. 2025 Jul 22;10(17):e194440.

doi: 10.1172/jci.insight.194440. eCollection 2025 Sep 9.

Integrating pulmonary and systemic transcriptomes to characterize lung injury after pediatric hematopoietic stem cell transplant

Emma M Pearce¹, Erica Evans¹, Madeline Y Mayday^{1

2}, Gustavo Reyes¹, Miriam R Simon¹, Jacob Blum¹, Hanna Kim¹, Jessica Mu¹, Peter J Shaw^{3

4}, Courtney M Rowan^{4

5}, Jeffery J Auletta^{4

6

7}, Paul L Martin^{4

8}, Caitlin Hurley^{4

9}, Erin M Kreml^{4

10}, Muna Qayed^{4

11}, Hisham Abdel-Azim^{4

12

13}, Amy K Keating^{4

14

15}, Geoffrey DE Cuvelier^{4

16}, Janet R Hume^{4

17}, James S Killinger^{4

18}, Kamar Godder^{4

19}, Rabi Hanna^{4

20}, Christine N Duncan^{4

14}, Troy C Quigg^{4

21

22}, Paul Castillo^{4

23}, Nahal R Lalefar^{4

24}, Julie C Fitzgerald^{4

25}, Kris M Mahadeo^{4

8

26}, Prakash Satwani^{4

27}, Theodore B Moore^{4

28}, Benjamin Hanisch^{4

29}, Aly Abdel-Mageed^{4

22}, Dereck B Davis^{4

30}, Michelle P Hudspeth^{4

31}, Greg A Yanik^{4

32}, Michael A Pulsipher^{4

33}, Christopher C Dvorak^{4

34}, Joseph L DeRisi^{35

36}, Matt S Zinter^{1

4

34}

Affiliations

¹ Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA.
² Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, Connecticut, USA.
³ The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
⁴ Pediatric Transplantation and Cell Therapy Consortium.
⁵ Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, Indiana, USA.
⁶ Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, Ohio, USA.
⁷ Center for International Blood and Marrow Transplant Research (CIBMTR), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA.
⁸ Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, North Carolina, USA.
⁹ Division of Critical Care, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
¹⁰ Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, Arizona, USA.
¹¹ Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA.
¹² Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
¹³ Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, California, USA.
¹⁴ Harvard Medical School, Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.
¹⁵ Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, Colorado, USA.
¹⁶ CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada.
¹⁷ University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, Minneapolis, Minnesota, USA.
¹⁸ Division of Pediatric Critical Care, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA.
¹⁹ Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, Florida, USA.
²⁰ Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, Ohio, USA.
²¹ Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, Texas, USA.
²² Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.
²³ University of Florida, Gainesville, UF Health Shands Children's Hospital, Gainesville, Florida, USA.
²⁴ Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, California, USA.
²⁵ Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
²⁶ Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, Texas, USA.
²⁷ Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, New York, USA.
²⁸ Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, California, USA.
²⁹ Children's National Hospital, Washington DC, USA.
³⁰ Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, Mississippi, USA.
³¹ Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, South Carolina, USA.
³² Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.
³³ Division of Pediatric Hematology and Oncology, Intermountain Primary Children's Hospital, Huntsman Cancer Institute, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, Utah, USA.
³⁴ Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, and.
³⁵ Department of Biochemistry and Biophysics, UCSF, San Francisco, California, USA.
³⁶ Chan Zuckerberg Biohub, San Francisco, California, USA.

PMID: 40694427
PMCID: PMC12487673
DOI: 10.1172/jci.insight.194440

Integrating pulmonary and systemic transcriptomes to characterize lung injury after pediatric hematopoietic stem cell transplant

Emma M Pearce et al. JCI Insight. 2025.

. 2025 Jul 22;10(17):e194440.

doi: 10.1172/jci.insight.194440. eCollection 2025 Sep 9.

Authors

Affiliations

¹ Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA.
² Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, Connecticut, USA.
³ The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
⁴ Pediatric Transplantation and Cell Therapy Consortium.
⁵ Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, Indiana, USA.
⁶ Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, Ohio, USA.
⁷ Center for International Blood and Marrow Transplant Research (CIBMTR), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA.
⁸ Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, North Carolina, USA.
⁹ Division of Critical Care, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
¹⁰ Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, Arizona, USA.
¹¹ Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA.
¹² Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
¹³ Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, California, USA.
¹⁴ Harvard Medical School, Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.
¹⁵ Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, Colorado, USA.
¹⁶ CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada.
¹⁷ University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, Minneapolis, Minnesota, USA.
¹⁸ Division of Pediatric Critical Care, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA.
¹⁹ Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, Florida, USA.
²⁰ Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, Ohio, USA.
²¹ Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, Texas, USA.
²² Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.
²³ University of Florida, Gainesville, UF Health Shands Children's Hospital, Gainesville, Florida, USA.
²⁴ Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, California, USA.
²⁵ Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
²⁶ Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, Texas, USA.
²⁷ Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, New York, USA.
²⁸ Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, California, USA.
²⁹ Children's National Hospital, Washington DC, USA.
³⁰ Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, Mississippi, USA.
³¹ Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, South Carolina, USA.
³² Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.
³³ Division of Pediatric Hematology and Oncology, Intermountain Primary Children's Hospital, Huntsman Cancer Institute, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, Utah, USA.
³⁴ Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, and.
³⁵ Department of Biochemistry and Biophysics, UCSF, San Francisco, California, USA.
³⁶ Chan Zuckerberg Biohub, San Francisco, California, USA.

