Central aspects of the innate immune response are shared between Drosophila and mammals, but despite this extraordinary conservation, natural populations of both organisms harbor considerable genetic variability in efficacy of the immune response. Much of the functional variation results from differences in the transcriptional dynamics of the immune response. Evolution has tuned both positive and negative regulation of the immune system for robust control even in the presence of environmental and genetic perturbations. The first Specific Aim of this proposed project is to use naturally occurring variation in D. melanogaster to reverse engineer the cis- and trans-regulatory components that control transcription of the innate immune response. Both pyrosequencing and RNA-seq will be applied to F1 hybrid lines from the Drosophila Genetic Reference Panel before and after infection to obtain a quantitative profile of expression dynamics. GRO-seq of fat body tissue in phenotypically extreme lines will specify the role of paused polymerase in both the speed of response to septic injury and the precision of the transcriptional regulation. Network reconstruction and an ODE dynamical model of the network will be fitted using differences causes by genetic polymorphism among lines as perturbations to the gene regulatory network. The models will seek to reveal heretofore cryptic feedback loops and other regulatory constraints.
The second Aim i s to establish and dissect the role of microRNAs in regulating the innate immune response. High-throughput sequencing of libraries of short RNA molecules will be analyzed at various times before, during, and after infection to establish the time-course of microRNA expression over an experimental infection. Transcript targets of immune-responsive microRNAs will be computationally inferred and functionally validated. Variation among DGRP lines in the microRNA response will be joined with the RNA-seq and GRO-seq data obtained under Aim 1 to determine the impact of miRNA regulation on immune-related gene expression. Tests of association will be performed to identify segregating polymorphisms in the miRNA genes and their targets that may result in differences in expression dynamics.
The third Aim i s to define the kinetics of innate immune system shutdown after infectious threat is eliminated, and to assess whether the rapid shutdown is driven by the physiological or autoimmune cost of inappropriate immune system activity. Dynamics of transcript decay and negative regulation of immune-activating pathways will be quantified. The correlation of shutdown kinetics with fitness traits such as reduced fecundity and lifespan will be tested under the hypothesis that genetic lines which exhibit excessively slow shutdown dynamics incur fitness costs. Ultimately this project seeks to determine how evolutionary modulation of the innate immune response has struck the critical balance between robust anti- pathogen defense and protection of self-tissue from autoimmunological damage.

Public Health Relevance

This project aims to experimentally define and quantitatively model the regulation of the innate immune response, emphasizing the balance of cis-acting and trans-acting genetic variation and the role of regulatory microRNAs. A well-characterized reference set of Drosophila melanogaster genetic lines will be exploited for experimental work and for development of the quantitative model. This project is aimed at understanding how genetic variation in populations mediates individual differences in the efficacy of immune defense against microbial infection.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
4R01AI064950-10
Application #
9053431
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Singleton, Kentner L
Project Start
2005-02-15
Project End
2017-04-30
Budget Start
2016-05-01
Budget End
2017-04-30
Support Year
10
Fiscal Year
2016
Total Cost
Indirect Cost
Name
Cornell University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Troha, Katia; Im, Joo Hyun; Revah, Jonathan et al. (2018) Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster. PLoS Pathog 14:e1006847
Lazzaro, Brian P; Fox, Gabriel M (2017) Host-Microbe Interactions: Winning the Colonization Lottery. Curr Biol 27:R642-R644
Early, Angela M; Shanmugarajah, Niroshan; Buchon, Nicolas et al. (2017) Drosophila Genotype Influences Commensal Bacterial Levels. PLoS One 12:e0170332
Sackton, Timothy B; Lazzaro, Brian P; Clark, Andrew G (2017) Rapid Expansion of Immune-Related Gene Families in the House Fly, Musca domestica. Mol Biol Evol 34:857-872
Early, Angela M; Clark, Andrew G (2017) Genomic signatures of local adaptation in the Drosophila immune response. Fly (Austin) 11:277-283
Early, Angela M; Arguello, J Roman; Cardoso-Moreira, Margarida et al. (2017) Survey of Global Genetic Diversity Within the Drosophila Immune System. Genetics 205:353-366
Unckless, Robert L; Lazzaro, Brian P (2016) The potential for adaptive maintenance of diversity in insect antimicrobial peptides. Philos Trans R Soc Lond B Biol Sci 371:
Unckless, Robert L; Howick, Virginia M; Lazzaro, Brian P (2016) Convergent Balancing Selection on an Antimicrobial Peptide in Drosophila. Curr Biol 26:257-262
Grenier, Jennifer K; Arguello, J Roman; Moreira, Margarida Cardoso et al. (2015) Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains. G3 (Bethesda) 5:593-603
Khalil, Sarah; Jacobson, Eliana; Chambers, Moria C et al. (2015) Systemic bacterial infection and immune defense phenotypes in Drosophila melanogaster. J Vis Exp :e52613

Showing the most recent 10 out of 36 publications