title: Two-stage, in silico deconvolution of the lymphocyte compartment of the peripheral whole blood transcriptome in the context of acute kidney allograft rejection.
abstract: Acute rejection is a major complication of solid organ transplantation that prevents the long-term assimilation of the allograft. Various populations of lymphocytes are principal mediators of this process, infiltrating graft tissues and driving cell-mediated cytotoxicity. Understanding the lymphocyte-specific biology associated with rejection is therefore critical. Measuring genome-wide changes in transcript abundance in peripheral whole blood cells can deliver a comprehensive view of the status of the immune system. The heterogeneous nature of the tissue significantly affects the sensitivity and interpretability of traditional analyses, however. Experimental separation of cell types is an obvious solution, but is often impractical and, more worrying, may affect expression, leading to spurious results. Statistical deconvolution of the cell type-specific signal is an attractive alternative, but existing approaches still present some challenges, particularly in a clinical research setting. Obtaining time-matched sample composition to biologically interesting, phenotypically homogeneous cell sub-populations is costly and adds significant complexity to study design. We used a two-stage, in silico deconvolution approach that first predicts sample composition to biologically meaningful and homogeneous leukocyte sub-populations, and then performs cell type-specific differential expression analysis in these same sub-populations, from peripheral whole blood expression data. We applied this approach to a peripheral whole blood expression study of kidney allograft rejection. The patterns of differential composition uncovered are consistent with previous studies carried out using flow cytometry and provide a relevant biological context when interpreting cell type-specific differential expression results. We identified cell type-specific differential expression in a variety of leukocyte sub-populations at the time of rejection. The tissue-specificity of these differentially expressed probe-set lists is consistent with the originating tissue and their functional enrichment consistent with allograft rejection. Finally, we demonstrate that the strategy described here can be used to derive useful hypotheses by validating a cell type-specific ratio in an independent cohort using the nanoString nCounter assay.
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; UBC James Hogg Centre for Heart Lung Innovations, Vancouver, BC, Canada.
authors.forename: Casey P
authors.initials: CP
authors.lastname: Shannon
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Balshaw
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada; UBC James Hogg Centre for Heart Lung Innovations, Vancouver, BC, Canada.
authors.forename: Raymond T
authors.initials: RT
authors.lastname: Ng
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; UBC James Hogg Centre for Heart Lung Innovations, Vancouver, BC, Canada.
authors.forename: Janet E
authors.initials: JE
authors.lastname: Wilson-McManus
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; Department of Medicine, Division of Nephrology, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Keown
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: McMaster
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; UBC James Hogg Centre for Heart Lung Innovations, Vancouver, BC, Canada.
authors.forename: Bruce M
authors.initials: BM
authors.lastname: McManus
authors.affiliation: Division of Nephrology, St. Paul's Hospital, and University of British Columbia, Vancouver, BC, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Landsberg
authors.affiliation: Department of Nephrology, Princess Alexandra Hospital, and University of Queensland, Brisbane, Australia.
authors.forename: Nicole M
authors.initials: NM
authors.lastname: Isbel
authors.affiliation: Ottawa Hospital Research Institute, Ottawa, On, Canada.
authors.forename: Greg
authors.initials: G
authors.lastname: Knoll
authors.affiliation: PROOF Centre of Excellence, Vancouver, BC, Canada; Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada; UBC James Hogg Centre for Heart Lung Innovations, Vancouver, BC, Canada.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Tebbutt
mesh_terms: D064591:Allografts / Q000378:metabolism*; D002451:Cell Compartmentation / Q000235:genetics*; D015331:Cohort Studies; D003198:Computer Simulation; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D006084:Graft Rejection / Q000097:blood* / Q000235:genetics*; D006801:Humans; D016030:Kidney Transplantation; D007958:Leukocyte Count; D008214:Lymphocytes / Q000166:cytology*; D015203:Reproducibility of Results; D013997:Time Factors; D059467:Transcriptome / Q000235:genetics*
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