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

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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

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120 C-MockC-TLR3 WT C-TLR3 P554S

12h 24h

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IFN

-β (I

U/m

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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


NEMO CD40 CD40L

IRF8

gp91phox


ISG15 ?

Medical implicationImpaired production of IFN-γ → Amenable to treatment by IFN-γ



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


NEMO CD40 CD40L

IRF8

gp91phox


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

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~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.