// Amanda R. Oran 1 , Clare M. Adams 1 , Xiao-yong Zhang 1 , Victoria J. Gennaro 1 , Harla K. Pfeiffer 1 , Hestia S. Mellert 2 , Hans E. Seidel 3 , Kirsten Mascioli 1 , Jordan Kaplan 1 , Mahmoud R. Gaballa 1 , Chen Shen 4,5 , Isidore Rigoutsos 1 , Michael P. King 6 , Justin L. Cotney 7 , Jamie J. Arnold 8 , Suresh D. Sharma 8 , Ubaldo E. Martinez-Outschoorn 1 , Christopher R. Vakoc 4 , Lewis A. Chodosh 3 , James E. Thompson 9 , James E. Bradner 10 , Craig E. Cameron 8 , Gerald S. Shadel 11,12 , Christine M. Eischen 1 and Steven B. McMahon 1 1 Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA 2 Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA, USA 3 Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, USA 4 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA 5 Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA 6 Department of Biochemistry, Thomas Jefferson University, Philadelphia, PA, USA 7 Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT, USA 8 Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA 9 Leukemia Service, Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA 10 Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA,USA 11 Department of Pathology, Yale School of Medicine, New Haven, CT, USA 12 Department of Genetics, Yale School of Medicine, New Haven, CT, USA Correspondence to: Steven B. McMahon, email: // Keywords : MYC, mitochondria, mitochondrial gene expression, tigecycline, synthetic lethality Received : June 08, 2016 Accepted : August 25, 2016 Published : August 31, 2016 Abstract Despite ubiquitous activation in human cancer, essential downstream effector pathways of the MYC transcription factor have been difficult to define and target. Using a structure/function-based approach, we identified the mitochondrial RNA polymerase (POLRMT) locus as a critical downstream target of MYC. The multifunctional POLRMT enzyme controls mitochondrial gene expression, a process required both for mitochondrial function and mitochondrial biogenesis. We further demonstrate that inhibition of this newly defined MYC effector pathway causes robust and selective tumor cell apoptosis, via an acute, checkpoint-like mechanism linked to aberrant electron transport chain complex assembly and mitochondrial reactive oxygen species (ROS) production. Fortuitously, MYC-dependent tumor cell death can be induced by inhibiting the mitochondrial gene expression pathway using a variety of strategies, including treatment with FDA-approved antibiotics. In vivo studies using a mouse model of Burkitt's Lymphoma provide pre-clinical evidence that these antibiotics can successfully block progression of MYC-dependent tumors.
Context.— Next-generation sequencing is a high-throughput method for detecting genetic abnormalities and providing prognostic and therapeutic information for patients with cancer. Oncogenic fusion transcripts are among the various classifications of genetic abnormalities present in tumors and are typically detected clinically with fluorescence in situ hybridization (FISH). However, FISH probes only exist for a limited number of targets, do not provide any information about fusion partners, cannot be multiplex, and have been shown to be limited in specificity for common targets such as ALK. Objective.— To validate an anchored multiplex polymerase chain reaction–based panel for the detection of fusion transcripts in a university hospital–based clinical molecular diagnostics laboratory. Design.— We used 109 unique clinical specimens to validate a custom panel targeting 104 exon boundaries from 17 genes involved in fusions in solid tumors. The panel can accept as little as 100 ng of total nucleic acid from PreservCyt-fixed tissue, and formalin-fixed, paraffin-embedded specimens with as little as 10% tumor nuclei. Results.— Using FISH as the gold standard, this assay has a sensitivity of 88.46% and a specificity of 95.83% for the detection of fusion transcripts involving ALK, RET, and ROS1 in lung adenocarcinomas. Using a validated next-generation sequencing assay as the orthogonal gold standard for the detection of EGFR variant III (EGFRvIII) in glioblastomas, the assay is 92.31% sensitive and 100% specific. Conclusions.— This multiplexed assay is tumor and fusion partner agnostic and will provide clinical utility in therapy selection for patients with solid tumors.
