A systems genomics approach to identify risk loci and pathways to Candida infection

Candidaemia is a bloodstream yeast infection caused by the opportunistic fungal pathogen Candida albicans (C. albicans). Candida is now ranked the fourth most common cause of nosocomial infections. However, not all at-risk patients will develop fungal disease, suggesting that inter-individual differences – both genetic and non-genetic factors – play a critical role in determining disease susceptibility. However, it is difficult to identify genetic factors using genome-wide association studies alone because of the limited size of candidaemia patient cohorts and use of inappropriate controls (such as individuals with asymptomatic infections). Given the complexity of human host-C. albicans interactions, we followed an integrative approach to obtain a comprehensive picture of these interactions. We integrated multi-omics data (genetics, transcriptomics and proteomics) to identify genes and molecular pathways that are implicated in the anti-Candida host immune response. To generate Candida-specific data in addition to our candidaemia cohort, we made use of larger population-based cohorts (the 500FG and Lifelines cohorts). Our results suggested an important role for the processes of complement and hemostasis in candidaemia susceptibility. In addition, we observed that increased risk to candidaemia could be explained by a disturbed lipid homeostasis, which regulates pro-inflammatory cytokines in response to Candida infection. Although there are still challenges to face before fully embracing genomics in a clinical setting, and challenges to fully unravelling the true risks of disease remain, stratification of patients based on their genetic profile is a promising route toward designing host-directed therapies that would be more effective than the currently available traditional therapeutic approaches

Challenges and Opportunities in Understanding Genetics of Fungal Diseases:Towards a Functional Genomics Approach

Item does not contain fulltextInfectious diseases are a leading cause of morbidity and mortality worldwide, and human pathogens have long been recognized as one of the main sources of evolutionary pressure, resulting in a high variable genetic background in immune-related genes. The study of the genetic contribution to infectious diseases has undergone tremendous advances over the last decades. Here, focusing on genetic predisposition to fungal diseases, we provide an overview of the available approaches for studying human genetic susceptibility to infections, reviewing current methodological and practical limitations. We describe how the classical methods available, such as family-based studies and candidate gene studies, have contributed to the discovery of crucial susceptibility factors for fungal infections. We will also discuss the contribution of novel unbiased approaches to the field, highlighting their success but also their limitations for the fungal immunology field. Finally, we show how a systems genomics approach can overcome those limitations and can lead to efficient prioritization and identification of genes and pathways with a critical role in susceptibility to fungal diseases. This knowledge will help to stratify at-risk patient groups and, subsequently, develop early appropriate prophylactic and treatment strategies

Impact of Human Genetic Variation on C-Reactive Protein Concentrations and Acute Appendicitis

BACKGROUND: Acute appendicitis is one of the most common abdominal emergencies worldwide. Both environmental and genetic factors contribute to the disease. C-reactive protein (CRP) is an important biomarker in the diagnosis of acute appendicitis. CRP concentrations are significantly affected by genetic variation. However, whether such genetic variation is causally related to appendicitis risk remains unclear. In this study, the causal relationship between single-nucleotide polymorphisms (SNPs) associated with circulating CRP concentrations and the risk and severity of acute appendicitis was investigated. METHODS: CRP concentrations in serum of appendicitis patients (n = 325) were measured. Appendicitis was categorized as complicated/uncomplicated and gangrenous/non-gangrenous. Imputed SNP data (n = 287) were generated. A genome-wide association study (GWAS) on CRP concentrations and appendicitis severity was performed. Intersection and colocalization of the GWAS results were performed with appendicitis and CRP-associated loci from the Pan-UKBB cohort. A functional-genomics approach to prioritize genes was employed. RESULTS: Thirteen percent of significant CRP quantitative trait loci (QTLs) that were previously identified in a large cohort of healthy individuals were replicated in our small patient cohort. Significant enrichment of CRP-QTLs in association with appendicitis was observed. Among these shared loci, the two top loci at chromosomes 1q41 and 8p23.1 were characterized. The top SNP at chromosome 1q41 is located within the promoter of H2.0 Like Homeobox (HLX) gene, which is involved in blood cell differentiation, and liver and gut organogeneses. The expression of HLX is increased in the appendix of appendicitis patients compared to controls. The locus at 8p23.1 contains multiple genes, including cathepsin B (CTSB), which is overexpressed in appendix tissue from appendicitis patients. The risk allele of the top SNP in this locus also increases CTSB expression in the sigmoid colon of healthy individuals. CTSB is involved in collagen degradation, MHC class II antigen presentation, and neutrophil degranulation. CONCLUSIONS: The results of this study prioritize HLX and CTSB as potential causal genes for appendicitis and suggest a shared genetic mechanism between appendicitis and CRP concentrations

