A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes

Background: Changes in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect shifts in tissue composition. Methods: Here we derive a DNA methylation reference matrix for 12 immune-cell types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix, we perform a directional Stouffer and fixed effects meta-analysis comprising 23,053 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes. In a separate cohort of 4386 blood samples, we assess associations between immune-cell fractions and health outcomes. Results: Our meta-analysis reveals many associations of cell-type fractions with age, sex, smoking and obesity, many of which we validate with single-cell RNA sequencing. We discover that naïve and regulatory T-cell subsets are higher in women compared to men, while the reverse is true for monocyte, natural killer, basophil, and eosinophil fractions. Decreased natural killer counts associated with smoking, obesity, and stress levels, while an increased count correlates with exercise and sleep. Analysis of health outcomes revealed that increased naïve CD4 + T-cell and N-cell fractions associated with a reduced risk of all-cause mortality independently of all major epidemiological risk factors and baseline co-morbidity. A machine learning predictor built only with immune-cell fractions achieved a C-index value for all-cause mortality of 0.69 (95%CI 0.67–0.72), which increased to 0.83 (0.80–0.86) upon inclusion of epidemiological risk factors and baseline co-morbidity. Conclusions: This work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes

The Wnt Receptor Ryk Reduces Neuronal and Cell Survival Capacity by Repressing FOXO Activity During the Early Phases of Mutant Huntingtin Pathogenicity

The Wnt receptor Ryk is an evolutionary-conserved protein important during neuronal differentiation through several mechanisms, including γ-secretase cleavage and nuclear translocation of its intracellular domain (Ryk-ICD). Although the Wnt pathway may be neuroprotective, the role of Ryk in neurodegenerative disease remains unknown. We found that Ryk is up-regulated in neurons expressing mutant huntingtin (HTT) in several models of Huntington's disease (HD). Further investigation in Caenorhabditis elegans and mouse striatal cell models of HD provided a model in which the early-stage increase of Ryk promotes neuronal dysfunction by repressing the neuroprotective activity of the longevity-promoting factor FOXO through a noncanonical mechanism that implicates the Ryk-ICD fragment and its binding to the FOXO co-factor β-catenin. The Ryk-ICD fragment suppressed neuroprotection by lin-18/Ryk loss-of-function in expanded-polyQ nematodes, repressed FOXO transcriptional activity, and abolished β-catenin protection of mutant htt striatal cells against cell death vulnerability. Additionally, Ryk-ICD was increased in the nucleus of mutant htt cells, and reducing γ-secretase PS1 levels compensated for the cytotoxicity of full-length Ryk in these cells. These findings reveal that the Ryk-ICD pathway may impair FOXO protective activity in mutant polyglutamine neurons, suggesting that neurons are unable to efficiently maintain function and resist disease from the earliest phases of the pathogenic process in HD. © 2014 Tourette et al

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Role of FOXO3 in the regulation of the early phases of Huntington's disease during neuronal differentiation

FOXO3 est un facteur de transcription important pour la réponse au stress, la régulation de la différenciation et de la survie cellulaires qui a des effets neuroprotecteurs dans plusieurs modèles de maladies neurodégénératives, dont la maladie de Huntington (MH). Les effets neuroprotecteurs de FOXO3 sont réprimés dans la MH par une activité anormale de Ryk, un récepteur Wnt important pour la neurogenèse, par la liaison du domaine intracellulaire de Ryk à la ?-caténine, un co-facteur de FOXO3. L'objectif principal de ce travail est d'étudier les effets de la huntingtine mutée (mHTT) sur le répertoire des cibles directes humaines de FOXO3 à l'aide d'un modèle des phases développementales de la MH, à savoir des cellules souches neurales isogéniques issues de cellules souches pluripotentes induites. En formant un complexe tripartite avec la ?-caténine et FOXO3, Ryk agit comme un co-régulateur de FOXO3 en conditions normales ou pathologiques. L'analyse des cibles directes de FOXO3 montre une reprogrammation de ces cibles avec des pertes et des gains dans des voies de signalisation qui sont connues pour leur rôle dans la MH, notamment les voies de régulation de la prolifération cellulaire. Ces résultats montrent que la régulation des gènes par FOXO3 est fortement modifiée dans les cellules qui expriment la mHTT. Cela ouvre la voie à l'étude des mécanismes d'homéostase cellulaire sous contrôle de FOXO3 dans les neurones en différenciation et leur impact sur l'activité des neurones adultes. Plus largement, ces résultats permettent de mieux comprendre la dynamique moléculaire de la MH et les effets de reprogrammation moléculaire sur la différenciation et l'activité neuronale.FOXO3 is an important transcription factor for stress response, the regulation of differentiation and cell survival that has neuroprotective effects in several models of neurodegenerative diseases, including Huntington’s disease (HD). The neuroprotective effects of FOXO3 in HD are repressed by abnormal signaling from the Wnt receptor Ryk by the binding of the intracellular domain of Ryk to the β-catenin, a cofactor of FOXO3.The aim of this work was to explore the effect of the mutant huntingtin (mHTT) on the repertoire of direct FOXO3 targets (F3Ts) using a model of developmental stage of HD, namely HD isogenic neural stem cells derived from Huntington’s Induced Pluripotent Stem cells. Forming a tripartite complex with β-catenin and FOXO3, Ryk acts as a co-regulator of FOXO3 in normal or pathological condition. Analysis of direct FOXO3 targets shows reprogramming of these targets with losses and gains in signaling pathways that are known to role in HD, including regulatory pathways of cell proliferation. These results show that gene regulation by FOXO3 is heavily modified in cells expressing the mutant huntingtin. Our findings open the way for a comprehensive study of cellular homeostasis mechanisms under the control of FOXO3 in neural differentiation and their impact on the activity of adult neurons. More broadly, these results provide insight into the molecular dynamics of MH and the effects of molecular reprogramming in differentiation and neuronal activity

