Human Genetics of Infectious Diseases - Laurent Abel
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Transcript of Human Genetics of Infectious Diseases - Laurent Abel
Human Genetics of Infectious Diseases
Laurent Abel
Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, Imagine Institute, Paris, and Rockefeller University, New-York
Host genetics in infectious diseases?
Experimental Experimental modelsmodels
Human Human GeneticsGenetics
Epidemiological Epidemiological observationsobservations
Proof ofProof ofconceptconcept
ConceptConcept
0
10
20
30
40
50
60
Mor
talit
y pe
r 100
,000
0--1
1--2
3--5
6--1
0
11--1
5
16--2
0
21--3
0
31--4
0
41--5
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51--6
0
61--7
0
over
70
years
generalized TBpulmonary TB
Ranke, K. 1910. Archiv für Kinderheilkunde
The discovery of asymptomatic infections (1910s)
The variability in clinical expression
Variability of response to exposure and infection
VIRULENCEFACTORS
MICROBE INFECTION CLINICALPHENOTYPES
EXPOSUREFACTORS
NON-GENETICFACTORS
GENETICFACTORS
MICROBE
HOST
Variability of response to exposure and infection
What are the critical immunological pathwaysin natural conditions of infection?
Why do some exposed individuals (and not others) get infected and develop infectious diseases?
Human genetics of infectious diseases
→ How to identify the genetic variants of interest?
Phenotype Severe/acute(children)
Milder/chronic(adults)
Approach Mendelian Genetics
Complex Genetics
Sample Small Large
Methods of investigation in humans
Rare mutationsStrong individual effect
Common polymorphismsModest individual effect
Using the very last genomic technology advances:- High throughput genotyping (Genome-wide linkage/association studies)- Deep sequencing (Exome/Genome)
Rare primary immunodeficienciesClinical, Mendelian genetics‘One gene, multiple pathogens’
Common infectious diseasesPopulation, complex genetics‘One infection, multiple genes’
Spectrum of genetic predisposition
PolygenicPolygenicpredisposition
NewNewPIDs MajorMajor
genes
1 Number of genes
1 N
umbe
r of m
icro
bes
0
One gene, One infection
New PIDsHighly selective Mendelian predisposition to a given microbe→ HSV1, mycobacteria
Major genesIntermediate predisposition to a given microbe→ mycobacteria (TB)
Am J Pathol, 1941
Herpes simplex encephalitis (HSE):a devastating viral illness of unclear pathogenesis
HSV-1 infects > 85% adults world-wide, with asymptomatic or benign infections
Sporadic HSE affects 2-4 persons per million per year, in particular children
No increased susceptibility to other infectious agents
No known primary immunodeficiency with HSE
→ Could HSE be a genetic disease?
HSE Cohort
Candidate Pathway Genome-wide >150 patients 21 consanguineous families
IFN-, ProductionIFN-, Response
Genetic Screening
Linkage ScanFine Mapping
Candidate Genes
Exome sequencing
Strategy
Autosomal Recessive (AR) UNC-93B deficiency: First genetic etiology of isolated HSE
TGA1034del4IIII II IV V VI VII VIII
4475’ 1034 del4
1 NH2 597 COOH
3’TGAATG
WT
781G>A
IIII II IV V VI VII VIII IX X XIIIII II IV V VI VII VIII IX X XI
781G>AIIII II IV VTGA
416
TLR3
UNC-93B
TLR7/8/9
↓ Type I IFNs
Casrouge et al, Science, 2006
→ Impaired production of IFN-, -, and –λ→ no response to TLR3, TLR7, TLR8, TLR9
10
102
103
104C+UNC-93B-/-
IFN
-(
pg/m
l)NS
Poly(I:C)
(TLR3)
1
Fibroblasts
NSPoly(I:C
)
(TLR3/RIG-I/MDA5)
3M-13
(TLR7) 3M-2
(TLR8) R-848
(TLR7/8)CpG-C
(TLR9)
1
10
102
103
104
IFN
-(
pg/m
l)
UNC-93B-/-C+
PBMCs
2 patients homozygousfor LOF UNC93B
mutations
Autosomal Dominant (AD) TLR3 deficiency: Second genetic etiology of HSE
IRF-3 NF-B
TLR3
TRIFUNC-93B
↓ IFNs
IκBα
Fibroblasts (WT)
Zhang et al., Science 2007
P554S
0
40
80
120 C-MockC-TLR3 WT C-TLR3 P554S
12h 24h
0
1
5
25
0
1
5
25
IFN
- (p
g/m
l)
12h 24h 0 1 5 25 0 1 5 25
poly(I:C)
0
20
40
60
IFN
-β (I
U/m
l)
C+TRL3+/- P1TLR3+/- P2
→ Impaired production of IFN-, -, and –λ→ no response to TLR3
New TLR3 alleles in children with HSE
G743D
R811ID592NM374T
E746X
P554SSS
1 2
P1
1 2 3
E? E?
E746X/WT P554S/WT
P554S/E746X
Autosomal recessive TLR3 deficiency
Guo et al, J Exp Med, 2011
Novel HSE genes in the TLR3 pathway
TLR7/8/9
UNC93B
TLR3
IKKcomplex
γα β
TBK1IKKε
IRF3 IRF7 NFκB
Impaired production of IFN-α,-β → IFN- treatment in addition to acyclovir?
ssRNA
CpGdsRNA
TRAF3TRIF MYD88
IRAK4
NEMO
Genome-wide search for the role of other genes/pathways- Positional cloning in consanguineous families- Whole exome sequencing
UNC93B: ARTLR3: AD and ARTRIF: AD and ARTRAF3: ADTBK1: AD
Immunological lessonUNC93B/TLR3 deficient patients present a highly selective predisposition to CNS infection by HSV-1 (Lafaille et al, Nature 2012)
TLR3 and 7/8/9 are redundant for defense against many viruses in natural conditions of infections (the ‘human model’)
Summary for HSE – General Implications
Genetic lessonHSE is a new PID due to a collection of rare single gene variants Most severe forms of common infections could be due to single-gene inborn errors of immunity as a rule Other examples: severe flu (IRF7), invasive pneumoccal disease (IRAK4, MYD88), severe mycobacterial diseases…
Mendelian susceptibilityto mycobacterial diseases (MSMD)
* Infections by BCG and environmental Mycobacteria
* Otherwise healthy individuals
* Very rare (10-5 – 10-6) but often familial (consanguinity)
MSMD: genetic defects in IL12/IFNγ pathway
MycobacteriaIL-12R1
IL-12R2
IFN-γR1
IL-12 p35
p40
IFN-γIFN-γR2STAT-1
NEMO CD40 CD40L
IRF8
gp91phox
Dendritic cells/Phagocytes T Lymphocytes/NK cells
ISG15 ?
MycobacteriaIL-12R1
IL-12R2
IFN-γR1
IL-12 p35
p40
IFN-γIFN-γR2STAT-1
NEMO CD40 CD40L
IRF8
gp91phox
Dendritic cells/Phagocytes T Lymphocytes/NK cells
ISG15 ?
Medical implicationImpaired production of IFN-γ → Amenable to treatment by IFN-γ
MSMD: genetic defects in IL12/IFNγ pathway
MSMD: genetic defects in IL12/IFNγ pathway
Abdominal TBMSMD
IL12RB1 mutation: R213W
First evidence of Mendelian TB from genetic dissection of MSMD
MycobacteriaIL-12R1
IL-12R2
IFN-γR1
IL-12 p35
p40
IFN-γIFN-γR2STAT-1
NEMO CD40 CD40L
IRF8
gp91phox
Dendritic cells/Phagocytes T Lymphocytes/NK cells
ISG15 ?
The proportion of Mendelian TB in disseminated forms of children could be far from negligible
Systematic sequencing of IL12RB1 in a sample of 50 children (<15 yrs) with severe TB from Morocco, Turkey and Iran.
2 patients with complete IL12-R1 deficiency
P2: severepulmonary TBParaspinal abcess
E?WT/WT
R173W/WT
R173W/WT
R173W/R173WE?
E?E?
