Upper and Lower Respiratory Tract Compartmentalization in Pediatric Stem Cell Transplantation

  1. Erica M. Evans
  2. Madeline Y. Mayday
  3. Emma M. Pearce
  4. K Iwanaga
  5. NP Ly
  6. GD Church
  7. Gustavo Reyes
  8. Miriam R. Simon
  9. Jacob Blum
  10. Hanna Kim
  11. Jessica Mu
  12. Jazmin Baez-Maidana
  13. Jeffrey J. Auletta
  14. Peter J. Shaw
  15. Erin M. Kreml
  16. Paul L. Martin
  17. Christine N. Duncan
  18. Courtney M. Rowan
  19. Kamar Godder
  20. Caitlin Hurley
  21. Geoffrey D.E. Cuvelier
  22. Muna Qayed
  23. Hisham Abdel-Azim
  24. Amy K. Keating
  25. Julie C. Fitzgerald
  26. Rabi Hanna
  27. James S. Killinger
  28. Janet R. Hume
  29. Troy C. Quigg
  30. Paul Castillo
  31. Prakash Satwani
  32. Theodore B. Moore
  33. Christopher C. Dvorak
  34. Matt S. Zinter
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Abstract

Rationale

Lung injury after hematopoietic stem cell transplantation (HCT) occurs due to infection, chemotherapy toxicity, and alloreactive inflammation. Analyses of bronchoalveolar lavage (BAL) fluid have revealed dominant pathobiologic signatures, but minimally-invasive diagnostics are needed.

Objectives

To determine whether microbiome and gene expression perturbations are shared along the respiratory tract or isolated to the alveoli in pediatric HCT patients with lung injury.

Methods

We performed bulk RNA sequencing on 189 paired nasal and BAL samples from 160 patients enrolled at 28 children’s hospitals (2016-2021). Microbial and human transcripts were compared using multivariable models accounting for age, sex, and paired sampling.

Measurements and Main Results

BAL and nasal transcriptomes differed across 13,698 genes, 48 cellular components, and network interactions linking inflammation, reactive oxygen species, and immunometabolism. Minimal BAL-nasal correlation was observed in gene expression levels (median ρ=0.03, IQR –0.03 to 0.08) or fractional abundance of key cells such as neutrophils and CD8+ T-cells. BAL microbiomes harbored fewer commensal bacteria and more fungi and DNA viruses. BAL bacterial RNA was associated with diminished immune signaling whereas nasal bacterial RNA aligned with inflammatory gene expression. Further, only BAL microbial RNA was linked to transcriptional shifts in epithelial injury response, keratinization, and collagen deposition. Finally, BAL commensal microbiome depletion, epithelial injury, and immune dysregulation signatures were associated with death or ≥7 days of mechanical ventilation in 30% of patients, whereas nasal samples provided minimal prognostic information.

Conclusions

These data support alveolar compartmentalization in pediatric HCT and emphasize the ongoing need for minimally-invasive but informative diagnostics.

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