Prevalence and spectrum of AKT1, PIK3CA, PTEN and TP53 somatic mutations in Chinese breast cancer patients

RESEARCH ARTICLE Prevalence and spectrum of AKT1, PIK3CA, PTEN and TP53 somatic mutations in Chinese breast cancer patients Guoli Li1, Xinwu Guo2, Ming Chen2, Lili Tang3, Hui Jiang1, Julia X. Day2, Yueliang Xie1, Limin Peng2, Xunxun Xu2, Jinliang Li2, Shouman Wang3, Zhi Xiao3, Lizhong Dai2,4,5, Jun Wang1,2* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 School of Life Sciences, Central South University, Changsha, Hunan, China, 2 Sanway Gene Technology Inc., Changsha, Hunan, China, 3 Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China, 4 Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, China, 5 Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, China * Abstract OPEN ACCESS Citation: Li G, Guo X, Chen M, Tang L, Jiang H, Day JX, et al. (2018) Prevalence and spectrum of AKT1, PIK3CA, PTEN and TP53 somatic mutations in Chinese breast cancer patients. PLoS ONE 13(9): e0203495. https://doi.org/10.1371/journal. pone.0203495 Editor: Alvaro Galli, CNR, ITALY Received: May 22, 2018 Accepted: July 17, 2018 Published: September 13, 2018 Copyright: © 2018 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Sequencing data have been uploaded to the Genome Sequence Archive in BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences and are available using accession number HRA000026. The data can also be accessed at http://bigd.big.ac.cn/gsa-human/s/deYtxeTa. All relevant data are within the paper and its Supporting Information files Funding: This work was supported in part by grant from the Natural Science Foundation of China (No. 81372228), and grants from China Hunan Breast cancer, one of the most frequently occurring cancers worldwide, is the leading cause of cancer-related death among women. AKT1, PIK3CA, PTEN and TP53 mutations were common observed in breast cancer representing potential clinical biomarkers for cancer classification and treatment. A comprehensive knowledge of AKT1, PIK3CA, PTEN and TP53 mutations in breast cancer was still insufficient in Chinese population. In this study, the complete coding regions and exon-intron boundaries of AKT1, PIK3CA, PTEN and TP53 genes were sequenced in paired breast tumor and normal tissues from 313 Chinese breast cancer patients using microfluidic PCR-based target enrichment and next-generation sequencing technology. Total 120 somatic mutations were identified in 190 of the 313 patients (60.7%), with the mutation frequency of AKT1 as 3.2%, PIK3CA as 36.4%, PTEN as 4.8%, and TP53 as 33.9%. Among these mutations, 1 in PIK3CA (p.I69N), 3 in PTEN (p. K62X, c.635-12_636delTTAACCATGCAGAT and p.N340IfsTer4) and 5 in TP53 (p. Q136AfsTer5, p.K139_P142del, p.Y234dup, p.V274LfsTer31 and p.N310TfsTer35) were novel. Notably, PIK3CA somatic mutations were significantly associated with ER-positive or PR-positive tumors. TP53 somatic mutations were significantly associated with ER-negative, PR-negative, HER2-positive, BRCA1 mutation, Ki67 high expression and basal-like tumors. Our findings provided a comprehensive mutation profiling of AKT1, PIK3CA, PTEN and TP53 genes in Chinese breast cancer patients, which have potential implications in clinical management. Introduction Breast cancer is the most common cancer types and the leading cause of cancer mortality in females in the world [1]. It was estimated that approximately 278,800 new breast cancer cases PLOS ONE | https://doi.org/10.1371/journal.pone.0203495 September 13, 2018 1 / 18 4 gene mutations in Chinese breast cancer patients Provincial Science and Technology Department (No. 2016GK3022, 2016XK2033 and 2016JC2068). Sanway Gene Technology Inc. provided support in the form of salaries for the specified authors (XWG, MC, LMP, XXX, JLL, LZD and JW), but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the “Author Contributions” section. Competing interests: Xinwu Guo, Ming Chen, Limin Peng, Xunxun Xu, Jinliang Li, Lizhong Dai and Jun Wang are employees of Sanway Gene Technology Inc. Julia Xiaoning Day is a student from La Jolla Country Day School (La Jolla, CA, USA), who worked as an intern at Sanway Gene Technology Inc. This does not alter our adherence to PLOS ONE policies on sharing data and materials. with 64,600 deaths occurred in China in 2013 [2]. It is well known that cancer progression is driven by mutations in cancer genome [3]. Somatic mutations in AKT1, PIK3CA PTEN and TP53 genes were found at high frequency in breast cancer, with PIK3CA as 26.4%, TP53 as 24.7%, PTEN as 3.8% and AKT1 as 2.8% in the Catalogue of Somatic Mutations in Cancer (COSMIC) database [4]. Recent large genomic landscape studies have showed that TP53 and PIK3CA were the two most frequently mutated driver genes in primary breast cancer and the mutation spectrum of these four genes displayed subgroup specificity with great clinical significance in cancer classification and treatment [5, 6]. However, the spectrum of these four gene mutations in breast cancer is still largely unknown in Chinese population. Thus a comprehensive understanding of the prevalence and clinical characteristics of AKT1, PIK3CA, PTEN and TP53 gene mutations in Chinese breast cancer patients is urgently needed. With the advance of next-generation sequencing (NGS) technologies, mutation analysis has become effective and feasible for routine clinical application in breast cancer [7]. In this study, paired tumor and normal tissues from a cohort of 313 Chinese breast cancer patients were screened for ATK1, PIK3CA, PTEN and TP53 mutations using microfluidic PCR-based target enrichment and NGS technology. Furthermore, clinicopathological characteristics of breast cancer associated with the mutations of these four genes were analyzed in parallel. Material and methods Patients and tissue samples Fresh tumor and paired adjacent normal tissues (located at least 2 cm away from the site of tumor tissue) from 313 primary breast cancer patients were collected at Xiangya Hospital, Central South University from year 2013 to 2015. The clinicopathological characteristics of the 313 patients were summarized in Table 1. All breast specimens were reviewed by experienced pathologists. The breast cancer molecular subtypes were characterized based on the guideline of St Gallen International Expert Consensus (2013) [8]. All of the 313 patients have been tested for BRCA1 and BRCA2 mutations by NGS and validated using Sanger sequencing in our previous study [9]. All the patients in this study were females of Chinese Han popu (...truncated)