Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle.

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testis-specific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits.

To efficiently transform genetic associations into drug targets requires evidence that a particular gene, and its encoded protein, contribute causally to a disease. To achieve this, we employ a three-step proteome-by-phenome Mendelian Randomization (MR) approach. In step one, 154 protein quantitative trait loci (pQTLs) were identified and independently replicated. From these pQTLs, 64 replicated locally-acting variants were used as instrumental variables for proteome-by-phenome MR across 846 traits (step two). When its assumptions are met, proteome-by-phenome MR, is equivalent to simultaneously running many randomized controlled trials. Step 2 yielded 38 proteins that significantly predicted variation in traits and diseases in 509 instances. Step 3 revealed that amongst the 271 instances from GeneAtlas (UK Biobank), 77 showed little evidence of pleiotropy (HEIDI), and 92 evidence of colocalization (eCAVIAR). Results were wide ranging: including, for example, new evidence for a causal role of tyrosine-protein phosphatase non-receptor type substrate 1 (SHPS1; SIRPA) in schizophrenia, and a new finding that intestinal fatty acid binding protein (FABP2) abundance contributes to the pathogenesis of cardiovascular disease. We also demonstrated confirmatory evidence for the causal role of four further proteins (FGF5, IL6R, LPL, LTA) in cardiovascular disease risk.

TiFoSi: an efficient tool for mechanobiology simulations of epithelia.

MOTIVATION: Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks between gene expression and cell biomechanics. In that context, in silico experiments are a powerful tool to understand fundamental mechanisms and to formulate and test hypotheses. RESULTS: Here, we present TiFoSi, a computational tool to simulate the cellular dynamics of planar epithelia. TiFoSi allows to model feedbacks between cellular mechanics and gene expression (either in a deterministic or a stochastic way), the interaction between different cell populations, the custom design of the cell cycle and cleavage properties, the protein number partitioning upon cell division, and the modeling of cell communication (juxtacrine and paracrine signaling). AVAILABILITY AND IMPLEMENTATION: http://tifosi.thesimbiosys.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indirect assortative mating for human disease and longevity.

Phenotypic correlations among partners for traits such as longevity or late-onset disease have been found to be comparable to phenotypic correlations in first-degree relatives. How these correlations arise in late life is poorly understood. Here we introduce a novel paradigm to establish the presence of indirect assortment on factors correlated across generations, by examining correlations between parents of couples, i.e., in-laws. Using correlations in additive genetic values we further corroborate the presence of indirect assortment on heritable factors. Specifically, using couples from the UK Biobank cohort, we show that longevity and disease history of the parents of White British couples are correlated, with correlations of up to 0.09. The correlations in parental longevity are replicated in the FamiLinx cohort, a larger and geographically more diverse historical ancestry dataset spanning a broader time frame. These correlations in parental longevity significantly (pval < 0.0093 for all pairs of parents) exceed what would be expected due to variations in lifespan based on year and location of birth. For cardiovascular diseases, in particular hypertension, we find significant correlations (r = 0.028, pval = 0.005) in genetic values among partners, supporting a model where partners assort for risk factors to some extent genetically correlated with cardiovascular disease. Partitioning the relative importance of indirect assortative mating and shared common environment will require large, well-characterized longitudinal cohorts aimed at understanding phenotypic correlations among none-blood relatives. Identifying the factors that mediate indirect assortment on longevity and human disease risk will help to unravel factors affecting human disease and ultimately longevity.

A compendium of genetic regulatory effects across pig tissues.

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions.

