Hematopoietic stem cell transplantation (HCT) is potentially curative for numerous malignant and non-malignant diseases but can lead to lung injury due to chemoradiation toxicity, infection, and immune dysregulation. Bronchoalveolar lavage (BAL) is the most commonly used procedure for diagnostic sampling of the lung but is invasive, cannot be performed in medically fragile patients, and is challenging to perform serially. We previously showed that BAL transcriptomes representing pulmonary inflammation and cellular injury can phenotype post-HCT lung injury and predict mortality outcomes. However, whether peripheral blood testing is a suitable minimally-invasive surrogate for pulmonary sampling in the HCT population remains unknown. To address this question, we compared 210 paired BAL and peripheral blood transcriptomes obtained from 166 pediatric HCT patients at 27 children’s hospitals. BAL and blood mRNA abundance showed minimal overall correlation at the level of individual genes, gene set enrichment scores, imputed cell fractions, and T- and B-cell receptor clonotypes. Instead, we identified significant site-specific transcriptional programs. In BAL, expression of innate and adaptive immune pathways was tightly co-regulated with expression of epithelial mesenchymal transition and hypoxia pathways, and these signatures were associated with mortality. In contrast, in blood, expression of endothelial injury, DNA repair, and cellular metabolism pathways was associated with mortality. Integration of paired BAL and blood transcriptomes dichotomized patients into two groups, of which one group showed twice the rate of hypoxia and significantly worse outcomes within 7 days of enrollment. These findings reveal a compartmentalized injury response, where BAL and peripheral blood transcriptomes provide distinct but complementary insights into local and systemic mechanisms of post-HCT lung injury.

M.S.Z. discloses consulting and advisory board work (Roche). C.C.D. discloses consulting and advisory board work (Jazz Pharmaceuticals; Alexion Inc.). J.J.A. discloses consulting and advisory board work (AscellaHealth; Takeda). T.C.Q. discloses consulting and advisory board work (Alexion AstraZeneca Rare Disease; Jazz Pharmaceuticals). H.A-A. discloses research support (Adaptive). R.P. discloses consulting and advisory board work (BlueBird Bio) and research support (Amgen). M.A.P. discloses consulting and advisory board work (Novartis; Pfizer; Cargo; BlueBird Bio; Vertex) and research support (Miltenyi; Adaptive). L.N.S. discloses consulting and advisory board work (Sanofi). J.J.B. discloses consulting and advisory board work (Sanofi; BlueRock; Sobi; SmartImmune; Immusoft; Advanced Clinical; Merck). J.L.D. discloses salary support and research support (Chan Zuckerberg Biohub).

M.S.Z. received research funding from NHLBI K23HL146936, NHLBI R03HL171423, NICHD K12HD000850, the American Thoracic Society, the Pediatric Transplantation and Cell Therapy Foundation, and the National Marrow Donor Program Amy Strelzer Manasevit Grant. M.Y.M received research funding from NCI F31CA271571. H.A-A. received grant funding from the Gateway Foundation and St. Baldrick's Foundation. J.S.K. and J.J.B. received research funding from NCI P30CA008748. M.A.P. received research funding from NCI P30CA040214. J.L.D. received research funding from the Chan Zuckerberg Biohub. Additional funding for the study was provided by NHLBI UG1HL069254 and a Johnny Crisstopher Children's Charitable Foundation St. Baldrick's Consortium Grant.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Patients or their guardians were approached prospectively for consent under local IRB approval at each site (UCSF IRB #14-13546, #16-18908) in accordance with the Declaration of Helsinki and permission was obtained to collect leftover BAL fluid as well as paired blood.

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