The High-throughput Molecular Profiling Core provides the global genomic and proteomic measurements that are essential for applying a systems biology approach to defining innate and adaptive immune responses to virus infection. Each of the Research Projects will provide numerous biological samples for high-throughput analysis. The majority of samples will come from Collaborative Cross lines infected with SARS-CoV (Project 1), influenza virus (Project 2), or West Nile virus (Projects 3 and 4). Global gene expression data obtained from these samples will provide the basis for expression quantitative trait loci (eQTL) analysis and gene expression network inference. Information obtained from these analyses will be indispensable for the identification of genes and gene networks that regulate virus-induced inflammation and innate and adaptive immune responses.
The Specific Aims of the Core are as follows:
Aim 1 : Provide microarray-based gene expression profiling to support expression quantitative trait loci (eQTL) analysis and gene expression network inference in the Collaborative Cross. The Core will provide large-scale sample handling, RNA isolation, quality control, and transcriptomic measurements. Gene expression profiling will be performed using the Affymetrix GeneChip Mouse Gene 1.1 ST Array. Gene expression data will be provided to the Bioinformatics Core, which will be responsible for data management, functional interpretation of gene expression changes, and internal and public data dissemination. eQTL analysis and gene expression network inference will be conducted by the Systems Immunogenetics Core.
Aim 2 : Provide targeted next generation sequencing and proteomic profiling on select Collaborative Cross lines. The Core will provide additional high-throughput transcriptomic and proteomic measurements on a small number of select Collaborative Cross lines identified by Program investigators as having immune response phenotypes of particular interest. This will include next-generation sequencing to identify and quantify large and small noncoding RNAs and quantitative proteomic approaches for protein abundance profiling, targeted proteomics, or the analysis of specific post-translational modifications.
Data generated by these analyses will provide deeper understanding of the genetic traits and molecular events that contribute to specific immune responses to viral pathogens. Improved knowledge of these responses will help to identify new targets for antiviral therapies or develop improved vaccines.
|Gunn, Bronwyn M; Jones, Jennifer E; Shabman, Reed S et al. (2018) Ross River virus envelope glycans contribute to disease through activation of the host complement system. Virology 515:250-260|
|Kollmus, Heike; Pilzner, Carolin; Leist, Sarah R et al. (2018) Of mice and men: the host response to influenza virus infection. Mamm Genome 29:446-470|
|Gorman, Matthew J; Caine, Elizabeth A; Zaitsev, Konstantin et al. (2018) An Immunocompetent Mouse Model of Zika Virus Infection. Cell Host Microbe 23:672-685.e6|
|Baxter, Victoria K; Heise, Mark T (2018) Genetic control of alphavirus pathogenesis. Mamm Genome 29:408-424|
|Chow, Kwan T; Driscoll, Connor; Loo, Yueh-Ming et al. (2018) IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection. J Leukoc Biol :|
|Gralinski, Lisa E; Sheahan, Timothy P; Morrison, Thomas E et al. (2018) Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis. MBio 9:|
|Menachery, Vineet D; Gralinski, Lisa E; Mitchell, Hugh D et al. (2018) Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines. J Virol 92:|
|McMullan, Rachel C; Ferris, Martin T; Bell, Timothy A et al. (2018) CC002/Unc females are mouse models of exercise-induced paradoxical fat response. Physiol Rep 6:e13716|
|Menachery, Vineet D; Schäfer, Alexandra; Burnum-Johnson, Kristin E et al. (2018) MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proc Natl Acad Sci U S A 115:E1012-E1021|
|Adams Waldorf, Kristina M; Nelson, Branden R; Stencel-Baerenwald, Jennifer E et al. (2018) Congenital Zika virus infection as a silent pathology with loss of neurogenic output in the fetal brain. Nat Med 24:368-374|
Showing the most recent 10 out of 77 publications