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POLE Mutations Improve the Prognosis

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POLE Mutations Improve the Prognosis Li et al. BMC Medical Genetics (2019) 20:202 https://doi.org/10.1186/s12881-019-0936-2 RESEARCH ARTICLE Open Access POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction Yiran Li1, Yiding Bian1, Kai Wang2 and Xiao-Ping Wan1* Abstract Background: The morbidity and mortality of endometrial tumors, a common type of malignant cancer in women, have increased in recent years. POLE encodes the DNA polymerase ε, which is responsible for the leading strand DNA replication. Somatic mutations of POLE have been acknowledged in numerous cancers, resulting in the accumulation of DNA errors, leading to ultra-mutated tumors. Mutations in the exonuclease domain of POLE have been reported to improve progression-free survival in endometrial cancer. However, the potential relationship and underlying mechanism between POLE mutations and the prognosis of endometrial cancer patients remains unclear. Methods: The whole exome sequencing data, RNA sequencing data, and clinical information were obtained from the TCGA database and employed for the analyses in this study. The detailed mutational information was analyzed using whole exome sequencing data and the mutated genes were shown with OncoPlot. The survival curves and cox proportional hazards regression analysis were used to accessed patient prognosis, the association of clinical characteristics and prognosis. Differentially expressed genes were analyzed by the edgeR R/Bioconductor package, then the GSEA Pre-ranked tool was used for Gene Set Enrichment Analysis (GSEA) to estimate the function of genes. Expression values were clustered using hierarchical clustering with Euclidean distance and ward linkage by the dendextend R package. Results: POLE mutational status was proven to be an independent prognostic factor for endometrial cancer patients. Patients with somatic POLE mutations presented a favorable prognosis. POLE mutations regulated glycolysis and cytokine secretion, affecting cell metabolism and immune response. Autocrine motility factor (AMF)/PGI and AMFR/gp78 exhibited higher expression levels in POLE mutant patients. The comprehensive high expressions of AMFR/gp78 and low expression of POLE were associated with the favorable prognosis of endometrial cancer patients. Conclusions: This study showed the POLE mutations a vital factor in endometrial cancer patients, leading to a higher expression of AMF/PGI and AMFR/gp78. These results suggested comprehensive consideration of the POLE mutations, expression of AMF/PGI and AMFR/gp78 may provide a more feasible and effective approach for the treatment of endometrial cancer, which might improve the prognosis. Keywords: Endometrial cancer, Polymerase ɛ (POLE) mutation, Glucose metabolism, Autocrine motility factor (AMF), Prognosis * Correspondence: [email protected] 1Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Li et al. BMC Medical Genetics (2019) 20:202 Page 2 of 13 Background of POLE have been confirmed to be significantly associ- Endometrial cancer (EC), arising from the lining of the ated with favorable prognosis and improved progression- uterus, is one of the most common malignancy among free survival in endometrial cancer [25–27]. These results women in developed countries. The incidence and mor- all suggest that POLE exonuclease domain mutations can tality of endometrial cancer have risen in the United serve as an important prognostic molecular marker associ- States in recent years, with estimated 74,200 new cases ated with excellent outcomes and guide the management and 151,30 deaths in 2017, and about 76,470 new cases of endometrial cancer patients. The role of POLE and and 15,520 deaths in 2018 [1–4]. Although most patients POLE mutants in carcinogenesis and the progression of present low-grade, early-stage diseases with favorable endometrial carcinoma is not fully clear. In this study, we prognosis, the high-grade group accounts for a large integrated whole exome sequencing data, patient clinical proportion of deaths in endometrial cancer patients [5]. information, and the RNA sequencing data of the Uterine In addition, the mutation frequency profile was also re- Corpus Endometrial Carcinoma (UCEC) project in the lated to different ethnicities and tumor grades in endo- TCGA database for combinational analysis to elucidate metrial