title: mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.
abstract: BACKGROUND
  Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in eukaryotic cellular function. However, the effects mitochondrial DNA (mtDNA) levels have on the nuclear transcriptome have not been defined under physiological conditions. In order to address this issue, we characterized the gene expression profiles of A549 lung cancer cells and their mtDNA-depleted rho0 counterparts grown in culture and as tumor xenografts in immune-deficient mice.
  
  
  RESULTS
  Cultured A549 rho0 cells were respiration-deficient and showed enhanced levels of transcripts relevant to metal homeostasis, initiation of the epithelial-mesenchymal transition, and glucuronidation pathways. Several well-established HIF-regulated transcripts showed increased or decreased abundance relative to the parental cell line. Furthermore, growth in culture versus xenograft has a significantly greater influence on expression profiles, including transcripts involved in mitochondrial structure and both aerobic and anaerobic energy metabolism. However, both in vitro and in vivo, mtDNA levels explained the majority of the variance observed in the expression of transcripts in glucuronidation, tRNA synthetase, and immune surveillance related pathways. mtDNA levels in A549 xenografts also affected the expression of genes, such as AMACR and PHYH, involved in peroxisomal lipid metabolic pathways.
  
  
  CONCLUSIONS
  We have identified mtDNA-dependent gene expression profiles that are shared in cultured cells and in xenografts. These profiles indicate that mtDNA-depleted cells could provide informative model systems for the testing the efficacy of select classes of therapeutics, such as anti-angiogenesis agents. Furthermore, mtDNA-depleted cells grown culture and in xenografts provide a powerful means to investigate possible relationships between mitochondrial activity and gene expression profiles in normal and pathological cells.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA 90089, USA. dmagda@pcyc.com
authors.forename: Darren
authors.initials: D
authors.lastname: Magda
authors.forename: Philip
authors.initials: P
authors.lastname: Lecane
authors.forename: Julia
authors.initials: J
authors.lastname: Prescott
authors.forename: Patricia
authors.initials: P
authors.lastname: Thiemann
authors.forename: Xuan
authors.initials: X
authors.lastname: Ma
authors.forename: Patricia K
authors.initials: PK
authors.lastname: Dranchak
authors.forename: Donna M
authors.initials: DM
authors.lastname: Toleno
authors.forename: Krishna
authors.initials: K
authors.lastname: Ramaswamy
authors.forename: Kimberly D
authors.initials: KD
authors.lastname: Siegmund
authors.forename: Joseph G
authors.initials: JG
authors.lastname: Hacia
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics; D002477:Cells; D002478:Cells, Cultured; D004272:DNA, Mitochondrial; D020869:Gene Expression Profiling; D015894:Genome, Human / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D014183:Transplantation, Heterologous
chemical_list: D004272:DNA, Mitochondrial