Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes

D. C. Thach, B. K. Agan, C. Olsen, J. Diao, B. Lin, J. Gomez, M. Jesse, M. Jenkins, R. Rowley, E. Hanson, C. Tibbetts, D. A. Stenger, E. Walter, P. Demitry, T. Difato, R. Holliday, R. Kruzelock, L. Daum, D. Metzgar, D. NiemeyerK. Russell, M. Archer, R. Bravo, N. Freed, J. Fuller, K. Gratwick, B. Johnson, E. Lawrence, C. Meador, H. Melgarejo, K. Mueller, D. Pearson, A. Purkayastha, J. Santiago, D. Seto, F. Stotler, J. Thornton, Z. Wang, D. Watson, S. Worthy, G. Vora, K. Grant, C. James

    Research output: Contribution to journalArticle

    21 Scopus citations

    Abstract

    Gene expression profiles permit analysis of host immune response at the transcriptome level. We used the Pax gene Blood RNA (PAX) System and Affymetrix microarrays (HG-U133A&B) to survey profiles in basic military trainees and to classify them as healthy, febrile respiratory illness (FRI) without adenovirus, FRI with adenovirus, and convalescent from FRI with adenovirus. We assessed quality metrics of RNA processing for microarrays. Class prediction analysis discovered nested sets of transcripts that could categorize the phenotypes with optimized accuracy of 99% (nonfebrile vs febrile, P<0.0005), 87% (healthy vs convalescent, P=0.001), and 91% (febrile without vs with adenovirus, P<0.0005). The discovered set for classification of nonfebrile vs febrile patients consisted of 40 transcripts with functions related to interferon induced genes, complement cascades, and TNF and IL1 signaling. The set of seven transcripts for distinguishing healthy vs convalescent individuals included those associated with ribosomal structure, humoral immunity, and cell adhesion. The set of 10 transcripts for distinguishing FRI without vs with adenovirus had functions related to interferon induced genes, IL1 receptor accessory protein, and cell interactions. These results are the first in vivo demonstration of classification of infectious diseases via host signature transcripts and move us towards using the transcriptome in biosurveillance.

    Original languageEnglish (US)
    Pages (from-to)588-595
    Number of pages8
    JournalGenes and Immunity
    Volume6
    Issue number7
    DOIs
    StatePublished - Oct 2005

    Keywords

    • Infection phenotypes
    • Surveillance
    • Transcriptome

    ASJC Scopus subject areas

    • Immunology
    • Genetics
    • Genetics(clinical)

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    Thach, D. C., Agan, B. K., Olsen, C., Diao, J., Lin, B., Gomez, J., Jesse, M., Jenkins, M., Rowley, R., Hanson, E., Tibbetts, C., Stenger, D. A., Walter, E., Demitry, P., Difato, T., Holliday, R., Kruzelock, R., Daum, L., Metzgar, D., ... James, C. (2005). Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes. Genes and Immunity, 6(7), 588-595. https://doi.org/10.1038/sj.gene.6364244