologies have mainly focused on identifying new driver mutations. There is nevertheless a need to investigate the spectrum of copy number aberrations in order to identify potential target genes in the altered chromosomal regions. The aim of this study was to characterize the patterns of chromosomal copy-number alterations (CNAs) in ICC. Methods 53 patients having ICC with frozen material were selected. In 47 cases, DNA hybridization has been performed on a genomewide SNP array. A procedure with a segmentation step and a calling step classified genomic regions into copy-number aberration states. We identified the exclusively amplified and deleted recurrent genomic areas. These areas are those showing the highest estimated propensity level for copy loss (resp. copy gain) together with the lowest level for copy gain (resp. copy loss). We investigated ICC clustering. We analyzed the relationships between CNAs and clinico-pathological characteristics. Results The overall genomic profile of ICC showed many alterations with higher rates for the deletions. Exclusively deleted genomic areas were 1p, 3p and 14q. The main exclusively amplified genomic areas were 1q, 7p, 7q and 8q. Based on the exclusively deleted/amplified genomic areas, a clustering analysis identified three tumors groups: the first group characterized by copy loss of 1p and copy gain of 7p, the second group characterized by 1p and 3p copy losses without 7p copy gain, the last group characterized mainly by very few CNAs. From univariate analyses, the number of tumors, the size of the largest tumor and the stage were significantly associated with shorter time recurrence. We found no relationship between the number of altered cytobands or tumor groups and time to recurrence. Conclusion This study describes the spectrum of chromosomal aberrations across the whole genome. Some of the recurrent exclusive CNAs harbor candidate target genes. Despite the absence of correlation between CNAs and clinico-pathological characteristics, the co-occurence of 7p gain and 1p loss in a subgroup of patients may suggest a differential activation of EGFR and its downstream pathways, which may have a potential effect on targeted therapies.