Doppler tissue imaging unmasks right ventricular function abnormalities in HIV-infected patients

Background: We sought to investigate right ventricular (RV) function with Doppler tissue imaging (DTI) in human immunodeficiency virus (HIV)-infected patients receiving highly-active antiretroviral treatment, without any heart-related symptoms. Methods: We studied 38 asymptomatic HIV patients (aged 44.5 ± 9.2 years, 22 of them men) and 25 age-matched and sex-matched controls. All subjects underwent conventional and DTI estimation of left ventricular (LV) systolic and diastolic function, measuring peak systolic and diastolic myocardial velocities at the mitral annulus (Sm, Em, Am). Two-dimensional (2-D) echocardiographic study of the right ventricle (RV) was performed from the four-chamber view, and RV end-diastolic dimensions were measured. DTI recordings from the RV free wall at the tricuspid annulus were used to determine systolic (SmRV) and diastolic function (EmRV and AmRV). Results: HIV-infected patients compared to controls exhibited significantly lower peak systolic velocities at the septal-SmIVS (7.9 ± 1.3 vs 9.1 ± 1.4 cm/s, p = 0.002) and lateral mitral annulus - SmLAT (9.8 ± 1.7 vs 11.2 ± 1.3 cm/s, p = 0.025); no difference was observed regarding conventional 2-D examination of LV systolic and diastolic function and DTI-derived Em and Am. No significant difference occurred between HIV patients and controls regarding RV end-diastolic dimensions and pulmonary artery systolic pressure. However, SmRV (13.8 ± 1.6 vs 14.9 ± 2.2 cm/s, p = 0.040), EmRV (11.6 ± 3 vs 13.5 ± 2.6 cm/s, p = 0.028) and AmRV (10.9 ± 2.5 vs 13.8 ± 4 cm/s, p = 0.003) were significantly reduced in HIV patients as compared to controls. Conclusions: DTI unmasks subtle and otherwise undetectable abnormalities of the longitudinal LV systolic function and both RV systolic and diastolic function, in asymptomatic HIV patients receiving highly-active antiretroviral treatment. (Cardiol J 2010; 17, 6: 587-593

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.

The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs. Building on this regulatory map, we explored GWAS signals for 4083 traits, detecting colocalization for 180 disease loci with eQTLs. We show that eQTL analyses taking HLA type haplotypes into account have substantially greater power compared with only using single variants. We examined the association between the 8.1 ancestral haplotype and delayed colonization in Cystic Fibrosis, postulating that downregulation of RNF5 expression is the likely causal mechanism. Our study provides insights into the genetic architecture of the MHC region and pinpoints disease associations that are due to differential expression of HLA genes and non-HLA genes

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response

Contains fulltext : 220669.pdf (publisher's version ) (Open Access)Candida bloodstream infection, i.e. candidemia, is the most frequently encountered life-threatening fungal infection worldwide, with mortality rates up to almost 50%. In the majority of candidemia cases, Candida albicans is responsible. Worryingly, a global increase in the number of patients who are susceptible to infection (e.g. immunocompromised patients), has led to a rise in the incidence of candidemia in the last few decades. Therefore, a better understanding of the anti-Candida host response is essential to overcome this poor prognosis and to lower disease incidence. Here, we integrated genome-wide association studies with bulk and single-cell transcriptomic analyses of immune cells stimulated with Candida albicans to further our understanding of the anti-Candida host response. We show that differential expression analysis upon Candida stimulation in single-cell expression data can reveal the important cell types involved in the host response against Candida. This confirmed the known major role of monocytes, but more interestingly, also uncovered an important role for NK cells. Moreover, combining the power of bulk RNA-seq with the high resolution of single-cell RNA-seq data led to the identification of 27 Candida-response QTLs and revealed the cell types potentially involved herein. Integration of these response QTLs with a GWAS on candidemia susceptibility uncovered a potential new role for LY86 in candidemia susceptibility. Finally, experimental follow-up confirmed that LY86 knockdown results in reduced monocyte migration towards the chemokine MCP-1, thereby implying that this reduced migration may underlie the increased susceptibility to candidemia. Altogether, our integrative systems genetics approach identifies previously unknown mechanisms underlying the immune response to Candida infection

