Abstract
Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are highly conserved cellular mechanisms that modulate gene expression. Here we introduce NMD pipeline that computes how splicing events introduce premature termination codons to mRNA transcripts via frameshift, then predicts the rate of PTC-dependent NMD. We utilize whole blood, deep RNA-sequencing data from critically ill patients to study gene expression in sepsis. Statistical significance was determined as adjusted p value < 0.05 and |log2foldchange| > 2 for differential gene expression and probability >= 0.9 and |DeltaPsi| > 0.1 for AS. NMD pipeline was developed based on AS data from Whippet. We demonstrate that the rate of NMD is higher in sepsis and deceased groups compared to control and survived groups, which signify purposeful downregulation of transcripts by AS-NMD or aberrant splicing due to altered physiology. Predominance of non-exon skipping events was associated with disease and mortality states. The NMD pipeline also revealed proteins with potential novel roles in sepsis. Together, these results emphasize the utility of NMD pipeline in studying AS-NMD along with differential gene expression and discovering potential protein targets in sepsis.
Competing Interest Statement
The authors have declared no competing interest.
Funding Statement
Armand D. Versaci Research Scholar in Surgical Sciences Award (JS) National Institutes of Health grant P20GM121344 (AMF, GJN) National Institutes of Health grant T32GM065085-20 (BEA) National Institutes of Health grant R35GM118097-09 (AA) National Institutes of Health grant T32HL134625 (MC) National Institutes of Health grant R01GM127472-06 (WGF) National Institutes of Health grant R01HL162954-03 (MML) National Institutes of Health grant T32HL134625-08 (KKL) National Institutes of Health grant R35GM142638-04 (SFM)
Author Declarations
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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:
The Institutional Review Board of Rhode Island Hospital gave ethical approval for this work with protocol number 411616.
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Footnotes
Conflict of Interest statement: The authors have declared that no conflict of interest exists.
Removed an ancillary section in Methods; Added a clarifying paragraph to Discussion; Supplemental files uploaded.
Data Availability
All data produced in the present study are available upon reasonable request to the authors.
Data availability
Our data sets and code utilized and developed for the computational pipeline will be available in the appropriate public repository.
