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Balancing the genetic risk of
APOL1 kidney disease variants
Sophie Limou, PhD
Paris, ANJH, May 21st, 2019
• 10-15% of the population is affected• 1/57 deaths worldwide due to CKD• No curative treatment
Created from “The American Cancer Society, Cancer Facts & Figures 2015” and
“United States Renal Data System, 2015 USRDS annual data report”.
Chronic and End-stage kidney disease, a major health burden
2
“United States Renal Data System, 2016 USRDS annual data report”.
Chronic and End-stage kidney disease, a major health disparity
3
ESK
D r
ate
/mill
ion
po
pu
lati
on
AA
EA
ESKD primary causeRR
AA:EA
All causes 3.5
Diabetes 4
Hypertension 5
Glomerulonephritis 3
Lupus nephritis 7
FSGS 5
HIVAN >20
Chronic and End-stage kidney disease, a major health disparity
4
ESKD primary causeRR
AA:EA
All causes 3.5
Diabetes 4
Hypertension 5
Glomerulonephritis 3
Lupus nephritis 7
FSGS 5
HIVAN >20
10% increase in African
ancestry in cases
Kopp et al., Nature Genetics 2008.
Mapping the gene(s) for FSGS/HIVAN in AA
5
Mapping the gene(s) for FSGS/HIVAN in AA
Kopp et al., Nature Genetics 2008. 6
Limou et al., ACKD 2014.
G1 G2
APOL1 risk variants are mutually exclusive
Haplotypefrequency
G0 (WT) 0.63
G1 0.24
G2 0.13
Risk allele count
0 RA 40%1 RA 46%2 RA (HR) 14%
7
Riskalleles
G1 G2
HIVAN FSGS Hypertension ESKD
High-risk
genotype
OR 29 (89 in South Africa) 17 7
Cases
72%
Pop. Controls
13%
Cases
HIV+
hypernorma
l controls
8%
72%
Cases
47%
Pop. Controls
12%
Genovese et al., Science 2010; Kopp et al., JASN 2011; Kasembeli et al., JASN 2015; Limou et al., ACKD 2014.
APOL1 genetic variants account for up to 70% of the excess kidney disease risk in AA
8
9
APOL1
APOL1 risk variants exhibit high frequency and unusuallyhigh effect sizes for a common disease
McCarthy et al. Nat Rev Genet 2008.
EA
AA
G1
G2
+
Kopp et al., JASN 2011.
APOL1 variants are restricted to individuals of African descent
10
EA
AA
G1
G2
+
Nadkarni et al., NEJM 2018. 11
<1%1-5%>5-10%>10%
APOL1 variants are restricted to individuals of African descent
G1 allele distribution
Limou et al. ACKD 2014; Cooper et al. eLife 2017.
G2 allele distribution
12
APOL1 variants are restricted to individuals of African descent
• Sequencing of 53 worldwide populations (>2,200 chr.)
Limou et al., KI 2015.
APOL1 selection signature
13
• Pairwise FST fixation index estimates
Limou et al., KI 2015.
0.0 0.1 0.2 0.3 0.4
05
10
15
20
25
Genome-wide Fst estimates
De
nsity
o West Africa populations are significantly differentiated than other SubSaharan African populations for APOL1 G1 (0.20 < FST <0.41)
o Only trends of population differentiation for APOL1 G2 in SubSaharan Africa
Yoruba, Nigeria vs. Bantu, Kenya
G1 FST = 0.32 (top 0.16%)
APOL1 selection signature
14
G2
Limou et al., KI 2015.
APOL1 selection signature
• EHH/iHS long-haplotype testso Evidence of a recent selective sweep in West Africa for APOL1 G1 and G2
15
• APOL1 = human resistance factor against T. brucei infections
T.b. brucei
APOL1
entry
Membrane
insertion
Pore
formation
Trafficking and endo-lysosomal acidification
Parasite
death
Perez-Morga et al., Science 2005.
