An overview of the role of genetics in infectious disease response

1. Human Genetics of Infectious Diseases
Laurent Abel
Laboratory of Human Genetics of Infectious Diseases,
Inserm U1163, Imagine Institute, Paris,
and Rockefeller University, New-York

2. Host genetics in infectious diseases?
ExperimentalExperimental
modelsmodels
HumanHuman
GeneticsGenetics
EpidemiologicalEpidemiological
observationsobservations
Proof ofProof of
conceptconcept
ConceptConcept

3. Ranke, K. 1910. Archiv für Kinderheilkunde
The discovery of
asymptomatic infections (1910s)
The variability in
clinical expression
Variability of response to exposure and infection

4. VIRULENCE
FACTORS
MICROBE INFECTION CLINICAL
PHENOTYPES
EXPOSURE
FACTORS
NON-GENETIC
FACTORS
GENETIC
FACTORS
MICROBE
HOST
Variability of response to exposure and infection

5. What are the critical immunological pathways
in 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?

6. Phenotype Severe/acute
(children)
Milder/chronic
(adults)
Approach Mendelian
Genetics
Complex
Genetics
Sample Small Large
Methods of investigation in humans
Rare mutations
Strong individual effect
Common polymorphisms
Modest individual effect
Using the very last genomic technology advances:
- High throughput genotyping (Genome-wide linkage/association studies)
- Deep sequencing (Exome/Genome)

7. Rare primary immunodeficiencies
Clinical, Mendelian genetics
‘One gene, multiple pathogens’
Common infectious diseases
Population, complex genetics
‘One infection, multiple genes’
Spectrum of genetic predisposition
PolygenicPolygenic
predisposition
NewNew
PIDs
MajorMajor
genes
1 Number of genes
1
Numberofmicrobes
0
One gene, One infection
New PIDs
Highly selective Mendelian
predisposition to a given microbe
→ HSV1, mycobacteria
Major genes
Intermediate predisposition
to a given microbe
→ mycobacteria (TB)

8. 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?

9. HSE Cohort
Candidate Pathway Genome-wide
>150 patients 21 consanguineous families
IFN-α,β Production
IFN-α,β Response
→ Genetic Screening
Linkage Scan
Fine Mapping
→ Candidate Genes
Exome sequencing
Strategy

10. Autosomal Recessive (AR) UNC-93B deficiency:
First genetic etiology of isolated HSE
TGA
1034del4IIII II IV V VI VII VIII
447
5’ 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 V
TGA
416
TLR3
UNC-93B
TLR7/8/9
↓ Type I
IFNs
Casrouge et al, Science, 2006
→ Impaired production of IFN-α, -β, and –λ
→ no response to TLR3, TLR7, TLR8, TLR9
10
102
103
104
C+
UNC-93B-/-
IFN-λ(pg/ml)
NS
Poly(I:C)
(TLR3)
1
Fibroblasts
NS
Poly(I:C)
(TLR3/RIG-I/M
DA5)
3M
-13
(TLR7) 3M
-2
(TLR8)
R-848
(TLR7/8)
CpG-C
(TLR9)
1
10
102
103
104
IFN-α(pg/ml)
UNC-93B-/-
C+
PBMCs
2 patients homozygous
for LOF UNC93B
mutations

11. Autosomal Dominant (AD) TLR3 deficiency:
Second genetic etiology of HSE
IRF-3 NF-κB
TLR3
TRIF
UNC-93B
↓ IFNs
IκBα
Fibroblasts (WT)
Zhang et al., Science 2007
P554S
0
40
80
120 C-Mock
C-TLR3 WT
C-TLR3 P554S
12h 24h
0 1 5
25
0 1 5
25
IFN-λ(pg/ml)
12h 24h
0 1 5 25 0 1 5 25poly(I:C
)
0
20
40
60
IFN-β(IU/ml)
C+
TRL3+/- P1
TLR3+/- P2
→ Impaired production of IFN-α, -β, and –λ
→ no response to TLR3

12. New TLR3 alleles in children with HSE
G743D
R811ID592NM374T
E746X
P554S
SS
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

13. Novel HSE genes in the TLR3 pathway
TLR7/8/9
UNC93B
TLR3
IKK
complex
γ
α β
TBK1IKKε
IRF3 IRF7 NFκB
Impaired production of IFN-α,-β → IFN-α treatment in addition to acyclovir?
ssRNA
CpG
dsRNA
TRAF3
TRIF
MYD88
IRAK4
NEMO
Genome-wide search for the role of other
genes/pathways
- Positional cloning in consanguineous families
- Whole exome sequencing
UNC93B: AR
TLR3: AD and AR
TRIF: AD and AR
TRAF3: AD
TBK1: AD

14. Immunological lesson
UNC93B/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 lesson
HSE 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…

15. Mendelian susceptibility
to mycobacterial diseases (MSMD)
* Infections by BCG and
environmental Mycobacteria
* Otherwise healthy individuals
* Very rare (10-5
– 10-6
) but
often familial (consanguinity)

16. MSMD: genetic defects in IL12/IFNγ pathway
Mycobacteria
IL-12Rβ1
IL-12Rβ2
IFN-γR1
IL-12 p35
p40
IFN-γ
IFN-γR2STAT-1
NEMO CD40 CD40L
IRF8
gp91phox
Dendritic cells/Phagocytes T Lymphocytes/NK cells
ISG15
?

17. Mycobacteria
IL-12Rβ1
IL-12Rβ2
IFN-γR1
IL-12 p35
p40
IFN-γ
IFN-γR2STAT-1
NEMO CD40 CD40L
IRF8
gp91phox
Dendritic cells/Phagocytes T Lymphocytes/NK cells
ISG15
?
Medical implication
Impaired production of IFN-γ → Amenable to treatment by IFN-γ
MSMD: genetic defects in IL12/IFNγ pathway

18. MSMD: genetic defects in IL12/IFNγ pathway
Abdominal TBMSMD
IL12RB1 mutation: R213W
First evidence of Mendelian TB
from genetic dissection of MSMD
Mycobacteria
IL-12Rβ1
IL-12Rβ2
IFN-γR1
IL-12 p35
p40
IFN-γ
IFN-γR2STAT-1
NEMO CD40 CD40L
IRF8
gp91phox
Dendritic cells/Phagocytes T Lymphocytes/NK cells
ISG15
?

19. 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-Rβ1 deficiency
P2: severe
pulmonary TB
Paraspinal abcess
E?
WT/
WT
R173W/
WT
R173W/
WT
R173W/
R173W
E?
E?E?
Kindred B (Iran)
E? K305X/WT
K305X/
K305X
P1: severe fatal
pulmonary 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

20. Autosomal recessive TYK2 deficiency in 4 new families
Minegishi et al.
Immunity 2006
Kreins et al.
J Exp Med 2014

21. Autosomal recessive TYK2 deficiency in 4 new families
Abdominal TB Miliary

22. TYK2 is involved in several signaling pathways
Impaired response to IL12
in 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-10Rs
IL-12/23
TYK2
STAT3
Critical
cytokine
Receptors
superfamilies
Signaling
molecules
Receptors
STAT1

23. M. tuberculosis Infection
Latency
Primary
Extrapulmonary
TB}
Reactivation
Pulmonary
TB}
~5%
~95% ~5%
Rare mutations (IL12RB1, TYK2, others…)
Role of IL12/IFNγ pathway
Genetic predisposition to clinical TB
~90%

24. 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 different
ethnicities (3000 total, 1500 PTB)

25. 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 TB
Grant et al, 2013
Am J Hum Genet. Validated in Madagascar

26. TOX
Thymocyte 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

27. ~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

28. (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 TB
Leprosy, HCV clearance (IL28B)
Genetic predisposition to infectious diseases
→ continuous spectrum

29. Mendelian
Major gene
Age
Polygenic
80%
Genetic cases
Primary infection Reinfection/reactivation
Genetic spectrum depends on age

30. Jean-Laurent Casanova and Laurent Abel
Laboratory of Human Genetics of Infectious Diseases
Mycobacteria group
Audrey Grant
Alexandra Kreins
Alexandre Alcaïs
Aurélie Cobat
Janet Markle
Jacinta C. Bustamante
S. Boisson-Dupuis
Virus group
Michael Ciancanelli
Melina Herman
E. Jouanguy
Lazaro Lorenzo
R. Perez de Diego
V. Sancho-Shimizu
Shen-Ying Zhang

31. V. Rasolofo
Pasteur Institute, Antananarivo
M. Orlova, E. Schurr
McGill University,
L. Barreiro
Ste Justine,Montreal Univ.
J. El Baghdadi, A. Benslimane
Military Hospital, Rabat
A. Bousfiha, J. Najib
Casablanca Medical School, Casablanca
Huge number of collaborators
Medical clinicians around the world
M. Tardieu
Pediatric Neurology, Kremlin-Bicêtre hosp.
F. Rozenberg, P. Lebon
Virology, St Vincent de Paul hosp.