A comprehensive characterization of rare mitochondrial DNA variants in neuroblastoma

// Francesco Maria Calabrese 1, * , Rosanna Clima 2, * , Piero Pignataro 3, 4 , Vito Alessandro Lasorsa 3, 4 , Michael D. Hogarty 5 , Aurora Castellano 6 , Massimo Conte 7 , Gian Paolo Tonini 8 , Achille Iolascon 3, 4 , Giuseppe Gasparre 2, # , Mario Capasso 3, 4, 9, # 1 Department of Biology, University of Bari “Aldo Moro”, Bari, Italy 2 Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, Bologna, Italy 3 Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy 4 CEINGE Biotecnologie Avanzate, Napoli, Italy 5 Department of Pediatrics, Division of Oncology, Children’s Hospital of Philadelphia, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, USA 6 Paediatric Haematology/Oncology Department, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy 7 Oncology Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy 8 Pediatric Research Institute (IRP) – Fondazione Città della Speranza, Neuroblastoma Laboratory, Padua, Italy 9 IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, Naples, Italy * These authors contributed equally to this work # Co-last authors Correspondence to: Mario Capasso, email: mario.capasso@unina.it Keywords: neuroblastoma, mitochondrial DNA mutations, WES, somatic mutations, germline mutations Received: April 21, 2016      Accepted: June 09, 2016      Published: June 24, 2016 ABSTRACT Background: Neuroblastoma, a tumor of the developing sympathetic nervous system, is a common childhood neoplasm that is often lethal. Mitochondrial DNA (mtDNA) mutations have been found in most tumors including neuroblastoma. We extracted mtDNA data from a cohort of neuroblastoma samples that had undergone Whole Exome Sequencing (WES) and also used snap-frozen samples in which mtDNA was entirely sequenced by Sanger technology. We next undertook the challenge of determining those mutations that are relevant to, or arisen during tumor development. The bioinformatics pipeline used to extract mitochondrial variants from matched tumor/blood samples was enriched by a set of filters inclusive of heteroplasmic fraction, nucleotide variability, and in silico prediction of pathogenicity. Results: Our in silico multistep workflow applied both on WES and Sanger-sequenced neuroblastoma samples, allowed us to identify a limited burden of somatic and germline mitochondrial mutations with a potential pathogenic impact. Conclusions: The few singleton germline and somatic mitochondrial mutations emerged, according to our in silico analysis, do not appear to impact on the development of neuroblastoma. Our findings are consistent with the hypothesis that most mitochondrial somatic mutations can be considered as ‘passengers’ and consequently have no discernible effect in this type of cancer.