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An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers.

Blein S, Bardel C, Danjean V, McGuffog L, Healey S, Barrowdale D, Lee A, Dennis J, Kuchenbaecker KB, Soucy P, Terry MB, Chung WK, Goldgar DE, Buys SS, Breast Cancer Family RegistryJanavicius R, Tihomirova L, Tung N, Dorfling CM, van Rensburg EJ, Neuhausen SL, Ding YC, Gerdes AM, Ejlertsen B, Nielsen FC, Hansen TV, Osorio A, Benitez J, Conejero RA, Segota E, Weitzel JN, Thelander M, Peterlongo P, Radice P, Pensotti V, Dolcetti R, Bonanni B, Peissel B, Zaffaroni D, Scuvera G, Manoukian S, Varesco L, Capone GL, Papi L, Ottini L, Yannoukakos D, Konstantopoulou I, Garber J, Hamann U, Donaldson A, Brady A, Brewer C, Foo C, Evans DG, Frost D, Eccles D, EMBRACEDouglas F, Cook J, Adlard J, Barwell J, Walker L, Izatt L, Side LE, Kennedy MJ, Tischkowitz M, Rogers MT, Porteous ME, Morrison PJ, Platte R, Eeles R, Davidson R, Hodgson S, Cole T, Godwin AK, Isaacs C, Claes K, De Leeneer K, Meindl A, Gehrig A, Wappenschmidt B, Sutter C, Engel C, Niederacher D, Steinemann D, Plendl H, Kast K, Rhiem K, Ditsch N, Arnold N, Varon-Mateeva R, Schmutzler RK, Preisler-Adams S, Markov NB, Wang-Gohrke S, de Pauw A, Lefol C, Lasset C, Leroux D, Rouleau E, Damiola F, GEMO Study CollaboratorsDreyfus H, Barjhoux L, Golmard L, Uhrhammer N, Bonadona V, Sornin V, Bignon YJ, Carter J, Van Le L, Piedmonte M, DiSilvestro PA, de la Hoya M, Caldes T, Nevanlinna H, Aittomäki K, Jager A, van den Ouweland AM, Kets CM, Aalfs CM, van Leeuwen FE, Hogervorst FB, Meijers-Heijboer HE, HEBONOosterwijk JC, van Roozendaal KE, Rookus MA, Devilee P, van der Luijt RB, Olah E, Diez O, Teulé A, Lazaro C, Blanco I, Del Valle J, Jakubowska A, Sukiennicki G, Gronwald J, Lubinski J, Durda K, Jaworska-Bieniek K, Agnarsson BA, Maugard C, Amadori A, Montagna M, Teixeira MR, Spurdle AB, Foulkes W, Olswold C, Lindor NM, Pankratz VS, Szabo CI, Lincoln A, Jacobs L, Corines M, Robson M, Vijai J, Berger A, Fink-Retter A, Singer CF, Rappaport C, Kaulich DG, Pfeiler G, Tea MK, Greene MH, Mai PL, Rennert G, Imyanitov EN, Mulligan AM, Glendon G, Andrulis IL, Tchatchou S, Toland AE, Pedersen IS, Thomassen M, Kruse TA, Jensen UB, Caligo MA, Friedman E, Zidan J, Laitman Y, Lindblom A, Melin B, Arver B, Loman N, Rosenquist R, Olopade OI, Nussbaum RL, Ramus SJ, Nathanson KL, Domchek SM, Rebbeck TR, Arun BK, Mitchell G, Karlan BY, Lester J, Orsulic S, Stoppa-Lyonnet D, Thomas G, Simard J, Couch FJ, Offit K, Easton DF, Chenevix-Trench G, Antoniou AC, Mazoyer S, Phelan CM, Sinilnikova OM, Cox DG - Breast Cancer Res. (2015)

Bottom Line: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01).Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03).This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

View Article: PubMed Central - PubMed

Affiliation: INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France. sophie.blein@gmail.com.

ABSTRACT

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers.

Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals.

Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk.

Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of subclade T tested for association with ALTree. (a) Phylogenetic tree of subclade T with all observed haplogroups. A homogeneity test is performed at each level of the tree. (b) First level of the phylogenetic tree of subclade T. Averaged counts, ranges and proportions of affected and unaffected observed in resamplings are indicated below each subclade. T2* represents the entire T2 subclade.
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Fig2: Phylogenetic tree of subclade T tested for association with ALTree. (a) Phylogenetic tree of subclade T with all observed haplogroups. A homogeneity test is performed at each level of the tree. (b) First level of the phylogenetic tree of subclade T. Averaged counts, ranges and proportions of affected and unaffected observed in resamplings are indicated below each subclade. T2* represents the entire T2 subclade.

Mentions: The phylogenetic tree of subclade T (see Figure 2a) contains only three levels; thus, only three tests were performed within this clade. Raw P-values were examined to determine at which level of the tree ALTree detects a difference of enrichment in affected or unaffected individuals (see Table 3). Only the P-value associated with the test performed at the first level of the tree is significant. We looked more closely at the mean frequencies of affected and unaffected individuals in the tree at this level (see Figure 2b). In the T1a1 subclade, the mean count of affected and unaffected are 32 and 47, respectively. In the T2* subclade, we observed, on average, 217 and 148 affected and unaffected individuals, respectively, whereas in the T subclade, we observed, on average, 13 and 11 affected and unaffected individuals, respectively. The ranges observed for each of these values over the 1,000 resamplings are represented in Figure 2b. On the basis of these observations, we conclude that subclade T1a1 is depleted in affected carriers compared with the neighboring subclades T and T2.Figure 2


An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers.

