Evolutionary analyses of entire genomes do not support the association of mtdna mutations with ras/mapk pathway syndromes

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Gómez Carballa, Alberto ^a   Cerezo, María ^a   Balboa, Emilia ^b   Heredia, Claudia ^c   Castro Feijóo, Lidia ^c   Rica, Itxaso ^d   Barreiro, Jesús ^c   Eirís, Jesús ^c   Cabanas, Paloma ^c   Martínez Soto, Isabel ^e   Fernández Toral, Joaquín ^f   Castro Gago, Manuel ^c   Pombo, Manuel ^c   Carracedo, Ángel ^a,b   Barros, Francisco ^b   Salas, Antonio ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^b CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^c UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^d HOSPITAL DE CRUCES   (Spain)

^e Instituto de Salud Carlos III   (Spain)

^f HOSPITAL UNIVERSITARIO CENTRAL DE ASTURIAS   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; K RAS PROTEIN; MITOCHONDRIAL DNA; MITOGEN ACTIVATED PROTEIN KINASE; PROTEIN SERINE THREONINE KINASE; PROTEIN SHOC2; PROTEIN TYROSINE PHOSPHATASE SHP 2; RAS PROTEIN; SOS PROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; CAUCASIAN; CLINICAL FEATURE; CONTROLLED STUDY; DNA SEQUENCE; GENE MUTATION; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC RISK; GENETIC VARIABILITY; GENOME ANALYSIS; HAPLOTYPE; HETEROPLASMY; HUMAN; HYPERTROPHIC CARDIOMYOPATHY; LEOPARD SYNDROME; MALE; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NOONAN SYNDROME; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHENOTYPE; PHYLOGENY; PHYLOGEOGRAPHY; PLESIOMORPHY; RISK FACTOR; SIGNAL TRANSDUCTION; CELL NUCLEUS; GENETICS; HUMAN GENOME; MUTATION; OPEN READING FRAME; SYNDROME;

CELL NUCLEUS; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MAP KINASE SIGNALING SYSTEM; MITOGEN-ACTIVATED PROTEIN KINASES; MUTATION; OPEN READING FRAMES; PHYLOGENY; PHYLOGEOGRAPHY; RAS PROTEINS; RNA, TRANSFER; SYNDROME;

EID: 79955443042     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018348     Document Type: Article

References (66)

