A novel somatic mutation of SIN3A detected in breast cancer by whole-exome sequencing enhances cell proliferation through ER\u03b1 expression

Kenji Watanabe,Keishiro Isayama,Syuiti Sakaguti,Hiroaki Nagano,Yoichi Mizukami,Masaaki Oka,Shigeru Yamamoto

doi:10.1038/s41598-018-34290-1

Abstract

Breast cancer is the most frequent tumor in women, and in nearly two-thirds of cases, the tumors express estrogen receptor α (ERα, encoded by ESR1). Here, we performed whole-exome sequencing of 16 breast cancer tissues classified according to ESR1 expression and 12 samples of whole blood, and detected 310 somatic mutations in cancer tissues with high levels of ESR1 expression. Of the somatic mutations validated by a different deep sequencer, a novel nonsense somatic mutation, c.2830 C>T; p.Gln944*, in transcriptional regulator switch-independent 3 family member A (SIN3A) was detected in breast cancer of a patient. Part of the mutant protein localized in the cytoplasm in contrast to the nuclear localization of ERα, and induced a significant increase in ESR1 mRNA. The SIN3A mutation obviously enhanced MCF7 cell proliferation. In tissue sections from the breast cancer patient with the SIN3A c.2830 C>T mutation, cytoplasmic SIN3A localization was detected within the tumor regions where nuclear enlargement was observed. The reduction in SIN3A mRNA correlates with the recurrence of ER-positive breast cancers on Kaplan-Meier plots. These observations reveal that the SIN3A mutation has lost its transcriptional repression function due to its cytoplasmic localization, and that this repression may contribute to the progression of breast cancer.

Highlights

Breast cancer is the most frequent primary tumor in women with an estimated 1.7 million cases diagnosed annually, and is the fifth leading cause of death among women
To examine somatic mutations involved in the high expression of ESR1 in breast cancer tissues, tissues were classified into 3 groups according to their ESR1 expression
We found 213 non-synonymous somatic mutations on the exon regions in 208 genes of DNAs extracted from breast cancers showing high expressions of ERα using different types of next-generation sequencers

Summary

Introduction

Breast cancer is the most frequent primary tumor in women with an estimated 1.7 million cases diagnosed annually, and is the fifth leading cause of death among women. Common features of tumors are their various genetic alterations, such as base substitutions, insertions/deletions, and rearrangements that are observed in relation to disease progression[11,12] These mutations are divided into driver mutations that affect the disease and passenger mutations that have no effects on the disease[11]. We carried out whole-exome sequencing (WES) analysis of breast cancers classified by ESR1 expression, and identified novel somatic mutations by exclusion of SNPs in the whole blood cells of patients with breast cancer. Of the somatic mutations validated by different types of DNA deep sequencers, genes directly related to ESR1 expression were selected from an Ingenuity Pathway Analysis (IPA) pathway database. We found a novel nonsense mutation of a transcriptional regulator, SIN3A, that can associate with HDACs but has lost its binding region for MeCP2 in breast cancers showing high ERα expression. The somatic mutation SIN3A c.2830 C>T; p.Gln944* enhances the increase in ESR1 expression, which, in turn, accelerates cell proliferation in MCF7 cells accompanied by cytoplasmic localization separate from the nuclear localization of ERα

Methods

Results

Conclusion