HNOBac Manuscript

Authors

Leah Kafer

Andrea Boyd

Isabel F. Escapa

Published

April 28, 2025

Introduction

This repository includes the code used for data analysis for the manuscript Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids. A preprint of this manuscript is available at bioRxiv.

All dataframes generated in the analysis from the raw data and metadata (see data input section for each code notebook) are available here as both .csv and .rds files.

  • Figure 1: Human nasal epithelial organoids tolerate nasal microbiont colonization and restrict bacteria to the mucus layer.
    • Figure 1B: The code for data analysis for the CFU data at 34 °C is available here.
    • Figure 1G: The code for data analysis for the LDH data at 34 °C is available here.
    • Additional images from independent experiments for this figure are available here.
  • Supplemental Figure 1: Nasal microbionts colonize HNOs at human internal body temperature, 37 °C.
    • Figure S1A: The code for data analysis for the RNASeq is available here.
    • Figure S1B: The code for data analysis for Cell Counts & TEER is available here.
    • Figure S1C: The code for data analysis for the CFU data at 37 °C, as well as analysis at 34 vs 37 °C, is available here.
    • Figure S1D: The code for data analysis for the LDH data at 37 °C, as well as analysis at 34 vs 37 °C, is available here.
  • Figure 2: HNOs exhibit many characteristics of human nasal respiratory epithelium that are lacking in Calu-3 and RPMI 2650 cells. Additional images from independent experiments for this figure are available here.
  • Figure 3: HNOs, Calu-3 cells, and RPMI 2650 cells at ALI exhibit similar levels of bacterial colonization and epithelial cell damage at 6 hours.
    • Figure 3A: The code for data analysis for the CFU data is available here.
    • Figure 3B: The code for data analysis for the LDH data is available here.
  • Figure 4: The human nasal respiratory epithelium of HNOs produce general and species-specific cytokine responses to bacterial colonization. The code for data analysis for this figure is available here.
  • Figure 5: The human nasal epithelium of HNOs produces key cytokines in amounts orders of magnitude above the limit detection. The code for data analysis for this figure is available here.
  • Supplemental Figure 2: In response to live S. aureus monocolonization, HNO production of IL-1α activity dominates over IL-1RN activity resulting in IL-1 receptor activation apically and basally. The code for data analysis for this figure is available here.