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Integrative genomic and transcriptomic characterization of papillary carcinomas of the breast

View Article: PubMed Central - PubMed

ABSTRACT

Papillary carcinoma (PC) is a rare type of breast cancer, which comprises three histologic subtypes: encapsulated PC (EPC), solid PC (SPC) and invasive PC (IPC). Microarray-based gene expression and Affymetrix SNP 6.0 gene copy number profiling, and RNA-sequencing revealed that PCs are luminal breast cancers that display transcriptomic profiles distinct from those of grade- and estrogen receptor (ER)-matched invasive ductal carcinomas of no special type (IDC-NSTs), and that the papillary histologic pattern is unlikely to be underpinned by a highly recurrent expressed fusion gene or a highly recurrent expressed mutation. Despite displaying similar patterns of gene copy number alterations, significant differences in the transcriptomic profiles of EPCs, SPCs and IPCs were found, and may account for their different histologic features.

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Unsupervised hierarchical clustering of gene copy number profiles of papillary carcinomas. Clustering was performed using SNP6-derived categorical states (i.e. gains, losses and amplifications) of 16 PCs, using Ward's algorithm and Euclidean distance. Amp, amplification; Del, homozygous deletion; EPC, encapsulated papillary carcinoma; Gain, copy number gain; IPC, invasive papillary carcinoma; Loss, copy number loss; NC, no copy number change; PC, papillary carcinoma; SPC, solid papillary carcinoma.
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fig3: Unsupervised hierarchical clustering of gene copy number profiles of papillary carcinomas. Clustering was performed using SNP6-derived categorical states (i.e. gains, losses and amplifications) of 16 PCs, using Ward's algorithm and Euclidean distance. Amp, amplification; Del, homozygous deletion; EPC, encapsulated papillary carcinoma; Gain, copy number gain; IPC, invasive papillary carcinoma; Loss, copy number loss; NC, no copy number change; PC, papillary carcinoma; SPC, solid papillary carcinoma.

Mentions: We have previously demonstrated that the patterns of gene copy number alterations found in PCs are relatively simple and similar to those found in IDC-NSTs of the same histologic grade and ER-status (Duprez et al., 2012). Here, using a platform with a higher resolution, we confirmed our previous observations that PCs displayed genomic features consistent with those of low-grade, ER-positive IDC-NSTs (i.e. 16q losses, 16p gains and 1q gains; Figure 3 and Supplementary Figure S1). After excluding regions mapping to known copy number polymorphisms (http://dgv.tcag.ca/dgv/app/home), we observed recurrent amplifications in 11q13.3 (n = 2) and 8p11.23-p11.22 (n = 2) loci (Supplementary Figure S1 and Supplementary Table S6). Consistent with our previous observations (Duprez et al., 2012), HER2 and ESR1 gene amplification was not observed in the PCs studied.


Integrative genomic and transcriptomic characterization of papillary carcinomas of the breast
Unsupervised hierarchical clustering of gene copy number profiles of papillary carcinomas. Clustering was performed using SNP6-derived categorical states (i.e. gains, losses and amplifications) of 16 PCs, using Ward's algorithm and Euclidean distance. Amp, amplification; Del, homozygous deletion; EPC, encapsulated papillary carcinoma; Gain, copy number gain; IPC, invasive papillary carcinoma; Loss, copy number loss; NC, no copy number change; PC, papillary carcinoma; SPC, solid papillary carcinoma.
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Related In: Results  -  Collection

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fig3: Unsupervised hierarchical clustering of gene copy number profiles of papillary carcinomas. Clustering was performed using SNP6-derived categorical states (i.e. gains, losses and amplifications) of 16 PCs, using Ward's algorithm and Euclidean distance. Amp, amplification; Del, homozygous deletion; EPC, encapsulated papillary carcinoma; Gain, copy number gain; IPC, invasive papillary carcinoma; Loss, copy number loss; NC, no copy number change; PC, papillary carcinoma; SPC, solid papillary carcinoma.
Mentions: We have previously demonstrated that the patterns of gene copy number alterations found in PCs are relatively simple and similar to those found in IDC-NSTs of the same histologic grade and ER-status (Duprez et al., 2012). Here, using a platform with a higher resolution, we confirmed our previous observations that PCs displayed genomic features consistent with those of low-grade, ER-positive IDC-NSTs (i.e. 16q losses, 16p gains and 1q gains; Figure 3 and Supplementary Figure S1). After excluding regions mapping to known copy number polymorphisms (http://dgv.tcag.ca/dgv/app/home), we observed recurrent amplifications in 11q13.3 (n = 2) and 8p11.23-p11.22 (n = 2) loci (Supplementary Figure S1 and Supplementary Table S6). Consistent with our previous observations (Duprez et al., 2012), HER2 and ESR1 gene amplification was not observed in the PCs studied.

View Article: PubMed Central - PubMed

ABSTRACT

Papillary carcinoma (PC) is a rare type of breast cancer, which comprises three histologic subtypes: encapsulated PC (EPC), solid PC (SPC) and invasive PC (IPC). Microarray-based gene expression and Affymetrix SNP 6.0 gene copy number profiling, and RNA-sequencing revealed that PCs are luminal breast cancers that display transcriptomic profiles distinct from those of grade- and estrogen receptor (ER)-matched invasive ductal carcinomas of no special type (IDC-NSTs), and that the papillary histologic pattern is unlikely to be underpinned by a highly recurrent expressed fusion gene or a highly recurrent expressed mutation. Despite displaying similar patterns of gene copy number alterations, significant differences in the transcriptomic profiles of EPCs, SPCs and IPCs were found, and may account for their different histologic features.

No MeSH data available.


Related in: MedlinePlus