1471-2350-9-41 1471-2350 Research article <p>New evidence of a mitochondrial genetic background paradox: Impact of the J haplogroup on the A3243G mutation</p> Pierron Denis d.pierron@anthropologie.u-bordeaux1.fr Rocher Christophe crocher@u-bordeaux2.fr Amati-Bonneau Patricia PaBonneau@chu-angers.fr Reynier Pascal PaReynier@chu-angers.fr Martin-Négrier Marie-Laure marie-laure.martin-negrier@umr5541.u-bordeaux2.fr Allouche Stéphane allouche-s@chu-caen.fr Batandier Cécile Cecile.Batandier@ujf-grenoble.fr de Camaret Mousson Benedicte mousson@univ-lyon1.fr Godinot Catherine godinot1@yahoo.com Rotig Agnes roetig@necker.fr Feldmann Delphine delphine.feldmann@trs.ap-hop-paris.fr Bellanne-Chantelot Christine christine.bellanne@sat.ap-hop-paris.fr Arveiler Benoit Benoit.Arveiler@u-bordeaux2.fr Pennarun Erwann erwan@ebc.ee Rossignol Rodrigue rodrigue.rossignol@phys-mito.u-bordeaux2.fr Crouzet Marc marc.crouzet@lbms.u-bordeaux2.fr Murail Pascal p.murail@anthropologie.u-bordeaux1.fr Thoraval Didier didier.thoraval@lbms.u-bordeaux2.fr Letellier Thierry thierry.letellier@phys-mito.u-bordeaux2.fr

Université Bordeaux 1, Laboratoire d'Anthropologie des Populations du Passé, UMR 5199 PACEA, 33400 Talence, France

Institut de Biochimie et Génétique Cellulaires, UMR 5095, CNRS, Université Victor Segalen-Bordeaux 2, 33076 Bordeaux, France

INSERM, U688 Laboratoire de Physiopathologie Mitochondriale; Université Victor Segalen-Bordeaux 2, 33076 Bordeaux, France

INSERM, U694, Angers, F-49033 France; Departement de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, F-49033 France

Laboratoire d'Anatomie Pathologique, Centre Hospitalier Universitaire, Laboratoire d'Histologie-Embryologie, UFRII, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France

Laboratoire de Biologie cellulaire et moléculaire de la signalisation, UPRES-EA 3919, Université de Caen, 14033 Caen, France

Laboratoire de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Grenoble, 38054 Grenoble, France

Laboratoire de Biochimie Pédiatrique, Hôpital Debrousse, 69322 Lyon, France

Centre de Génétique Moléculaire et Cellulaire, UMR 5534, CNRS, Université Claude Bernard de Lyon 1, 69622 Villeurbanne, France

Department of Genetics, INSERM U781 Hôpital Necker-Enfants Malades, 75743 Paris, France

Service de Biochimie et de Biologie Moléculaire, INSERM U587 Hôpital d'Enfants Armand-Trousseau, AP-HP, 75571 Paris, France

Department of Cytogenetics, Hôpital Saint-Antoine-AP-HP, 75012 Paris, France

Pôle Génotypage-Séquençage, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France

Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia

 BMC Medical Genetics 1471-2350 2008 9 1 41 http://www.biomedcentral.com/1471-2350/9/41 18462486 10.1186/1471-2350-9-41 19 12 2007 07 5 2008 07 5 2008 2008 Pierron et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

The A3243G mutation in the tRNALeu gene (UUR), is one of the most common pathogenic mitochondrial DNA (mtDNA) mutations in France, and is associated with highly variable and heterogeneous disease phenotypes. To define the relationships between the A3243G mutation and mtDNA backgrounds, we determined the haplogroup affiliation of 142 unrelated French patients – diagnosed as carriers of the A3243G mutation – by control-region sequencing and RFLP survey of their mtDNAs.