A functional genomics approach in Tanzanian population identifies distinct genetic regulators of cytokine production compared to European population

Humans exhibit remarkable interindividual and interpopulation immune response variability upon microbial challenges. Cytokines play a vital role in regulating inflammation and immune responses, but dysregulation of cytokine responses has been implicated in different disease states. Host genetic factors were previously shown to significantly impact cytokine response heterogeneity mainly in European-based studies, but it is unclear whether these findings are transferable to non-European individuals. Here, we aimed to identify genetic variants modulating cytokine responses in healthy adults of East African ancestry from Tanzania. We leveraged both cytokine and genetic data and performed genome-wide cytokine quantitative trait loci (cQTLs) mapping. The results were compared with another cohort of healthy adults of Western European ancestry via direct overlap and functional enrichment analyses. We also performed meta-analyses to identify cQTLs with congruent effect direction in both populations. In the Tanzanians, cQTL mapping identified 80 independent suggestive loci and one genome-wide significant locus (TBC1D22A) at chromosome 22; SNP rs12169244 was associated with IL-1b release after Salmonella enteritidis stimulation. Remarkably, the identified cQTLs varied significantly when compared to the European cohort, and there was a very limited percentage of overlap (1.6% to 1.9%). We further observed ancestry-specific pathways regulating induced cytokine responses, and there was significant enrichment of the interferon pathway specifically in the Tanzanians. Furthermore, contrary to the Europeans, genetic variants in the TLR10-TLR1-TLR6 locus showed no effect on cytokine response. Our data reveal both ancestry-specific effects of genetic variants and pathways on cytokine response heterogeneity, hence arguing for the importance of initiatives to include diverse populations into genomics research

Tissue metabolic changes drive cytokine responses to Mycobacterium tuberculosis

Cellular metabolism can influence host immune responses to Mycobacterium tuberculosis (Mtb). Using a systems biology approach, differential expression of 292 metabolic genes involved in glycolysis, glutathione, pyrimidine and inositol phosphate pathways was evident at the site of a human tuberculin skin test challenge in patients with active tuberculosis infection. For 28 metabolic genes, we identified single nucleotide polymorphisms (SNPs) that were trans-acting for in vitro cytokine responses to Mtb stimulation, including glutathione and pyrimidine metabolism genes that alter production of Th1 and Th17 cytokines. Our findings identify novel therapeutic targets in host metabolism that may shape protective immunity to tuberculosis

Genetic regulators of cytokine responses upon BCG vaccination in children from West Africa

Genetic variation is a key factor influencing cytokine production capacity, but which genetic loci regulate cytokine production before and after vaccination, particularly in African population is unknown. Here, we aimed to identify single-nucleotide polymorphisms (SNPs) controlling cytokine responses (cQTLs) after microbial stimulation in infants of West-African ancestry, comprising of low-birth-weight neonates randomized to bacillus Calmette–Guérin (BCG) vaccine-at-birth (intervention) or to the usual delayed BCG (control). Genome-wide cytokine QTL mapping revealed 12 independent cQTLs loci, of which the LINC01082-LINC00917 locus influenced more than half of the cytokine-stimulation pairs assessed. Furthermore, nine distinct cQTLs were found among infants randomized to BCG. Functional validation confirmed that several complement genes affect cytokine response after BCG vaccination. We observed a limited overlap of common cQTLs between the West-African infants and cohorts of Western European individuals. These data reveal strong population-specific genetic effects on cytokine production and may indicate new opportunities for therapeutic intervention and vaccine development in African populations.</p