Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response

Abstract

Background Immune responses need to be initiated rapidly, and maintained as needed, to prevent establishment and growth of infections. At the same time, resources need to be balanced with other physiological processes. On the level of transcription, studies have shown that this balancing act is reflected in tight control of the initiation kinetics and shutdown dynamics of specific immune genes. Results To investigate genome-wide expression dynamics and trade-offs after infection at a high temporal resolution, we performed an RNA-seq time course on D. melanogaster with 20 time points post Imd stimulation. A combination of methods, including spline fitting, cluster analysis, and Granger causality inference, allowed detailed dissection of expression profiles, lead-lag interactions, and functional annotation of genes through guilt-by-association. We identified Imd-responsive genes and co-expressed, less well characterized genes, with an immediate-early response and sustained up-regulation up to 5 days after stimulation. In contrast, stress response and Toll-responsive genes, among which were Bomanins, demonstrated early and transient responses. We further observed a strong trade-off with metabolic genes, which strikingly recovered to pre-infection levels before the immune response was fully resolved. Conclusions This high-dimensional dataset enabled the comprehensive study of immune response dynamics through the parallel application of multiple temporal data analysis methods. The well annotated data set should also serve as a useful resource for further investigation of the D. melanogaster innate immune response, and for the development of methods for analysis of a post-stress transcriptional response time-series at whole-genome scale.

The Drosophila Baramicin polypeptide gene protects against fungal infection

“…coli ( Fig 1C ). This result is consistent with a recent time course study that found Toll-regulated genes (including BaraA ) were rapidly induced after injection stimulating the Imd pathway, but this principally Imd-based induction resolves to nearly basal levels within 48 hours [ 22 ] (and see S1B and S1C Fig ). Additionally, larvae pricked with M .…”

“…Monitoring GFP in BaraA-Gal4>UAS-mCD8-GFP flies (referred to as BaraA>mGFP) confirms that the BaraA reporter is highly induced in the fat body after infection by M. luteus, but less so by E. coli (Fig 1C). This result is consistent with a recent time course study that found Toll-regulated genes (including BaraA) were rapidly induced after injection stimulating the Imd pathway, but this principally Imd-based induction resolves to nearly basal levels within 48 hours [22] (and see S1B and S1C Fig) There was also sporadic GFP signal in other tissues that included the larval hindgut, the dorsal abdomen of developing pupae, and the seminal vesicle of males. [11]).…”

“…The expression profile of BaraA is complex and poorly defined in existing transcriptomic datasets, likely owing to the gene duplication of BaraA1 and BaraA2 complicating read mapping [ 22 , 25 ]. As BaraA is expressed in various tissues including the head/eye, crop, and fat body ( Fig 1 and [ 23 ]), it is unclear if BaraA absence in the brain, neuromusculature, or non-neuronal tissues (such as the fat body) could underlie the predisposal to erect wing.…”

Infection increases activity via Toll dependent and independent mechanisms in Drosophila melanogaster

“…Activity on the first day of infection was predictive of lifespan, with more active flies exhibiting increased lifespan (Figure 1E). In addition, there was a positive correlation between total activity and survival (Figure 1 – figure supplement 1F); we used day one activity as a predictor because previous work has found immune activity to be strongest at this time (De Gregorio et al, 2002a; Lemaitre et al, 1997; Schlamp et al, 2021) and thus would be an appropriate metric in looking at infections of shorter duration. Furthermore, day 1 activity levels were positively correlated with total activity levels (Figure 1 – figure supplement 1G), giving us confidence that activity on day 1 is representative of total activity levels in assessing infections of longer duration.…”

Wild-type Caenorhabditis elegans Isolates Exhibit Distinct Gene Expression Profiles in Response to Microbial Infection

“…Analysis of gene expression at regular intervals throughout an infection has demonstrated that the host immune response is a dynamic process which needs to be initiated and sustained to fight an infection. 48,49 At 24 hours post-infection, the timepoint at which RNA was collected for gene expression analysis, animals infected with P. aeruginosa were much closer to dying than animals infected with P. rettgeri (N2 P. aeruginosa LT50 = 3.8 ± 0.3 days, CB4856 P. aeruginosa LT50 = 3.5 ± 0.3 days; N2 P. rettgeri LT50 = 7.8 ± 0.7 days, CB4856 P. rettgeri LT50 = 7.2 ± 0.6 days). Perhaps animals exposed to P. aeruginosa or P. rettgeri are at two different stages in combatting their respective infections and the overlap in gene expression between N2 and CB4856 animals grows larger as animals progress from earlier to later stages of infection.…”