Results

The analysis revealed 111 different haplotypes encompassing all European haplogroups, indicating that the 3243 site might be a mutational hot spot. However, contrary to previous findings, we observed a statistically significant underepresentation of the A3243G mutation on haplogroup J in patients (p = 0.01, OR = 0.26, C.I. 95%: 0.08–0.83), suggesting that might be due to a strong negative selection at the embryo or germ line stages.

Conclusion

Thus, our study supports the existence of mutational hotspot on mtDNA and a "haplogroup J paradox," a haplogroup that may increase the expression of mtDNA pathogenic mutations, but also be beneficial in certain environmental contexts.

Background

The mitochondrion is unique in that its bioenergetic and biosynthetic systems are assembled from two different information storage and retrieval systems: the nuclear-cytosolic system, expressing nuclear DNA-encoded mitochondrial genes, and the mitochondrial system, expressing mitochondrial DNA-encoded genes. Maternally inherited, mitochondrial DNA (mtDNA) encodes the 12S and 16S mitochondrial rRNAs, 22 tRNAs, and 13 polypeptides, which form essential subunits of OXPHOS enzyme complexes 12.

Over the past twenty years, genetic variations in mtDNA have been linked to a number of multifactorial diseases and aging 3, however, a large number of mutations were considered neutral and used to define haplogroups in order to investigate human origins 4, migrations, and demographic events 5. Indeed, human populations can be divided into several mtDNA haplogroups on the basis of specific nucleotid polymorphisms scattered throughout the mitochondrial genome, reflecting mutation events accumulated over time by a discrete maternal lineage. Thus, for example, 95% of Europeans belong to 10 major haplogroups 6 while 100% of Native Americans belong to 5 major haplogroups 78.

Several recent studies have pointed out the possible impact of haplogroups on mitochondrial physiology. Indeed, Ruiz-Pesini et al. 9 revealed a possible impact of haplogroups on the oxidative phosphorylation activity that facilitates human adaptation to colder climates, resulting in regional enrichment of specific mtDNA lineages (haplogroups). Moreover, haplogroups have been shown to play a role in the phenotypic expression of diseases 10. Indeed, a link has been observed between haplogroups and various disorders and phenotypes; for example, the haplogroup may influence the disease expression of a mitochondrial pathogenic mutation, such as T14484C and G11778A, found in Leber hereditary optic neuropathy (LHON) 1112131415.

The A3243G mutation 161718 on the tRNALeu gene (UUR) is one of the most common mitochondrial DNA mutations worldwide and in France (unpublished data from the French mitochondrial disease network). The phenotypic expression of this mutation is quite variable, ranging from mild to severe clinical phenotypes. Indeed, while mtDNA the A3243G mutation is usually associated with the MELAS syndrome (mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes: MIM 540000) or MIDD (maternally inherited diabetes and deafness: MIM 520000) 19. This mutation is also found in patients without any typical symptoms, but who had clinical manifestations ranging from a mixture of chronic progressive external ophthalmoplegia symptoms, to strokelike episodes, cardiomyopathy, and progressive kidney disease 20212223.

Several molecular mechanisms have been proposed to explain the phenotypic expression of this mutation, such as a reduced association of mRNA with ribosomes, possibly due to the tRNALeu (UUR) aminoacylation defect 24. However, Kirino et al. recently proposed that a wobble modification deficiency resulting in defective translation could be a key molecular factor responsible for the phenotypic features of MELAS that would explain why the different MELAS-associated mutations produce indistinguishable clinical features 25.

Several studies suggested that certain mtDNA haplogroups affected the phenotypic expression of this mutation 2627, but Torroni et al. and Deschauer et al. recently concluded that European mtDNA backgrounds did not have any substantial impact 2829, however, these studies involved only a small number of individuals or poorly-defined populations. Thus it was impossible to confirm the relationship between mutations responsible for pathological conditions and haplogroups. Indeed, as mentioned by Samuels et al. 30, large cohorts are required to identify a reliable connection with complex human diseases and geographical variations in haplogroup frequencies.

