COMBINING MENDELIAN AND EPIDEMIOLOGY GENETICS IN...
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COMBINING MENDELIAN AND EPIDEMIOLOGY GENETICS IN AAA Juliette ALBUISSON MD PhD INSERM U970 GENETICS OF RARE VASCULAR DISORDERS GENETICS DEPARTMENT EUROPEAN HOSPITAL GEORGES POMPIDOU REFERENCE CENTER FOR RARE VASCULAR DISORDERS [email protected]
Transcript of COMBINING MENDELIAN AND EPIDEMIOLOGY GENETICS IN...
COMBINING MENDELIAN AND EPIDEMIOLOGY
GENETICS IN AAA
Juliette ALBUISSONMD PhD
INSERM U970 GENETICS OF RARE VASCULAR DISORDERSGENETICS DEPARTMENT EUROPEAN HOSPITAL GEORGES POMPIDOU
REFERENCE CENTER FOR RARE VASCULAR DISORDERS
Disclosure of Interest
Speaker name: JULIETTE ALBUISSON
• I do not have any potential conflict of interest
Very rare Mendeliancases
GENETICS AND HERITABILITY OF AAA, A COMMON DISEASE
Mostly sporadic cases
0.7-0.8 heritability (twins)
Shibamura 2004; Ogata, 2005; Nischan 2010; Wahlgren 2010; Joergensen 2016
20% declare family history
OR= 8 of AAA when 1st degree relative affected
Very rare Mendeliancases
Isolates
.
..
.
Sequencing of the extremes
GWAS (common variants)
EPIDEMIOLOGY GENETICS IN COMMON DISEASES: STRATEGIES
Mendelian cases
GENETICS OF AAA: STRATEGIES
Mendelian cases
GENETICS OF AAA: RESULTS
4q13 Z-Score=3.73
19q13 Z-Score=4.64 (KLK1)
Van Vlijmen et al 2002, Shibamura et al, 2004
1p13.3 OR=1.23 (SORT1)
9p21.3 OR~1.3 (ANRIL)
12q13.3 OR=1.15 (LRP1)
9q33.2 OR=1.21 (DAB2IP)
19p13.2 OR=1.321 (LDLR)
Gretasdottir et al, 2010; Bown et al, 2011; Bradley et al, 2013; Jones et al, 2013; van’t Hof et al, 2016
18q11p13.2 OR=1.11 (RBBP8)
15q21 OR=1.07 (FBN1)
GENETICS OF AAA: HERITABILITY IS MISSING
GENETICS OF AAA: WHAT ABOUT rare variants?
Rare Variants-
Common diseases
Common variants
-Common diseases
Adapted from Manolio et al, 2009
Mean age at diagnosis: 62 (Males), 78 (Females)
Atheroma, Tobacco, HTN are present
EXOME SEQUENCING IN A MENDELIAN FORM OF AAA
Albuisson et al, in preparation
EXOME SEQUENCING IN A MENDELIAN FORM OF AAA
Albuisson et al, in preparation
EXOME SEQUENCING IN A MENDELIAN FORM OF AAA
Albuisson et al, in preparation
NFKBIZGly80Cys
PLA2G3R303*
APOL3R377W
Inconsistentsegregation
EXAC: 0.5% LOF in caucasians
Murine KO: protectsfrom atherosclerosis
Z-score =4.14
Expressed in normal and atherosclerotic
endothelium, induced by
inflammation
Horrevoets et al, 1999
EXAC: 1-20% LOF
R377W: toxic? dominant negative effect?
