Transcriptome analysis in acute gastrointestinal graft-<i>versus</i> host disease reveals a unique signature in children and shared biology with pediatric inflammatory bowel disease
Pooja Khandelwal,
Dana T Lounder,
Allison Bartlett,
Yael Haberman,
Anil G. Jegga,
Sudhir Ghandikota,
Jane Koo,
Nathan Luebbering,
Daniel Leino,
Sheyar Abdullah,
Michaela Loveless,
Phillip Minar,
Kelly Lake,
Bridget Litts,
Rebekah Karns,
Adam S. Nelson,
Lee A. Denson,
Stella M. Davies
Affiliations
Pooja Khandelwal
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Dana T Lounder
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Allison Bartlett
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Yael Haberman
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Gastroenterology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Sheba Medical Center, Hashomer, affiliated with the Aviv University, Israel 52620
Anil G. Jegga
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
Sudhir Ghandikota
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
Jane Koo
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Nathan Luebbering
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Daniel Leino
Department of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
Sheyar Abdullah
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Michaela Loveless
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Phillip Minar
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Gastroenterology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
Kelly Lake
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Bridget Litts
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Rebekah Karns
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Gastroenterology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
Adam S. Nelson
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
Lee A. Denson
Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Gastroenterology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
Stella M. Davies
Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229
We performed transcriptomic analyses on freshly frozen (n=21) and paraffin-embedded (n=35) gastrointestinal (GI) biopsies from children with and without acute acute GI graft-versus-host disease (GvHD) to study differential gene expressions. We identified 164 significant genes, 141 upregulated and 23 downregulated, in acute GvHD from freshy frozen biopsies. CHI3L1 was the top differentially expressed gene in acute GvHD, involved in macrophage recruitment and bacterial adhesion. Mitochondrial genes were among the top downregulated genes. Immune deconvolution identified a macrophage cellular signature. Weighted gene co-expression network analysis showed enrichment of genes in the ERK1/2 cascade. Transcriptome data from 206 ulcerative colitis (UC) patients were included to uncover genes and pathways shared between GvHD and UC. Comparison with the UC transcriptome showed both shared and distinct pathways. Both UC and GvHD transcriptomes shared an innate antimicrobial signature and FCγ1RA/CD64 was upregulated in both acute GvHD (log-fold increase 1.7, P=0.001) and UC. Upregulation of the ERK1/2 cascade pathway was specific to GvHD. We performed additional experiments to confirm transcriptomics. Firstly, we examined phosphorylation of ERK (pERK) by immunohistochemistry on GI biopsies (acute GvHD n=10, no GvHD n=10). pERK staining was increased in acute GvHD biopsies compared to biopsies without acute GvHD (P=0.001). Secondly, plasma CD64, measured by enzyme-linked immunsorbant assay (n=85) was elevated in acute GI GvHD (P<0.001) compared with those without and was elevated in GVHD compared with inflammatory bowel disease (n=47) (P<0.001), confirming the upregulated expression seen in the transcriptome.
