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Patterns of chromosomal copy-number alterations in intrahepatic cholangiocarcinoma.

Dalmasso C, Carpentier W, Guettier C, Camilleri-Broët S, Borelli WV, Campos Dos Santos CR, Castaing D, Duclos-Vallée JC, Broët P - BMC Cancer (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, UMR CNRS 8071, USC INRA, Evry, France. cyril.dalmasso@genopole.cnrs.fr.

ABSTRACT

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.

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Related in: MedlinePlus

LRR values and BAF values all along the 22 autosomes for four samples with different proportions of tumoral cells: less than 20% (top left panel), 30% (top right panel), 40% (bottom left panel) and 60% (bottom right panel). Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively.
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Fig2: LRR values and BAF values all along the 22 autosomes for four samples with different proportions of tumoral cells: less than 20% (top left panel), 30% (top right panel), 40% (bottom left panel) and 60% (bottom right panel). Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively.

Mentions: In five cases with no or very few tumor cells, we observed no CNA which reflects the high specificity of our procedure. We tested the relationship between CNAs and the percentage of tumor cells distributions across the tumor samples. There was no significant relationship (p=0.40) between the fraction of the genome altered (copy loss or gain) and the percentage of tumor cells which reflects the good behavior of our classification procedure for the chosen cut-off (20% of tumor cells). Figure 2 displays BAF and LRR values together with the allocation states for four samples with different proportions of tumoral cells contents: less than 20% (top left panel), 30% (top right panel), 40% (bottom left panel) and 60% (bottom right panel). Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively. From this figure, we can see the interest of considering simultaneously BAF and LRR values for the calling procedure. Out of the 42 cases analyzed, 15 tumors showed some copy-neutral events with very few recurrent event (less than three).Figure 2


Patterns of chromosomal copy-number alterations in intrahepatic cholangiocarcinoma.

Dalmasso C, Carpentier W, Guettier C, Camilleri-Broët S, Borelli WV, Campos Dos Santos CR, Castaing D, Duclos-Vallée JC, Broët P - BMC Cancer (2015)

LRR values and BAF values all along the 22 autosomes for four samples with different proportions of tumoral cells: less than 20% (top left panel), 30% (top right panel), 40% (bottom left panel) and 60% (bottom right panel). Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373066&req=5

Fig2: LRR values and BAF values all along the 22 autosomes for four samples with different proportions of tumoral cells: less than 20% (top left panel), 30% (top right panel), 40% (bottom left panel) and 60% (bottom right panel). Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively.
Mentions: In five cases with no or very few tumor cells, we observed no CNA which reflects the high specificity of our procedure. We tested the relationship between CNAs and the percentage of tumor cells distributions across the tumor samples. There was no significant relationship (p=0.40) between the fraction of the genome altered (copy loss or gain) and the percentage of tumor cells which reflects the good behavior of our classification procedure for the chosen cut-off (20% of tumor cells). Figure 2 displays BAF and LRR values together with the allocation states for four samples with different proportions of tumoral cells contents: less than 20% (top left panel), 30% (top right panel), 40% (bottom left panel) and 60% (bottom right panel). Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively. From this figure, we can see the interest of considering simultaneously BAF and LRR values for the calling procedure. Out of the 42 cases analyzed, 15 tumors showed some copy-neutral events with very few recurrent event (less than three).Figure 2

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, UMR CNRS 8071, USC INRA, Evry, France. cyril.dalmasso@genopole.cnrs.fr.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus