Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients

Background: The development of next-generation sequencing (NGS) technologies has a great impact in the human variation detection given their high-throughput. These techniques are particularly helpful for the evaluation of the genetic background in disorders of complex genetic etiology such as Hirschsprung disease (HSCR). The purpose of this study was the design of a panel of HSCR associated genes as a rapid and efficient tool to perform genetic screening in a series of patients. Methods: We have performed NGS-based targeted sequencing (454-GS Junior) using a panel containing 26 associated or candidate genes for HSCR in a group of 11 selected HSCR patients. Results: The average percentage of covered bases was of 97 %, the 91.4 % of the targeted bases were covered with depth above 20X and the mean coverage was 422X. In addition, we have found a total of 13 new coding variants and 11 new variants within regulatory regions among our patients. These outcomes allowed us to re-evaluate the genetic component associated to HSCR in these patients. Conclusions: Our validated NGS panel constitutes an optimum method for the identification of new variants in our patients. This approach could be used for a fast, reliable and more thorough genetic screening in future series of patients.Instituto de Salud Carlos III (ISCIII)Spanish Ministry of Economy and Competitiveness, Spain (PI13/01560)Consejería de Innovación Ciencia y Empresa de la Junta de Andalucía (CTS-7447)CIBERER is an initiative of the ISCIII, Spanish Ministry of Economy and Competitivenes

Genetic variation in NDFIP1 modifies the metabolic patterns in immune cells of multiple sclerosis patients

Autoinmunidad; Marcadores genéticos; Trastornos neurológicosAutoimmunitat; Marcadors genètics; Trastorns neurològicsAutoimmunity; Genetic markers; Neurological disordersOne of the 233 polymorphisms associated with multiple sclerosis (MS) susceptibility lies within the NDFIP1 gene, and it was previously identified as eQTL in healthy controls. NDFIP1 shows interesting immune functions and is involved in the development of the central nervous system. We aimed at studying the NDFIP1 variant on activation and metabolism of immune cells. NDFIP1 mRNA and protein expression were assessed in PBMCs by qPCR and western blot in 87 MS patients and 84 healthy controls genotyped for rs4912622. Immune activation after PHA stimulation was evaluated by CD69 upregulation, and metabolic function of both basal and PHA-activated lymphocytes was studied by Seahorse Xfp-Analyzer. In minor-allele homozygous controls but not in patients, we found higher NDFIP1 expression, significantly reduced protein levels, and CD69 upregulation in B- and T-cells. PBMCs from minor-allele homozygous controls showed significantly higher basal mitochondrial respiration and ATP production compared to major-allele carriers, while minor-allele homozygous patients showed significantly lower metabolic activity than carriers of the major allele. In conclusion, we describe associations in minor-allele homozygous controls with lower levels of NDFIP1 protein, CD69 upregulation, and raised mitochondrial activity, which are not replicated in MS patients, suggesting a NDFIP1 differential effect in health and disease.This work was supported by the projects PI16/01259 and PI20/01634, integrated in the Plan Nacional de I + D + I, AES 2013–2016 and 2017–2020; funded by the ISCIII and co-funded by the European Regional Development Fund (ERDF) "A way to make Europe”. LEP is recipient of a contract from “REEM: Red Española de Esclerosis Múltiple” (RETICS-REEM RD16/0015/0013; www.reem.es). AGJ and JAZ hold contracts from the program “Promoción de empleo joven y garantía juvenil-CAM” (PEJ2018-003125-A and PEJD-2019-PRE/SAL-16662)

Two vs. three weeks of treatment with amoxicillin-clavulanate for stabilized community-acquired complicated parapneumonic effusions. A preliminary non-inferiority, double-blind, randomized, controlled trial

Background: The optimal duration of antibiotic treatment for complicated parapneumonic effusions (CPPEs) has not been properly defined. Our aim was to compare the efficacy of amoxicillin-clavulanate for 2 vs. 3 weeks in patients with CPPE (i.e. those which required chest tube drainage). Methods: In this non-inferiority, randomized, double-blind, controlled trial, patients with community-acquired CPPE were recruited from two centers in Spain and, after having obtained clinical stability following 2 weeks of amoxicillin-clavulanate, they were randomly assigned to placebo or antibiotic for an additional week. The primary objective was clinical success, tested for a non-inferiority margin of10 mm at 3 months, and adverse events. The study was registered with EudraCT, number 2014-003137-25. We originally planned to randomly assign 284 patients. Results: After recruiting 55 patients, the study was terminated early owing to slow enrolment. A total of 25 patients were assigned to 2 weeks and 30 patients to 3 weeks of amoxicillin-clavulanate. Clinical success occurred in the 25 (100%) patients treated for 2 weeks and 29 (97%) treated for 3 weeks (difference 3%, 95% CI -3 to 9.7%). Respective between-group differences in the rate of residual pleural thickening (-12%, 95%CI -39 to 14%) and adverse events (-7%, 95%CI -16 to 2%) did not reach statistical significance. Conclusions: In this small series of selected adult patients with community-acquired CPPE, amoxicillin-clavulanate treatment could be safely discontinued by day 14 if clinical stability was obtained

