152 research outputs found
Estudi immunogenètic de les quimiocines CCL4 i CCL4L : exemple i model de la complexitat de la superfamília de les quimiocines
No full textDescripció del recurs: el 19-08-2008Consultable des del TDXTítol obtingut de la portada digitalitzadaEls resultats d'aquesta tesi doctoral, presentada per compendi de publicacions, es divideixen en 2 grups: A) Basats en la variabilitat de CCL4 i CCL4L: Article: Multiple Products Derived from Two CCL4 Loci: High Incidence of a New Polymorphism in HIV+ Patients. Roger Colobran, Patricia Adreani, Yaqoub Ashhab, Anuska Llano, José A. Esté, Orlando Dominguez, Ricardo Pujol-Borrell, and Manel Juan. The Journal of Immunology, 2005, 174: 5655-5664. Els locus CCL4 i CCL4L originen les quimiocines CCL4 i CCL4L, que estan altament relacionades. En aquest treball es demostra que ambdós gens produeixen trànscrits originats per splicing alternatiu mancats de l'exó 2 (anomenats CCL4Δ2 i CCL4LΔ2). Per altra banda, el locus CCL4L presenta un polimorfisme de nucleòtid únic (rs4796195) situat a la seqüència acceptora de tall-i-unió (splicing) de l'intró 2, donant lloc a dues variants al·lèliques: CCL4L1 (la originalment descrita) i CCL4L2, on aquesta seqüència acceptora de tall desapareix i l'ús de noves seqüències de tall acceptores al voltant de la original, dóna lloc a la generació de múltiples trànscrits diferents als generats per CCL4L1. En un estudi cas-control es demostra que la variant CCL4L2 està significativament augmentada en els pacients HIV+ respecte una població control. Això demostra que CCL4L2 és un factor de susceptibilitat per a la infecció per HIV. Article: Confusión entre CCL4 y CCL4L1: Un ejemplo a tener en cuenta cuando se usan reactivos de terceras partes. R. Colobran, M. Juan. Inmunología, Vol. 26 / Núm 1/ Enero-Marzo 2007: 51-54. En aquest treball es descriuen errors en la seqüència aminoacídica de les proteïnes CCL4 i CCL4L1 comercialitzades per algunes empreses. Article: Population Structure in Copy Number Variation (CNV) and SNPs in the CCL4L Chemokine Gene. Roger Colobran, David Comas, Rosa Faner, Edurne Pedrosa, Roger Anglada, Ricardo Pujol-Borrell, Jaume Bertranpetit, Manel Juan. Genes and Immunity, Submitted. En aquest treball s'integra l'anàlisis de variacions de nombre de còpia (CNV) i SNPs (rs4796195 and rs3744595) en el gen CCL4L. S'ha quantificat el nombre de còpies del gen CCL4L i s'han genotipat els dos SNPs en el panell HGDP-CEPH, que conté 1064 individus de 52 poblacions mundials. Per primera vegada presentem dades de poblacions mundials que combinen els dos tipus de variació genòmica (CNVs i SNPs) i els nostres resultats mostren una clara estructura poblacional: les poblacions de l'Àfrica Subsahariana són les que tenen un nombre més elevat de còpies de CCL4L (mitja = 4,32) i les poblacions Europees són les que en tenen menys (mitja = 1,89). B) Basats en la variabilitat global de la superfamília de les quimiocines: Article: The chemokine network. I. How the genomic organization of chemokines contains clues for deciphering their functional complexity. R. Colobran, R. Pujol-Borrell, Ma P. Armengol and M. Juan. Clinical and Experimental Immunology, 2007, 148: 208-217. En aquesta primera revisió analitzem les dades actuals sobre la família de les quimiocines, bàsicament sobre la seva organització genòmica. S'interpreta aquesta organització genòmica en relació a les principals funcions adquirides pels seus membres individuals o pels clusters de gens que es formen. Article: The chemokine network. II. On how polymorphisms and alternative splicing increase the number of molecular species and configure intricate patterns of disease susceptibility. R. Colobran, R. Pujol-Borrell, Ma P. Armengol and M. Juan. Clinical and Experimental Immunology, 2007, 150: 1-12. En aquesta segona revisió sobre quimiocines, ens centrem en els polimorfismes i els fenòmens d'splicing alternatiu i les seves conseqüències en malaltia.The results of this doctoral thesis, presented as compendium of works, can be divided in two main groups: A) Based on the variability of CCL4 and CCL4L: Manuscript: Multiple Products Derived from Two CCL4 Loci: High Incidence of a New Polymorphism in HIV+ Patients. Roger Colobran, Patricia Adreani, Yaqoub Ashhab, Anuska Llano, José A. Esté, Orlando Dominguez, Ricardo Pujol-Borrell, and Manel Juan. The Journal of Immunology, 2005, 174: 5655-5664. CCL4 and CCL4L loci codify for CCL4 and CCL4L chemokines, that are highly related. In this work we demonstrate that both loci produce alternatively spliced transcripts that lacks intron 2 (called CCL4Δ2 and CCL4LΔ2). Moreover, CCL4L locus show a single nucleotide polymorphism (SNP, rs4796195) located in the acceptor splice site of intron 2, splitting CCL4L into two allelic variants: CCL4L1 (the originally described one) and CCL4L2. In CCL4L2 the original acceptor splice site desappears and several new acceptor splice sites surrounding the original one are used, displaying