1. Noonan J, Ehmke D, (1963) Associated non cardiac malformations in children with congenital heart disease. J Pediatr pp. 468-470.
2. Tartaglia M, Gelb BD, (2005) Noonan syndrome and related disorders: genetics and pathogenesis. Annu Rev Genomics Hum Genet 6: 45-68.
3. Takahashi K, Kogaki S, Kurotobi S, Nasuno S, Ohta M, et al. (2005) A novel mutation in the PTPN11 gene in a patient with Noonan syndrome and rapidly progressive hypertrophic cardiomyopathy. Eur J Pediatr 164: 497-500.
4. Bertola DR, Kim CA, Sugayama SM, Albano LM, Wagenfuhr J, et al. (2000) Cardiac findings in 31 patients with Noonan's syndrome. Arq Bras Cardiol 75: 409-412.
5. Burch M, Sharland M, Shinebourne E, Smith G, Patton M, et al. (1993) Cardiologic abnormalities in Noonan syndrome: phenotypic diagnosis and echocardiographic assessment of 118 patients. J Am Coll Cardiol 22: 1189-1192.
6. Marino B, Digilio MC, Toscano A, Giannotti A, Dallapiccola B, (1999) Congenital heart diseases in children with Noonan syndrome: An expanded cardiac spectrum with high prevalence of atrioventricular canal. J Pediatr 135: 703-706.
7. Tartaglia M, Mehler EL, Goldberg R, Zampino G, Brunner HG, et al. (2001) Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome. Nat Genet 29: 465-468.
8. Schubbert S, Zenker M, Rowe SL, Boll S, Klein C, et al. (2006) Germline KRAS mutations cause Noonan syndrome. Nat Genet 38: 331-336.
9. Roberts AE, Araki T, Swanson KD, Montgomery KT, Schiripo TA, et al. (2007) Germline gain-of-function mutations in SOS1 cause Noonan syndrome. Nat Genet 39: 70-74.
10. Tartaglia M, Pennacchio LA, Zhao C, Yadav KK, Fodale V, et al. (2007) Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet 39: 75-79.
11. Razzaque MA, Nishizawa T, Komoike Y, Yagi H, Furutani M, et al. (2007) Germline gain-of-function mutations in RAF1 cause Noonan syndrome. Nat Genet 39: 1013-1017.
12. Pandit B, Sarkozy A, Pennacchio LA, Carta C, Oishi K, et al. (2007) Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet 39: 1007-1012.
13. Gelb BD, Tartaglia M, (2006) Noonan syndrome and related disorders: dysregulated RAS-mitogen activated protein kinase signal transduction. Hum Mol Genet 15 Spec No 2: R220-226.
14. Araki T, Chan G, Newbigging S, Morikawa L, Bronson RT, et al. (2009) Noonan syndrome cardiac defects are caused by PTPN11 acting in endocardium to enhance endocardial-mesenchymal transformation. Proc Natl Acad Sci U S A 106: 4736-4741.
15. Shchelochkov OA, Patel A, Weissenberger GM, Chinault AC, Wiszniewska J, et al. (2008) Duplication of chromosome band 12q24.11q24.23 results in apparent Noonan syndrome. Am J Med Genet A 146A: 1042-1048.
16. Tartaglia M, Zampino G, Gelb BD, (2010) Noonan syndrome: clinical aspects and molecular pathogenesis. Mol Syndromol 1: 2-26.
17. Tidyman WE, Rauen KA, (2009) The RASopathies: developmental syndromes of Ras/MAPK pathway dysregulation. Curr Opin Genet Dev 19: 230-236.
18. Dhandapany PS, Sadayappan S, Vanniarajan A, Karthikeyan B, Nagaraj C, et al. (2007) Novel mitochondrial DNA mutations implicated in Noonan syndrome. Int J Cardiol 120: 284-285.
19. Prasad GN, Vanniarajan A, Emmanuel C, Cherian KM, Singh L, et al. (2006) Novel mitochondrial DNA mutations in a rare variety of hypertrophic cardiomyopathy. Int J Cardiol 109: 432-433.
20. Bandelt H-J, Salas A, Bravi CM, (2006) What is a 'novel' mtDNA mutation-and does 'novelty' really matter? J Hum Genet 51: 1073-1082.
21. Bandelt H-J, Yao Y-G, Salas A, (2008) The search of 'novel' mtDNA mutations in hypertrophic cardiomyopathy: MITOMAPping as a risk factor. Int J Cardiol 126: 439-442.
22. Bandelt H-J, Salas A, Taylor RW, Yao Y-G, (2009) The exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches. Hum Mutat 30: 191-196.
23. Castro MG, Huerta C, Reguero JR, Soto MI, Domenech E, et al. (2006) Mitochondrial DNA haplogroups in Spanish patients with hypertrophic cardiomyopathy. Int J Cardiol 112: 202-206.
24. Rani DS, Dhandapany PS, Nallari P, Govindaraj P, Singh L, et al. (2010) Mitochondrial DNA haplogroup 'R' is associated with Noonan syndrome of south India. Mitochondrion 10: 166-173.
25. Pereira L, Goncalves J, Franco-Duarte R, Silva J, Rocha T, et al. (2007) No evidence for an mtDNA role in sperm motility: data from complete sequencing of asthenozoospermic males. Mol Biol Evol 24: 868-874.
26. Samuels DC, Carothers AD, Horton R, Chinnery PF, (2006) The power to detect disease associations with mitochondrial DNA haplogroups. Am J Hum Genet 78: 713-720.
27. Mosquera-Miguel A, Álvarez-Iglesias V, Vega A, Milne R, Cabrera de León A, et al. (2008) Is mitochondrial DNA variation associated with sporadic breast cancer risk? Cancer Res 68: 623-625.
28. Álvarez-Iglesias V, Mosquera-Miguel A, Cerezo M, Quintáns B, Zarrabeitia MT, et al. (2009) New population and phylogenetic features of the internal variation within mitochondrial DNA macro-haplogroup R0. PLoS ONE 4: e5112.
29. Torroni A, Rengo C, Guida V, Cruciani F, Sellitto D, et al. (2001) Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am J Hum Genet 69: 1348-1356.
30. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147.
31. Palanichamy Mg, Sun C, Agrawal S, Bandelt H-J, Kong Q-P, et al. (2004) Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet 75: 966-978.
32. Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, et al. (2004) The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75: 910-918.