Proinflammatory cytokine profile differences between primary open angle and pseudoexfoliative glaucoma

Introduction: Few studies have investigated glaucoma biomarkers in aqueous humor and tear and have found elevations of proinflammatory cytokines in patients with primary open-angle glaucoma (POAG) and pseudoexfoliative glaucoma (PXG). In this study we investigate differences in inflammatory cytokines between POAG and PXG patients to find specific disease biomarkers. Methods: For this purpose, tear and aqueous humor samples of 14 eyes with POAG and 15 eyes with PXG undergoing cataract surgery were immunoassayed for 27 pro-inflammatory cytokines. The concentrations of cytokines in tear and aqueous humor and their association with clinical variables were analysed, correlated and compared between the groups. Results: We found that the levels of three cytokines differed significantly in the aqueous humor of POAG and PXG patients: IL-12 and IL-13 were higher in the POAG group, while MCP-1(MCAF) was higher in the PXG group. The number of topical hypotensive medications was correlated with diminished levels of two cytokines (IL-7 and basic fibroblast growth factor) in aqueous humor in the POAG group and with diminished levels of IL-12 in tear in the PXG group. Conclusion: We conclude that both POAG and PXG show elevated concentrations of proinflammatory cytokines in tear and aqueous humor that could be used as biomarkers for these types of glaucoma and that the concentrations in aqueous humor of three cytokines: IL-12, IL-13 and MCP-1(MCAF) could be used to differentiate POAG and PXG

CX3CL1–CX3CR1 Axis: A New Player in Coeliac Disease Pathogenesis

Background: The CX3CL1–CX3CR1 axis has been related to numerous diseases. The aim of our study was to investigate its involvement in coeliac disease (CD) pathogenesis, particularly in the early phase of the disease. Methods: We collected peripheral blood from CD patients and controls, enrolled in a 3-day gluten challenge, to study soluble CX3CL1, I-TAC and MIG by Luminex, CX3CL1 and CX3CR1 gene expression by qPCR, and CX3CR1 protein expression in monocytes and CD8+, CD4+ and γδ+ T cells, by flow cytometry. We also analysed the expression of the CX3CL1 and CX3CR1 mRNA and protein in the duodenal biopsies of CD patients with active and treated disease, and in non-CD control individuals, by qPCR and immunohistochemistry. Results: After the gluten challenge, increased levels of CX3CL1, I-TAC and MIG proteins were observed in the peripheral blood of CD patients, with no changes in CX3CL1 mRNA, or CX3CR1 mRNA and protein. Regarding duodenal tissue, CX3CL1 was absent or barely present in the superficial and basal epithelium of CD patients, contrasting with the moderate to high levels present in controls. Conclusions: CX3CL1 seems to be involved in the appearance and progression of CD, and it appears to be a potential diagnostic biomarker. Its use as an alternative therapeutic target in CD deserves further research

Hypercytokinemia in COVID-19: Tear cytokine profile in hospitalized COVID-19 patients

The aim of this study is to analyze the concentrations of cytokines in tear of hospitalized COVID-19 patients compared to healthy controls. Tear samples were obtained from 41 healthy controls and 62 COVID-19 patients. Twenty-seven cytokines were assessed: interleukin (IL)-1b, IL-1RA, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL9, IL-10, IL-12, IL-13, IL-15, IL-17, eotaxin, fibroblast growth factor basic, granulocyte colony-stimulating factor (G-CSF), granulocyte-monocyte colony-stimulating factor (GM-CSF), interferon (IFN)-γ, interferon gamma-induced protein, monocyte chemo-attractant protein-1, macrophage inflammatory protein (MIP)-1a, MIP-1b, platelet-derived growth factor (PDGF), regulated on activation normal T cell expressed and secreted, tumor necrosis factor-α and vascular endothelial growth factor (VEGF). In tear samples of COVID-19 patients, an increase in IL-9, IL-15, G-CSF, GM-CSF, IFN-γ, PDGF and VEGF was observed, along with a decrease in eotaxin compared to the control group (p < 0.05). A poor correlation between IL-6 levels in tear and blood was found. IL-1RA and GM-CSF were significantly lower in severe patients and those who needed treatment targeting the immune system (p < 0.05). Tear cytokine levels corroborate the inflammatory nature of SARS-CoV-2

The Rare IL22RA2 Signal Peptide Coding Variant rs28385692 Decreases Secretion of IL-22BP Isoform-1, -2 and -3 and Is Associated with Risk for Multiple Sclerosis.

