RT Journal Article
SR Electronic
T1 The abundance of Nudix hydrolase 16 transcripts is elevated in human sepsis: perspectives gained during a hands-on reductionist investigation workshop
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 490565
DO 10.1101/490565
A1 Mathieu Garand
A1 Darawan Rinchai
A1 Basirudeen Syed Ahamed Kabeer
A1 Mohammed Toufiq
A1 Mohamed Alfaki
A1 Jessica Roelands
A1 Wouter Hendrickx
A1 Sabri Boughorbel
A1 Nico Marr
A1 Davide Bedognetti
A1 Damien Chaussabel
YR 2018
UL http://biorxiv.org/content/early/2018/12/09/490565.abstract
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.