Long runs of homozygosity are associated with Alzheimer's disease

Altres ajuts: The Genome Research at Fundació ACE project (GR@ACE) is supported by Fundación bancaria "La Caixa," Grifols SA and Fundació ACE. L.M.R. is supported by Consejería de Salud de la Junta de Andalucía (Grant PI-0001/2017).Long runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes, which are a footprint of inbreeding and recessive inheritance. The presence of recessive loci is suggested for Alzheimer's disease (AD); however, their search has been poorly assessed to date. To investigate homozygosity in AD, here we performed a fine-scale ROH analysis using 10 independent cohorts of European ancestry (11,919 AD cases and 9181 controls.) We detected an increase of homozygosity in AD cases compared to controls [ β (CI 95%) = 0.070 (0.037-0.104); P = 3.91 × 10 −5 ; β (CI95%) = 0.043 (0.009-0.076); P = 0.013]. ROHs increasing the risk of AD (OR > 1) were significantly overrepresented compared to ROHs increasing protection (p < 2.20 × 10 −16). A significant ROH association with AD risk was detected upstream the HS3ST1 locus (chr4:11,189,482‒11,305,456), (β (CI 95%) = 1.09 (0.48 ‒ 1.48), p value = 9.03 × 10 −4), previously related to AD. Next, to search for recessive candidate variants in ROHs, we constructed a homozygosity map of inbred AD cases extracted from an outbred population and explored ROH regions in whole-exome sequencing data (N = 1449). We detected a candidate marker, rs117458494, mapped in the SPON1 locus, which has been previously associated with amyloid metabolism. Here, we provide a research framework to look for recessive variants in AD using outbred populations. Our results showed that AD cases have enriched homozygosity, suggesting that recessive effects may explain a proportion of AD heritability

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks : The GR@ACE project

Introduction: Large variability among Alzheimer's disease (AD) cases might impact genetic discoveries and complicate dissection of underlying biological pathways. Methods: Genome Research at Fundacio ACE (GR@ACE) is a genome-wide study of dementia and its clinical endophenotypes, defined based on AD's clinical certainty and vascular burden. We assessed the impact of known AD loci across endophenotypes to generate loci categories. We incorporated gene coexpression data and conducted pathway analysis per category. Finally, to evaluate the effect of heterogeneity in genetic studies, GR@ACE series were meta-analyzed with additional genome-wide association study data sets. Results: We classified known AD loci into three categories, which might reflect the disease clinical heterogeneity. Vascular processes were only detected as a causal mechanism in probable AD. The meta-analysis strategy revealed the ANKRD31-rs4704171 and NDUFAF6-rs10098778 and confirmed SCIMP-rs7225151 and CD33-rs3865444. Discussion: The regulation of vasculature is a prominent causal component of probable AD. GR@ACE meta-analysis revealed novel AD genetic signals, strongly driven by the presence of clinical heterogeneity in the AD series

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

Droughts and climate warming desynchronize Black pine growth across the Mediterranean Basin.

The effects of climate change on forest growth are not homogeneous across tree species distribution ranges because of inter-population variability and spatial heterogeneity. Although latitudinal and thermal gradients in growth patterns have been widely investigated, changes in these patterns along longitudinal gradients due to the different timing and severity of regional droughts are less studied. Here, we investigated these responses in Mediterranean Black pine (Pinus nigra Arn.). We built a tree-ring width dataset comprising 77 forests (1202 trees) across the Mediterranean Basin. The biogeographical patterns in growth patterns and the relationships between growth and mean temperature, precipitation, drought and atmospheric circulations patterns (NAO -North Atlantic Oscillation-, SOI -Southern Oscillation Index- and MOI -Mediterranean Oscillation index-) were analyzed. Then, we evaluated the spatial and temporal growth synchrony between and within east and west populations. We found different growth and climate patterns in west vs. east Black pine populations, although in both regions growth was driven by similar temperature and precipitation variables. MOI significantly influenced tree growth, whilst NAO and SOI showed weaker effects. Growth of east and west Black pine populations desynchronized after the 1970s when several and uncoupled regional droughts occurred across the Mediterranean Basin. We detected a climate shift from the 1970s to the 1980s affecting growth patterns, changing growth-climate relationships, and reducing forest growth from west to east Black pine forests. Afterwards, climate and growth of east and west populations became increasingly more divergent. Our findings imply that integral bioclimatic and biogeographical analyses across the species distribution area must be considered to adequately assess the impact of climate change on tree growth under warming and more arid conditions

