genetic heterogeneity of mitochondrial disorders - agnès rötig

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Genetic heterogeneity of mitochondrial disorders Agnès Rötig Institut Imagine Paris

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Genetic heterogeneityof mitochondrial disorders

Agnès RötigInstitut Imagine

Paris

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

►►►►►►►

►►►

►►

►►

►►

►►►►

►►

►►►►►►

►►►

►>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