Sato et al, 2008
RARE VARIANTS ANALYSIS AND GENE-CENTERED ASSOCIATION STUDY
1500 sporadic cases250 familial cases
CODING VARIANTS
5 common (1-50%)
7 rare (0.1-1%)
6 very rare (<0.1%)
BURDEN: p=0.02SKAT-O: p=0.03
700 population-basedcontrols (EXOME-CHIP)
3000 age- and sex-matched controls(AA<25mm)
Albuisson et al, in preparation
RARE VARIANTS ANALYSIS AND GENE-CENTERED ASSOCIATION STUDY
SKAT-O: ns
700 population-basedcontrols (EXOME-CHIP)
1700 casesReplication cohort
(EXOME CHIP)
Albuisson et al, in preparation
APOL FAMILY
LZ
PORE MAD SID
BH3
-Apol 1-6: conserved domains
- "BH3" only proteins: Apoptosis/Autophagy regulators
-Induced by inflammation, virus stimuli
-Induce permeabilization of the lysosome and mitochondria
Secreted in serum: trypanolytic factor
Expressed in podocytes: G1/G2 mutants induce celldeath, potentiated by inflammation and viruses
Adapted from Pays et al, 2014
APOL1 ROLE AND MUTANTS
APOL3 R377W AND APOL1 G1 AND G2 THE LZ DOMAIN
APOL1 WT APOL3 WT
APOL1 G1
APOL1 G2
APOL3 R377W
R377W G1 G2
Adapted from Lecordier et al, 2009
Albuisson et al, in preparation
APOL3 : ENDOTHELIAL AND DENDRITIC CELLS FACTOR INDUCTION BY VIRUSES AND INFLAMMATION
Aorta fromR377W AAA
case
mammaryartery
Normal Aorta
ARTERIAL EXPRESSION
Popliteaartery
Albuisson et al, in preparation
Collab. Uzereau
INDUCTION OF APOLS IN AORTIC ENDOTHELIUM BY VARIOUS TLR STIMULATION
INDUCTION OF APOLs IN DENDRITIC CELLS BY TLR3 STIMULATION
Uzereau et al, 2016
Sub-endothelial area
Endothelium
Elastic lamina
Media
Dendritic cell
B CellT Cell
PATHOPHYSIOLOGICAL MODEL FOR APOL 3-INDUCED AAA
T Cell
Viral stimulus
Cell death signal
APOL3 R377W ENDOTHELIAL PHENOTYPECRISPR KNOCK-IN IN PROGRESS
0
10
20
30
40
50
COL3A1 Mut Temoin
Cell death, Apoptosis biomarkers
R377W WT
GENETICS OF AAA: CONCLUSION
• Combining different genetic strategies : efficient approach to
investigate common diseases
• APOL3 very rare variants probably contribute to Mendelian AND
sporadic forms of AAA
• APOL3 R377W: deregulation of apoptosis in endothelial and immune
cells in abdominal aorta, in response to viral and inflammatory stimuli?
THANKS
U970
Xavier Jeunemaitre Nabila Bouatia-Naji
Romuald Kiando Cyrielle Tréard
Sophie Aili-Tan Irmine Ferreira
NIHR Biomedical Research Unit in
Cardiovascular Disease
Nilesh Samani Matt Bown
Jean-Michael Mazzella
Michael Franck
Dépt. de Génétique
Marie-Laure Baranne
Mathilde Padilla
Dépt. de parasitologie moléculaire
Etienne Pays
Sophie Uzereau
Elisabeth Tournier-Lasserve
Clinical Genetics dpt.
Danielle Majoor
Pierre Julia
Patrick Bruneval
(2) SÉQUENCAGE SANGER DE CAS SPORADIQUES ET FAMILIAUX D’AAA
RESULTATS (2) IDENTIFICATION DE VARIANTS RARES ET FREQUENTS
APOL3 MADLZPORE ?
BH3
SID
V25V
S39R
N188N
A196T
A228T
V232M
T244T
R262R G319G R377Q
PHENOTYPE GENERAL DE LA FAMILLE SE
INDIVIDUPHÉNOTYPE AORTIQUE (ÂGE DE DIAGNOSTIC)
ATHÉROME TABAC HTA DYSLIPIDÉMIE COMORBIDITES
II1 AAA (64 ans) + + + - ?