APOL1 and trypanosomes, a co-evolutionary arms race
16
• T.b. rhodesiense and T.b. gambiense have evolved resistance mechanisms against APOL1 lysis
T.b. gambiense
APOL1
entry
TgsGP-mediated
membrane thickening
APOL1
degradation
Parasite
survival
T.b. rhodesiense
APOL1
entry
SRA-mediated
inhibition
APOL1
degradation
Parasite
survival
African sleeping sickness
Vanhamme et al., Nature 2003; Uzureau et al., Nature 2013.
APOL1 and trypanosomes, a co-evolutionary arms race
17
• APOL1 G1 et G2 restore lysis against T.b. rhodesiense
protection against acute trypanosomiasis
WT/WT
WT
G1 G2
Genovese et al., Science 2010; Limou et al., KI 2015.
APOL1 and trypanosomes, a co-evolutionary arms race
18
E. Pays
T.b. rhodesiense
APOL1
G1/G2 entry
No SRA-mediated
inhibition and APOL1
membrane insertion
Pore
formation
Parasite
death
G1 G2
APOL1 and trypanosomes, a co-evolutionary arms race
• APOL1 G1 et G2 restore lysis against T.b. rhodesiense
19
protection against acute trypanosomiasis
APOL1 kidney risk alleles (1 or 2) protect from trypanosomiasis
20
Two APOL1 risk alleles (high-risk genotypes) associate with increased CKD/ESKD risk
21
Balancing the risk: African sleeping sickness vs. CKD
22
CKD/ESKD riskTrypanosomiasis risk
Mouse
Ψ
Ψ Ψ Ψ
Ψ
Ψ
APOL1 APOL2 APOL4 APOL3 APOL5 APOL6
Human
Orangutan
Chimpanzee
Gorilla
Macaque1
Baboon2
Ψ
23
APOL gene family in primates
• Broad innate immunity factor
• Mitochondrial dysfunction
• Autophagy flux and vesicle trafficking
• Controversy around a suPAR-dependent complex
• APOL1 RNA and PKR activation
APOL1 cellular function
Beckerman et al., Nature Med 2017; see Review and previous talk. 24
Recessive model of inheritance? Second hit?
• APOL1 recipient genotype does not impact kidney graft failure
• APOL1 high-risk kidney allografts have more risk to fail
donor recipient
Allo
graf
t su
rviv
al (
%)
Low risk
High risk
Donor genotype
P=0.001
Clinical applications for APOL1 genotyping in kidney transplantation
Reeves-Daniel et al., AJT 2011; Lee et al., AJT 2012; Freedman et al., Transplantation 2016. 25
• Donors w/ APOL1 high-risk genotypes have lower eGFR at donation
• Decline in post-donation eGFR is faster among donors w/ APOL1 high-risk genotypes
Doshi et al. JASN 2018 26
APOL1 and living kidney donation
P=0.02
livingdonor
APOL1 HR
post-donation ESKD risk
• Donation does not increase the rate of kidney function decline
Doshi et al. JASN 2018 27
APOL1 and living kidney donation
• Considering APOL1 genotypes instead of race drastically change the risk associated with kidneys transplanted from AA donors
Better prediction of post-transplantation outcomes
Improved organ allocation
Julian et al. AJT 2017
Low-risk APOL1 genotypes High-risk APOL1 genotypes
Current score(race-based)
Revised score (APOL1-based)
Current score (race-based)
Revised score (APOL1-based)
KDRI 1.5 1.2 1.5 1.9
InterpretationWe exclude
perfectly good donorsWe underestimate
the risk for these donors
28
APOL1 and kidney transplantation risk
Translation to clinics: the APOLLO network
• Prospective collection of APOL1 data and outcome follow-up in African-American donors and recipients
• Open questions regarding APOL1 genotyping benefits/ethics:
Kidney allograft survival?
ESKD risk for living kidney donors?
Impact of APOL1-based KDRI score for allograft outcomes?
Freedman et al. CJASN 2018.
B. Freedman
29
Conclusions and Perspectives
• Population studies have revealed strong associations between common
APOL1 genetic variants and CKD/ESKD risk in African Americans
• APOL1 G1 and G2 variants were selected by pathogens (likely Tryps)
• Potential translation to clinics for kidney transplantation
• Genomic approach in populations can unravel novel pathways for kidney
allograft survival
Definitive (?) answers from the APOLLO networkPromise of personalized medicine approach
30
Acknowledgments
31