Final Report Summary - GUT IMMUNITY GRNS (Characterizing the Gene Regulatory Networks Mediating Gut Immunocompetence in Drosophila)
The emergence of a gastrointestinal tract within the body cavity is one of the major innovations in animal evolution, allowing the transition from an intra- to an extracellular mode of digestion. With this emergence came the opportunity for infectious agents to exploit this intestinal ecosystem for their own transmission. Gut-bearing organisms therefore evolved complex mechanisms to defend themselves against these agents, making them “gut immunocompetent”. Important progress has been made to elucidate the biological processes underlying gut immunocompetence, revealing an intricate interplay between immunological, stress, and neuronal signaling as well as gut regeneration and wound repair. However, how this multilayered gut immunocompetence network is encoded at the molecular level and how genetic variation of the host species influences the activity of this network is still poorly understood.
In this project, we used a global and interdisciplinary study, combining regulatory genomics and bioinformatics, to elucidate the genetic and molecular mechanisms underlying gut immunocompetence and its variation in Drosophila melanogaster, a model organism that is developing into an important and economical model system to inform human intestinal pathophysiology.
First, to understand how the gut regulatory networks respond to pathogenic microorganisms from the environment, we measured global gene expression levels in control flies and flies infected with two insect-specific bacterial strains, Pseudomonas entomophila (Pe) and Erwinia carotovora carotovora (Ecc15). We generated data sets from guts isolated from flies infected with Pe and Ecc15, at two time points and two biological replicates, yielding a total of 12 RNA-seq samples. Our results show that the immune response to lethal Pe differs from that to nonlethal Ecc15. While both pathogens induce genes involved in antimicrobial response, stress response, and epithelium renewal, induction of most of these genes was higher in flies infected with Pe than Ecc15. In addition, Pe specifically induced additional genes related to stress and damage pathways, suggesting that the amplitude of transcriptional changes correlates with the pathogenicity of bacteria. Interestingly, the overactivation of stress pathways could also contribute to pathogenesis and as many human diseases are associated with deleterious and often overactive immune responses (inflammation/autoimmunity), our results in flies might help to understand such diseases in humans.
Distinct cell types and cell states derive from differentially controlled gene expression. These programs are coordinated by the genome within the context of chromatin, whose fundamental subunit is the nucleosome. Each nucleosome consists of an octamer of two copies of different histones, around which the DNA is wrapped. Post-translational modifications of histones and DNA methylation regulate nucleosome compaction that facilitates or impedes the binding of regulatory proteins called transcription factors. For example, while histone modifications such as H3 lysine 4 mono- and tri-methylation (H3K4me1 and H3K4me3) and H3 lysine 27 acetylation (H3K27ac) and H3 lysine 18 acetylation (H3K18ac) facilitate TF binding and the access of the transcriptional machinery to DNA, DNA methylation and H3K27me3 are normally associated with reduced DNA binding access and gene repression. Therefore, to understand how the transcriptional changes driven by infection were encoded in the fly genome, we measured H3K4me1, H3K4me3, H3K18ac, H3K27ac and H3K27me3 levels in control and flies infected with Pe. Unexpectedly, our results showed that, although a potent modulator of host transcription, Pe has essentially no impact on the chromatin landscape of the fly gut. These findings support the notion that infection-regulated genes are already primed for expression in the fly gut, and that gene expression changes are controlled by TFs that operate in a permissive (and thus relatively stable) chromatin environment.
In addition to our efforts in elucidating the genetic basis of gut immunocompetence, we developed a microfluidics based approach to examine histone modifications from rare or small number of cells, given the challenge of probing these molecular marks in many flies across many genotypes and conditions (infection versus control). The ChIP-on-chip method allows the identification of histone modifications in an easy, low input, fast and cheap manner, which will allow us to move on to the last part of the project that is the characterization of the genetic variants that may cause gut immunocompetence variation by affecting gene expression or the chromatin landscape. This would not only constitute a breakthrough in the field of innate immunity, but would also provide a sound foundation for more generally understanding the molecular driving forces that mediate the relationship between genotypic and phenotypic variation.
