Download presentation
Presentation is loading. Please wait.
1
Infection and Immunity
Personalized Health Symposium 22 Sept 2016 Human Genomics of Infection and Immunity Jacques Fellay EPFL School of Life Sciences Swiss Institute of Bioinformatics Service of Infectious Diseases, CHUV @jacques.fellay
2
© ALAIN HERZOG First reason: we, humans, are amazingly diverse. You’ve got 4 million variants in your genome. Reason 2: we have the tools to dive into that diversity, to track it down, relate it to phenotypic traits.
3
Exploiting human genetic variation to improve human health
Identification of relevant genetic variant Prediction models Understanding of underlying biology Individualized healthcare New drug or vaccine targets
4
Hunting for host genetic variants
>1-3% <<1% Allele frequency of variant Sequencing Genotyping Hunting for host genetic variants When searching for human genetic variants with phenotypic consequences, one has to consider this inverse relationship between allele frequency in the population adn potential clinical impact at the invidual level. From a technical perspective, genotyping is used on the rigth hand side, while sequencing is required to cover the full spectrum of allelic frequencies. We combine these approaches. +++ + ++ Clinical impact
5
Allele frequency of variant
>1-3% <<1% Allele frequency of variant Fulminant viral hepatitis Opportunistic infections & cancers Spontaneous control of HIV Severe viral respiratory infections Pediatric sepsis IgG responses to common infections Generation of broadly neutralizing antibodies Here is a list of ongoing studies in my lab that use a mix of DNA analysis strategies, often coupled with RNA sequencing. I will not describe them al, but will give you an overview of 2 of them: serological response to viruses, and severe clinical presentation of respiratory infections. Chronic viral hepatitis Ectyma gangrenosum +++ + ++ Clinical impact Decay of the HIV reservoir
6
Severe viral respiratory infections
<1 in 1000 live birth 1-2% hospitalization 10% PICU admission 50% no known risk factors 2nd vignette: severe clinical presentation of common viral respiratory infections. We’re all exposed to common cold… Healthy children who develop unusually severe symptoms upon infection with common respiratory viruses carry rare causal genetic defects
7
Study participants 120 samples (blood for DNA & RNA + NPA)
Inclusion criteria Exclusion criteria Consent of legal guardian Age 0-3 years Ventilation support needed Prematurity Immunosuppression Chronic disease Sickle cell anemia Comorbidity 120 samples (blood for DNA & RNA + NPA) Exome sequencing, RNA sequencing, viral PCR
8
DNA extraction and normalization
Target enrichment Exome sequencing Pathogen sequencing Short read alignment DNA extraction and normalization DNA pooling and bar-coding Patient recruitment Variant calling Functional characterization & experimental confirmation Variant annotation & frequency estimation CAA GTA AAC ATA GGA CTT CTT CAA GTA AAC ATA GGA CAT CTT G>A Stop-gain ExAC
9
Putative loss-of-function variants in the IFIH1 gene
Splice-site 3 het Stop-gained 1 het 1 hom, 3 het ATP-dependant binding to RNA CARDs: N-terminal Caspase Activation And Recruitment Domains (downstream signalling transduction) Hel: RNA helicase-DEAD box motifs (ATP binding and hydrolysis) Pincer: Bridging Domain (connection of the Hel-2 domain to the CTD) CTD: C-Terminal regulatory Domain (RNA binding domain)
10
IFIH1 (MDA5) is a pattern recognition receptor for long dsRNA
Reikine S. et al. Front Immunol, 2014
11
IFIH1-Δ8: 39 aa missing IFIH1-Δ14: 153 aa missing IFIH1-ΔCTD: 399 aa missing
12
Protein expression in vivo
Both IFIH1-wt and IFIH1-Δ14 are expressed in BPMCs upon RSV infection
13
IFIH1-LoFs are less stable & they reduce wt stability
Protein stability emphesis IFIH1-LoFs are less stable & they reduce wt stability
14
Interferon β induction
Explain gels IFIH1-LoFs cannot induce IFNβ and interfere with wt function
15
LoF variants in IFIH1 cause a pathogen-specific primary immunodeficiency
Scientific relevance: human genetics informs on immunological principles, which can help identify therapeutic or vaccine targets Clinical relevance: immediate impact for patients and families, potential inclusion in screening programs
16
Recruitment, sample collection
Clinical observation Recruitment, sample collection Genomics, transcriptomics Functional follow-up Clinical impact
17
Study participants & families, Pediatric ICUs
Samira Asgari Istvan Bartha Chris Hammer Christian Thorball Petar Scepanovic Nimisha Chaturvedi Olivier Naret Thomas Junier Alessandro Borghesi Flavia Hodel Study participants & families, Pediatric ICUs Dominique Garcin and Caroline Tapparel, University of Geneva Keith Harshman & team, Lausanne Genomic Technologies Facility Ioannis Xenarios & team, Vital-IT Computing Center
Similar presentations