33. Loogväli E-L, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, et al. (2004) Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol 21: 2012-2021.
34. Macaulay V, Richards M, Hickey E, Vega E, Cruciani F, et al. (1999) The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. Am J Hum Genet 64: 232-249.
35. Richards M, Macaulay V, Hickey E, Vega E, Sykes B, et al. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67: 1251-1276.
36. van Oven M, Kayser M, (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386-394.
37. Bandelt H-J, Olivieri A, Bravi C, Yao Y-G, Torroni A, et al. (2007) 'Distorted' mitochondrial DNA sequences in schizophrenic patients. Eur J Hum Genet 15: 400-402; author reply 402-404.
38. Bandelt H-J, Achilli A, Kong Q-P, Salas A, Lutz-Bonengel S, et al. (2005) Low "penetrance" of phylogenetic knowledge in mitochondrial disease studies. Biochem Biophys Res Commun 333: 122-130.
39. Salas A, Yao Y-G, Macaulay V, Vega A, Carracedo A, et al. (2005) A critical reassessment of the role of mitochondria in tumorigenesis. PLoS Med 2: e296.
40. Salas A, Carracedo Á, Macaulay V, Richards M, Bandelt H-J, (2005) A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun 335: 891-899.
41. Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V, (2002) The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71: 1150-1160.
42. Kong Q-P, Bandelt H-J, Sun C, Yao Y-G, Salas A, et al. (2006) Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15: 2076-2086.
43. Elson JL, Turnbull DM, Howell N, (2004) Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection. Am J Hum Genet 74: 229-238.
44. Soares P, Ermini L, Thomson N, Mormina M, Rito T, et al. (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84: 740-759.
45. Heredia CE, Balboa E, Castro-Feijóo L, Rica I, Barreiro J, et al. (2009) PTPN11, SOS1, KRAS and RAF: genotype-phenotype correlations in Noonan syndrome. Horm Res 72 (Suppl.3): 317.
46. Salas A, Richards M, De la Fé T, Lareu MV, Sobrino B, et al. (2002) The making of the African mtDNA landscape. Am J Hum Genet 71: 1082-1111.
47. Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, et al. (2008) The dawn of human matrilineal diversity. Am J Hum Genet 82: 1130-1140.
48. Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, et al. (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet 75: 752-770.
49. Olivieri A, Achilli A, Pala M, Battaglia V, Fornarino S, et al. (2006) The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314: 1767-1770.
50. Crespillo M, Luque JA, Paredes M, Fernández R, Ramirez E, et al. (2000) Mitochondrial DNA sequences for 118 individuals from northeastern Spain. Int J Legal Med 114: 130-132.
51. Salas A, Comas D, Lareu MV, Bertranpetit J, Carracedo Á, (1998) mtDNA analysis of the Galician population: a genetic edge of European variation. Eur J Hum Genet 6: 365-375.
52. Kivisild T, Shen P, Wall DP, Do B, Sung R, et al. (2006) The role of selection in the evolution of human mitochondrial genomes. Genetics 172: 373-387.
53. Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, et al. (2009) The diversity present in 5140 human mitochondrial genomes. Am J Hum Genet 84: 628-640.
54. Bandelt H-J, Kong Q-P, Richards M, Macaulay V, (2006) Estimation of mutation rates and coalescence times: some caveats. In: Bandelt H-J, Richards M, Macaulay V, editors. Human mitochondrial DNA and the evolution of Homo sapiens Berlin Springer-Verlag pp. 47-90.
55. Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, et al. (2004) Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 118: 137-146.
56. Yao Y-G, Salas A, Logan I, Bandelt H-J, (2009) mtDNA data mining in GenBank needs surveying. Am J Hum Genet 85 933: 929-933; author reply 933.
57. Helm M, Brule H, Friede D, Giege R, Putz D, et al. (2000) Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 6: 1356-1379.
58. Ingman M, Kaessmann H, Pääbo S, Gyllensten U, (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-713.
59. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, et al. (2002) Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences from the major African, Asian, and European haplogroups. Am J Hum Genet 70: 1152-1171.
60. McFarland R, Elson JL, Taylor RW, Howell N, Turnbull DM, (2004) Assigning pathogenicity to mitochondrial tRNA mutations: when "definitely maybe" is not good enough. Trends Genet 20: 591-596.
61. Salas A, Carracedo Á, (2007) Studies of association in complex diseases: statistical problems related to the analysis of genetic polymorphisms. Rev Clin Esp 207: 563-565.
62. Ingman M, Gyllensten U, (2006) mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res 34: D749-751.
63. Attimonelli M, Accetturo M, Santamaria M, Lascaro D, Scioscia G, et al. (2005) HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research. BMC Bioinformatics 6 (Suppl 4): S4.
64. Gasparre G, Hervouet E, de Laplanche E, Demont J, Pennisi LF, et al. (2008) Clonal expansion of mutated mitochondrial DNA is associated with tumor formation and complex I deficiency in the benign renal oncocytoma. Hum Mol Genet 17: 986-995.
65. Porcelli AM, Ghelli A, Ceccarelli C, Lang M, Cenacchi G, et al. (2010) The genetic and metabolic signature of oncocytic transformation implicates HIF1alpha destabilization. Hum Mol Genet 19: 1019-1032.
66. Zheng W, Khrapko K, Coller HA, Thilly WG, Copeland WC, (2006) Origins of human mitochondrial point mutations as DNA polymerase gamma-mediated errors. Mutat Res 599: 11-20.