The detection of gene-gene interactions (i.e., epistasis) in the human genome is becoming decisive for the complete characterization of the genetic factors associated with complex binary traits. Despite the fact that many methods have been developed to address this challenging issue, their performance still remains insufficient. We will show how case and control groups store complementary information regarding interactions, and the use of this fundamental property in the design of a new, rapid, and highly powerful epistasis analysis method. Unlike previous approaches where statistical methods are tested over a very limited range of situations, we have performed an exhaustive evaluation of the power of our new method. To this end, we also propose a more comprehensive interpretation of epistasis in which genotype interactions may be of risk, protective, or neutral. In this extended view of genetic interactions, we demonstrate that our method has superior performance than existing approaches, thus, providing a highly powerful tool for the identification of gene-gene interactions associated with binary traits.

Fine-mapping of retinal vascular complexity loci identifies Notch regulation as a shared mechanism with myocardial infarction outcomes.

There is increasing evidence that the complexity of the retinal vasculature measured as fractal dimension, Df, might offer earlier insights into the progression of coronary artery disease (CAD) before traditional biomarkers can be detected. This association could be partly explained by a common genetic basis; however, the genetic component of Df is poorly understood. We present a genome-wide association study (GWAS) of 38,000 individuals with white British ancestry from the UK Biobank aimed to comprehensively study the genetic component of Df and analyse its relationship with CAD. We replicated 5 Df loci and found 4 additional loci with suggestive significance (P < 1e-05) to contribute to Df variation, which previously were reported in retinal tortuosity and complexity, hypertension, and CAD studies. Significant negative genetic correlation estimates support the inverse relationship between Df and CAD, and between Df and myocardial infarction (MI), one of CAD's fatal outcomes. Fine-mapping of Df loci revealed Notch signalling regulatory variants supporting a shared mechanism with MI outcomes. We developed a predictive model for MI incident cases, recorded over a 10-year period following clinical and ophthalmic evaluation, combining clinical information, Df, and a CAD polygenic risk score. Internal cross-validation demonstrated a considerable improvement in the area under the curve (AUC) of our predictive model (AUC = 0.770 ± 0.001) when comparing with an established risk model, SCORE, (AUC = 0.741 ± 0.002) and extensions thereof leveraging the PRS (AUC = 0.728 ± 0.001). This evidences that Df provides risk information beyond demographic, lifestyle, and genetic risk factors. Our findings shed new light on the genetic basis of Df, unveiling a common control with MI, and highlighting the benefits of its application in individualised MI risk prediction.

Dynamics and mechanical stability of the developing dorsoventral organizer of the wing imaginal disc.

Shaping the primordia during development relies on forces and mechanisms able to control cell segregation. In the imaginal discs of Drosophila the cellular populations that will give rise to the dorsal and ventral parts on the wing blade are segregated and do not intermingle. A cellular population that becomes specified by the boundary of the dorsal and ventral cellular domains, the so-called organizer, controls this process. In this paper we study the dynamics and stability of the dorsal-ventral organizer of the wing imaginal disc of Drosophila as cell proliferation advances. Our approach is based on a vertex model to perform in silico experiments that are fully dynamical and take into account the available experimental data such as: cell packing properties, orientation of the cellular divisions, response upon membrane ablation, and robustness to mechanical perturbations induced by fast growing clones. Our results shed light on the complex interplay between the cytoskeleton mechanics, the cell cycle, the cell growth, and the cellular interactions in order to shape the dorsal-ventral organizer as a robust source of positional information and a lineage controller. Specifically, we elucidate the necessary and sufficient ingredients that enforce its functionality: distinctive mechanical properties, including increased tension, longer cell cycle duration, and a cleavage criterion that satisfies the Hertwig rule. Our results provide novel insights into the developmental mechanisms that drive the dynamics of the DV organizer and set a definition of the so-called Notch fence model in quantitative terms.

Comparative transcriptome in large-scale human and cattle populations.

BACKGROUND: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. RESULTS: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. CONCLUSIONS: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.

A multi-tissue atlas of regulatory variants in cattle.

Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.

Evidence of horizontal indirect genetic effects in humans.