PMID: 40694427
PMCID: PMC12487673
DOI: 10.1172/jci.insight.194440

Abstract

Hematopoietic stem cell transplantation (HCT) is a potentially life-saving therapy but can lead to lung injury due to chemoradiation toxicity, infection, and immune dysregulationWe previously showed that bronchoalveolar lavage (BAL) transcriptomes representing pulmonary inflammation and cellular injury can phenotype post-HCT lung injury and predict mortality. To test whether peripheral blood might be a suitable surrogate for BAL, we compared 210 paired BAL and blood transcriptomes obtained from 166 pediatric patients with HCT at 27 hospitals. BAL and blood RNA abundance showed minimal 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, pathways related to immunity, hypoxia, and epithelial mesenchymal transition were tightly coexpressed and linked to 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 2 groups with significantly different rates of hypoxia and clinical outcomes within 1 week of BAL. These findings reveal a compartmentalized injury response, where BAL and blood transcriptomes provide distinct but complementary insights into local and systemic mechanisms of post-HCT lung injury.

Keywords: Bone marrow transplantation; Immunology; Inflammation; Pulmonology; Stem cell transplantation; Transcriptomics.

PubMed Disclaimer

Conflict of interest statement

Conflict of interest: MSZ discloses consulting and advisory board work (Roche, DelveBio). CCD discloses consulting and advisory board work (Jazz Pharmaceuticals; Alexion Inc.). JJA discloses consulting and advisory board work (AscellaHealth, Takeda). TCQ discloses speaker bureau, consulting and advisory board work (Alexion AstraZeneca Rare Disease, Jazz Pharmaceuticals). HAA discloses research support (Adaptive). MAP discloses consulting and advisory board work (Novartis, Garuda, Autolous, Pfizer, Cargo, BlueBird Bio, Vertex) and research support (Miltenyi, Adaptive). JLD discloses salary support and research support (Chan Zuckerberg Biohub).

Figures

**Figure 1. Study design.**
(A) Geographic location of participating children’s hospitals. (B) Patients were followed from the time of conditioning chemotherapy for the development of pulmonary symptoms. If bronchoscopy with bronchoalveolar lavage was planned for clinical reasons, patients were enrolled and BAL with a paired blood sample was collected. Patients were then followed clinically through hospital discharge.

**Figure 2. Differential gene expression and coexpression in BAL and paired blood samples.**
(A) Genes differentially expressed in BAL versus peripheral blood are shown. (B) Expression levels of select genes specific to lung (SFTPC, MUC5AC) and blood (HBA2, HBB). (C) Gene set enrichment scores to the 50 MSigDB Hallmark Pathways were calculated, and correlation between expression of each gene set was calculated within each body site and then contrasted to identify site-specific coregulation. Here we show unique coexpression of Hallmark Hypoxia and IFN-γ gene sets in BAL but not blood as well as unique coexpression of Hallmark DNA Repair and E2F targets in blood but not BAL. (D) Correlation of MSigDB Hallmark pathways within blood (top right triangle) and within BAL (bottom left triangle) are shown. See Supplemental Figure 1 for detailed labels. (E) BAL-blood correlation was calculated for expression levels of n = 7,169 protein-coding genes, and the distribution of correlation coefficients is plotted. Expression levels of CXCL8 in BAL and blood are shown as an example of minimal correlation. Gene set enrichment scores for the MSigDB Hallmark Inflammatory Response gene set measured in BAL and blood are also shown as an example of minimal BAL-blood correlation. BAL and peripheral blood cell type fractions were imputed using CIBERSORTx and reference atlases, and cell fractions across body sites were correlated using Spearman correlation coefficients, with neutrophils and CD8⁺ T cells shown as examples. T and B cell receptor clonotypes were measured using ImReP, and the number of unique clonotypes across body sites were correlated using Spearman correlation coefficients, with TRA shown as an example.

**Figure 3. Differential gene expression by survival status.**
(A) BAL gene expression differences in nonsurvivors. (B) Peripheral blood gene expression differences in nonsurvivors. (C) Overlap between BAL and blood genes associated with mortality.

