Predicting Nonsense-mediated mRNA Decay from Splicing Events in Sepsis using RNA-Sequencing Data

Area of Science:

• Molecular Biology
• Genetics
• Bioinformatics

Background:

• Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are crucial conserved mechanisms regulating gene expression.
• Understanding AS-NMD interplay is vital for deciphering cellular responses to disease states.

Purpose of the Study:

• To introduce and validate an NMD pipeline for predicting premature termination codon (PTC)-dependent NMD rates.
• To investigate the role of AS-NMD in sepsis using whole blood RNA-sequencing data.

Main Methods:

• Development of an NMD pipeline utilizing Whippet for AS data analysis.
• Application of deep RNA-sequencing on whole blood samples from sepsis patients and controls.
• Statistical analysis for differential gene expression and AS events, with significance thresholds set for adjusted p-value < 0.05, |log2foldchange| > 2, probability >= 0.9, and |DeltaPsi| > 0.1.

Main Results:

• The NMD pipeline demonstrated a higher rate of NMD in sepsis and deceased patient groups compared to control and survived groups.
• Predominance of non-exon skipping AS events correlated with disease severity and mortality.
• Identification of proteins with potential novel roles in sepsis through the NMD pipeline analysis.

Conclusions:

• The developed NMD pipeline is a valuable tool for studying AS-NMD mechanisms alongside differential gene expression.
• Elevated NMD rates in sepsis may indicate purposeful transcript downregulation or aberrant splicing due to physiological changes.
• The study highlights potential novel protein targets for sepsis intervention.