Rôle de FOXO3 dans la régulation des phases précoces de la maladie de Huntington lors de la différenciation neuronale

FOXO3 is an important transcription factor for stress response, the regulation of differentiation and cell survival that has neuroprotective effects in several models of neurodegenerative diseases, including Huntington’s disease (HD). The neuroprotective effects of FOXO3 in HD are repressed by abnormal signaling from the Wnt receptor Ryk by the binding of the intracellular domain of Ryk to the β-catenin, a cofactor of FOXO3.The aim of this work was to explore the effect of the mutant huntingtin (mHTT) on the repertoire of direct FOXO3 targets (F3Ts) using a model of developmental stage of HD, namely HD isogenic neural stem cells derived from Huntington’s Induced Pluripotent Stem cells. Forming a tripartite complex with β-catenin and FOXO3, Ryk acts as a co-regulator of FOXO3 in normal or pathological condition. Analysis of direct FOXO3 targets shows reprogramming of these targets with losses and gains in signaling pathways that are known to role in HD, including regulatory pathways of cell proliferation. These results show that gene regulation by FOXO3 is heavily modified in cells expressing the mutant huntingtin. Our findings open the way for a comprehensive study of cellular homeostasis mechanisms under the control of FOXO3 in neural differentiation and their impact on the activity of adult neurons. More broadly, these results provide insight into the molecular dynamics of MH and the effects of molecular reprogramming in differentiation and neuronal activity.FOXO3 est un facteur de transcription important pour la réponse au stress, la régulation de la différenciation et de la survie cellulaires qui a des effets neuroprotecteurs dans plusieurs modèles de maladies neurodégénératives, dont la maladie de Huntington (MH). Les effets neuroprotecteurs de FOXO3 sont réprimés dans la MH par une activité anormale de Ryk, un récepteur Wnt important pour la neurogenèse, par la liaison du domaine intracellulaire de Ryk à la ?-caténine, un co-facteur de FOXO3. L'objectif principal de ce travail est d'étudier les effets de la huntingtine mutée (mHTT) sur le répertoire des cibles directes humaines de FOXO3 à l'aide d'un modèle des phases développementales de la MH, à savoir des cellules souches neurales isogéniques issues de cellules souches pluripotentes induites. En formant un complexe tripartite avec la ?-caténine et FOXO3, Ryk agit comme un co-régulateur de FOXO3 en conditions normales ou pathologiques. L'analyse des cibles directes de FOXO3 montre une reprogrammation de ces cibles avec des pertes et des gains dans des voies de signalisation qui sont connues pour leur rôle dans la MH, notamment les voies de régulation de la prolifération cellulaire. Ces résultats montrent que la régulation des gènes par FOXO3 est fortement modifiée dans les cellules qui expriment la mHTT. Cela ouvre la voie à l'étude des mécanismes d'homéostase cellulaire sous contrôle de FOXO3 dans les neurones en différenciation et leur impact sur l'activité des neurones adultes. Plus largement, ces résultats permettent de mieux comprendre la dynamique moléculaire de la MH et les effets de reprogrammation moléculaire sur la différenciation et l'activité neuronale

