title: RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.
abstract: Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression.
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: Kirsten E
authors.initials: KE
authors.lastname: McLoughlin
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: Nicolas C
authors.initials: NC
authors.lastname: Nalpas
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: Kévin
authors.initials: K
authors.lastname: Rue-Albrecht
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: John A
authors.initials: JA
authors.lastname: Browne
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: David A
authors.initials: DA
authors.lastname: Magee
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: Kate E
authors.initials: KE
authors.lastname: Killick
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland.
authors.forename: Stephen D E
authors.initials: SD
authors.lastname: Park
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin , Dublin , Ireland.
authors.forename: Karsten
authors.initials: K
authors.lastname: Hokamp
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre , Dunsany , Ireland.
authors.forename: Kieran G
authors.initials: KG
authors.lastname: Meade
authors.affiliation: Comparative Immunology Group, School of Biochemistry and Immunology, Trinity Biosciences Institute, Trinity College Dublin , Dublin , Ireland.
authors.forename: Cliona
authors.initials: C
authors.lastname: O'Farrelly
authors.affiliation: Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland.
authors.forename: Eamonn
authors.initials: E
authors.lastname: Gormley
authors.affiliation: UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland ; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland.
authors.forename: Stephen V
authors.initials: SV
authors.lastname: Gordon
authors.affiliation: Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland.
authors.forename: David E
authors.initials: DE
authors.lastname: MacHugh
keywords: Mycobacterium bovis; RNA-seq; biomarker; cattle; microarray; peripheral blood; tuberculosis