PT  - JOURNAL ARTICLE
AU  - Mathieu Garand
AU  - Darawan Rinchai
AU  - Basirudeen Syed Ahamed Kabeer
AU  - Mohammed Toufiq
AU  - Mohamed Alfaki
AU  - Jessica Roelands
AU  - Wouter Hendrickx
AU  - Sabri Boughorbel
AU  - Nico Marr
AU  - Davide Bedognetti
AU  - Damien Chaussabel
TI  - The abundance of Nudix hydrolase 16 transcripts is elevated in human sepsis: perspectives gained during a hands-on reductionist investigation workshop
AID  - 10.1101/490565
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 490565
4099  - http://biorxiv.org/content/early/2018/12/09/490565.short
4100  - http://biorxiv.org/content/early/2018/12/09/490565.full
AB  - A hands-on training workshop was devised with omics data used as source material to emulate reductionist investigation approaches. NUDT16, a member of the Nudix hydrolase family was selected as a candidate gene on the basis of: 1) it being upregulated in neutrophils exposed in vitro to serum of patients with sepsis, AND 2) the absence of overlap between the NUDT16 and sepsis, inflammation or neutrophil literature. We next sought to corroborate the initial finding in five public transcriptome sepsis datasets in which NUDT16 transcript levels were measured. In each of these dataset NUDT16 transcript abundance was found to be significantly increased in septic patients in vivo in comparison to uninfected controls. Next, biological concepts were extracted from the NUDT16 literature. The main concepts to emerge from profiling this literature were RNA decapping, inosine triphosphate, and inosine diphosphate. Through these concepts, indirect links could be established between NUDT16 and the sepsis/inflammation/neutrophil literature. A potential role for NUDT16 could, in turn, be inferred in the degradation of mRNAs in activated neutrophils. Follow on experiments that would be necessary in order to further explore such inference are discussed.