Genetic architecture of natural variation of cardiac performance from flies to humans.

Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome-wide associations studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict transcription factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart-specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.

Epi-MEIF: detecting higher order epistatic interactions for complex traits using mixed effect conditional inference forests.

Understanding the relationship between genetic variations and variations in complex and quantitative phenotypes remains an ongoing challenge. While Genome-wide association studies (GWAS) have become a vital tool for identifying single-locus associations, we lack methods for identifying epistatic interactions. In this article, we propose a novel method for higher-order epistasis detection using mixed effect conditional inference forest (epiMEIF). The proposed method is fitted on a group of single nucleotide polymorphisms (SNPs) potentially associated with the phenotype and the tree structure in the forest facilitates the identification of n-way interactions between the SNPs. Additional testing strategies further improve the robustness of the method. We demonstrate its ability to detect true n-way interactions via extensive simulations in both cross-sectional and longitudinal synthetic datasets. This is further illustrated in an application to reveal epistatic interactions from natural variations of cardiac traits in flies (Drosophila). Overall, the method provides a generalized way to identify higher-order interactions from any GWAS data, thereby greatly improving the detection of the genetic architecture underlying complex phenotypes.

Interplay between trauma and Pseudomonas entomophila infection in flies: a central role of the JNK pathway and of CrebA.

In mammals, both sterile wounding and infection induce inflammation and activate the innate immune system, and the combination of both challenges may lead to severe health defects, revealing the importance of the balance between the intensity and resolution of the inflammatory response for the organism's fitness. Underlying mechanisms remain however elusive. Using Drosophila, we show that, upon infection with the entomopathogenic bacterium Pseudomonas entomophila (Pe), a sterile wounding induces a reduced resistance and increased host mortality. To identify the molecular mechanisms underlying the susceptibility of wounded flies to bacterial infection, we analyzed the very first steps of the process by comparing the transcriptome landscape of infected (simple hit flies, SH), wounded and infected (double hit flies, DH) and wounded (control) flies. We observed that overexpressed genes in DH flies compared to SH ones are significantly enriched in genes related to stress, including members of the JNK pathway. We demonstrated that the JNK pathway plays a central role in the DH phenotype by manipulating the Jra/dJun activity. Moreover, the CrebA/Creb3-like transcription factor (TF) and its targets were up-regulated in SH flies and we show that CrebA is required for mounting an appropriate immune response. Drosophila thus appears as a relevant model to investigate interactions between trauma and infection and allows to unravel key pathways involved.

Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network.

Developmental patterning and tissue formation are regulated through complex gene regulatory networks (GRNs) driven through the action of transcription factors (TFs) converging on enhancer elements. Here, as a point of entry to dissect the poorly defined GRN underlying cardiomyocyte differentiation, we apply an integrated approach to identify active enhancers and TFs involved in Drosophila heart development. The Drosophila heart consists of 104 cardiomyocytes, representing less than 0.5% of all cells in the embryo. By modifying BiTS-ChIP for rare cells, we examined H3K4me3 and H3K27ac chromatin landscapes to identify active promoters and enhancers specifically in cardiomyocytes. These in vivo data were complemented by a machine learning approach and extensive in vivo validation in transgenic embryos, which identified many new heart enhancers and their associated TF motifs. Our results implicate many new TFs in late stages of heart development, including Bagpipe, an Nkx3.2 ortholog, which we show is essential for differentiated heart function.

[Cardiac pathologies and aging: lessons from a tiny heart]. / Pathologies et vieillissement cardiaque - Les leçons d'un tout petit cœur.

The high level of conservation of the cardiogenic gene regulatory network as well as of the cellular and physiological characteristics of the cardiomyocytes between fly and human, makes the small heart of this invertebrate the simplest and most flexible genetic system to dissect the fundamental molecular mechanisms that are brought into play during the development, the establishment and the maintenance of the cardiac function. The recent improvements in techniques of measurements of cardiac function made it possible to validate Drosophila as a model of cardiomyopathies and arrhythmias of genetic and metabolic origin or dependent of ageing. The heart of the fly thus represents a model of choice to identify genes and their interactions implicated in cardiac pathologies.

