Proceedings of the National Academy of Sciences · 2018 · 112 citations · 38 references
Life SciencesGeneticsOncologyCellular MetabolismMitochondrial BiologyMolecular OncologyCancer GenomicsKidney CancerMetabolic ReprogrammingMetabolic Reprogramming In CancerMitochondrial MetabolismMitochondrial PhysiologyAdaptive Metabolic ReprogrammingMitochondrial Respiration ControlMitochondrial Respiratory Complex IOncocytoma CharacterizationReduced GlutathioneRenal OncocytomaTumor Cell ProliferationTumor Metabolism
Significance Renal oncocytomas are benign kidney tumors with numerous mitochondria. Here, we analyze the mitochondrial (mtDNA) and nuclear genomes of these tumors. Our analysis finds mtDNA mutations in complex I (the first step in mitochondrial respiration) to be early genetic events that likely contribute to tumor formation. Since mtDNA mutations can lead to severe degenerative disorders, the cellular responses allowing renal oncocytoma cells to grow are important to consider. To properly understand authentic gene expression changes in tumors, we found it important to consider the gene expression pattern of the tumor’s cell of origin, the distal nephron. By doing so, we uncover alterations in glutathione synthesis and turnover that likely represent an adaptive metabolic response in renal oncocytoma.
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
Robust enumeration of cell subsets from tissue expression profiles
Aaron M. Newman, Chih Long Liu, Michael R. Green et al. · Nature Methods · 2015 · 14.1K citations · Full text
Comprehensive molecular characterization of clear cell renal cell carcinoma