Blein S, Bardel C, Danjean V, McGuffog L, Healey S, Barrowdale D, Lee A, Dennis J, Kuchenbaecker KB, Soucy P, Terry MB, Chung WK, Goldgar DE, Buys SS, Breast Cancer Family RegistryJanavicius R, Tihomirova L, Tung N, Dorfling CM, van Rensburg EJ, Neuhausen SL, Ding YC, Gerdes AM, Ejlertsen B, Nielsen FC, Hansen TV, Osorio A, Benitez J, Conejero RA, Segota E, Weitzel JN, Thelander M, Peterlongo P, Radice P, Pensotti V, Dolcetti R, Bonanni B, Peissel B, Zaffaroni D, Scuvera G, Manoukian S, Varesco L, Capone GL, Papi L, Ottini L, Yannoukakos D, Konstantopoulou I, Garber J, Hamann U, Donaldson A, Brady A, Brewer C, Foo C, Evans DG, Frost D, Eccles D, EMBRACEDouglas F, Cook J, Adlard J, Barwell J, Walker L, Izatt L, Side LE, Kennedy MJ, Tischkowitz M, Rogers MT, Porteous ME, Morrison PJ, Platte R, Eeles R, Davidson R, Hodgson S, Cole T, Godwin AK, Isaacs C, Claes K, De Leeneer K, Meindl A, Gehrig A, Wappenschmidt B, Sutter C, Engel C, Niederacher D, Steinemann D, Plendl H, Kast K, Rhiem K, Ditsch N, Arnold N, Varon-Mateeva R, Schmutzler RK, Preisler-Adams S, Markov NB, Wang-Gohrke S, de Pauw A, Lefol C, Lasset C, Leroux D, Rouleau E, Damiola F, GEMO Study CollaboratorsDreyfus H, Barjhoux L, Golmard L, Uhrhammer N, Bonadona V, Sornin V, Bignon YJ, Carter J, Van Le L, Piedmonte M, DiSilvestro PA, de la Hoya M, Caldes T, Nevanlinna H, Aittomäki K, Jager A, van den Ouweland AM, Kets CM, Aalfs CM, van Leeuwen FE, Hogervorst FB, Meijers-Heijboer HE, HEBONOosterwijk JC, van Roozendaal KE, Rookus MA, Devilee P, van der Luijt RB, Olah E, Diez O, Teulé A, Lazaro C, Blanco I, Del Valle J, Jakubowska A, Sukiennicki G, Gronwald J, Lubinski J, Durda K, Jaworska-Bieniek K, Agnarsson BA, Maugard C, Amadori A, Montagna M, Teixeira MR, Spurdle AB, Foulkes W, Olswold C, Lindor NM, Pankratz VS, Szabo CI, Lincoln A, Jacobs L, Corines M, Robson M, Vijai J, Berger A, Fink-Retter A, Singer CF, Rappaport C, Kaulich DG, Pfeiler G, Tea MK, Greene MH, Mai PL, Rennert G, Imyanitov EN, Mulligan AM, Glendon G, Andrulis IL, Tchatchou S, Toland AE, Pedersen IS, Thomassen M, Kruse TA, Jensen UB, Caligo MA, Friedman E, Zidan J, Laitman Y, Lindblom A, Melin B, Arver B, Loman N, Rosenquist R, Olopade OI, Nussbaum RL, Ramus SJ, Nathanson KL, Domchek SM, Rebbeck TR, Arun BK, Mitchell G, Karlan BY, Lester J, Orsulic S, Stoppa-Lyonnet D, Thomas G, Simard J, Couch FJ, Offit K, Easton DF, Chenevix-Trench G, Antoniou AC, Mazoyer S, Phelan CM, Sinilnikova OM, Cox DG - Breast Cancer Res. (2015)

Phylogenetic tree of subclade T tested for association with ALTree. (a) Phylogenetic tree of subclade T with all observed haplogroups. A homogeneity test is performed at each level of the tree. (b) First level of the phylogenetic tree of subclade T. Averaged counts, ranges and proportions of affected and unaffected observed in resamplings are indicated below each subclade. T2* represents the entire T2 subclade.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4478717&req=5

Fig2: Phylogenetic tree of subclade T tested for association with ALTree. (a) Phylogenetic tree of subclade T with all observed haplogroups. A homogeneity test is performed at each level of the tree. (b) First level of the phylogenetic tree of subclade T. Averaged counts, ranges and proportions of affected and unaffected observed in resamplings are indicated below each subclade. T2* represents the entire T2 subclade.
Mentions: The phylogenetic tree of subclade T (see Figure 2a) contains only three levels; thus, only three tests were performed within this clade. Raw P-values were examined to determine at which level of the tree ALTree detects a difference of enrichment in affected or unaffected individuals (see Table 3). Only the P-value associated with the test performed at the first level of the tree is significant. We looked more closely at the mean frequencies of affected and unaffected individuals in the tree at this level (see Figure 2b). In the T1a1 subclade, the mean count of affected and unaffected are 32 and 47, respectively. In the T2* subclade, we observed, on average, 217 and 148 affected and unaffected individuals, respectively, whereas in the T subclade, we observed, on average, 13 and 11 affected and unaffected individuals, respectively. The ranges observed for each of these values over the 1,000 resamplings are represented in Figure 2b. On the basis of these observations, we conclude that subclade T1a1 is depleted in affected carriers compared with the neighboring subclades T and T2.Figure 2

Bottom Line: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01).Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03).This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

View Article: PubMed Central - PubMed

Affiliation: INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France. sophie.blein@gmail.com.

ABSTRACT

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers.

Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals.

Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk.

Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

No MeSH data available.


Related in: MedlinePlus