multiple transcripts differents to those generated to CCL4L1. In a case-control study we demonstrate that the variant CCL4L2 is significantly increased in HIV patients with respect to the control population. Therefore, CCL4L2 is a susceptibility factor for HIV infection. Manuscript: Confusion Between CCL4 and CCL4L1: An Example to Bear in Mind when Using Third-Party Reagents. R. Colobran, M. Juan. Inmunología, Vol. 26 / Núm 1/ Enero-Marzo 2007: 51-54. In this work, we describe errors in the aminoacidic sequences of CCL4 and CCL4L1 proteins delivered by several companies. Manuscript: Population Structure in Copy Number Variation (CNV) and SNPs in the CCL4L Chemokine Gene. Roger Colobran, David Comas, Rosa Faner, Edurne Pedrosa, Roger Anglada, Ricardo Pujol-Borrell, Jaume Bertranpetit, Manel Juan. Genes and Immunity, Submitted. In this study we integrate the analysis of CNV and SNPs, combining the assessment of gene copy number with the genotyping of relevant SNPs in human CCL4L chemokine gene. We have quantified the CCL4L copy number and genotyped both SNPs in samples from HGDP-CEPH Diversity Panel, that contains 1064 individuals of 52 worldwide populations. For the first time, we report worldwide population data combining both types of variation, CNV and SNPs, and our results show a clear population structure: Subsaharian Africa populations have the higher number of CCL4L copies (mean = 4,32) and European populations have the lower number of CCL4L copies (mean = 1,89). B) Based on the global variability of chemokine superfamily: Manuscript: The chemokine network. I. How the genomic organization of chemokines contains clues for deciphering their functional complexity. R. Colobran, R. Pujol-Borrell, Ma P. Armengol and M. Juan. Clinical and Experimental Immunology, 2007, 148: 208-217. In this first review, we analyse currently available data on the chemokine superfamily, focusing on its complex genomic organization. We will try to interpret this genomic organization of chemokines in relation to the main functions acquired by each individual member or by each cluster. Manuscript: The chemokine network. II. On how polymorphisms and alternative splicing increase the number of molecular species and configure intricate patterns of disease susceptibility. R. Colobran, R. Pujol-Borrell, Ma P. Armengol and M. Juan. Clinical and Experimental Immunology, 2007, 150: 1-12. In this second review on chemokines, we focus on the polymorphisms and alternative splicings and on their consequences in disease
Síndromes poliendocrinos autoinmunes que revelan mecanismos de tolerancia y autoinmunidad
No full text
Estudio de la reconstitución de poblaciones de linfocitos T mediante marcadores epigenéticos
No full textDurante su desarrollo los linfocitos tienen una serie de elecciones secuenciales para definir su identidad. Primero, la selección entre el linaje T (LT) o B (LB), luego la definición de su TCR como αβ o γδ posteriormente definir su identidad con los correceptores CD4 vs CD8 y, en periferia después de la activación del LT naive definir los linajes Th1, Th2, células T reguladores (Treg) o Th17. Algunos estadios de diferenciación en las células T son complejos de identificar y cuantificar. Especialmente, en sangre periférica, un ejemplo claro son las Treg o las células emigrantes tímicas recientes (RTEs). El control de la diferenciación y desarrollo de los LT se inician sin cambios en la secuencia del DNA pero con una constante activación y represión de transcritos de muchos genes. La regulación epigenética tiene un papel clave en la dinámica del genoma de los LT. Los cambios epigenéticos mantienen la estructura de la cromatina y regulan la transcripción de genes durante su desarrollo y diferenciación, principalmente por la metilación del DNA. La metilación se da en dinucleótidos CG. Sin embargo, hay unas regiones ricas en estos dinucleótidos conocidas como islas CpG (CGI), que no se metilan comúnmente y que se ubican en regiones promotoras, intergénicas o intragénicas. La metilación diferencial de estas regiones en muchos genes establecer perfiles de metilación de cada estadio de diferenciación celular y podrían ser marcadores de estadios celulares. Nuestra hipótesis es que la metilación del DNA, juega un papel clave en la diferenciación e identidad celular en humanos y que los perfiles de metilación del DNA de algunos genes, expresados diferencialmente en los estadios de maduración de los LT, como los genes que codifican para CD4 y CD8 pueden ser un marcador celular especialmente para el estadio de RTEs. Los objetivos fueron: i) analizar los patrones de metilación de los genes CD4, CD8A y CD8B durante el desarrollo de LT tímicos y periféricos; ii) diseñar una prueba molecular sensible y específica para identificar gradientes de metilación en poblaciones de LT y asociarlas con su grado de diferenciación. Estudiamos una CGI en el gen CD4 y tres CGIs en el gen CD8A en diferentes poblaciones de LT