Genes and networks regulating cardiac development and function in flies: genetic and functional genomic approaches.

The Drosophila heart has emerged as a powerful model system for cardiovascular research. This simple organ, composed of only 104 cardiomyocytes and associated pericardiac cells, has been the focus of numerous candidate gene approaches in the last 2 decades, which have unraveled a number of transcription factors and signaling pathways involved in the regulation of early cardiac development. Importantly, these regulators seem to have largely conserved functions in mammals. Recent studies also demonstrated the usefulness of the fly circulatory system to investigate molecular mechanisms involved in the control of the establishment and maintenance of the cardiac function. In this review, we have focused on how new technological and conceptual advances in the field of functional genomics have impacted research on the cardiovascular system in Drosophila. Genome-scale genetic screens were conducted taking advantage of recently developed ribonucleic acid interference transgenic lines and molecularly defined genetic deficiencies, which have provided new insights into the genetics of both the developmental control of heart formation and cardiac function. In addition, a comprehensive picture of the transcriptional network controlling heart formation is emerging, thanks to newly developed genomic approaches which allow global and unbiased identification of the underlying components of gene regulatory circuits.

Expression of cardiac myosin-binding protein-C (cMyBP-C) in Drosophila as a model for the study of human cardiomyopathies.

Mutations in the MYBPC3 gene encoding human cardiac myosin-binding protein-C (cMyBP-C) are associated with familial hypertrophic cardiomyopathy (FHC), but the molecular mechanisms involved are not fully understood. In addition, development of FHC is sensitive to genetic background, and the search for candidate modifier genes is crucial with a view to proposing diagnosis and exploring new therapies. We used Drosophila as the model to investigate the in vivo consequences of human cMyBP-C mutations. We first produced transgenic flies that specifically express human wild-type or two C-terminal truncated cMyBP-Cs in indirect flight muscles (IFM), a tissue particularly amenable to genetic and molecular analyses. First, incorporation of human cMyBP-C into the IFM led to sarcomeric structural abnormalities and to a flightless phenotype aggravated by age and human gene dosage. Second, transcriptome analysis of transgenic IFM using nylon microarrays showed the remodelling of a transcriptional program involving 97 out of 3570 Drosophila genes. Among them, the Calmodulin gene encoding a key component of muscle contraction, found up-regulated in transgenic IFM, was evaluated as a potential modifier gene. Calmodulin mutant alleles rescued the flightless phenotype, and therefore behave as dominant suppressors of the flightless phenotype suggesting that Calmodulin might be a modifier gene in the context of human FHC. In conclusion, we suggest that the combination of heterologous transgenesis and transcriptome analysis in Drosophila could be of great value as a way to glean insights into the molecular mechanisms underlying FHC and to propose potential candidate modifier genes.

The spatial expression ofDrosophila rotund gene reveals that the imaginal discs are organized in domains along the proximal-distal axis.

InDrosophila imaginal discs, pattern formation requires the activity of three positional information systems, antero-posterior (A/P), dorso-ventral (D/V) and proximo-distal (P/D). Three genes,Decapentaplegic, Distal-less androtund (rn), involved in pattern formation along the P/D axis have been characterized. Thern gene is required in a sub-distal region, localized at a similar position along the P/D axis in all appendages; it encodes two major transcripts, m1.7 and m5.3, both expressed in the central region of all the major imaginal discs. The present study of these transcripts in severalrn mutant favours m5.3 as encodingrn morphogenetic function in the imaginal discs. The fine characterization of its distribution partitions all major imaginal discs in domains along the P/D axis. The ventral and dorsal discs appear to be similarly but not identically organized: two P/D domains are evident in the wing and haltere discs whilst the leg and antenna discs appear to be composed of at least three. We also show that m5.3 is sex-regulated in the genital disc and thatrn function is required for proper development of a sub-distal structure of the female genitalia. This suggests that the primordia of the female genitalia may be organized in a similar way to the other imaginal discs, and strongly supports the hypothesis thatrn function is specific to pattern formation along the P/D axis and that it may be involved in the establishment or maintenance of this pattern.