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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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Integrative transcriptomic, evolutionary, and causal inference framework for region-level analysis: Application to

Dan Zhou1,2,3, Eric R Gamazon4,5,6,7,8

  • 1Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.

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Host genetics significantly impact COVID-19 severity. An introgressed archaic segment on chromosome 3p21.31 substantially increases severe disease risk by influencing gene expression, highlighting its role in COVID-19 outcomes.

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Area of Science:

  • Genetics
  • Genomics
  • Evolutionary Biology

Background:

  • Understanding host genetic factors is crucial for COVID-19 severity.
  • Previous studies have identified genetic loci associated with COVID-19, but causal mechanisms remain unclear.

Purpose of the Study:

  • To develop and apply an integrative framework for region-level genetic analysis.
  • To investigate the host genetics underlying COVID-19 severity, focusing on the 3p21.31 locus.

Main Methods:

  • Developed an integrative framework combining transcriptomic, evolutionary, and causal inference methods.
  • Integrated published approaches with a novel summary-statistics-based methodology.
  • Applied the framework to COVID-19 severity data and performed phenome-wide scans.

Main Results:

  • Identified putative causal genes (SLC6A20, CXCR6, CCR9, CCR5) in the 3p21.31 locus influencing COVID-19 severity.
  • Confirmed that an introgressed archaic segment in this locus significantly increases severe COVID-19 risk.
  • Quantified the contribution of this segment to expression-mediated heritability, explaining 15.7% of the causal effect.

Conclusions:

  • The developed region-level framework (SEGMENT-SCAN) provides deep insights into disease genetics.
  • Introgressed archaic segments can play a substantial role in complex disease phenotypes like COVID-19 severity.
  • Findings have implications for understanding disease mechanisms and developing therapeutics.