Indeed, Drosophila has contributed to elucidate interactions between gut cells and microbiota, and is gaining importance as a useful model to study the etiology of gut-related diseases. We therefore expect that our results will contribute to a level of mechanistic and analytical understanding that is currently unattainable in humans.
In this project, we used a global and interdisciplinary study, combining regulatory genomics and bioinformatics, to elucidate the genetic and molecular mechanisms underlying gut immunocompetence and its variation in Drosophila melanogaster, a model organism that is developing into an important and economical model system to inform human intestinal pathophysiology.
First, to understand how the gut regulatory networks respond to pathogenic microorganisms from the environment, we measured global gene expression levels in control flies and flies infected with two insect-specific bacterial strains, Pseudomonas entomophila (Pe) and Erwinia carotovora carotovora (Ecc15). We generated data sets from guts isolated from flies infected with Pe and Ecc15, at two time points and two biological replicates, yielding a total of 12 RNA-seq samples. Our results show that the immune response to lethal Pe differs from that to nonlethal Ecc15. While both pathogens induce genes involved in antimicrobial response, stress response, and epithelium renewal, induction of most of these genes was higher in flies infected with Pe than Ecc15. In addition, Pe specifically induced additional genes related to stress and damage pathways, suggesting that the amplitude of transcriptional changes correlates with the pathogenicity of bacteria. Interestingly, the overactivation of stress pathways could also contribute to pathogenesis and as many human diseases are associated with deleterious and often overactive immune responses (inflammation/autoimmunity), our results in flies might help to understand such diseases in humans.
Distinct cell types and cell states derive from differentially controlled gene expression. These programs are coordinated by the genome within the context of chromatin, whose fundamental subunit is the nucleosome. Each nucleosome consists of an octamer of two copies of different histones, around which the DNA is wrapped. Post-translational modifications of histones and DNA methylation regulate nucleosome compaction that facilitates or impedes the binding of regulatory proteins called transcription factors. For example, while histone modifications such as H3 lysine 4 mono- and tri-methylation (H3K4me1 and H3K4me3) and H3 lysine 27 acetylation (H3K27ac) and H3 lysine 18 acetylation (H3K18ac) facilitate TF binding and the access of the transcriptional machinery to DNA, DNA methylation and H3K27me3 are normally associated with reduced DNA binding access and gene repression. Therefore, to understand how the transcriptional changes driven by infection were encoded in the fly genome, we measured H3K4me1, H3K4me3, H3K18ac, H3K27ac and H3K27me3 levels in control and flies infected with Pe. Unexpectedly, our results showed that, although a potent modulator of host transcription, Pe has essentially no impact on the chromatin landscape of the fly gut. These findings support the notion that infection-regulated genes are already primed for expression in the fly gut, and that gene expression changes are controlled by TFs that operate in a permissive (and thus relatively stable) chromatin environment.
In addition to our efforts in elucidating the genetic basis of gut immunocompetence, we developed a microfluidics based approach to examine histone modifications from rare or small number of cells, given the challenge of probing these molecular marks in many flies across many genotypes and conditions (infection versus control). The ChIP-on-chip method allows the identification of histone modifications in an easy, low input, fast and cheap manner, which will allow us to move on to the last part of the project that is the characterization of the genetic variants that may cause gut immunocompetence variation by affecting gene expression or the chromatin landscape. This would not only constitute a breakthrough in the field of innate immunity, but would also provide a sound foundation for more generally understanding the molecular driving forces that mediate the relationship between genotypic and phenotypic variation.
Indeed, Drosophila has contributed to elucidate interactions between gut cells and microbiota, and is gaining importance as a useful model to study the etiology of gut-related diseases. We therefore expect that our results will contribute to a level of mechanistic and analytical understanding that is currently unattainable in humans.