Indirect genetic effects, the effects of the genotype of one individual on the phenotype of other individuals, are environmental factors associated with human disease and complex trait variation that could help to expand our understanding of the environment linked to complex traits. Here, we study indirect genetic effects in 80,889 human couples of European ancestry for 105 complex traits. Using a linear mixed model approach, we estimate partner indirect heritability and find evidence of partner heritability on ~50% of the analysed traits. Follow-up analysis suggests that in at least ~25% of these traits, the partner heritability is consistent with the existence of indirect genetic effects including a wide variety of traits such as dietary traits, mental health and disease. This shows that the environment linked to complex traits is partially explained by the genotype of other individuals and motivates the need to find new ways of studying the environment.

Sex differences in genetic architecture in the UK Biobank.

Males and females present differences in complex traits and in the risk of a wide array of diseases. Genotype by sex (GxS) interactions are thought to account for some of these differences. However, the extent and basis of GxS are poorly understood. In the present study, we provide insights into both the scope and the mechanism of GxS across the genome of about 450,000 individuals of European ancestry and 530 complex traits in the UK Biobank. We found small yet widespread differences in genetic architecture across traits. We also found that, in some cases, sex-agnostic analyses may be missing trait-associated loci and looked into possible improvements in the prediction of high-level phenotypes. Finally, we studied the potential functional role of the differences observed through sex-biased gene expression and gene-level analyses. Our results suggest the need to consider sex-aware analyses for future studies to shed light onto possible sex-specific molecular mechanisms.

Interplay between intrinsic noise and the stochasticity of the cell cycle in bacterial colonies.

Herein we report on the effects that different stochastic contributions induce in bacterial colonies in terms of protein concentration and production. In particular, we consider for what we believe to be the first time cell-to-cell diversity due to the unavoidable randomness of the cell-cycle duration and its interplay with other noise sources. To that end, we model a recent experimental setup that implements a protein dilution protocol by means of division events to characterize the gene regulatory function at the single cell level. This approach allows us to investigate the effect of different stochastic terms upon the total randomness experimentally reported for the gene regulatory function. In addition, we show that the interplay between intrinsic fluctuations and the stochasticity of the cell-cycle duration leads to different constructive roles. On the one hand, we show that there is an optimal value of protein concentration (alternatively an optimal value of the cell cycle phase) such that the noise in protein concentration attains a minimum. On the other hand, we reveal that there is an optimal value of the stochasticity of the cell cycle duration such that the coherence of the protein production with respect to the colony average production is maximized. The latter can be considered as a novel example of the recently reported phenomenon of diversity induced resonance.

Statistical and Functional Studies Identify Epistasis of Cardiovascular Risk Genomic Variants From Genome-Wide Association Studies.

Background Epistasis describes how gene-gene interactions affect phenotypes, and could have a profound impact on human diseases such as coronary artery disease (CAD). The goal of this study was to identify gene-gene interactions in CAD using an easily generalizable multi-stage approach. Methods and Results Our forward genetic approach consists of multiple steps that combine statistical and functional approaches, and analyze information from global gene expression profiling, functional interactions, and genetic interactions to robustly identify gene-gene interactions. Global gene expression profiling shows that knockdown of ANRIL (DQ485454) at 9p21.3 GWAS (genome-wide association studies) CAD locus upregulates TMEM100 and TMEM106B. Functional studies indicate that the increased monocyte adhesion to endothelial cells and transendothelial migration of monocytes, 2 critical processes in the initiation of CAD, by ANRIL knockdown are reversed by knockdown of TMEM106B, but not of TMEM100. Furthermore, the decreased monocyte adhesion to endothelial cells and transendothelial migration of monocytes induced by ANRIL overexpression was reversed by overexpressing TMEM106B. TMEM106B expression was upregulated by >2-fold in CAD coronary arteries. A significant association was found between variants in TMEM106B (but not in TMEM100) and CAD (P=1.9×10-8). Significant gene-gene interaction was detected between ANRIL variant rs2383207 and TMEM106B variant rs3807865 (P=0.009). A similar approach also identifies significant interaction between rs6903956 in ADTRP and rs17465637 in MIA3 (P=0.005). Conclusions We demonstrate 2 pairs of epistatic interactions between GWAS loci for CAD and offer important insights into the genetic architecture and molecular mechanisms for the pathogenesis of CAD. Our strategy has broad applicability to the identification of epistasis in other human diseases.

