Genomic analysis of mitochondrial mutations in chromophobe renal cell carcinoma by using low-depth whole genome sequencing.

Abstract

553 Background: Mitochondria have a circular genome that is independent of the nuclear genome of the nucleus. Mutations of mitochondrial DNA rarely occur during tumorigenesis. Chromophobe renal cell carcinoma (chRCCC) is a type of kidney tumor characterized by a morphologic abnormality of mitochondria. However, there is still little research on the existence of mitochondrial mutation in chRCC and how it plays a role in tumorigenesis. Here, we investigated the mutation patterns of mitochondria genome in chRCC using low-depth sequencing technique. Methods: We evaluated 17 patients with chRCC who underwent radical nephrectomy from December 2010 to January 2017. Mitochondrial genomic analysis was performed by low-depth sequencing. Varscan and MToolBox analysis programs were used to search for mutations. Germline mutation information reported in MtDB, Phylotree, and Mitomap databases was used to allocate patient haplogroups and exclude germline mutations. Results: Whole genome sequencing of 17 chRCC tissues at an average depth of 1x based on whole genome revealed that the mitochondrial genome was sequenced to an average of 630x. A total of 1,206 Haplotype frequency > 0.25 mutations were found, of which 30 were mutations not reported in the database. Seven of them were identified as synonymous mutations (average of 0.41 and 41% per tumor), and three were truncating mutations (average of 0.18 per tumor; 18%). Truncating mutations were specifically identified as two frameshift indel and one stop gain mutation. Conclusions: In summary, our study showed that the frequency of truncating mutation of mitochondrial DNA was higher in chRCC compared to other solid tumors which have a low frequency of 1-2%. This finding suggests that dysfunctional mitochondria may play an oncogenic role in tumorigenesis of chRCC, while other tumors are predicted to undergo negative selection of mitochondrial truncating mutations during tumorigenesis. Based on these results, we are performing prospective study for evaluating mutational characteristics and associated morphological changes of mitochondria under electron microscopy.