Deconvolution of bulk blood eQTL effects into immune cell subpopulations.

BACKGROUND: Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole blood and tissue biopsies, which are likely to mask the cell type-context of the eQTL regulatory effects. Although this context can be investigated by generating transcriptional profiles from purified cell subpopulations, current methods to do this are labor-intensive and expensive. We introduce a new method, Decon2, as a framework for estimating cell proportions using expression profiles from bulk blood samples (Decon-cell) followed by deconvolution of cell type eQTLs (Decon-eQTL). RESULTS: The estimated cell proportions from Decon-cell agree with experimental measurements across cohorts (R ≥ 0.77). Using Decon-cell, we could predict the proportions of 34 circulating cell types for 3194 samples from a population-based cohort. Next, we identified 16,362 whole-blood eQTLs and deconvoluted cell type interaction (CTi) eQTLs using the predicted cell proportions from Decon-cell. CTi eQTLs show excellent allelic directional concordance with eQTL (≥ 96-100%) and chromatin mark QTL (≥87-92%) studies that used either purified cell subpopulations or single-cell RNA-seq, outperforming the conventional interaction effect. CONCLUSIONS: Decon2 provides a method to detect cell type interaction effects from bulk blood eQTLs that is useful for pinpointing the most relevant cell type for a given complex disease. Decon2 is available as an R package and Java application (https://github.com/molgenis/systemsgenetics/tree/master/Decon2) and as a web tool (www.molgenis.org/deconvolution).

Tissue alarmins and adaptive cytokine induce dynamic and distinct transcriptional responses in tissue-resident intraepithelial cytotoxic T lymphocytes.

The respective effects of tissue alarmins interleukin (IL)-15 and interferon beta (IFNß), and IL-21 produced by T cells on the reprogramming of cytotoxic T lymphocytes (CTLs) that cause tissue destruction in celiac disease is poorly understood. Transcriptomic and epigenetic profiling of primary intestinal CTLs showed massive and distinct temporal transcriptional changes in response to tissue alarmins, while the impact of IL-21 was limited. Only anti-viral pathways were induced in response to all the three stimuli, albeit with differences in dynamics and strength. Moreover, changes in gene expression were primarily independent of changes in H3K27ac, suggesting that other regulatory mechanisms drive the robust transcriptional response. Finally, we found that IL-15/IFNß/IL-21 transcriptional signatures could be linked to transcriptional alterations in risk loci for complex immune diseases. Together these results provide new insights into molecular mechanisms that fuel the activation of CTLs under conditions that emulate the inflammatory environment in patients with autoimmune diseases.

Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease.

Celiac disease (CeD) is a common immune-mediated disease of the small intestine that is triggered by exposure to dietary gluten. While the HLA locus plays a major role in disease susceptibility, 39 non-HLA loci were also identified in a study of 24,269 individuals. We now build on this earlier study by adding 4125 additional Caucasian samples including an Argentinian cohort. In doing so, we not only confirm the previous associations, we also identify two novel independent genome-wide significant associations at loci: 12p13.31 and 22q13.1. By applying a genomics approach and differential expression analysis in CeD intestinal biopsies, we prioritize potential causal genes at these novel loci, including LTBR, CYTH4, and RAC2. Nineteen prioritized causal genes are overlapping known drug targets. Pathway enrichment analysis and expression of these genes in CeD biopsies suggest that they have roles in regulating multiple pathways such as the tumor necrosis factor (TNF) mediated signaling pathway and positive regulation of I-κB kinase/NF-κB signaling.

Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease.

Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. Although genome-wide association studies have identified numerous genomic regions associated with CeD, it is difficult to accurately pinpoint which genes in these loci are most likely to cause CeD. We used four different in silico approaches-Mendelian randomization inverse variance weighting, COLOC, LD overlap, and DEPICT-to integrate information gathered from a large transcriptomics dataset. This identified 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway analysis of these genes indicated an association with adaptive and innate cytokine signaling and T cell activation pathways. Fifty-one of these genes are targets of known drug compounds or likely druggable genes, suggesting that our methods can be used to pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations that were affected by our CeD-prioritized genes in trans. Notably, 41 of these trans-mediated genes appear to be under control of one master regulator, TRAF-type zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an immune regulator acting in trans. Our strategy confirmed the role of adaptive immunity in CeD and revealed a genetic link between CeD and IFNγ signaling as well as with MHC I antigen processing, both major players of immune activation and CeD pathogenesis.