separadas por FACS sorting, de timo, sangre de cordón y sangre periférica de adultos sanos. Extrajimos el DNA, el cual se trato con bisulfito de sodio y luego se secuenció cada CGI. Nuestros resultados muestran que las CGI del gen CD4 no se metila diferencialmente en LT. La CGI-2 del gen CD8A no se metila en ningún caso, la CGI-3 presenta el mayor grado de metilación, pero sin diferencias entre linajes ni poblaciones y en la CGI-1 del gen CD8A identificamos una región diferencialmente metilada (DMR). Sobre esta región diseñamos por primera vez una prueba de PCR cuantitativa con sondas FRET, que permiten discriminar cambios en las temperaturas de melt cuando las CpG están o no metiladas en cada población de LT. Usando esta prueba pudimos analizar la DMR y pudimos discriminar claramente entre LT CD4 y CD8. Además, permite identificar en sangre periférica de adultos entre RTE CD8 y LT CD8 naive. También observamos que los LT CD4 incrementan la metilación de esta región a medida que van madurando En conclusión encontramos una región en el gen CD8A, ubicada en el extremo 5' de la CGI-1 que puede ser un marcador epigenético para diferenciar LT CD4 y CD8 y algunos estadios de desarrollo celular. Esta región puede estar involucrada en mecanismos de regulación de la expresión del gen CD8 y con la identidad celular.During development the lymphocytes have many choices by taking in order to define their identity. The first choice is about T (LT) or B (LB) lineage. Then the lymphocytes select their TCR αβ or γδ. Later they define their identity with CD4 vs CD8 co-receptors. Finally, in periphery they define among Th1, Th2, Th17, or regulatory T cells (Treg) lineages. Some stages of T cells differentiation are complex to identify such as Treg or Recent Thymic Emigrants (RTEs). The T cell differentiation and development are control by activation and repression a lot of specific genes. The Epigenetica and specifically the DNA methylation has a pivotal role in genome dynamics. In the human genome DNA methylation plays an important role in establishing and maintaining chromatin structures and in regulating gene transcription during development and differentiation. DNA methylation predominantly occurs at cytosine guanine dinucleotide (CpG). However, some areas are CpG rich and they are not always methylated. These regions are calling CpG islands (CGIs) and are present in many promoter genes or intragenic places. This mechanism has an important role in T-cell and lineage commitment and differentiation. The CD4 and CD8 co-receptor is coded by the CD4, and CD8A, and CD8B genes, and is the main lineage differentiation protein for T cells. CD4 gene has a CGIs upstream on the promoter and CD8A gene has three well-defined CGIs amenable to perform quantitative DNA methylation analysis. The aim of the present work is to analyze the methylation pattern of CD4 and CD8A genes and assess its possible use for staging the maturation state of CD4 and CD8 T lymphocytes. We studied three CpG islands located within promoter region of CD8A gene. The methylation analysis was performed in purified T cell populations from human thymus, cord blood and adult peripheral blood. T lymphocytes were sorted by FACS and included: i) single positive CD4 and CD8 T cells from thymus and ii) recent thymic emigrants (RTEs), naïve and memory T cells from cord blood and from adult blood. Genomic DNA from each population was treated with bisulfite and amplified by Nested-PCR with specific primers for each CpG island. The PCR products were cloned and sequenced for quantitative methylation analysis. Initial results showed that CpG Island 2 is not methylated in any of the T cell populations studied, while the CpG islands 1 and 3 have a variable degree of methylation. We identified a specific region of CD8A CpG island 1 that is differentially methylated in T cell populations. This region is clearly more methylated in CD4 T cells than in CD8 T cells. Moreover, within CD8 T cell populations there were differences between naïve and memory cells. It was also feasible to design a protocol for the rapid detection of methylation in this region. This protocol is based on the ability of FRET probes to discriminate nucleotide changes in a melting step by qPCR. Using it we were able to analyze 4 CpG positions and we determined the exact number of methylated positions (0-4) in each sample. In conclusion, we have identified a specific region in CD8A gene that is differentially methylated in T cell populations, which could be an epigenetic marker for T cell differentiation between CD4 and CD8 lymphocytes. The methylation patterns of this region are probably part of the maturation mechanisms that occur in the transition from naïve to memory cells among CD8 T lymphocytes
Decreased AIRE and promiscuous gene expression in thymus from Down syndrome individuals may explain predisposition to autoimmunity
No full textShorter androgen receptor polyQ alleles protect against life-threatening COVID-19 disease in European males