Primary cilia expression in bone marrow in response to mechanical stimulation in explant bioreactor culture

Bone marrow contains a multitude of mechanically sensitive cells that may participate in mechanotransduction. Primary cilia are sensory organelles expressed on mesenchymal stem cells (MSCs), osteoblasts, osteocytes, and other cell types that sense fluid flow in monolayer culture. In marrow, cilia could similarly facilitate the sensation of relative motion between adjacent cells or interstitial fluid. The goal of this study was to determine the response of cilia to mechanical stimulation of the marrow. Bioreactors were used to supply trabecular bone explants with low magnitude mechanical stimulation (LMMS) of 0.3 xg at 30 Hz for 1 h/d, 5 d/week, inducing shear stresses in the marrow. Four groups were studied: unstimulated (UNSTIM), stimulated (LMMS), and with and without chloral hydrate (UNSTIM+CH and LMMS+CH, respectively), which was used to disrupt cilia. After 19 days of culture, immunohistochemistry for acetylated alpha-tubulin revealed that more cells expressed cilia in culture compared to in vivo controls. Stimulation decreased the number of cells expressing cilia in untreated explants, but not in CH-treated explants. MSCs represented a greater fraction of marrow cells in the untreated explants than CH-treated explants. MSCs harvested from the stimulated groups were more proliferative than in the unstimulated explants, but this effect was absent in CH treated explants. In contrast to the marrow, neither LMMS nor CH treatment affected bone formation as measured by mineralising surface. Computational models indicated that LMMS does not induce bone strain, and the reported effects were thus attributed to shear stress in the marrow. From a clinical perspective, genetic or pharmaceutical alterations of cilia expression may affect marrow health and function.This research was supported by grants from Science Foundation Ireland 07/EN/E015B Travel Fellowship TRC, ERC Grant no. 258992 (BONEMECHBIO) LMMcN. and MV, and U.S. National Science Foundation CMMI-110207 and 1435467 TRC and GLNpeer-reviewe

Primary cilia expression in bone marrow in response to mechanical stimulation in explant bioreactor culture

Bone marrow contains a multitude of mechanically sensitive cells that may participate in mechanotransduction. Primary cilia are sensory organelles expressed on mesenchymal stem cells (MSCs), osteoblasts, osteocytes, and other cell types that sense fluid flow in monolayer culture. In marrow, cilia could similarly facilitate the sensation of relative motion between adjacent cells or interstitial fluid. The goal of this study was to determine the response of cilia to mechanical stimulation of the marrow. Bioreactors were used to supply trabecular bone explants with low magnitude mechanical stimulation (LMMS) of 0.3 xg at 30 Hz for 1 h/d, 5 d/week, inducing shear stresses in the marrow. Four groups were studied: unstimulated (UNSTIM), stimulated (LMMS), and with and without chloral hydrate (UNSTIM+CH and LMMS+CH, respectively), which was used to disrupt cilia. After 19 days of culture, immunohistochemistry for acetylated alpha-tubulin revealed that more cells expressed cilia in culture compared to in vivo controls. Stimulation decreased the number of cells expressing cilia in untreated explants, but not in CH-treated explants. MSCs represented a greater fraction of marrow cells in the untreated explants than CH-treated explants. MSCs harvested from the stimulated groups were more proliferative than in the unstimulated explants, but this effect was absent in CH treated explants. In contrast to the marrow, neither LMMS nor CH treatment affected bone formation as measured by mineralising surface. Computational models indicated that LMMS does not induce bone strain, and the reported effects were thus attributed to shear stress in the marrow. From a clinical perspective, genetic or pharmaceutical alterations of cilia expression may affect marrow health and function.This research was supported by grants from Science Foundation Ireland 07/EN/E015B Travel Fellowship TRC, ERC Grant no. 258992 (BONEMECHBIO) LMMcN. and MV, and U.S. National Science Foundation CMMI-110207 and 1435467 TRC and GL

GO terms classification of genes (N = 51) whose promoter-specific DNA methylation was significantly different between baseline (i.e before Roux-en Y gastric bypass surgery) and at six month after surgery.

<p>An enrichment analysis of GO-terms biological processes using DAVID functional analysis revealed an enrichment for genes involved in metabolic processes (GO: 0008152) (P<0.05).</p