genetic heterogeneity of mitochondrial disorders - agnès rötig
TRANSCRIPT
1/8000 live birth
Primary mitochondrial disordersMutations in 250 nuclear genesMutations in 13 mitochondrial genes
Secondary mitochondrial disordersSecondary RC deficiency ( oxidation)False diagnosis
Human genome: 30000-50000 genes1000-1500 genes encoding mitochondrial proteins
Mitochondrial disorders
CII
CIII CIV CVCI
O2 H2O
c
ADP ATP
Respiratory chain
CNSheartmusclegutkidneylivereyebloodeardiabetesIUGR
CNSliver
heart
Clinical features in respiratory chain deficiency
Necker hospitalPediatric patients
noyau
~1500 mitochondrial proteins
mtDNA37 genes
CII
CIII CIV CVCI
O2 H2O
c
ADP ATP
Genes of mitochondrial disorders
• Sporadic• Maternal• AD• AR• X linked
mtDNA
TCAcycle
Translocases Chaperones
Carriers
mtDNAmaintenance
Proteases
Assembly
Cofactorssynthesis
TranslationFusionFission
RC subunits
TCAdeficiencies
Mechanisms of mitochondrial disorders
250 nuclear genes of mitochondrial diseases
Genetic heterogeneityClinical heterogeneity
Mitochondrial disorders
mtDNA mutations excluded
mtDNAnuclearunknown
CI CII CIII CIV CV multiple Q0
100
200
300
400
500
600
unknownnuclearmtDNA
Necker hospital patients
10%
22%
Leigh Syndrome LHON Neurogenic Muscle Weakness Ataxia and Retinitis Pigmentosa Encephalomyopathy, MELAS Epilepsy MM, Exercise Intolerance Cardiomyopathy Deafness Diabetes Mellitus Alzheimer & Parkinson Disease Idiopathic Sideroblastic Anemia
mtDNA point mutations
Reported in Mitomap:rRNA/tRNA mutations: 306 mutationsCoding and Control Region Point Mutations: 311mtDNA deletions: 134
MITOMAPA human mitochondrial genome databasehttp://www.mitomap.org/MITOMAP
mtDNA variations
Polymorphisms
usually homoplasmictransmitted
homoplasmy homoplasmyheteroplasmy
Mutations
usually heteroplasmictransmitted or de novo
high mutant load in patientlow mutant load in mother
0% mutation in mother
high mutant load in affected organslow mutant load in non affected organs
mtDNA mutations: 10% of pediatric patients
23 haplogroups associatingspecific polymorphisms
Leigh syndromeHyperlactatemiaImprovement at 3 yrs
Leigh syndromeHyperlactatemiaMultiple RC deficiencyDeath at 6 mo
mt-tRNAGlu
100% 14674T>C
100%14674T>C
100%14674T>C
100%14674T>C
100%14674T>C
100%14674T>C
Onset: first days or weeks of lifeHypotoniaRespiratory and feeding difficultiesHyperlactatemia
One patient died of severe hypotonia at 39 daysAll other improved spontaneously (4-20 months)
100% 14674T>C mt-tRNAGlu
in all patients in all maternal relatives
mtDNA mutation or polymorphism?
Horvath et al, Brain 2009
Leber hereditary optic neuropathy
Onset 15-30 yrsMost common of the primary mtDNA diseasesPrevalence: 1/40 000 in Europe2% of visually impaired people suffer LHON
Incomplete penetrance50% of males and 10% of females with LHON mutation develop the optic neuropathy genetic and/or environmental factors
ND4 (G11778A)ND6 (T14484C)cytb (G15257A)maternal transmissionhomoplasmic/heteroplasmic
mtDNA polymorphisms11778G>A and 14484T>C mutations higher risk of visual failure with haplogroup J3460G>A mutation higher risk of visual failure with haplogroup K11778G>A mutation lower risk of visual loss with haplogroup H
Leber hereditary optic neuropathy
Environmental factors
discordant monozygotic twins? increased risk of visual loss with high tobacco and alcohol consumption? nutritional deprivation, exposure to industrial toxins, antiretroviral drugs, psychologicalstress or acute illness