No full textCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Gen receptor d'andrògens; Infecció vírica i genoma de l’hosteCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Gen receptor de andrógenos; Infección viral y genoma del huéspedCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Androgen receptor gene; Viral infection and host genomeBackground While SARS-CoV-2 similarly infects men and women, COVID-19 outcome is less favorable in men. Variability in COVID-19 severity may be explained by differences in the host genome. Methods We compared poly-amino acids variability from WES data in severely affected COVID-19 patients versus SARS-CoV-2 PCR-positive oligo-asymptomatic subjects. Findings Shorter polyQ alleles (≤22) in the androgen receptor (AR) conferred protection against severe outcome in COVID-19 in the first tested cohort (both males and females) of 638 Italian subjects. The association between long polyQ alleles (≥23) and severe clinical outcome (p = 0.024) was also validated in an independent cohort of Spanish men <60 years of age (p = 0.014). Testosterone was higher in subjects with AR long-polyQ, possibly indicating receptor resistance (p = 0.042 Mann-Whitney U test). Inappropriately low serum testosterone level among carriers of the long-polyQ alleles (p = 0.0004 Mann-Whitney U test) predicted the need for intensive care in COVID-19 infected men. In agreement with the known anti-inflammatory action of testosterone, patients with long-polyQ and age ≥60 years had increased levels of CRP (p = 0.018, not accounting for multiple testing). Interpretation We identify the first genetic polymorphism that appears to predispose some men to develop more severe disease. Failure of the endocrine feedback to overcome AR signaling defects by increasing testosterone levels during the infection leads to the polyQ tract becoming dominant to serum testosterone levels for the clinical outcome. These results may contribute to designing reliable clinical and public health measures and provide a rationale to test testosterone as adjuvant therapy in men with COVID-19 expressing long AR polyQ repeats.MIUR project “Dipartimenti di Eccellenza 2018-2020” to Department of Medical Biotechnologies University of Siena, Italy (Italian D.L. n.18 March 17, 2020) and “Bando Ricerca COVID-19 Toscana” project to Azienda Ospedaliero-Universitaria Senese. Private donors for COVID-19 research and charity funds from Intesa San Paolo
Complement factor 5 (C5) p.A252T mutation is prevalent in, but not restricted to, Sub-Saharan Africa: Implications for the susceptibility to meningococcal disease
No full textEpigenome-wide association study of COVID-19 severity with respiratory failure
No full textCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Metilació de l'ADN; EpigenèticaCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Metilación del ADN; EpigenéticaCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; DNA methylation; EpigeneticsBackground
Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a wide spectrum of disease behaviour. Since DNA methylation has been implicated in the regulation of viral infections and the immune system, we performed an epigenome-wide association study (EWAS) to identify candidate loci regulated by this epigenetic mark that could be involved in the onset of COVID-19 in patients without comorbidities.
Methods
Peripheral blood samples were obtained from 407 confirmed COVID-19 patients ≤ 61 years of age and without comorbidities, 194 (47.7%) of whom had mild symptomatology that did not involve hospitalization and 213 (52.3%) had a severe clinical course that required respiratory support. The set of cases was divided into discovery (n = 207) and validation (n = 200) cohorts, balanced for age and sex of individuals. We analysed the DNA methylation status of 850,000 CpG sites in these patients.
Findings
The DNA methylation status of 44 CpG sites was associated with the clinical severity of COVID-19. Of these loci, 23 (52.3%) were located in 20 annotated coding genes. These genes, such as the inflammasome component Absent in Melanoma 2 (AIM2) and the Major Histocompatibility Complex, class I C (HLA-C) candidates, were mainly involved in the response of interferon to viral infection. We used the EWAS-identified sites to establish a DNA methylation signature (EPICOVID) that is associated with the severity of the disease.
Interpretation
We identified DNA methylation sites as epigenetic susceptibility loci for respiratory failure in COVID-19 patients. These candidate biomarkers, combined with other clinical, cellular and genetic factors, could be useful in the clinical stratification and management of patients infected with the SARS-CoV-2.The Unstoppable campaign of the Josep Carreras Leukaemia Foundation, the Cellex Foundation and the CERCA Programme/Generalitat de Catalunya
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