Parent of origin genetic effects on methylation in humans are common and influence complex trait variation.

Parent-of-origin effects (POE) exist when there is differential expression of alleles inherited from the two parents. A genome-wide scan for POE on DNA methylation at 639,238 CpGs in 5,101 individuals identifies 733 independent methylation CpGs potentially influenced by POE at a false discovery rate ≤ 0.05 of which 331 had not previously been identified. Cis and trans methylation quantitative trait loci (mQTL) regulate methylation variation through POE at 54% (399/733) of the identified POE-influenced CpGs. The combined results provide strong evidence for previously unidentified POE-influenced CpGs at 171 independent loci. Methylation variation at 14 of the POE-influenced CpGs is associated with multiple metabolic traits. A phenome-wide association analysis using the POE mQTL SNPs identifies a previously unidentified imprinted locus associated with waist circumference. These results provide a high resolution population-level map for POE on DNA methylation sites, their local and distant regulators and potential consequences for complex traits.

Publisher Correction: Parent of origin genetic effects on methylation in humans are common and influence complex trait variation.

In the original version of this Article, the legend in the upper panel of Figure 2 incorrectly read 'paternal imprinting' and should have read 'maternal imprinting'. This has been corrected in both the PDF and HTML versions of the Article.

A spatial toggle switch drives boundary formation in development.

Herein we introduce a multicellular network motif that performs as a spatial toggle switch and explains how boundary formation can be faithfully accomplished in developmental processes. Importantly, we show that expression and activity patterns of proteins must be simultaneously characterized for a proper understanding and description of the underlying mechanism. Our in silico experiments, in agreement with in vivo results, evaluate different genetic backgrounds and shed light on the dynamics of boundary formation. In addition, we provide an estimation of relevant biological parameters and a robustness analysis.

An atlas of genetic associations in UK Biobank.

Genome-wide association studies (GWAS) have identified many loci contributing to variation in complex traits, yet the majority of loci that contribute to the heritability of complex traits remain elusive. Large study populations with sufficient statistical power are required to detect the small effect sizes of the yet unidentified genetic variants. However, the analysis of huge cohorts, like UK Biobank, is challenging. Here, we present an atlas of genetic associations for 118 non-binary and 660 binary traits of 452,264 UK Biobank participants of European ancestry. Results are compiled in a publicly accessible database that allows querying genome-wide association results for 9,113,133 genetic variants, as well as downloading GWAS summary statistics for over 30 million imputed genetic variants (>23 billion phenotype-genotype pairs). Our atlas of associations (GeneATLAS, http://geneatlas.roslin.ed.ac.uk ) will help researchers to query UK Biobank results in an easy and uniform way without the need to incur high computational costs.

Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability.

Natural hair colour within European populations is a complex genetic trait. Previous work has established that MC1R variants are the principal genetic cause of red hair colour, but with variable penetrance. Here, we have extensively mapped the genes responsible for hair colour in the white, British ancestry, participants in UK Biobank. MC1R only explains 73% of the SNP heritability for red hair in UK Biobank, and in fact most individuals with two MC1R variants have blonde or light brown hair. We identify other genes contributing to red hair, the combined effect of which accounts for ~90% of the SNP heritability. Blonde hair is associated with over 200 genetic variants and we find a continuum from black through dark and light brown to blonde and account for 73% of the SNP heritability of blonde hair. Many of the associated genes are involved in hair growth or texture, emphasising the cellular connections between keratinocytes and melanocytes in the determination of hair colour.