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Integrative genomic and transcriptomic characterization of papillary carcinomas of the breast

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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.


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Unsupervised hierarchical clustering of gene expression data of histologic subtypes of papillary carcinomas. A) Clustering was performed on 2310 probes using Ward's algorithm and Pearson correlation as distance metric. B) Clustering was performed on 2310 probes using complete linkage algorithm and Pearson correlation as distance metric. EPC, encapsulated papillary carcinoma; IPC, invasive papillary carcinoma; SPC, solid papillary carcinoma.
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fig5: Unsupervised hierarchical clustering of gene expression data of histologic subtypes of papillary carcinomas. A) Clustering was performed on 2310 probes using Ward's algorithm and Pearson correlation as distance metric. B) Clustering was performed on 2310 probes using complete linkage algorithm and Pearson correlation as distance metric. EPC, encapsulated papillary carcinoma; IPC, invasive papillary carcinoma; SPC, solid papillary carcinoma.

Mentions: We next carried out a hypothesis-generating, comparative exploratory analysis of the transcriptomic profiles of PC subtypes to ascertain whether histologic subtypes of PCs (i.e. EPC, SPC and IPC) would have distinctive transcriptomic profiles. Unsupervised hierarchical clustering demonstrated that EPCs preferentially clustered together (Fisher's exact test, p = 0.0406, Figure 5A), irrespective of the clustering algorithm employed (Figure 5B). It should be noted, however, that all EPCs were of histologic grade 1, and a significant enrichment for tumors of histologic grade 1 (Fisher's exact test, p = 0.04) was also observed in the cluster enriched for EPCs.


Integrative genomic and transcriptomic characterization of papillary carcinomas of the breast
Unsupervised hierarchical clustering of gene expression data of histologic subtypes of papillary carcinomas. A) Clustering was performed on 2310 probes using Ward's algorithm and Pearson correlation as distance metric. B) Clustering was performed on 2310 probes using complete linkage algorithm and Pearson correlation as distance metric. EPC, encapsulated papillary carcinoma; IPC, invasive papillary carcinoma; SPC, solid papillary carcinoma.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5037246&req=5

fig5: Unsupervised hierarchical clustering of gene expression data of histologic subtypes of papillary carcinomas. A) Clustering was performed on 2310 probes using Ward's algorithm and Pearson correlation as distance metric. B) Clustering was performed on 2310 probes using complete linkage algorithm and Pearson correlation as distance metric. EPC, encapsulated papillary carcinoma; IPC, invasive papillary carcinoma; SPC, solid papillary carcinoma.
Mentions: We next carried out a hypothesis-generating, comparative exploratory analysis of the transcriptomic profiles of PC subtypes to ascertain whether histologic subtypes of PCs (i.e. EPC, SPC and IPC) would have distinctive transcriptomic profiles. Unsupervised hierarchical clustering demonstrated that EPCs preferentially clustered together (Fisher's exact test, p = 0.0406, Figure 5A), irrespective of the clustering algorithm employed (Figure 5B). It should be noted, however, that all EPCs were of histologic grade 1, and a significant enrichment for tumors of histologic grade 1 (Fisher's exact test, p = 0.04) was also observed in the cluster enriched for EPCs.

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