Kindred B (Iran)
E? K305X/WT
K305X/K305X
P1: severe fatalpulmonary TB
Kindred A (Morocco)
K305X/WT
Two Mendelian defects out of 50 patients (4%) by testing a single gene
Investigation of a larger sample of patients by Whole exome sequencing Several interesting mutations under functional validation
Autosomal recessive TYK2 deficiency in 4 new families
Minegishi et al. Immunity 2006
Kreins et al. J Exp Med 2014
Autosomal recessive TYK2 deficiency in 4 new families
Abdominal TB Miliary
TYK2 is involved in several signaling pathways
Impaired response to IL12in Saimiri T cells
IL-12/23Rβ1IFN-α/βR
IL-6Rs
Principal pathogens
Viruses Mycobacteria S. aureus
IFN-α/β IFN-γ/IL-17 IL-6/10
IL-10RsIL-12/23
TYK2
STAT3
Critical cytokine
Receptorssuperfamilies
Signalingmolecules
Receptors
STAT1
M. tuberculosis Infection
Latency
Primary Extrapulmonary
TB}
Reactivation Pulmonary
TB}
~5%
~95% ~5%
Rare mutations (IL12RB1, TYK2, others…) Role of IL12/IFN pathway
Genetic predisposition to clinical TB
0
10
20
30
40
50
60
Mor
talit
y pe
r 100
,000
0--1
1--2
3--5
6--1
0
11--1
5
16--2
0
21--3
0
31--4
0
41--5
0
51--6
0
61--7
0
over
70
years
generalized TBpulmonary TB
~90%
Pulmonary TB (PTB): Genome-wide (GW) studies
1) Positional cloning (GW linkage followed by association)
Bacteriologically confirmed PTB
Primary family-based sample from endemic areas of Morocco
Replication samples of differentethnicities (3000 total, 1500 PTB)
PTB: Positional cloning strategy
44 SNPs at p<0.01 tested for replication
Two replicated SNPs in TOX
Linkage to chromosome 8q12-q13
Ultra-fine association of the linked region
population marker OR P
Full rs1568952 2.1 1 10-5
rs2726600 1.8 9 10-5
< 25 years rs1568952 3.3 4 10-8
rs2726600 2.2 3 10-5
>25 years rs1568952 1.4 0.15
rs2726600 1.4 0.09
Stronger effect in early-onset TBGrant et al, 2013
Am J Hum Genet. Validated in Madagascar
TOXThymocyte selection-associated high mobility group box protein
TOX is involved in the development of CD4 T cells.
CD4 T cells are of major importance to maintain latent infection as shown by high incidence of pulmonary TB in HIV+ subjects
rs2726600 is located in an important regulatory region (ENCODE)
→ Functional studies investigating the expression of TOX in T cells according to rs276600 genotypes→ Investigation of TOX in other populations
~3500 patients and ~7000 controls from The Gambia and Ghana
2) GW association studies in pulmonary TB
OR ~1.19 OR ~ 0.8
→ No strong signals in pulmonary TB with common polymorphisms (Same kind of results in Morocco) → Search for rare variants by deep sequencing Focusing on specific PTB patients: familial cases, early-onset
OR ~ 0.85
~6600 patients and ~8400 controls from Russia
(Manolio et al, Nature, 2009)
Extreme phenotypes of common infections (TB)Direct clinical and therapeutic implications
Major gene effect in specific phenotypes: early-onset, familial…
Limited role in TBLeprosy, HCV clearance (IL28B)
Genetic predisposition to infectious diseases continuous spectrum
Mendelian
Major gene
Age
Polygenic
80%
Genetic cases
Primary infection Reinfection/reactivation
Genetic spectrum depends on age
Jean-Laurent Casanova and Laurent Abel Laboratory of Human Genetics of Infectious Diseases
Mycobacteria groupAudrey GrantAlexandra KreinsAlexandre AlcaïsAurélie CobatJanet MarkleJacinta C. BustamanteS. Boisson-Dupuis
Virus groupMichael CiancanelliMelina HermanE. JouanguyLazaro LorenzoR. Perez de DiegoV. Sancho-ShimizuShen-Ying Zhang
V. RasolofoPasteur Institute, Antananarivo
M. Orlova, E. SchurrMcGill University,
L. BarreiroSte Justine,Montreal Univ.
J. El Baghdadi, A. Benslimane Military Hospital, RabatA. Bousfiha, J. Najib
Casablanca Medical School, Casablanca
Huge number of collaborators
Medical clinicians around the world
M. TardieuPediatric Neurology, Kremlin-Bicêtre hosp.
F. Rozenberg, P. LebonVirology, St Vincent de Paul hosp.