Droughts and climate warming desynchronize Black pine growth across the Mediterranean Basin

The effects of climate change on forest growth are not homogeneous across tree species distribution ranges because of inter-population variability and spatial heterogeneity. Although latitudinal and thermal gradients in growth patterns have been widely investigated, changes in these patterns along longitudinal gradients due to the different timing and severity of regional droughts are less studied. Here, we investigated these responses in Mediterranean Black pine (Pinus nigra Arn.). We built a tree-ring width dataset comprising 77 forests (1202 trees) across the Mediterranean Basin. The biogeographical patterns in growth patterns and the relationships between growth and mean temperature, precipitation, drought and atmospheric circulations patterns (NAO -North Atlantic Oscillation-, SOI -Southern Oscillation Index- and MOI -Mediterranean Oscillation index-) were analyzed. Then, we evaluated the spatial and temporal growth synchrony between and within east and west populations. We found different growth and climate patterns in west vs. east Black pine populations, although in both regions growth was driven by similar temperature and precipitation variables. MOI significantly influenced tree growth, whilst NAO and SOI showed weaker effects. Growth of east and west Black pine populations desynchronized after the 1970s when several and uncoupled regional droughts occurred across the Mediterranean Basin. We detected a climate shift from the 1970s to the 1980s affecting growth patterns, changing growth-climate relationships, and reducing forest growth from west to east Black pine forests. Afterwards, climate and growth of east and west populations became increasingly more divergent. Our findings imply that integral bioclimatic and biogeographical analyses across the species distribution area must be considered to adequately assess the impact of climate change on tree growth under warming and more arid conditions

La lectura como medio de socialización

Se realiza un proyecto de innovación educativa sobre la lectura como medio de socialización en el C.R.A. Valdelavía de Navalperal de Pinares, en Ávila. Se pretende mejorar la biblioteca del centro y las bibliotecas de aula, creando un marco óptimo para el fomento de la lectura. Para ello se programan actividades para el fomento de la lectura y el desarrollo de la comprensión lectora con el fin de mejorar los procesos de socialización entre el alumnado de diferentes orígenes socio-culturales. Dentro de las actividades propuestas en el proyecto de innovación están: la creación de bibliotecas en los diferentes centros que componen el C.R.A.; la creación de 'maletas viajeras' con libros para las diferentes localidades se localice el centro; la actividad llamada 'mis historias' en la el alumnado elabora un libro en el que cuenta una historia que acompaña de dibujos en la se quiere mejorar la expresión oral, escrita y enriquecer el vocabulario; se realiza un concurso de relatos del día de la paz; cuando llega el carnaval o la navidad se lee un cuento y sobre él gira la temática en torno a la cual se tienen que disfrazar; en la semana cultural se relaciona una actividad con alguna temática de la lectura; se realizan actividades basadas en el juego como un álbum de personajes, un Twister de cuentos o revuelto de historias. La experiencia ha sido muy positiva en el alumnado, puesto que se ha mejorado la imagen de la biblioteca, se ha iniciado la lectura de libros infantiles y se ha comenzado a animar y a desarrollar el gusto por la lectura desde pequeños.Castilla y LeónConsejería de Educación. Dirección General de Universidades e Investigación; Monasterio de Nuestra Señora de Prado, Autovía Puente Colgante s. n.; 47071 Valladolid; +34983411881; +34983411939ES

Discovering HIV related information by means of association rules and machine learning

Acquired immunodeficiency syndrome (AIDS) is still one of the main health problems worldwide. It is therefore essential to keep making progress in improving the prognosis and quality of life of affected patients. One way to advance along this pathway is to uncover connections between other disorders associated with HIV/AIDS-so that they can be anticipated and possibly mitigated. We propose to achieve this by using Association Rules (ARs). They allow us to represent the dependencies between a number of diseases and other specific diseases. However, classical techniques systematically generate every AR meeting some minimal conditions on data frequency, hence generating a vast amount of uninteresting ARs, which need to be filtered out. The lack of manually annotated ARs has favored unsupervised filtering, even though they produce limited results. In this paper, we propose a semi-supervised system, able to identify relevant ARs among HIV-related diseases with a minimal amount of annotated training data. Our system has been able to extract a good number of relationships between HIV-related diseases that have been previously detected in the literature but are scattered and are often little known. Furthermore, a number of plausible new relationships have shown up which deserve further investigation by qualified medical experts

Nat Commun

Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE ɛ4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease