Reverse phase protein array identification of triple-negative breast cancer subtypes and comparison with mRNA molecular subtypes.

Hiroko Masuda,Naoki Hayashi,Naoto T Ueno,Debu Tripathy,Yuan Qi,Shuying Liu,Takahiro Kogawa,Gabriel N Hortobagyi

doi:10.18632/oncotarget.19719

Hiroko Masuda, Naoki Hayashi + Show 6 more

Open Access

https://doi.org/10.18632/oncotarget.19719

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Abstract

BackgroundReverse phase protein array (RPPA) analysis, allows investigation of potential targets at the functional protein level,. We identified TNBC subtypes at the protein level using RPPA and compared them with mRNA molecular subtypes (TNBCtype, TNBCtype-4, and PAM50) that is unique in its availability of both RPPA and mRNA analyses.MethodsWe classified the samples from 80 TNBC patients using both k-means and hierarchical consensus clustering analysis and performed Ingenuity Pathway Analysis. We also investigated whether we could reproduce the mRNA molecular subtypes using the RPPA dataset.ResultsBoth clustering methods divided all samples into 2 clusters that were biologically the same. The top canonical pathways included inflammation, hormonal receptors, and MAPK signaling pathways for the first cluster [“inflammation and hormonal-related (I/H) subtype”] and the GADD45, DNA damage, and p53 signaling pathways for the second cluster [“DNA damage (DD)-related subtype”]. Further k-means cluster analysis identified 5 TNBC clusters. Comparison between sample classification using the 5 RPPA-based k-means cluster subtypes and 6 gene-expression-based TNBCtype molecular subtypes showed significant association between the 2 classifications (p = 0.017).ConclusionsThe I/H and DD subtypes identified by RPPA advance our understanding of TNBC’s heterogeneity from the functional proteomic perspective.

Highlights

Triple-negative breast cancer (TNBC) is not a simple, homogeneous breast cancer subtype; it collectively describes cancers that do not express the well-known target receptors estrogen receptor (ER), progesterone receptor (PR), and HER2
We identified 2 stable clusters (Figure 1A) that were significantly different from each other (SigClust p = 0.012)
Ingenuity pathway analysis of the protein signatures showed that the top canonical pathways associated with one of the clusters included the inflammation, hormonal receptor, and MAPK signaling pathways; we designated this cluster as the “inflammation and hormonal-related (I/H)-related subtype” The canonical pathways associated with the other cluster included the Growth Arrest and DNA Damage (GADD45), DNA damage, and p53 signaling pathways; we designated this cluster as the “DD-related subtype” (Tables 1 and 2, Figures 2 and 3)

Summary

Introduction

Triple-negative breast cancer (TNBC) is not a simple, homogeneous breast cancer subtype; it collectively describes cancers that do not express the well-known target receptors estrogen receptor (ER), progesterone receptor (PR), and HER2. In order to divide the heterogeneous TNBC into homogeneous subtypes, several groups have used gene expression analysis, an approach that allows comprehensive investigation of more than 20,000 genes and their expression patterns. Several TNBC subtype www.impactjournals.com/oncotarget classifications have been derived by clustering analysis using gene expression patterns, such as PAM50 intrinsic subtypes [2, 6, 7], claudin-low subtype [8], Burstein et al’s 4 subtypes [9], and Lehmann and colleagues’ molecular subtypes [4, 10]. We identified TNBC subtypes at the protein level using RPPA and compared them with mRNA molecular subtypes (TNBCtype, TNBCtype-4, and PAM50) that is unique in its availability of both RPPA and mRNA analyses

Methods

Results

Conclusion