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INPP4B and RAD50 have an interactive effect on survival after breast cancer

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Abstract

Genes sharing similar genomic landscape have the potential to interactively orchestrate certain clinicopathological features of a disease. Deletion of the RAD50 gene is a common event particularly in basal-like breast cancer, and often occurs together with deletions of BRCA1, RB1, TP53, PTEN, and INPP4B. In this study, we investigate whether these co-deleted genes have interactive effects on survival in breast cancer. Using publicly available TCGA data, we employed Cox’s proportional hazards models to test whether genomic deletions of these genes, or reduced protein or transcript levels associate with breast cancer patient survival in an interactive manner. Further validation was obtained at the transcriptional level by including 1,596 additional cases from 13 publicly available gene expression data sets from the KM-plotter database. Our results indicate that RAD50 and INPP4B associate interactively with breast cancer survival at the transcriptional, translational, and genomic levels in the TCGA data set (p (interaction) < 0.05). While neither of the genes was independently prognostic on its own, low INPP4B levels in combination with above median RAD50 abundance associated with increased hazard, both at the mRNA (HR 2.39, 95 % CI 1.20–4.76) and protein (HR 2.92, 95 % CI 1.42–6.00) levels, whereas concomitant deletion or low expression of both genes associated with unexpectedly improved survival. A similar pattern was observed in the KM-plotter data set (p (interaction) = 0.0067). We find that RAD50 and INPP4B expression levels have a synergistic influence on breast cancer survival, possibly through their effects on treatment response.

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Abbreviations

TCGA:

The Cancer Genome Atlas

CNV:

Copy number variation

HR:

Hazard ratio

CI:

Confidence interval

RPPA:

Reverse-phase protein microarray

OS:

Overall survival

RFS:

Relapse-free survival

ER:

Estrogen receptor

T:

Tumor size

N:

Lymph node metastasis

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Acknowledgments

This work was supported by the Helsinki University Central Hospital Research Fund, the Finnish Cancer Society, the Sigrid Juselius Foundation, and the Academy of Finland (266528). The results shown in this study are in part based upon data generated by the TCGA Research Network (http://cancergenome.nih.gov/) and the Kaplan–Meier Plotter database (http://kmplot.com/). We thank the specimen donors and research groups who have provided these data and made this study possible.

Conflicts of interest

All authors declare no conflicts of interest.

Author information

Authors and Affiliations

  1. Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, PO Box 700, 00029 HUS, Helsinki, Finland

    Xiaofeng Dai, Rainer Fagerholm, Sofia Khan & Heli Nevanlinna

  2. National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, JiangNan University, Wuxi, 214122, China

    Xiaofeng Dai

  3. Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland

    Carl Blomqvist

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  1. Xiaofeng Dai
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  2. Rainer Fagerholm
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Corresponding author

Correspondence to Heli Nevanlinna.

Additional information

Xiaofeng Dai and Rainer Fagerholm have contributed equally to this work.

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Dai, X., Fagerholm, R., Khan, S. et al. INPP4B and RAD50 have an interactive effect on survival after breast cancer. Breast Cancer Res Treat 149, 363–371 (2015). https://doi.org/10.1007/s10549-014-3241-y

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  • DOI: https://doi.org/10.1007/s10549-014-3241-y

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