Predicting nonsense-mediated mRNA decay from splicing events in sepsis using RNA-sequencing data

Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are highly conserved cellular mechanisms that modulate gene expression. Here, we introduce the NMD pipeline that computes how splicing events introduce premature termination codons to mRNA transcripts via frameshift, then predicts the rate of premature termination codon-dependent NMD. We use whole-blood, deep RNA-sequencing data from critically ill patients to study gene expression in sepsis. Statistical significance was determined as adjusted <i>P</i> < 0.05 and |log₂ fold change| > 2 for differential gene expression and probability ≥0.9 and |DeltaPsi| > 0.1 for AS. The NMD pipeline was developed based on the AS data from Whippet. We demonstrate that the rate of NMD is higher in the sepsis and deceased groups compared with the control and survived groups, which may signify aberrant splicing because of altered physiology in critical illness. Predominance of non-exon skipping events was associated with disease and mortality states. The NMD pipeline also revealed proteins with potential association with sepsis. Together, these results emphasize the utility of the NMD pipeline in studying AS-NMD along with differential gene expression analysis and uncovering proteins associated with sepsis.