Concordancia entre ecoscopia realizada por médicos no cardiólogos y ecocardiografía convencional / Agreement between "echoscopy" performed by non-cardiologist physicians and conventional cardiac ultrasound

Resumen Introducción: el ultrasonido cardiaco enfocado ha sido propuesto como una aproximación útil para mejorar la toma de decisiones clínicas, permitiendo identificar rápidamente signos ultrasonográficos de una lista específica de diagnósticos potenciales. Objetivo: evaluar un programa de entrenamiento para médicos sin experiencia en ecocardiografía a fin de realizar ultrasonido cardiaco enfocado por medio de un dispositivo portátil (ecoscopio). Materiales y métodos: se compararon los resultados obtenidos mediante ecoscopia realizada por los médicos que recibieron el entrenamiento, con los obtenidos mediante ecocardiografía convencional realizada por cardiólogos expertos. Métodos: un total de 5 médicos no cardiólogos incluyendo un estudiante de Medicina de último año, 2 residentes de Medicina Interna y 2 Intensivistas participaron en un curso de entrenamiento de cuatro semanas, dirigido por un Cardiólogo experto de nivel III así: Primera semana: teoría y bases de ecocardiografía (3 horas diarias) Segunda semana: teoría de la adquisición de imágenes. Hallazgos normales y anormales (50 estudios). Tercera semana: manejo del ecoscopio (50 estudios). Cuarta semana: recolección de datos. Se incluyeron pacientes programados para ecocardiografía convencional en el Laboratorio de métodos no invasivos. A cada paciente se le realizaron dos exámenes. El primero consistió en una ecoscopia hecha por médico que recibió el entrenamiento y el segundo consistió en un ecocardiograma realizado por un cardiólogo experto. Los parámetros ecocardiográficos evaluados fueron: fracción de eyección del ventrículo izquierdo, disfunción ventricular derecha, crecimiento auricular izquierdo, hipertensión pulmonar, enfermedad valvular cardiaca y derrame pericárdico. Por medio de análisis de concordancia (índice Kappa) se compararon los resultados encontrados en ecoscopia versus ecocardiografía. Resultados: de 221 estudios se obtuvo concordancia moderada en fracción de eyección del ventrículo izquierdo (к =0,541, p<0,000), función ventricular derecha (к =0,403, p<0,001), dilatación de la aurícula izquierda (к =0,413, p<0,001), valvulopatía mitral (к =0,466, p<0,001) y tricuspídea (к =0,437, p<0,001). La valvulopatía aórtica mostró un acuerdo débil. El derrame pericárdico y la hipertensión pulmonar tuvieron concordancia pobre y débil, respectivamente. Conclusiones: con un tiempo limitado de formación, los participantes sin experiencia previa en técnicas de ultrasonido y utilizando ecoscopia, alcanzaron un acuerdo moderado en la mayoría de las mediciones cuando se comparó con ecocardiografía convencional practicada por ecocardiografistas expertos. Es necesario un estudio con mayor número de participantes que determine el tiempo de formación ideal para obtener resultados comparables con ecocardiografía.

Abstract Introduction: Focused cardiac ultrasound has been proposed as a useful approach for improving clinical decision making, as well as to be able to rapidly identify the ultrasound signs of a specific list of potential diagnoses. Objective: To evaluate a training program for physicians with no experience in cardiac ultrasound with the aim performing focused cardiac ultrasound using a portable device (echoscopy). Materials and methods: The results obtained from echoscopy performed by the physicians that received training were compared with those obtained with conventional cardiac ultrasound carried out by expert cardiologists. A total of 5 non-cardiologist doctors, including 1 medical student, 2 Internal Medicine residents, and 2 from Intensive Medicine, took part in a four-week training course given by a Level III Cardiology specialist. The course included: First week: Theory and basis of cardiac ultrasound (3 hours daily) Second week: Theory of acquiring images. Normal and abnormal findings (50 studies). Third week: handling of the echoscope (50 studies). Fourth week: Data collection. The study included patients scheduled for conventional cardiac ultrasound in the Non-Invasive Methods Laboratory. Two examinations were carried out on each patient. The first consisted of an echoscopy performed by a doctor that had received the training, and the second consisted of a cardiac ultrasound carried out by an expert cardiologist. The ultrasound parameters evaluated were: left ventricular ejection fraction, right ventricular dysfunction, left atrial enlargement, pulmonary hypertension, cardiac valve disease, and pericardial effusion. The results found in echoscopy versus cardiac ultrasound were compared using concordance analysis (Kappa Index). Results: The following results were obtained on the 221 studies performed: moderate agreement in left ventricular ejection fraction (к =0.541, P<.000), right ventricular function (к =0.403, P<.001), left atrial enlargement (к =0.413, P<.001), mitral valve and tricuspid valve disease (к =0.437, P<.001 and (к =0.466, P<.001, respectively). There was weak agreement with aortic valve disease. Pericardiac effusion and the presence of pulmonary hypertension had a poor and week agreement, respectively. Conclusions: With a limited training period, the participants with no previous experience in ultrasound techniques and using echoscopy achieved a moderate agreement in the majority of measurements when compared with conventional cardiac ultrasound performed by experts in the technique. A study with a larger number of participants is required in order to determine the ideal training period to obtain results comparable with cardiac ultrasound.

