Identification and functional prediction of mitochondrial complex III and IV mutations associated with glioblastoma.
BACKGROUND
Glioblastoma (GBM) is the most common primary brain tumor in adults, with a dismal prognosis. Treatment is hampered by GBM's unique biology, including differential cell response to therapy. Although several mitochondrial abnormalities have been identified, how mitochondrial DNA (mtDNA) mutations contribute to GBM biology and therapeutic response remains poorly described. We sought to determine the spectrum of functional complex III and IV mtDNA mutations in GBM.


METHODS
The complete mitochondrial genomes of 10 GBM cell lines were obtained using next-generation sequencing and combined with another set obtained from 32 GBM tissues. Three-dimensional structural mapping and analysis of all the nonsynonymous mutations identified in complex III and IV proteins was then performed to investigate functional importance.


RESULTS
Over 200 mutations were identified in the mtDNAs, including a significant proportion with very low mutational loads. Twenty-five were nonsynonymous mutations in complex III and IV, 9 of which were predicted to be functional and affect mitochondrial respiratory chain activity. Most of the functional candidates were GBM specific and not found in the general population, and 2 were present in the germ-line. Patient-specific maps reveal that 43% of tumors carry at least one functional candidate.


CONCLUSIONS
We reveal that the spectrum of GBM-associated mtDNA mutations is wider than previously thought, as well as novel structural-functional links between specific mtDNA mutations, abnormal mitochondria, and the biology of GBM. These results could provide tangible new prognostic indicators as well as targets with which to guide the development of patient-specific mitochondrially mediated chemotherapeutic approaches.
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Rhiannon E
RE
Lloyd
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Kathleen
K
Keatley
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
D Timothy J
DT
Littlewood
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Brigitte
B
Meunier
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
William V
WV
Holt
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Qian
Q
An
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Samantha C
SC
Higgins
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Stavros
S
Polyzoidis
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Katie F
KF
Stephenson
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Keyoumars
K
Ashkan
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Helen L
HL
Fillmore
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
Geoffrey J
GJ
Pilkington
Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.).
John E
JE
McGeehan
D000293:Adolescent; D000328:Adult; D000368:Aged; D001932:Brain Neoplasms / Q000235:genetics*; D004272:DNA, Mitochondrial; D014450:Electron Transport Complex III / Q000235:genetics*; D003576:Electron Transport Complex IV / Q000235:genetics*; D005260:Female; D005909:Glioblastoma / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D062105:Molecular Docking Simulation; D009154:Mutation
D004272:DNA, Mitochondrial; D003576:Electron Transport Complex IV; D014450:Electron Transport Complex III
functional prediction; glioblastoma; mitochondrial DNA (mtDNA) mutation; structural analysis; subgrouping