title: Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming.
abstract: Variation in the intracellular percentage of normal and mutant mitochondrial DNAs (mtDNA) (heteroplasmy) can be associated with phenotypic heterogeneity in mtDNA diseases. Individuals that inherit the common disease-causing mtDNA tRNA(Leu(UUR)) 3243A>G mutation and harbor ∼10-30% 3243G mutant mtDNAs manifest diabetes and occasionally autism; individuals with ∼50-90% mutant mtDNAs manifest encephalomyopathies; and individuals with ∼90-100% mutant mtDNAs face perinatal lethality. To determine the basis of these abrupt phenotypic changes, we generated somatic cell cybrids harboring increasing levels of the 3243G mutant and analyzed the associated cellular phenotypes and nuclear DNA (nDNA) and mtDNA transcriptional profiles by RNA sequencing. Small increases in mutant mtDNAs caused relatively modest defects in oxidative capacity but resulted in sharp transitions in cellular phenotype and gene expression. Cybrids harboring 20-30% 3243G mtDNAs had reduced mtDNA mRNA levels, rounded mitochondria, and small cell size. Cybrids with 50-90% 3243G mtDNAs manifest induction of glycolytic genes, mitochondrial elongation, increased mtDNA mRNA levels, and alterations in expression of signal transduction, epigenomic regulatory, and neurodegenerative disease-associated genes. Finally, cybrids with 100% 3243G experienced reduced mtDNA transcripts, rounded mitochondria, and concomitant changes in nuclear gene expression. Thus, striking phase changes occurred in nDNA and mtDNA gene expression in response to the modest changes of the mtDNA 3243G mutant levels. Hence, a major factor in the phenotypic variation in heteroplasmic mtDNA mutations is the limited number of states that the nucleus can acquire in response to progressive changes in mitochondrial retrograde signaling.
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104;
authors.forename: Martin
authors.initials: M
authors.lastname: Picard
authors.affiliation: School of Biological Sciences, The University of Hong Kong, Hong Kong, People's Republic of China;
authors.forename: Jiangwen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Trovagene, San Diego, CA 92130;
authors.forename: Saege
authors.initials: S
authors.lastname: Hancock
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104;
authors.forename: Olga
authors.initials: O
authors.lastname: Derbeneva
authors.affiliation: Center for Applied Genomics, Division of Genetics, Department of Pediatrics, and.
authors.forename: Ryan
authors.initials: R
authors.lastname: Golhar
authors.affiliation: Institute of Genetics and Biotechnology, Warsaw University, 00-927, Warsaw, Poland;
authors.forename: Pawel
authors.initials: P
authors.lastname: Golik
authors.affiliation: Morton Mower Central Research Laboratory, Sinai Hospital of Baltimore, Baltimore, MD 21215;
authors.forename: Sean
authors.initials: S
authors.lastname: O'Hearn
authors.affiliation: Genomics Sevices Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806;
authors.forename: Shawn
authors.initials: S
authors.lastname: Levy
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104;
authors.forename: Prasanth
authors.initials: P
authors.lastname: Potluri
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104;
authors.forename: Maria
authors.initials: M
authors.lastname: Lvova
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104;
authors.forename: Antonio
authors.initials: A
authors.lastname: Davila
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104;
authors.forename: Chun Shi
authors.initials: CS
authors.lastname: Lin
authors.affiliation: Nucleic Acid/Protein Research Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA 19104;
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Perin
authors.affiliation: Nucleic Acid/Protein Research Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA 19104;
authors.forename: Eric F
authors.initials: EF
authors.lastname: Rappaport
authors.affiliation: Trovagene, San Diego, CA 92130;
authors.forename: Hakon
authors.initials: H
authors.lastname: Hakonarson
authors.affiliation: Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia; and.
authors.forename: Ian A
authors.initials: IA
authors.lastname: Trounce
authors.affiliation: Department of Biochemistry and Genetics, National Center for Neurodegenerative and Mitochondrial Diseases, Centre Hospitalier Universitaire d'Angers, 49933 Angers, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Procaccio
authors.affiliation: Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and the Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104; wallaced1@email.chop.edu.
authors.forename: Douglas C
authors.initials: DC
authors.lastname: Wallace
mesh_terms: D045744:Cell Line, Tumor; D004272:DNA, Mitochondrial / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D030342:Genetic Diseases, Inborn / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D006019:Glycolysis / Q000235:genetics; D006801:Humans; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D017354:Point Mutation; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D012356:RNA, Transfer, Leu / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D004272:DNA, Mitochondrial; D012333:RNA, Messenger; D012356:RNA, Transfer, Leu
keywords: RNA-Seq; electron microscopy; epigenetic; mitochondrial disease; mtDNA variant