Nuclear genetic factorspredominance of affected males in LHON recessive X-linked susceptibility gene?no skewed X chromosome inactivation in affected female carrierstwo loci Xp21–Xq21 and Xq25–27 but no identified gene
Genetic factors
Mitochondrial DNA mutationsGenes encoding subunits of the respiratory chain
CI
CII
CIII CIV CV
ND1ND2ND3ND4ND5ND6 cytb
ATP6ATP8
COXICOXIICOXIII
Necker hospital: 33 patients 1 patient 1 patient 20 patients
mtDNA mutations: 10% of pediatric patients
Mitochondrial disorders
Relative clinical homogeneity but high genetic heterogeneity:Complex I deficiency
High clinical and genetic heterogeneity:Translation deficiency
multiple 51%(555 patients)
CI 22% (250 patients)
CII 4%CIII 2,5%
CIV 13%
CV 7%
Q 1%
NADH + H+
NAD+
FMN
Fe-S pool
Q pool Q
Innermembrane
Matrix
Fp
IP
HP
FPNDUFV1NDUFV2NDUFV3
HPNDUFA1NDUFA2NDUFA3NDUFA4NDUFA6NDUFA7NDUFA8NDUFA9NDUFA10NDUFAB1NDUFB1NDUFB2NDUFB3NDUFB4NDUFB5NDUFB6NDUFB7NDUFB8NDUFB9NDUFB10NDUFC1NDUFC2NDUFS7NDUFS8
ND1ND2ND3ND4ND4LND5ND6
IPNDUFS1NDUFS2NDUFS3NDUFS4NDUFS5NDUFS6NDUFA5
Mitochondrial complex IComplex I: 44 subunits + 11 assembly factors- 37 encoded by nuclear genes- 7 encoded by mtDNA
Assembly factorsNDUFAF1 FOXRED1NDUFAF2 ECSITNDUFAF3 ACAD9NDUFAF4 TMEM126BNDUFAF6 C3ORF1IND1
mtD
NA
NADH + H+
NAD+
FMN
Fe-S pool
Q pool Q
Innermembrane
Matrix
Fp
IP
HP
FPNDUFV1NDUFV2NDUFV3
HPNDUFA1NDUFA2NDUFA3NDUFA4NDUFA6NDUFA7NDUFA8NDUFA9NDUFA10NDUFAB1NDUFB1NDUFB2NDUFB3NDUFB4NDUFB5NDUFB6NDUFB7NDUFB8NDUFB9NDUFB10NDUFC1NDUFC2NDUFS7NDUFS8
ND1ND2ND3ND4ND4LND5ND6
IPNDUFS1NDUFS2NDUFS3NDUFS4NDUFS5NDUFS6NDUFA5
Mitochondrial complex IComplex I: 44 subunits + 11 assembly factors- 37 encoded by nuclear genes- 7 encoded by mtDNA
Assembly factorsNDUFAF1 FOXRED1NDUFAF2 ECSITNDUFAF3 ACAD9NDUFAF4 TMEM126BNDUFAF6 NDUFAF5IND1
mtD
NA
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►>30 disease causing genes
unknown
nuclear
mtDNA
53%
26%
21%
Clinical presentation of complex I deficiencies
IUGRGrowth retardationOptic atrophyDeafnessTubulopathy Cardiomyopathy
CardiomyopathyMuscle weaknessCardiomyopathy
mtDNA mutations
ND1ND3ND4ND5ND6
Assembly factors
ACAD9 NDUFAF1IBA57 NDUFAF2NFU1 NDUFAF3NUBPL NDUFAF4NUBPL NDUFAF5NDUFAF6TMEM126B
Structural subunits
NDUFB3 NDUFB8NDUFS1 NDUFS3NDUFS4 NDUFS6NDUFS7 NDUFS8NDUFV1 NDUFV2NDUFA11NDUFA12
Neurological involvement:
Leigh syndrome Psychomotor retardation Epilepsy
- Abnormal brain MRI- Hyperlactatemia/hyperlactatorachia
Bilateral brainstem lesions (30/30)Lactate peak (30/30)Anomalies of the putamen (23/30)
Brain MRI in complex I deficient patients
Brain MRI (Axial T2)
brainstem lenticular nuclei and thalami
Magnetic resonancespectroscopy
30 patients with isolated complex I deficiency20 mtDNA mutations10 nuclear gene mutations
Lebre, JMG 2010
Patients with nuclear gene mutations Earlier brain MRI anomalies than patients with mtDNA mutations (2.8 years and 8.9, respectively, p<0.05)
Mutations in complex I genes cause a common pattern of brain MRI imagingBrainstem and basal ganglia anomalies
+ Lactate peakbut no corpus callosum dysmorphism
Stroke-like lesions 40% of patients with mtDNA mutations none of the patients with nuclear gene mutations
Supratentorial leucoencephalopathy 50% of patients with nuclear gene mutations none of the patients carrying mtDNA mutations
Brain MRI in complex I deficient patients
Lebre, JMG 2010
Mitochondrial disorders
Relative clinical homogeneity but high genetic heterogeneity:Complex I deficiency
High clinical and genetic heterogeneity:Translation deficiency
multiple 51%(555 patients)
CI 22% (246 patients)
CII 4%CIII 2,5%
CIV 13%
CV 7%
Q 1%
translation deficiency: 69 patients
Mitochondrial translation
CI
CII
CIII CIV CV
mtDNA
Mitochondrial ribosome (mitoribosome)large subunit 39S 31 proteins mt 16S rRNAsmall subunit 28S 21 proteins mt 12S rRNA
tRNA synthetases 30 proteins mt tRNAtRNA modification enzymes 30 proteinsOther factors 40 proteins
Nuclear genes Mitochondrial genes
13 respiratory chainsubunits
Abnormal mitochondrial translation
mtDNA
tRNA
tRNAprocessing
aminoacyl –tRNAsynthetases
ribosomalproteins
translationfactors
rRNA
mRNA
tRNALeuMELASsyndrome
AARS2 CardiomyopathyCARS2 Myoclonic epilepsyDARS2 LeukoencephalopathyEARS2 LeukoencephalopathyFARS2 Alpers syndromeGARS Myalgia, cardiomyopathyHARS2 Perrault syndromeIARS2 Cataract, deafness/Leigh SyndromeKARS CMT diseaseLARS2 Perrault SyndromeNARS2 Alpers syndrome / deafness and Leigh SyndromePARS2 Alpers syndromeRARS2 Pontocerebellar hypoplasiaSARS2 Pulmonary hypertension, renal failureYARS2 Myopathy, sideroblastic anemia
MRPL12 Growth retardation, encephalopathyMRPL3 Cardiomyopathy, mental retardationMRPL44 CardiomyopathyMRPS16 Agenesis of corpus callosum, dysmorphismMRPS22 Cardiomyopathy, tubulopathy/Cornelia de Lange like syndromeMRPS7 Deafness, hepatic and renal failure
GTPBP3 Cardiomyopathy, encephalopathyMTFMT Leigh syndromeMTO1 CardiomyopathyPUS1 Myopathy and sideroblastic anemiaTRMT5 Cardiomyopathy/exercise intoleranceTRMT10C Hypotonia, feeding difficulties, deafnessTRMU Liver failure, deafness
GFM1 Encephalopathy/hepatic failureGFM2 Neurodevelopmental disorderC12orf62 Dysmorphic featuresC12orf65 Optic atrophy, axonal neuropathy, paraparesisLRPPRC Leigh syndrome, French-Canadian typeRMND1 EncephalopathyTACO1 Leigh syndromeTSFM Encephalomyopathy/cardiomyopathy/liver failureTUFM Encephalopathy
Heterogeneity in mitochondrial translation deficiencyAminoacyl-tRNA synthetasesGene Number of
patientsClinical presentation
AARS2 2 families Cardiomyopathy1 family Encephalomyopahty
CARS2 1 family Myoclonic epilepsyDARS2 >30 families LeukoencephalopathyEARS2 6 families LeukoencephalopathyFARS2 2 patients Alpers syndrome
1 patient Early-onset epilepsy1 family Developmental delay, dysarthria1 family Spastic paraplegia
GARS 1 patient Myalgia, cardiomyopathyHARS2 1 family Perrault syndromeIARS2 3 patients Cataract, deafness
1 patient Leigh Syndrome1 patient Cardiomyopathy
KARS 2 patients CMT disease1 family visual loss, progressive microcephaly, developmental delay, seizures3 families nonsyndromic hearing impairment
LARS2 2 families Perrault Syndrome (POF, hearing loss)NARS2 1 patient Alpers syndrome
3 patients Deafness and Leigh SyndromePARS2 1 patient Alpers syndromeRARS2 10 patients Pontocerebellar hypoplasiaSARS2 3 families HUPRA syndrome: Pulmonary hypertension, renal failureYARS2 5 patients Myopathy, sideroblastic anemia
Gene ProteinRNF207 ring finger protein 207SEC16B SEC16 homolog B (S. cerevisiae)CCNT2 cyclin T2MTRF1L mitochondrial translational release factor 1-likeSERAC1 serine active site containing 1MXRA5 matrix-remodelling associated 5
Which gene?
IUGRD1 lactic acidosisD4 liver insufficiencyHypotoniaBrain MRI: thalamus, lactate peakDeath at 7 moMultiple RC deficiency in liver
Gene ProteinRNF207 ring finger protein 207SEC16B SEC16 homolog B (S. cerevisiae)CCNT2 cyclin T2MTRF1L mitochondrial translational release factor 1-likeSERAC1 phospholipid remodeling MXRA5 matrix-remodelling associated 5
homozygous c.107T>A, p.Leu36GlnSIFT: DeleteriousMutationTaster: Disease causingPolyphen: Probably damaging
MTRF1L A/T MTRF1L A/T
MTRF1L A/A MTRF1L A/A
Which gene?