In order to elucidate the relationships between mtDNA the A3243G mutation and mitochondrial genetic backgrounds, we used RFLP and sequencing to determine haplogroups of 142 patients diagnosed as carriers of the A3243G mutation by the French mitochondrial disease network.

Methods

A3243G patients

Screening for mitochondrial diseases was carried out by the French mitochondrial disease network. This network is made up of all the laboratories involved in genetic and biochemical diagnosis of mitochondrial pathologies in France. These laboratories collect samples from all French patients suspected to be affected by mitochondrial diseases, as the French health-care system makes it possible for each individual to receive appropriate treatment. Over the past fifteen years, 1,667 patients have been diagnosed as carriers of a mitochondrial mutation. Patients showing symptoms of MELAS, deafness, or mitochondrial diabetes were tested for the A3243G mutation, using standard procedures. Among the cohort of individuals diagnosed as carriers of the A3243G mutation over this period, we have listed 142 unrelated patients tested by laboratories in University Hospitals of Angers, Bordeaux, Caen, Grenoble, Lyon, and Paris. All these patients carried the A3243G mutation and presented a mitochondrial pathology (General phenotype are presented in Table 1). Despite we have detected qualitatively for all the A3243G patients the presence of heteroplamy (between 80 to 40%), the precise percentage of heteroplasmy was not available for all the patients. Genetic analyses were carried out with the appropriate consent of the patients.

<p>Table 1</p>

RFLP and control-region mtDNA haplotypes from the French A3243G carriers. The patients were regrouped in three major phenotypes (Clear MELAS Syndrome, Partial MELAS syndrome and Diabetes Syndrome).

Individu

haplotype

haplogroup

RFLP

POLYMORPHISM OBSERVED BETWEEN POSITION 16050–16569 AND 1- 205

PHENOTYPE

1

1

H

-7025AluI

16304,

clear MELAS syndrome

2

1

H

-7025AluI

16304,

Partial MELAS syndrome

3

1

H

-7025AluI

16304,

clear MELAS syndrome

4

2

H

-7025AluI

16354,

Diabetes Syndrome

5

2

H

-7025AluI

16354,

Diabetes Syndrome

6

3

H

-7025AluI

16519,

Partial MELAS syndrome

7

3

H

-7025AluI

16519,

Diabetes Syndrome

8

3

H

-7025AluI

16519,

clear MELAS syndrome

9

3

H

-7025AluI

16519,

Diabetes Syndrome

10

3

H

-7025AluI

16519,

Diabetes Syndrome

11

3

H

-7025AluI

16519,

clear MELAS syndrome

12

3

H

-7025AluI

16519,

Partial MELAS syndrome

13

3

H

-7025AluI

16519,

clear MELAS syndrome

14

3

H

-7025AluI

16519,

clear MELAS syndrome

15

3

H

-7025AluI

16519,

Partial MELAS syndrome

16

3

H

-7025AluI

16519,

Diabetes Syndrome

17

3

H

-7025AluI

16519,

clear MELAS syndrome

18

3

H

-7025AluI

16519,

Diabetes Syndrome

19

4

H

-7025AluI

16094,16278,16293,16311,195,

clear MELAS syndrome

20

5

H

-7025AluI

16114,16293,16311,16354,16519,195,

clear MELAS syndrome

21

5

H

-7025AluI

16114,16293,16311,16354,16519,195,

Diabetes Syndrome

22

6

H

-7025AluI

16126,16274,16519,

Diabetes Syndrome

23

7

H

-7025AluI

16126,16311,16519,

Diabetes Syndrome

24

8

H

-7025AluI

16126,16519,198,

clear MELAS syndrome

25

9

H

-7025AluI

16129,16316,16519,

Partial MELAS syndrome

26

10

H

-7025AluI

16129,16362,16482,16519,

Partial MELAS syndrome

27

11

H

-7025AluI

16129,16519,

Diabetes Syndrome

28

12

H

-7025AluI

16129,16519,10,

Partial MELAS syndrome

29

13

H

-7025AluI

16129,16519,10,189,

clear MELAS syndrome

30

14

H

-7025AluI

16129,16519,152,

clear MELAS syndrome

31

15

H

-7025AluI -12308HinfI; -4216NlaIII; +4577NlaIII

16162,16209,16519,73,

Diabetes Syndrome

32

16

H

-7025AluI

16166delA,

Diabetes Syndrome

33

17

H

-7025AluI

16169,16299,16519,

Diabetes Syndrome

34

18

H

-7025AluI

16183C,16189,16519,

clear MELAS syndrome

35

19

H

-7025AluI

16189,195,

Partial MELAS syndrome

36

19

H

-7025AluI

16189,195,

clear MELAS syndrome

37

19

H

-7025AluI

16189,195,

clear MELAS syndrome

38

20

H

-7025AluI

16213,16256,16519,9,

Partial MELAS syndrome

39

21

H

-7025AluI

16221,16519,

Partial MELAS syndrome

40

22

H

-7025AluI

16260,16357,16519,

Diabetes Syndrome

41

22

H

-7025AluI

16260,16357,16519,

Partial MELAS syndrome

42

23

H

-7025AluI

16261,16519,

clear MELAS syndrome

43

24

H

-7025AluI -12308HinfI; -4216NlaIII; +4577NlaIII

16278,16519,73,

Partial MELAS syndrome

44

25

H

-7025AluI

16290,16304,16519,

Diabetes Syndrome

45

26

H

-7025AluI

16290,16519,152,

Diabetes Syndrome

46

27

H

-7025AluI

16293,16519,

Diabetes Syndrome

47

27

H

-7025AluI

16293,16519,

Diabetes Syndrome

48

28

H

-7025AluI

16304,16325,

clear MELAS syndrome

49

29

H

-7025AluI

16311,16519,

Diabetes Syndrome

50

29

H

-7025AluI

16311,16519,

Diabetes Syndrome

51

29

H

-7025AluI

16311,16519,

Diabetes Syndrome

52

30

H

-7025AluI

16311,16519,93,

Diabetes Syndrome

53

31

H

-7025AluI

16362,16482,

clear MELAS syndrome

54

32

H

-7025AluI

16362,16482,16519,152,

Partial MELAS syndrome

55

33

H

-7025AluI

16519,143,152,

Partial MELAS syndrome

56

34

H

-7025AluI

16519,151,152,

Partial MELAS syndrome

57

34

H

-7025AluI

16519,151,152,

Partial MELAS syndrome

58

35

H

-7025AluI

16519,152,199,

Partial MELAS syndrome

59

35

H

-7025AluI

16519,152,199,

Partial MELAS syndrome

60

36

H

-7025AluI

16519,56i,93,

Diabetes Syndrome

61

37

H

-7025AluI -12308HinfI; -4216NlaIII; +4577NlaIII

16519,73,

clear MELAS syndrome

62

38

H

-7025AluI

16519,93,95C,

Partial MELAS syndrome

63

39

H

-7025AluI

93,204,

Partial MELAS syndrome

64

39

H

-7025AluI

93,204,

Diabetes Syndrome

65

40

H

-7025AluI

RCRS,

Diabetes Syndrome

66

40

H

-7025AluI

RCRS,

clear MELAS syndrome

67

41

R0*

+7025AluI -12308HinfI; -4216NlaIII; +4577NlaIII

16311,

Partial MELAS syndrome

68

42

R0*

+7025AluI -12308HinfI; -4216NlaIII; +4577NlaIII

16311,16354,

clear MELAS syndrome

69

43

R0a

+7025AluI +4577NlaIII

16126,16362,16519,64,

clear MELAS syndrome

70

44

V

+7025AluI -4577NlaIII

16086,16298,72,73,

Diabetes Syndrome

71

45

V

+7025AluI -4577NlaIII

16129,16298,16311,72,195,

Partial MELAS syndrome

72

46

V

+7025AluI -4577NlaIII

16162,16298,

clear MELAS syndrome

73

47

V

+7025AluI -4577NlaIII

16278,16298,72,

clear MELAS syndrome

74

48

V

+7025AluI -4577NlaIII

16292,16298,72,195,

Diabetes Syndrome

75

49

V

+7025AluI -4577NlaIII

16298,16301,72,

Partial MELAS syndrome

76

50

V

+7025AluI -4577NlaIII

16298,16311,72,

clear MELAS syndrome

77

51

V

+7025AluI -4577NlaIII

16298,72,

clear MELAS syndrome

78

52

V

+7025AluI -4577NlaIII

16298,72,200,

clear MELAS syndrome

79

53

V

+7025AluI -4577NlaIII

16298,72,93,

Diabetes Syndrome

80

54

HV0*

+7025AluI +4577NlaIII

16129,16298,72,195,

Diabetes Syndrome

81

55

HV0*

+7025AluI +4577NlaIII

16298,72,195,

Diabetes Syndrome

82

56

T1

+7025AluI +4216NlaIII; +13704BstOI

16126,16163,16186,16189,16294,16304,16519,73,152,195,

clear MELAS syndrome

83

57

T1

+7025AluI +4216NlaIII; +13704BstOI

16126,16163,16186,16189,16294,16355,16356,16519,73,

clear MELAS syndrome

84

58

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16147,16294,16296,16297,16304,16519,73,

clear MELAS syndrome

85

59

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16153,16294,16390,16519,41,73,150,

Diabetes Syndrome

86

60

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16172,16294,16296,16304,16519,73,

Diabetes Syndrome

87

61

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16189,16292,16294,16519,73,146,

Diabetes Syndrome

88

62

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16266,16294,16304,16519,73,

clear MELAS syndrome

89

63

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16294,16296,16304,16454,16455,16519,73,152,

Diabetes Syndrome

90

64

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16294,16296,16304,16519,73,

Diabetes Syndrome

91

65

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16294,16296,16304,16519,73,146,