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses.

The immune response to pathogens varies substantially among people. Whereas both genetic and nongenetic factors contribute to interperson variation, their relative contributions and potential predictive power have remained largely unknown. By systematically correlating host factors in 534 healthy volunteers, including baseline immunological parameters and molecular profiles (genome, metabolome and gut microbiome), with cytokine production after stimulation with 20 pathogens, we identified distinct patterns of co-regulation. Among the 91 different cytokine-stimulus pairs, 11 categories of host factors together explained up to 67% of interindividual variation in cytokine production induced by stimulation. A computational model based on genetic data predicted the genetic component of stimulus-induced cytokine production (correlation 0.28-0.89), and nongenetic factors influenced cytokine production as well.

A locus at 7p14.3 predisposes to refractory celiac disease progression from celiac disease.

BACKGROUND: Approximately 5% of patients with celiac disease (CeD) do not respond to a gluten-free diet and progress to refractory celiac disease (RCD), a severe progression that is characterized by infiltration of intraepithelial T lymphocytes. Patients with RCD type II (RCDII) show clonal expansions of intraepithelial T lymphocytes that result in a poor prognosis and a high mortality rate through development of aggressive enteropathy-associated T-cell lymphoma. It is not known whether genetic variations play a role in severe progression of CeD to RCDII. PATIENTS AND METHODS: We performed the first genome-wide association study to identify the causal genes for RCDII and the molecular pathways perturbed in RCDII. The genome-wide association study was performed in 38 Dutch patients with RCDII, and the 15 independent top-associated single nucleotide polymorphism (SNP) variants (P<5×10) were replicated in 56 independent French and Dutch patients with RCDII. RESULTS: After replication, SNP rs2041570 on chromosome 7 was significantly associated with progression to RCDII (P=2.37×10, odds ratio=2.36) but not with CeD susceptibility. SNP rs2041570 risk allele A was associated with lower levels of FAM188B expression in blood and small intestinal biopsies. Stratification of RCDII biopsies based on rs2041570 genotype showed differential expression of innate immune and antibacterial genes that are expressed in Paneth cells. CONCLUSION: We have identified a novel SNP associated with the severe progression of CeD to RCDII. Our data suggest that genetic susceptibility to CeD might be distinct from the progression to RCDII and suggest a role for Paneth cells in RCDII progression.

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits.

Effective immunity requires a complex network of cellular and humoral components that interact with each other and are influenced by different environmental and host factors. We used a systems biology approach to comprehensively assess the impact of environmental and genetic factors on immune cell populations in peripheral blood, including associations with immunoglobulin concentrations, from ∼500 healthy volunteers from the Human Functional Genomics Project. Genetic heritability estimation showed that variations in T cell numbers are more strongly driven by genetic factors, while B cell counts are more environmentally influenced. Quantitative trait loci (QTL) mapping identified eight independent genomic loci associated with leukocyte count variation, including four associations with T and B cell subtypes. The QTLs identified were enriched among genome-wide association study (GWAS) SNPs reported to increase susceptibility to immune-mediated diseases. Our systems approach provides insights into cellular and humoral immune trait variability in humans.

Encephalitozoon intestinalis Inhibits Dendritic Cell Differentiation through an IL-6-Dependent Mechanism.

Microsporidia are a group of intracellular pathogens causing self-limited and severe diseases in immunocompetent and immunocompromised individuals, respectively. A cellular type 1 adaptive response, mediated by IL-12, IFNγ, CD4+, and CD8+ T cells has been shown to be essential for host resistance, and dendritic cells (DC) play a key role at eliciting anti-microsporidial immunity. We investigated the in vitro response of DC and DC precursors/progenitors to infection with Encephalitozoon intestinalis (Ei), a common agent of human microsporidosis. Ei-exposed DC cultures up-regulated the surface expression of MHC class II and the costimulatory molecules CD86 and CD40, only when high loads of spores were used. A vigorous secretion of IL-6 but not of IL-1ß or IL-12p70 was also observed in these cultures. Ei-exposed DC cultures consisted of immature infected and mature bystander DC, as assessed by MHC class II and costimulatory molecules expression, suggesting that intracellular Ei spores deliver inhibitory signals in DC. Moreover, Ei selectively inhibited the secretion of IL-12p70 in LPS-stimulated DC. Whereas Ei-exposed DC promoted allogeneic naïve T cell proliferation and IL-2 and IFNγ secretion in DC-CD4+ T cell co-cultures, separated co-cultures with bystander or infected DCs showed stimulation or inhibition of IFNγ secretion, respectively. When DC precursors/progenitors were exposed to Ei spores, a significant inhibition of DC differentiation was observed without shifting the development toward cells phenotypically or functionally compatible with myeloid-derived suppressor cells. Neutralization experiments demonstrated that this inhibitory effect is IL-6-dependent. Altogether this investigation reveals a novel potential mechanism of immune escape of microsporidian parasites through the modulation of DC differentiation and maturation.

Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.

Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci in one or more of these diseases. As more than 90% of AID-associated SNPs are intergenic or intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 SNPs that are associated with 14 AID to causal genes using transcriptomic data from 629 blood samples. We were able to link 71 (39%) of the AID-SNPs to two or more nearby genes, providing evidence that for part of the AID loci multiple causal genes exist. While 54 of the AID loci are shared by one or more AID, 17% of them do not share candidate causal genes. In addition to finding novel genes such as ULK3, we also implicate novel disease mechanisms and pathways like autophagy in celiac disease pathogenesis. Furthermore, 42 of the AID SNPs specifically affected the expression of 53 non-coding RNA genes. To further understand how the non-coding genome contributes to AID, the SNPs were linked to functional regulatory elements, which suggest a model where AID genes are regulated by network of chromatin looping/non-coding RNAs interactions. The looping model also explains how a causal candidate gene is not necessarily the gene closest to the AID SNP, which was the case in nearly 50% of cases.

Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis.

Hundreds of genomic loci have been associated with a significant number of immune-mediated diseases, and a large proportion of these associated loci are shared among traits. Both the molecular mechanisms by which these loci confer disease susceptibility and the extent to which shared loci are implicated in a common pathogenesis are unknown. We therefore sought to dissect the functional components at loci shared between two autoimmune diseases: coeliac disease (CeD) and rheumatoid arthritis (RA). We used a cohort of 12 381 CeD cases and 7827 controls, and another cohort of 13 819 RA cases and 12 897 controls, all genotyped with the Immunochip platform. In the joint analysis, we replicated 19 previously identified loci shared by CeD and RA and discovered five new non-HLA loci shared by CeD and RA. Our fine-mapping results indicate that in nine of 24 shared loci the associated variants are distinct in the two diseases. Using cell-type-specific histone markers, we observed that loci which pointed to the same variants in both diseases were enriched for marks of promoters active in CD14+ and CD34+ immune cells (P < 0.001), while loci pointing to distinct variants in one of the two diseases showed enrichment for marks of more specialized cell types, like CD4+ regulatory T cells in CeD (P < 0.0001) compared with Th17 and CD15+ in RA (P = 0.0029).

Small and Long Regulatory RNAs in the Immune System and Immune Diseases.

Cellular differentiation is regulated on the level of gene expression, and it is known that dysregulation of gene expression can lead to deficiencies in differentiation that contribute to a variety of diseases, particularly of the immune system. Until recently, it was thought that the dysregulation was governed by changes in the binding or activity of a class of proteins called transcription factors. However, the discovery of micro-RNAs and recent descriptions of long non-coding RNAs (lncRNAs) have given enormous momentum to a whole new field of biology: the regulatory RNAs. In this review, we describe these two classes of regulatory RNAs and summarize what is known about how they regulate aspects of the adaptive and innate immune systems. Finally, we describe what is known about the involvement of micro-RNAs and lncRNAs in three different autoimmune diseases (celiac disease, inflammatory bowel disease, and multiple sclerosis).

In vitro susceptibility of Trypanosoma cruzi strains from Santander, Colombia, to hexadecylphosphocholine (miltefosine), nifurtimox and benznidazole