**Figure 4. Differential gene coexpression by survival status.**
(A) Network of genes coexpressed in BAL of nonsurvivors (right) but not coexpressed in survivors (left). Examples of hubs genes (CEACAM6, CXCL17, NFAM1) are shown. Examples of differentially coexpressed genes linked to each hub gene are shown (e.g., CEACAM6-FN1 coexpression) to illustrate differential gene-expression. To the right, pathway enrichment for hub genes are shown. (B) Network of genes coexpressed in peripheral blood of nonsurvivors (right) but not coexpressed in survivors (left). Examples of hub genes (ZNF707, GARRE1, TMEM86B) are shown. Examples of differentially coexpressed genes linked to each hub gene are shown (e.g., ZNF707-BUB1B coexpression) to illustrate differential gene-expression. To the right, pathway enrichment for hub genes are shown.

**Figure 5. BAL and peripheral blood transcriptome correlates of post-HCT lung injury subtypes.**
(A) Concept diagram for 4 post-HCT lung injury subtypes derived in the PTCTC SUP1601 cohort and validated in the University of Utrecht, Netherlands, cohort (58). (B) Example BAL and blood genes differentially expressed in lung injury subtypes 2, 3, and 4 relative to subtype 1. (C) Differentially expressed BAL and blood genes underwent pathway analysis, and pathways identified in BAL and blood gene are quantified to show greater overall differences detected in BAL as opposed to paired blood.

**Figure 6. Integrated BAL and blood transcriptomic signatures reveal 2 large patient groups.**
(A) Paired BAL and blood transcriptomes underwent multi-omics factor analysis (MOFA) followed by dimensionality reduction (UMAP) and k-means clustering to show 2 groups of patients. (B) Post-HCT lung injury subtype was mapped onto the 2 integrated transcriptome clusters, showing that most patients from subtypes 2, 3, and 4 mapped to Cluster B. (C and D) Approximately twice as many patients in Cluster B required oxygen prior to BAL sampling, and twice as many patients died or required ongoing mechanical ventilation within 7 days of BAL sampling.

See this image and copyright information in PMC

Update of

Integrating Pulmonary and Systemic Transcriptomic Profiles to Characterize Lung Injury after Pediatric Hematopoietic Stem Cell Transplant.
Pearce EM, Evans E, Mayday MY, Reyes G, Simon MR, Blum J, Kim H, Mu J, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Hurley C, Kreml EM, Qayed M, Abdel-Azim H, Keating AK, Cuvelier GDE, Hume JR, Killinger JS, Godder K, Hanna R, Duncan CN, Quigg TC, Castillo P, Lalefar NR, Fitzgerald JC, Mahadeo KM, Satwani P, Moore TB, Hanisch B, Abdel-Mageed A, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Dvorak CCJL, Zinter MS. Pearce EM, et al. medRxiv [Preprint]. 2025 Apr 1:2025.03.31.25324969. doi: 10.1101/2025.03.31.25324969. medRxiv. 2025. Update in: JCI Insight. 2025 Jul 22;10(17):e194440. doi: 10.1172/jci.insight.194440. PMID: 40236411 Free PMC article. Updated. Preprint.

References

1. D’Souza A, et al. Current use of and trends in hematopoietic cell transplantation in the United States. Biol Blood Marrow Transplant. 2020;26(8):e177–e182. doi: 10.1016/j.bbmt.2020.04.013. - DOI - PMC - PubMed
1. Panoskaltsis-Mortari A, et al. An official American Thoracic Society research statement: noninfectious lung injury after hematopoietic stem cell transplantation: idiopathic pneumonia syndrome. Am J Respir Crit Care Med. 2011;183(9):1262–1279. doi: 10.1164/rccm.2007-413ST. - DOI - PMC - PubMed
1. Gower WA, et al. Pulmonary dysfunction in pediatric hematopoietic stem cell transplant patients: non-infectious and long-term complications. Pediatr Blood Cancer. 2007;49(3):225–233. doi: 10.1002/pbc.21060. - DOI - PubMed
1. Zinter MS, et al. Pediatric hematopoietic cell transplant patients who survive critical illness frequently have significant but recoverable decline in functional status. Biol Blood Marrow Transplant. 2018;24(2):330–336. doi: 10.1016/j.bbmt.2017.10.036. - DOI - PMC - PubMed
1. Zinter MS, et al. Intensive care risk and long-term outcomes in pediatric allogeneic hematopoietic cell transplant recipients. Blood Adv. 2024;8(4):1002–1017. doi: 10.1182/bloodadvances.2023011002. - DOI - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

F31 CA271571/CA/NCI NIH HHS/United States

LinkOut - more resources

Full Text Sources
- American Society for Clinical Investigation
- PubMed Central

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Integrating pulmonary and systemic transcriptomes to characterize lung injury after pediatric hematopoietic stem cell transplant

Affiliations

Integrating pulmonary and systemic transcriptomes to characterize lung injury after pediatric hematopoietic stem cell transplant

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Update of

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources