Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma

Jason D. Christie, Mark M. Wurfel, Rui Feng, Grant E. O'Keefe, Jonathan Bradfield, Lorraine B. Ware, David C. Christiani, Carolyn S. Calfee, Mitchell J. Cohen, Michael Matthay, Nuala J. Meyer, Cecilia Kim, Mingyao Li, Joshua Akey, Kathleen C. Barnes, Jonathan Sevransky, Paul N. Lanken, Addison K. May, Richard Aplenc, James P. MaloneyHakon Hakonarson

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Abstract

Acute Lung Injury (ALI) is a syndrome with high associated mortality characterized by severe hypoxemia and pulmonary infiltrates in patients with critical illness. We conducted the first investigation to use the genome wide association (GWA) approach to identify putative risk variants for ALI. Genome wide genotyping was performed using the Illumina Human Quad 610 BeadChip. We performed a two-stage GWA study followed by a third stage of functional characterization. In the discovery phase (Phase 1), we compared 600 European American trauma-associated ALI cases with 2266 European American population-based controls. We carried forward the top 1% of single nucleotide polymorphisms (SNPs) at p<0.01 to a replication phase (Phase 2) comprised of a nested case-control design sample of 212 trauma-associated ALI cases and 283 at-risk trauma non-ALI controls from ongoing cohort studies. SNPs that replicated at the 0.05 level in Phase 2 were subject to functional validation (Phase 3) using expression quantitative trait loci (eQTL) analyses in stimulated B-lymphoblastoid cell lines (B-LCL) in family trios. 159 SNPs from the discovery phase replicated in Phase 2, including loci with prior evidence for a role in ALI pathogenesis. Functional evaluation of these replicated SNPs revealed rs471931 on 11q13.3 to exert a cis-regulatory effect on mRNA expression in the PPFIA1 gene (p = 0.0021). PPFIA1 encodes liprin alpha, a protein involved in cell adhesion, integrin expression, and cell-matrix interactions. This study supports the feasibility of future multi-center GWA investigations of ALI risk, and identifies PPFIA1 as a potential functional candidate ALI risk gene for future research.

Original languageEnglish (US)
Article numbere28268
JournalPloS one
Volume7
Issue number1
DOIs
StatePublished - Jan 25 2012

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Christie, J. D., Wurfel, M. M., Feng, R., O'Keefe, G. E., Bradfield, J., Ware, L. B., Christiani, D. C., Calfee, C. S., Cohen, M. J., Matthay, M., Meyer, N. J., Kim, C., Li, M., Akey, J., Barnes, K. C., Sevransky, J., Lanken, P. N., May, A. K., Aplenc, R., ... Hakonarson, H. (2012). Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma. PloS one, 7(1), [e28268]. https://doi.org/10.1371/journal.pone.0028268