Partial MELAS syndrome

92

66

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16294,16296,16519,73,

Partial MELAS syndrome

93

67

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16294,16304,16519,73,

clear MELAS syndrome

94

68

T

+7025AluI +4216NlaIII; +13704BstOI

16126,16294,16519,73,146,152,

Partial MELAS syndrome

95

69

J

+7025AluI +4216NlaIII; -13704BstOI

16069,16126,16234,16235,16519,73,185,188,

Partial MELAS syndrome

96

69

J

+7025AluI +4216NlaIII; -13704BstOI

16069,16126,16234,16235,16519,73,185,188,

Diabetes Syndrome

97

70

J

+7025AluI +4216NlaIII; -13704BstOI

16069,16126,16366,16390,16519,73,185,188,

clear MELAS syndrome

98

71

U2

+7025AluI +12308HinfI

16051,16129,16189,16256,16519,73,152,

Partial MELAS syndrome

99

72

U2

+7025AluI +12308HinfI

16051,16129C,16183C,16189,16319,16362,16519,73,152,

Diabetes Syndrome

100

73

U2

+7025AluI +12308HinfI

16051,16129C,16183C,16189,16355,16362,16519,73,152,

Diabetes Syndrome

101

74

U2

+7025AluI +12308HinfI

16051,16183C,16189,16234,16266,16294,16519,16525,16558,73,152,199,

Diabetes Syndrome

102

75

U2

+7025AluI +12308HinfI

16051,16183C,16189,16234,16266,16294,16519,16525,73,152,199,

clear MELAS syndrome

103

76

K

+7025AluI +12308HinfI

16093,16224,16260,16311,16519,44,73,

Partial MELAS syndrome

104

77

K

+7025AluI +12308HinfI

16093,16224,16311,16319,16519,73,195,

Diabetes Syndrome

105

78

K

+7025AluI +12308HinfI

16114A,16224,16311,16362,16519,73,195,

Diabetes Syndrome

106

79

K

+7025AluI +12308HinfI

16223,16224,16234,16311,16519,73,114,

clear MELAS syndrome

107

80

K

+7025AluI +12308HinfI

16224,16311,16519,64,73,146,152,

Diabetes Syndrome

108

81

K

+7025AluI +12308HinfI

16224,16311,16519,73,

Diabetes Syndrome

109

82

K

+7025AluI +12308HinfI

16224,16311,16519,73,146,

clear MELAS syndrome

110

83

K

+7025AluI +12308HinfI

16224,16311,16519,73,146,152,

Diabetes Syndrome

111

84

K

+7025AluI +12308HinfI

16224,16311,16519,73,146,185,

Partial MELAS syndrome

112

85

K

+7025AluI +12308HinfI

16224,16311,16519,73,146,195,

clear MELAS syndrome

113

85

K

+7025AluI +12308HinfI

16224,16311,16519,73,146,195,

clear MELAS syndrome

114

86

U5

+7025AluI +12308HinfI

16148,16239,16270,73,150,

Diabetes Syndrome

115

87

U5

+7025AluI +12308HinfI

16150,16172,16185,16189delT,16270,16274,16311,16465,16519,73,150,152,

Partial MELAS syndrome

116

88

U5

+7025AluI +12308HinfI

16168,16192,16256,16270,16526,73,

Partial MELAS syndrome

117

89

U5

+7025AluI +12308HinfI

16189,16192,16270,16398,73,150,

Diabetes Syndrome

118

90

U5

+7025AluI +12308HinfI

16192,16256,16270,16278,16294,16391,16526,64,73,

Diabetes Syndrome

119

91

U5

+7025AluI +12308HinfI

16192,16270,16319,16526,73,150,

Partial MELAS syndrome

120

92

U5

+7025AluI +12308HinfI

16192,16270,16319,73,150,

Diabetes Syndrome

121

93

U5

+7025AluI +12308HinfI

16256,16270,16399,73,

clear MELAS syndrome

122

94

U5

+7025AluI +12308HinfI

16270,16296,58,59G,64,73,150,200,

clear MELAS syndrome

123

95

U4

+7025AluI +12308HinfI

16219,16356,16519,73,195,

clear MELAS syndrome

124

95

U4

+7025AluI +12308HinfI

16219,16356,16519,73,195,

Diabetes Syndrome

125

95

U4

+7025AluI +12308HinfI

16219,16356,16519,73,195,

Diabetes Syndrome

126

96

U4

+7025AluI +12308HinfI

16295,16356,16519,73,195,

Diabetes Syndrome

127

97

U4

+7025AluI +12308HinfI

16356,16519,73,146,195,

clear MELAS syndrome

128

98

U4

+7025AluI +12308HinfI

16356,16519,73,195,

clear MELAS syndrome

129

99

U5

+7025AluI +12308HinfI

16189,16192,16270,16311,16336,55,73,150,

clear MELAS syndrome

130

100

X

+7025AluI +14465AccI

16129,16189,16223,16278,16290,16362,16519,73,153,195,

clear MELAS syndrome

131

101

X

+7025AluI +14465AccI

16186,16189,16223,16278,16297,16519,73,153,195,

Diabetes Syndrome

132

102

X

+7025AluI

16186,16189,16223,16278,16519,73,153,188,195,

Partial MELAS syndrome

133

103

I

+7025AluI -4529HaeII

16129,16223,16304,16391,16519,73,199,204,

Diabetes Syndrome

134

103

I

+7025AluI -4529HaeII

16129,16223,16304,16391,16519,73,199,204,

Partial MELAS syndrome

135

104

N1b

+7025AluI

16145,16176G,16223,16390,16519,73,151,152,

clear MELAS syndrome

136

105

N1a

+7025AluI

16147A,16172,16223,16248,16355,16519,73,199,204,

clear MELAS syndrome

137

106

L2

+7025AluI

16129,16189,16192,16223,16274,16278,16294,16309,16390,73,143,146,152,195,

Diabetes Syndrome

138