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An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility.

Publication ,  Journal Article
Matzaraki, V; Gresnigt, MS; Jaeger, M; Ricaño-Ponce, I; Johnson, MD; Oosting, M; Franke, L; Withoff, S; Perfect, JR; Joosten, LAB; Kullberg, BJ ...
Published in: PLoS One
2017

Candidaemia is a bloodstream infection caused by Candida species that primarily affects specific groups of at-risk patients. Because only small candidaemia patient cohorts are available, classical genome wide association cannot be used to identify Candida susceptibility genes. Therefore, we have applied an integrative genomics approach to identify novel susceptibility genes and pathways for candidaemia. Candida-induced transcriptome changes in human primary leukocytes were assessed by RNA sequencing. Genetic susceptibility to candidaemia was assessed using the Illumina immunochip platform for genotyping of a cohort of 217 patients. We then integrated genetics data with gene-expression profiles, Candida-induced cytokine production capacity, and circulating concentrations of cytokines. Based on the intersection of transcriptome pathways and genomic data, we prioritized 31 candidate genes for candidaemia susceptibility. This group of genes was enriched with genes involved in inflammation, innate immunity, complement, and hemostasis. We then validated the role of MAP3K8 in cytokine regulation in response to Candida stimulation. Here, we present a new framework for the identification of susceptibility genes for infectious diseases that uses an unbiased, hypothesis-free, systems genetics approach. By applying this approach to candidaemia, we identified novel susceptibility genes and pathways for candidaemia, and future studies should assess their potential as therapeutic targets.

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Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2017

Volume

12

Issue

7

Start / End Page

e0180824

Location

United States

Related Subject Headings

  • Transcriptome
  • Sequence Analysis, RNA
  • Male
  • Humans
  • Genotype
  • Genetic Predisposition to Disease
  • General Science & Technology
  • Gene Expression Profiling
  • Female
  • Candidemia
 

Citation

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Chicago
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Matzaraki, V., Gresnigt, M. S., Jaeger, M., Ricaño-Ponce, I., Johnson, M. D., Oosting, M., … Kumar, V. (2017). An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. PLoS One, 12(7), e0180824. https://doi.org/10.1371/journal.pone.0180824
Matzaraki, Vasiliki, Mark S. Gresnigt, Martin Jaeger, Isis Ricaño-Ponce, Melissa D. Johnson, Marije Oosting, Lude Franke, et al. “An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility.PLoS One 12, no. 7 (2017): e0180824. https://doi.org/10.1371/journal.pone.0180824.
Matzaraki V, Gresnigt MS, Jaeger M, Ricaño-Ponce I, Johnson MD, Oosting M, et al. An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. PLoS One. 2017;12(7):e0180824.
Matzaraki, Vasiliki, et al. “An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility.PLoS One, vol. 12, no. 7, 2017, p. e0180824. Pubmed, doi:10.1371/journal.pone.0180824.
Matzaraki V, Gresnigt MS, Jaeger M, Ricaño-Ponce I, Johnson MD, Oosting M, Franke L, Withoff S, Perfect JR, Joosten LAB, Kullberg BJ, van de Veerdonk FL, Jonkers I, Li Y, Wijmenga C, Netea MG, Kumar V. An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. PLoS One. 2017;12(7):e0180824.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2017

Volume

12

Issue

7

Start / End Page

e0180824

Location

United States

Related Subject Headings

  • Transcriptome
  • Sequence Analysis, RNA
  • Male
  • Humans
  • Genotype
  • Genetic Predisposition to Disease
  • General Science & Technology
  • Gene Expression Profiling
  • Female
  • Candidemia