Breast Cancer Research and Treatment

, Volume 162, Issue 3, pp 439–450 | Cite as

Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer

  • Gaurav A. Mehta
  • Joel S. Parker
  • Grace O. Silva
  • Katherine A. Hoadley
  • Charles M. Perou
  • Michael L. GatzaEmail author
Preclinical study



The PI3K/Akt signaling axis contributes to the dysregulation of many dominant features in breast cancer including cell proliferation, survival, metabolism, motility, and genomic instability. While multiple studies have demonstrated that basal-like or triple-negative breast tumors have uniformly high PI3K/Akt activity, genomic alterations that mediate dysregulation of this pathway in this subset of highly aggressive breast tumors remain to be determined.


In this study, we present an integrated genomic analysis based on the use of a PI3K gene expression signature as a framework to analyze orthogonal genomic data from human breast tumors, including RNA expression, DNA copy number alterations, and protein expression. In combination with data from a genome-wide RNA-mediated interference screen in human breast cancer cell lines, we identified essential genetic drivers of PI3K/Akt signaling.


Our in silico analyses identified SOX4 amplification as a novel modulator of PI3K/Akt signaling in breast cancers and in vitro studies confirmed its role in regulating Akt phosphorylation.


Taken together, these data establish a role for SOX4-mediated PI3K/Akt signaling in breast cancer and suggest that SOX4 may represent a novel therapeutic target and/or biomarker for current PI3K family therapies.


Breast cancer Genomics SOX4 PI3 kinase Akt 



We thank members of our laboratory for helpful discussion and suggestions. Research reported in this publication was supported by the National Cancer Institute of the US National Institutes of Health (R00-CA166228), V Foundation for Cancer Research (V2016-013), and from the New Jersey Health Foundation (PC-52-16) to M.L.G. Additional funding for research reported in this study was provided by the National Cancer Institute of the US National Institutes of Health Breast SPORE program grant P50-CA58223-09A1 and R01-CA148761-04, as well as grants from the Susan G. Komen for the Cure and the Breast Cancer Research Foundation to C.M.P.

Author contribution

GA.M., J.S.P., C.M.P., and M.L.G. conceived and designed the study. G.A.M., G.O.S., K.A.H., and M.L.G. performed analyses and experiments. G.A.M., C.M.P., and M.L.G. wrote the manuscript. All authors have reviewed and approved the final manuscript.

Compliance with ethical standards

Conflicts of interest

CM.P. is an equity stock holder and board of director member of BioClassifier LLC and GeneCentric Diagnostics. C.M.P. is also listed as an inventor on a patent application for the PAM50 molecular assay. J.S.P. is also listed as an inventor on a patent application for the PAM50 molecular assay. All other authors declare no conflicts of interest.

Supplementary material

10549_2017_4139_MOESM1_ESM.pdf (570 kb)
Supplementary Fig. 1 PI3K, PIK3CA, PTEN WT and PTEN Del signature patterns in breast cancer subtypes. Patterns of pathway activity were scored for a collection of 1031 breast cancer samples. Differences between pathway scores were calculated using a t test to compare each molecular subtype to all other samples and resulting p-values are reported (PDF 571 kb)
10549_2017_4139_MOESM2_ESM.pdf (1.2 mb)
Supplementary Fig. 2 Correlation between pathway signature score. A Spearman's Rank correlation was used to compare pathway scores between each pair of signatures (PI3K, PIK3CA, PTEN DEL, and PTEN WT) across the TCGA cohort (n = 1031). Resulting p-values and R-values are reported (PDF 1202 kb)
10549_2017_4139_MOESM3_ESM.pdf (214 kb)
Supplementary Fig. 3 Frequency of SOX4 copy number gains per molecular subtype. The frequency of copy number gains (including both high-level amplifications and gains) were calculated for each molecular subtype (n = 1031). Basal-like tumors (57.5%) were the only subtype to show a significant enrichment in SOX4 amplification frequency (p < 0.0001, Chi square test) (PDF 214 kb)
10549_2017_4139_MOESM4_ESM.pdf (928 kb)
Supplementary Fig. 4 Concordance of SOX4 copy number status and PI3K activity. The relationship between discrete SOX4 copy number status (i.e. gain/amplification, neutral, or LOH/ deletion) and PI3K score was calculated (p = 3.7 × 10−08) in the TCGA cohort (n = 1031) (PDF 929 kb)
10549_2017_4139_MOESM5_ESM.pdf (929 kb)
Supplementary Fig. 5 Correlation between SOX4 copy number, mRNA expression and PI3K signature score. Analysis of the METABRIC dataset (n = 1992) confirmed the positive correlation between SOX4 copy number status, mRNA levels and PI3K signature score. These results confirm the associations identified in the TCGA cohort (PDF 929 kb)
10549_2017_4139_MOESM6_ESM.pdf (1.3 mb)
Supplementary Fig. 6 Co-occurrence of copy number alterations in PI3K pathway components with SOX4. The incidence of the co-occurrence of copy number alterations including copy number gains for PIK3CA and SOX4 or copy number losses for PTEN and INPP4B was calculated in human breast tumors (n = 1031). These results demonstrate that SOX4 CNAs occur in neither a mutually inclusive nor exclusive pattern with each gene (PDF 1284 kb)
10549_2017_4139_MOESM7_ESM.pdf (913 kb)
Supplementary Fig. 7 PI3K score and SOX4 expression in breast cancer cell lines. A panel of 51 breast cancer cell lines (GSE12777) was scored for molecular subtype (basal or luminal), PI3K pathway score and SOX4 mRNA expression. Samples were ranked according to PI3K score and the top three cell lines MDAMB468, HCC1143, and HCC38 (indicated in red text) were selected for in vitro studies (PDF 914 kb)
10549_2017_4139_MOESM8_ESM.pdf (1.2 mb)
Supplementary Fig. 8 SOX4 mediates pAkt expression in HCC1143 cells. Immunofluorescence microscopy was used to analyze the effects of siC or siSOX4 in HCC1143 cells on SOX4 (Cy3) or pAkt (Cy5) protein expression and cell nuclei were visualized by DAPI. Images were captured at 40× magnification using Nikon Eclipse TE-2000U fluorescent microscope (PDF 1273 kb)
10549_2017_4139_MOESM9_ESM.xlsx (1.9 mb)
Supplementary Tables 1–4 (XLSX 1973 kb)


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Gaurav A. Mehta
    • 1
    • 2
    • 3
  • Joel S. Parker
    • 4
  • Grace O. Silva
    • 4
  • Katherine A. Hoadley
    • 4
  • Charles M. Perou
    • 4
  • Michael L. Gatza
    • 1
    • 2
    • 3
    Email author
  1. 1.Rutgers Cancer Institute of New JerseyNew BrunswickUSA
  2. 2.Department of Radiation OncologyRobert Wood Johnson Medical SchoolNew BrunswickUSA
  3. 3.Rutgers, The State University of New JerseyNew BrunswickUSA
  4. 4.Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillUSA

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