cancer patients [6]. PIK3CA, ARID1A, TP53, the possible mechanism of POLE mutations on endomet- PIK3R1, and MUC16 are the most frequent mutations in rial cancer. endometrial cancer patients, and all of them have been reported to be associated with prognosis. PIK3CA, Methods ARID1A, and MUC16 mutations were correlated with TCGA data downloading favorable prognosis, whereas TP53 and PIK3R1 muta- In this study, 530 endometrial cancer patients with tions were correlated with poor prognosis [6, 7]. whole exome sequencing data, 528 patients with clinical All cancers are caused by alterations in the DNA se- and survival information, and 526 patients with RNA ex- quence including somatic mutations of the genomes in pression data in the TCGA-UCEC project were down- normal cells. DNA polymerases (Pols) are important en- loaded from the TCGA database. In brief, the Mutation zymes involved in DNA replication and repair in vivo. Annotation Format (MAF) data generated by the According to the similarity of the protein sequence, Pols mutect2 algorithm from whole exome sequencing data, are categorized into six families: A, B, C, D, X and Y. RNA sequencing raw counts (HTSeq-Counts) data, RNA Pols α, δ, and ε are three DNA polymerases essential sequencing FPKM data (HTSeq-FPKM), clinical and sur- during DNA replication in eukaryotes [8]. POLE (p261) vival information were downloaded from the TCGA encodes the DNA polymerase ε, which is a heterotetra- database through the TCGAbiolinks R/Bioconductor mer (p261, p59, p17, p12) [9] and responsible for the package [28]. leading strand DNA replication [10, 11]. POLE contains the proof-reading exonuclease domain to ensure low Analyses and visualization of somatic mutations mutation rates in replicating cells [12]. Early studies The detailed mutational information was extracted demonstrated that POLE mutations were observed in from the MAF file by the Maftools R/Bioconductor colorectal cancer, pancreatic cancer, ovarian cancer, package [29]. Next, the plotmafSummary function was ultra-mutated giant cell high-grade glioma, and endo- used to plot the summary of the MAF file for display- metrial cancer [13–17]. Germline mutations in the exo- ing the number of variant type and variant classifica- nuclease domains of POLE were associated with a tion. The oncoplot function was used to plot the familial predisposition and increased risk of colorectal OncoPlot of the top 10 mutated genes and POLE. cancer and giant cell glioblastoma [18–20]. Somatic The lollipopPlot of POLE was plotted through the lol- mutations in POLE have also been reported in these lipopPlot function [29]. cancers [21]. These mutations lead to an accumula- tion of DNA errors during the replication process, Prognostic analyses resulting in ultra-mutated tumors associated with We used the Kaplan–Meier method and compared it microsatellite stability [22]. with the log-rank test to depict the survival curves. Cox Different forms of genomic instability in cancers are proportional hazards regression analysis was used for known to be associated with prognosis [23]. The somatic univariate and multivariate analyses to explore the asso- POLE mutations can lead to a genomically, histologically ciation of clinical characteristics, POLE mutational sta- and clinically distinct subgroup of high-grade gliomas tus, and patient prognosis. that are associated with a longer progression-free sur- vival [16]. In endometrial cancer, somatic POLE proof- Differentially expressed genes and enrichment analysis reading mutations were found in about 7% ECs, and the The differentially expressed genes (DEGs) between the results have shown a tight association with high histo- mutant and the wild type POLE endometrial cancer logic grade [24]. Mutations in the exonuclease domain samples were analyzed by the edgeR R/Bioconductor Li et al. BMC Medical Genetics (2019) 20:202 Page 3 of 13 package [30]. Gene ontology (GO) and the Kyoto improved prognosis when they held more mutations Encyclopedia of Genes and Genomes (KEGG) were used (P = 0.00033) (Fig. 1b). The patients with POLE somatic for the enrichment analysis of the function and signaling mutations had a higher tumor mutational burden com- pathway of the DEGs through the hypergeometric pared with patients without POLE mutations (P = algorithm. The value of p < 0.05 was considered signifi- 1.26e-76) (Fig. 1c). These results suggest that POLE cantly enriched.
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