IUGRD1 lactic acidosisD4 liver insufficiencyHypotoniaBrain MRI: thalamus, lactate peakDeath at 7 moMultiple RC deficiency in liver
Gene ProteinRNF207 ring finger protein 207SEC16B SEC16 homolog B (S. cerevisiae)CCNT2 cyclin T2MTRF1L mitochondrial translational release factor 1-likeSERAC1 phospholipid remodeling (interface mito/ER)MXRA5 matrix-remodelling associated 5
homozygous c.107T>A, p.Leu36GlnSIFT: DeleteriousMutationTaster: Disease causingPolyphen: Probably damaging
c.1122_1124dup, p.Tyr375*
IUGRD1 lactic acidosisD4 liver insufficiencyHypotoniaBrain MRI: thalamus, lactate peakDeath at 7 moMultiple RC deficiency in liver
MTRF1L A/T MTRF1L A/T
MTRF1L A/A MTRF1L A/A
SERAC1 dup/dupSERAC1 dup/dup
SERAC1 dup/wt SERAC1 dup/wt
Which gene?
SERAC1MTRF1LMitochondrial translational release factor 1-like
No reported mutationLiver: RC defect (I IV)
Phospholipid remodeling (interface mito/ER)
MEGDEL syndromedeafness, encephalopathy, and Leigh-like syndrome3-methylglutaconic aciduria
Wortmann Nat Genet 2012
Mitochondrial hepatopathy Sariq et al Am J Med Genet 2013
our patient:HepatopathyLeigh syndromeSlight 3-methylglutaconic aciduria
mtDNA depletion
isolated
syndromic
mtDNA translationTRMU
GFM1
TSFM
DGUOK
POLG
PEO1
MPV17
unknowngene
unknowngene
MTRF1L or SERAC1 ?
MTRF1L chr6:152,987,362-153,002,685
SERAC1 chr6:158,109,515-158,168,270homozygosity region: 150,535,865-165,801,958
28 patients:non mitochondrial disease
112 patients with suspected mitochondrial diseaseand whole exome or targeted exome sequencing
8/29 hyperlactatemia(27%)
84 patients:gene encoding mitochondrial protein
52/83 hyperlactatemia(63%)
Criteria for mitochondrial disease: Clinical presentation Course of the disease Brain MRI Metabolic data RC analysis/assembly
Exome sequencing allows us to better define criteria for mitochondrial disorders diagnosis
ABCB11 AP4M1 CDG1J COG5 ECHS1 EXOCS3 GFAP MUNC18 PCCB PPP2R5D PRPS1 SCA37 SEPSECS SLC6A8 SRRM2 WDR81
Exome sequencing allows us to better define criteria for mitochondrial disorders diagnosis
28 patients:non mitochondrial disease
84 patients:gene encoding mitochondrial protein
Criteria for mitochondrial disease: Clinical presentation Course of the disease Brain MRI Metabolic data RC analysis/assembly
mitochondrial non mitochondrial
criteria for mitochondrial disease0 1 2 3 4 5 6 7 0 0 1 2 3
0
5
10
15
20
25
nb patients
nb o
f pat
ient
s
112 patients with suspected mitochondrial diseaseand whole exome or targeted exome sequencing
Genotype/Phenotype correlations
Kearns-Sayre syndrome, Pearson syndrome(mtDNA deletions)
Liver insufficiencymtDNA depletion (DGUOK, POLG, PEO1)
Barth syndromecardiolipin deficiency, TAZ mutations
Leigh syndromeCI deficiency (mtDNA, nuclear NDUF…)CII deficiency (SDHA)CIV deficiency (SURF1)Multiple deficiency
…………………. but alsoAbsence of genotype/phenotype correlationsRare disease genes
Mitochondrial disorders
clinical heterogeneity genetic heterogeneity
one genotype
one phenotypeHepatic failure
one genotype
various phenotypesdominant
adPEO
recessiveAlpers syndrome
Hepatic failure
various genotypes
one phenotypeHepatic failure
DGUOK POLG DGUOKPOLGTRMU
genomit - ERA-Net E-Rare
Imagine Institut
Metodi METODIEVBenedetta RUZZENENTE
Anthony DRECOURTJuliette PULMANChristelle TAMBYLucas BIANCHI
Coralie ZANGARELLI
Christine BOLEPatrick NITSCHKE
Department of Geneticsand of Pediatrics
Zahra ASSOULINEGiulia BARCIA
Julie STEFFANNJean-Paul BONNEFONT
Marlène RIONathalie BODDAERTIsabelle DESGUERREPascale de LONLAY
Arnold MUNNICH