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Kalsbeek AMF, Chan EFK, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes AM, Horvath LG, Kench JG, Stricker PD, Hayes VM. Mutational load of the mitochondrial genome predicts pathological features and biochemical recurrence in prostate cancer. Aging (Albany NY) 2017; 8:2702-2712. [PMID: 27705925 PMCID: PMC5191864 DOI: 10.18632/aging.101044] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022]
Abstract
Prostate cancer management is complicated by extreme disease heterogeneity, which is further limited by availability of prognostic biomarkers. Recognition of prostate cancer as a genetic disease has prompted a focus on the nuclear genome for biomarker discovery, with little attention given to the mitochondrial genome. While it is evident that mitochondrial DNA (mtDNA) mutations are acquired during prostate tumorigenesis, no study has evaluated the prognostic value of mtDNA variation. Here we used next-generation sequencing to interrogate the mitochondrial genomes from prostate tissue biopsies and matched blood of 115 men having undergone a radical prostatectomy for which there was a mean of 107 months clinical follow-up. We identified 74 unique prostate cancer specific somatic mtDNA variants in 50 patients, providing significant expansion to the growing catalog of prostate cancer mtDNA mutations. While no single variant or variant cluster showed recurrence across multiple patients, we observe a significant positive correlation between the total burden of acquired mtDNA variation and elevated Gleason Score at diagnosis and biochemical relapse. We add to accumulating evidence that total acquired genomic burden, rather than specific mtDNA mutations, has diagnostic value. This is the first study to demonstrate the prognostic potential of mtDNA mutational burden in prostate cancer.
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Affiliation(s)
- Anton M F Kalsbeek
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia
| | - Eva F K Chan
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia
| | - Judith Grogan
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia.,Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Desiree C Petersen
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia.,Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Ruth J Lyons
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Maree Haynes
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Lisa G Horvath
- Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW 2050, Australia
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia.,Cancer Research Division, The Kinghorn Cancer Centre/Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - Vanessa M Hayes
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,School of Medical Sciences, University of New South Wales, Randwick, NSW 2031, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia
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Isaacs S, Geduld-Ullah T, Benjeddou M. Reconstruction of major maternal and paternal lineages of the Cape Muslim population. Genet Mol Biol 2013; 36:167-76. [PMID: 23885197 PMCID: PMC3715281 DOI: 10.1590/s1415-47572013005000019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/12/2013] [Indexed: 11/28/2022] Open
Abstract
The earliest Cape Muslims were brought to the Cape (Cape Town - South Africa) from Africa and Asia from 1652 to 1834. They were part of an involuntary migration of slaves, political prisoners and convicts, and they contributed to the ethnic diversity of the present Cape Muslim population of South Africa. The history of the Cape Muslims has been well documented and researched however no in-depth genetic studies have been undertaken. The aim of the present study was to determine the respective African, Asian and European contributions to the mtDNA (maternal) and Y-chromosomal (paternal) gene pool of the Cape Muslim population, by analyzing DNA samples of 100 unrelated Muslim males born in the Cape Metropolitan area. A panel of six mtDNA and eight Y-chromosome SNP markers were screened using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Overall admixture estimates for the maternal line indicated Asian (0.4168) and African mtDNA (0.4005) as the main contributors. The admixture estimates for the paternal line, however, showed a predominance of the Asian contribution (0.7852). The findings are in accordance with historical data on the origins of the early Cape Muslims.
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Affiliation(s)
- Shafieka Isaacs
- Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, South Africa
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Mitochondrial DNA haplogroups and incidence of lipodystrophy in HIV-infected patients on long-term antiretroviral therapy. J Acquir Immune Defic Syndr 2012; 59:113-20. [PMID: 22245716 DOI: 10.1097/qai.0b013e31823daff3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We investigated the rates of lipodystrophy events, according to mitochondrial DNA haplogroup, in 187 patients starting combination antiretroviral therapy and following it. Incidence rates of lipoatrophy and fat accumulation were 8.2 and 4.8 per 100 person-years of follow-up, respectively. In multivariable models, patients with haplogroup K were at higher risk of any lipodystrophy [adjusted relative risk (aRR) 4.02, P = 0.0009], lipoatrophy (competing-risk aRR 2.42, P = 0.09; cause-specific aRR 2.99, P = 0.031), and fat accumulation (competing-risk aRR, 2.63, P = 0.11; cause-specific aRR 5.27, P = 0.019) than those with haplogroup H. Mitochondrial haplogroups may explain part of the genetic predisposition to lipodystrophy during combination antiretroviral therapy.