Introduction. The current chemotherapy for Chagas disease is unsatisfactory with only two drugs available for treatment. Research to discover new drugs for Chagas disease is urgent. Hexadecyl-phosphocholine (HPC, miltefosine) has been demonstrated to have in vitro activity against Trypanosoma cruzi parasites, but its activity on different Colombian T. cruzi strains is not known. Objective. To evaluate the in vitro susceptibility of T. cruzi strains isolated from humans and vectors in Santander, Colombia, to miltefosine, nifurtimox and benznidazole. Materials and methods. Eight T. cruzi Colombian strains and three reference strains (Esmeraldo, SilvioX10 and Y) were studied. Drug activities against extracellular epimastigotes and intracellular amastigotes were determined by microscopic counting. The results were expressed as the concentrations that inhibited 50% and 90% growth (IC50 and IC90). Results. For miltefosine a similar range of drug activity was observed against all the Colombian strains, all parasites being more susceptible to miltefosine than to the reference drugs. The intracellular amastigotes were more susceptible to miltefosine (IC50 0.08 to 0.63 ìM and IC90 0.21 to 2.21 ìM) than extracellular forms (IC50 <0.92 to 2.29 ìM and IC90 1.38 to 4.76 ìM). For reference drugs, parasites were more susceptible to nifurtimox than to benznidazole and some differences in activity of benznidazole between T. cruzi strains was observed. Conclusions. The results showed the significant in vitro activity of miltefosine against T. cruzi stages, and the expected results for the reference drugs. Further in vivo studies with miltefosine are planned.

Introducción. Los tratamientos actuales para la enfermedad de Chagas son insatisfactorios y sólo existen dos medicamentos disponibles. La búsqueda de alternativas terapéuticas es prioritaria. La hexadecilfosfocolina (miltefosina) ha mostrado actividad in vitro contra Trypanosoma cruzi. Sin embargo, su actividad en aislamientos de T. cruzi obtenidos en Colombia aún no ha sido reportada. Objetivo. Evaluar la susceptibilidad in vitro a miltefosina, nifurtimox y benznidazole de cepas de T. cruzi aisladas de humanos y vectores en Santander, Colombia. Materiales y métodos. Se evaluó la susceptibilidad de los tres medicamentos en ocho cepas colombianas de T. cruzi y tres cepas de referencia: Esmeraldo, Silvio X10 y Y. La actividad de los compuestos fue determinada en epimastigotes extracelulares y amastigotes intracelulares, por conteo microscópico. Los resultados se expresaron en concentraciones inhibitorias 50 y 90 (CI50 y CI90). Resultados. Para la miltefosina, se observaron rangos similares en la actividad del medicamento entre las cepas colombianas; todos los parásitos fueron más susceptibles a la miltefosina que a los medicamentos de referencia. Los amastigotes intracelulares fueron más sensibles a la miltefosina (CI50, 0,08 a 0,63 µM y CI90, 0,21 a 2,21 µM) que las formas extracelulares (CI50, <0,92 a 2,29 µM y CI90, 1,38 a 4,76 µM). En los medicamentos de referencia, los parásitos fueron más susceptibles al nifurtimox que al benznidazole. Se observaron algunas diferencias en la actividad del benznidazole en las cepas estudiadas de T. cruzi. Conclusiones. Los resultados obtenidos de la actividad in vitro de miltefosina y de los medicamentos de referencia contra aislamientos de T. cruzi son satisfactorios y serán considerados en estudios posteriores in vivo.

In vitro susceptibility of Trypanosoma cruzi strains from Santander, Colombia, to hexadecylphosphocholine (miltefosine), nifurtimox and benznidazole.

INTRODUCTION: The current chemotherapy for Chagas disease is unsatisfactory with only two drugs available for treatment. Research to discover new drugs for Chagas disease is urgent. Hexadecyl-phosphocholine (HPC, miltefosine) has been demonstrated to have in vitro activity against Trypanosoma cruzi parasites, but its activity on different Colombian T. cruzi strains is not known. OBJECTIVE: To evaluate the in vitro susceptibility of T. cruzi strains isolated from humans and vectors in Santander, Colombia. to miltefosine, nifurtimox and benznidazole. MATERIALS AND METHODS: Eight T. cruzi Colombian strains and three reference strains (Esmeraldo, SilvioX10 and Y) were studied. Drug activities against extracellular epimastigotes and intracellular amastigotes were determined by microscopic counting. The results were expressed as the concentrations that inhibited 50% and 90% growth (IC50 and IC90). RESULTS: For miltefosine a similar range of drug activity was observed against all the Colombian strains, all parasites being more susceptible to miltefosine than to the reference drugs. The intracellular amastigotes were more susceptible to miltefosine (IC50 0.08 to 0.63 microM and IC90 0.21 to 2.21 microM) than extracellular forms (IC50 <0.92 to 2.29 microM and IC90 1.38 to 4.76 microM). For reference drugs, parasites were more susceptible to nifurtimox than to benznidazole and some differences in activity of benznidazole between T. cruzi strains was observed. CONCLUSIONS: The results showed the significant in vitro activity of miltefosine against T. cruzi stages, and the expected results for the reference drugs. Further in vivo studies with miltefosine are planned.