II2 ? ? - - - ?
II3 ? ? ? ? ? ?
II4 ? ? ? ? ? ?
II5Mega-dolicho-aorte
(80 ans)+ + - + ?
II6 ? ? ? ? ?Décédé à 65 ans (K
du poumon)
II7 ? ? + - +Décédé à 64 ans (K
ORL)
II8 ? ? ? ? ?Décédé à 67 ans (K
du poumon)
II9 AAA (62 ans) + + + - ?
II10 normal - + - - ?
II11 AAA (66 ans) + + + + ?
II12 AAA (85 ans) + - + - ?
II13Mega-dolicho-aorte
(78 ans)+ - + - ?
III21Mega-dolicho-aorte (55
ans)- + + - ?
III25 normal - - + - ?
III26 normal - - + + Diabète type 2
(1) ROLE D’APOL3 DANS LA PHYSIOPATHOLOGIE DE L’AAA
EXPRESSION TISSULAIRE
Collaboration S. Uzereau, parasitologie moléculaire, Université libre de Bruxelles
- Fortement induite par stimulus viral (Poly-IC)
Expression dans les cellules dendritiques
- spécifiques de la reconnaissance de signaux de nécrose et de la réponse antivirale (cellules
BDCA3+)
0,0
200,0
400,0
600,0
800,0
1000,0
1200,0
1400,0
BDCA1+ BDCA3+ CD16+ Plasmocytoides Myéloides Monocytaires
Exp
ress
ion
re
lati
ve (
au)
APOL3 IS SPECIFICALLY AND STRONGLY EXPRESSEND IN BDCA3+ DENDRITIC CELLS
Apol1
Apol2
Apol3
Apol4
Apol5
Apol6
Extrait de Robbins et al, Genome Biol 2008
APOL3
VARIANT FRÉQ EXAC SIFT POLYPHEN FORME
S230C 0 Délétère Probablement délétère Sporadique ?
A303N 0 Toléré Possiblement délétère Sporadique ?
S315L 8/106 Toléré Possiblement délétère familial
I326T 5/105 Toléré Bénin Sporadique ?
R377W 8/105 Délétère Probablement délétère Familial (famille SE)
R395H 8/105 Toléré Bénin Sporadique ?
C399G 0 Toléré Bénin sporadique
(2) SÉQUENCAGE SANGER DE CAS SPORADIQUES ET FAMILIAUX D’AAA
RESULTATS (1) IDENTIFICATION DE 6 VARIANTS TRES RARES
MADLZPORE ?
BH3
SID
(C. Tréard, ML. Baranne, Dpt de Génétique HEGP)
Contrôle qualité des données de génotypage
Individus de fond génétique européen (ACP)
Taux de génotypage : par individu ≥ 97% ; par marqueur ≥ 99%
Equilibre d’Hardy-Weinberg (P≥10-5
)
Analyse de l’association de 25 567 variants fréquents (MAF ≥ 5%), régression
logistique sous le modèle additif
Génotypage par l’Exome Chip : variants codants
Marqueurs (EC) Effectif
Non-synonymes ~ 220 000
Variants fréquents ~ 12%GWAS tags ~ 5000
Marqueur d’héritage ethnique 3 468
Total ~240 000
100% of variants
GWAS 30 ~80%
EXOME ~ 0.5%
GENOME ~ 90%
Frequent CNVsFrequent
SNPs
Rare CNVs Rare SNP
Gene Gene Gene Gene Gene
IDENTIFICATION OF VARIANTS BY HIGHT THROUGHPUT SEQUENCING
GENETIC VARIANTIONS IN THE CODING PART OF GENES
• ~20,000 variants : ~10,000 variants with possible or probable functional
effect
• ~95% common variants
• <5% « new » variants
• ~80-200 loss-of-function (LOF) variants
• ~5-10 new LOF