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Mehta P, Mellick GD, Rowe DB, Halliday GM, Jones MM, Manwaring N, Vandebona H, Silburn PA, Wang JJ, Mitchell P, Sue CM. Mitochondrial DNA haplogroups J and K are not protective for Parkinson's disease in the Australian community. Mov Disord 2009; 24:290-2. [PMID: 19086081 DOI: 10.1002/mds.22389] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
MtDNA haplogroups J and K have been associated with a decreased risk of developing Parkinson's disease (PD). To confirm this finding, we compared the distribution of mtDNA haplogroups J and K in a large sample of Australian patients with PD (n = 890) to population-based controls (n = 3,491). We assigned subjects to haplogroups J or K using standard PCR/RFLP techniques. Of the 890 subjects with PD, 10.6% were haplogroup J (95% CI 8.6-12.8, n = 94) and 7.1% were haplogroup K (95% CI 5.5-8.9, n = 63). In our controls, 10.2% belonged to haplogroup J (95% CI 9.2-11.2, n = 356), and 7.8% were in haplogroup K (95% CI 6.9-8.7, n = 272). There was no significant difference in the prevalence of mtDNA haplogroup J or K in PD patients compared to population-based controls. Our findings indicate that mtDNA haplogroups J and K are not associated with a lower risk of PD.
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Affiliation(s)
- Prachi Mehta
- Department of Neurology and Neurogenetics, Kolling Institute, Royal North Shore Hospital and University of Sydney, Sydney, Australia
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Light JE, Allen JM, Long LM, Carter TE, Barrow L, Suren G, Raoult D, Reed DL. Geographic distributions and origins of human head lice (Pediculus humanus capitis) based on mitochondrial data. J Parasitol 2009; 94:1275-81. [PMID: 18576877 DOI: 10.1645/ge-1618.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2008] [Accepted: 05/05/2008] [Indexed: 12/27/2022] Open
Abstract
Human head lice (Pediculus humanus capitis) are subdivided into 3 deeply divergent mitochondrial clades (Clades A, B, and C), each having unique geographical distributions. Determining the evolutionary history and geographic distribution of these mitochondrial clades can elucidate the evolutionary history of the lice as well as their human hosts. Previous data suggest that lice belonging to mitochondrial Clade B may have originated in North America or Asia; however, geographic sampling and sample sizes have been limited. With newly collected lice, we calculate the relative frequency, geographic distribution, and genetic diversity of louse mitochondrial clades to determine the geographic origin of lice belonging to Clade B. In agreement with previous studies, genetic diversity data support a North American origin of Clade B lice. It is likely that lice belonging to this mitochondrial clade recently migrated to other geographic localities, e.g., Europe and Australia, and, if not already present, may disperse further to occupy all geographic regions.
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Affiliation(s)
- Jessica E Light
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.
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McRae AF, Byrne EM, Zhao ZZ, Montgomery GW, Visscher PM. Power and SNP tagging in whole mitochondrial genome association studies. Genome Res 2008; 18:911-7. [PMID: 18356315 DOI: 10.1101/gr.074872.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The application of genetic association studies to detect mitochondrial variants responsible for phenotypic variation has recently been demonstrated. However, the only power estimates currently available are based on the use of mitochondrial haplogroups, which can only tag a small fraction of the common variation in the mitochondrial genome. Here, power estimates are derived for a SNP-based study design for both disease (case-control) and quantitative trait mapping studies. Power is estimated using simulations based on a collection of publicly available mitochondrial sequences of European origin. The power when testing all common mitochondrial SNPs is shown to be equivalent to that when testing only tagging SNPs, despite the relatively high ratio of tagging SNPs to total SNPs resulting from the tagging of all SNPs with a minor allele frequency greater than 1%. The sample size requirements of mitochondrial genome association studies are compared with that of nuclear whole-genome studies. Remarkably, the trade off between the number of tests being performed and the proportion of phenotypic variance explained for a fixed effect size results in approximately equal sample sizes required for both study types, although the per individual cost for the mitochondrial association study is much less. To test the representation of the sequences used in the power simulations, a sample of 3839 individuals from 1037 Australian families was genotyped for 69 tagging SNPs. The strong concordance in allele frequencies and linkage disequilibrium between the European sequences and the Australian sample indicates that the results presented here are transferable across populations of European descent.
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Affiliation(s)
- Allan F McRae
- Queensland Institute of Medical Research, Brisbane 4006, Australia.
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Manwaring N, Jones MM, Wang JJ, Rochtchina E, Howard C, Mitchell P, Sue CM. Population prevalence of the MELAS A3243G mutation. Mitochondrion 2007; 7:230-3. [PMID: 17300999 DOI: 10.1016/j.mito.2006.12.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Revised: 12/05/2006] [Accepted: 12/27/2006] [Indexed: 10/23/2022]
Abstract
We aimed to establish the population prevalence of the MELAS 3243A>G mtDNA mutation in a large Caucasian-based population (n=2954; 99% Caucasian, 57% women and mean age of 66.4 years). All participants underwent comprehensive clinical evaluation including audiologic testing. We detected the 3243A>G mutation in seven subjects using standard polymerase chain reaction/restriction fragment length polymorphism methods, establishing a population prevalence of 236/100000 (0.24%; 95% CI 0.10-0.49%); much higher than previously reported. All had mild to moderate hearing loss. Our findings indicate that subjects with the 3243A>G mtDNA mutation could be markedly under-recognised in the community.
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Affiliation(s)
- Neil Manwaring
- Kolling Institute, Department of Neurogenetics, University of Sydney, Clinic 4, Royal North Shore Hospital, Reserve Road, St. Leonards, NSW 2065, Australia
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