The IL22RA2 locus is associated with risk for multiple sclerosis (MS) but causative variants are yet to be determined. In a single nucleotide polymorphism (SNP) screen of this locus in a Basque population, rs28385692, a rare coding variant substituting Leu for Pro at position 16 emerged significantly (p = 0.02). This variant is located in the signal peptide (SP) shared by the three secreted protein isoforms produced by IL22RA2 (IL-22 binding protein-1(IL-22BPi1), IL-22BPi2 and IL-22BPi3). Genotyping was extended to a Europe-wide case-control dataset and yielded high significance in the full dataset (p = 3.17 × 10-4). Importantly, logistic regression analyses conditioning on the main known MS-associated SNP at this locus, rs17066096, revealed that this association was independent from the primary association signal in the full case-control dataset. In silico analysis predicted both disruption of the alpha helix of the H-region of the SP and decreased hydrophobicity of this region, ultimately affecting the SP cleavage site. We tested the effect of the p.Leu16Pro variant on the secretion of IL-22BPi1, IL-22BPi2 and IL-22BPi3 and observed that the Pro16 risk allele significantly lowers secretion levels of each of the isoforms to around 50%-60% in comparison to the Leu16 reference allele. Thus, our study suggests that genetically coded decreased levels of IL-22BP isoforms are associated with augmented risk for MS

Estudio de marcadores genéticos asociados a diabetes tipo 1 en población española con debut pediátrico y adulto

La diabetes tipo 1 (DT1) es una enfermedad autoinmune causada por la destrucción de las células productoras de insulina en el páncreas. Esta destrucción está mediada por linfocitos T autorreactivos y monocitos, y además existen componentes genéticos y ambientales que influyen en la susceptibilidad a padecer la enfermedad. Dentro del componente genético, el mayor determinante de la susceptibilidad a la DT1 se encuentra en la región HLA de clase II, en la que los haplotipos asociados a la enfermedad suponen el 50% de la carga genética. Los primeros estudios de asociación de genes candidatos establecieron 5 regiones que influyen en el riesgo a padecer DT1, pero el gran avance se ha dado en los últimos cinco años con el desarrollo de los estudios de barrido genómico (GWAS) que han permitido elevar a 50 el número de regiones asociadas a la enfermedad. en nuestro estudio en población española encontramos pequeñas diferencias en la susceptibilidad a DT1 conferida por los genes HLA de clase II que podrían indicar la presencia de diferencias poblacionales. Además, describimos la influencia de cuatro regiones cromosómicas en la edad de comienzo de la enfermedad. Este resultado apoya la necesidad de incluir este tipo de análisis en el estudio general de la genética de la DT1, con el objetivo de determinar los factores genéticos que puedan actuar como “aceleradores” de la enfermedad. Entre los genes candidatos seleccionados, describimos por primera vez la asociación del gen STAT4 a la DT1. Por último, la ausencia de asociación en el único gen no relacionado con el sistema inmunitario (G6PC2) concuerda con los estudios que apoyan que la base genética de la DT1 está formada principalmente por genes relacionados con la respuesta inmunitaria y que no existen defectos genéticos en el funcionamiento de las células beta que predispongan a la enfermedad. [ABSTRACT]Type 1 diabetes (T1D) is an autoimmune disease caused by the destruction of insulinproducing cells in the pancreas mediated by autorreactive T cells and monocytes. There is a genetic and an environmental component that influences T1D susceptibility. The strongest genetic modifier is located in the class II HLA region, in which certain haplotypes carry 50% of the genetic load of the disease. The association studies of candidate genes established 5 regions associated with T1D, but a more significant progress has been made in the last five years with the development of the genome-wide association studies (GWAS), which have increased the number of T1D genetic associations to 50 chromosome regions. Our study in a Spanish population provides with some interesting differences in the T1D susceptibility conferred by the HLA class II genes that could be caused by populational differences. We also describe the influence of four chromosome regions in the age at onset of T1D, a result that supports the need for including these analyses in the general study of T1D genetics to identify genetic factors that could accelerate or delay the disease onset. Among the selected candidate genes, we describe for the first time the association of STAT4 with the disease. Finally, no association was detected in G6PC2, the only selected gene that is not related with the immune system. This result is concordant with previous studies supporting that the genetic basis of T1D is composed mainly of genes related with the immune response

Polymorphisms in ARNTL/BMAL1 and CLOCK Are Not Associated with Multiple Sclerosis in Spanish Population

Disrupted circadian cycle has been reported in multiple sclerosis (MS). Previous genome-wide association studies (GWAS) singled out over 230 variants associated with MS. A study performed in a Slavic population identified two new single nucleotide polymorphisms (SNPs), rs6811520 (CLOCK) and rs3789327 (ARNTL/BMAL1), associated with MS risk. However, these regions that codify the capital regulators of circadian rhythm had not been linked to the disease before, so replication in independent populations is warranted to ascertain possible geographical differences. Our aim was to replicate the associations reported in the ARNTL/BMAL1 and CLOCK genes in a Spanish cohort with a maximum of 974 MS patients and 626 controls. In this study, 956 MS patients and 612 controls were successfully genotyped for rs6811520 and 943 MS patients and 598 controls for rs3789327.Clinical variables (age at disease onset, EDSS, or relapses) were collected in a maximum of 549 patients. No statistically significant differences were found between cases and controls for the analyzed SNPs, even after stratifications by sex, clinical form, or HLA-DRB1*15:01 status. No influence of the SNPs was found on age at disease onset, EDSS, or annual relapse rate at 5 years after onset. In conclusion, our study does not replicate the associations observed in the previously investigated Slavic population

Additional file 1: of Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients

Detailed description of covered regions in our panel of genes. (XLS 53 kb