Inactivating Mutations of the IK Gene Weaken Ku80/Ku70-Mediated DNA Repair and Sensitize Endometrial Cancer to Chemotherapy.

Chao Gao,Paola Amero,Ye Yan,Emine Bayraktar,Guangxu Jin,Anil K Sood,Yingmei Wang,Lingegowda S Mangala,Wei Zhang,Fengxia Xue,Cristian Rodríguez-Aguayo ,Russell R Broaddus ,Gabriel López-Berestein ,M Elizabeth Forbes

doi:10.3390/cancers13102487

Abstract

Simple SummarySome endometrial cancer (EC) patients have different prognoses and responses to treatment, even among those with the same stage and tumor grade as assessed by the International Federation of Gynecology and Obstetrics (FIGO) criteria. Molecular classification may make up for this deficiency to some extent. Our previous investigation of the 271 EC samples from the Cancer Genome Atlas (TCGA) dataset showed that IK somatic mutations were enriched in a cluster of patients with high-grade and high-stage cancers, and this group had longer overall survival. This current study continued to provide insight into how IK somatic mutations contribute to EC pathophysiology. We explored IK gene mutations in depth and used functional studies to characterize an unrecognized function of the IK gene in EC. Our findings may elucidate the molecular mechanism of IK in EC, which might guide future patient stratification and contribute targeted therapy for EC.IK is a mitotic factor that promotes cell cycle progression. Our previous investigation of 271 endometrial cancer (EC) samples from the Cancer Genome Atlas (TCGA) dataset showed IK somatic mutations were enriched in a cluster of patients with high-grade and high-stage cancers, and this group had longer survival. This study provides insight into how IK somatic mutations contribute to EC pathophysiology. We analyzed the somatic mutational landscape of IK gene in 547 EC patients using expanded TCGA dataset. Co-immunoprecipitation and mass spectrometry were used to identify protein interactions. In vitro and in vivo experiments were used to evaluate IK’s role in EC. The patients with IK-inactivating mutations had longer survival during 10-year follow-up. Frameshift and stop-gain were common mutations and were associated with decreased IK expression. IK knockdown led to enrichment of G2/M phase cells, inactivation of DNA repair signaling mediated by heterodimerization of Ku80 and Ku70, and sensitization of EC cells to cisplatin treatment. IK/Ku80 mutations were accompanied by higher mutation rates and associated with significantly better overall survival. Inactivating mutations of IK gene and loss of IK protein expression were associated with weakened Ku80/Ku70-mediated DNA repair, increased mutation burden, and better response to chemotherapy in patients with EC.

Highlights

Endometrial cancer (EC) is one of the three most prevalent gynecologic malignancies, and its incidence and mortality have risen in the last few decades [1,2]
We analyzed the cohort of 547 endometrial cancer (EEC) patients in the Cancer Genome Atlas (TCGA) (Table S1) and identified 38 somatic mutations of the IK gene, including six patients with R93fs deletion (c_267_267delinesGA), three patients with stop-gain nonsense mutations, and others with missense mutations (Figure 1a and Table S2)
To examine whether the R93fs deletion (c_267_267delines-GA) is a germline mutation or an artifact caused by technical errors, we analyzed germline mutations in normal tissues from the 547 EEC patients, fragments of paired-end reads aligned to the GA repetitive adjacent to c_267_267delines-GA, and forward and reverse strands of the aligned reads with the c_267_267delines-GA somatic mutation

Summary

Introduction

Endometrial cancer (EC) is one of the three most prevalent gynecologic malignancies, and its incidence and mortality have risen in the last few decades [1,2]. Compared with the other two types of gynecologic malignancies, EC has a relatively better prognosis. Those with EC have different prognoses and responses to treatment, even among those with the same stage and tumor grade as assessed by the International Federation of Gynecology and Obstetrics (FIGO) criteria [3]. A proactive molecular risk classification tool for endometrial cancers (ProMisE) was developed to improve EC subgroup assignment and risk assessment [4,5]. Based on sequencing and immunohistochemical results, ProMisE includes mismatch repair deficiency (MMRd), DNA polymerase epsilon (POLE) mutations, wild-type p53, and abnormal p53 as molecular markers. POLE mutations are associated with improved prognosis in EC [9]

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Results

Conclusion