Evidence map›Paper›PMID 36727399›Full record

ArticleHaematologica2023

Transcriptome analysis in acute gastrointestinal graft-

Pooja Khandelwal, Dana T Lounder, Allison Bartlett, Yael Haberman, Anil G Jegga, Sudhir Ghandikota, Jane Koo, Nathan Luebbering, Daniel Leino, Sheyar Abdullah and 8 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Haematologica, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.2field-weighted citation impact, top 56% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 3 institutions in 2 countries.

Pooja KhandelwalDivision 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. Pooja.khandelwal@cchmc.org.
Dana T LounderDivision 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 BartlettDivision 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 HabermanDepartment 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 JeggaDepartment 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 GhandikotaDepartment 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 KooDivision 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 LuebberingDivision 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 LeinoDepartment of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.
Sheyar AbdullahDivision 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 LovelessDivision 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 MinarDepartment of Pediatrics, University of Cincinnati College of Medicine, Cincinnati OH 45229; Division of Gastroenterology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.
Kelly LakeDivision 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 LittsDivision 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 KarnsDepartment 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 NelsonDivision 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 DensonDepartment 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 DaviesDivision 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.
University of Cincinnati Medical Center · USCincinnati Children's Hospital Medical Center · USSheba Medical Center · IL

Funding

Stem Cell/Organoid and Genome Editing CoreP30DK078392 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI LEE ARMISTEAD DENSON · 2007 to 2026
$24.4M
Predicting Response to Standardized Pediatric Colitis Therapy: PROTECT StudyU01DK095745 · NIDDK · CONNECTICUT CHILDREN'S MEDICAL CENTER · PI DENSON, LEE ARMISTEAD, HYAMS, JEFFREY SAMUEL · 2012 to 2016
$10.4M
NIDDK NIH HHS P30 DK078392NIDDK NIH HHS U01 DK095745
6 · The paper itself

Abstract

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.

Indexed as

Graft vs Host DiseaseHematopoietic Stem Cell TransplantationInflammatory Bowel DiseasesAcute DiseaseBiologyChildGene Expression ProfilingHumansTranscriptome

Identifiers

PMID36727399
PMCPMC10316272
OpenAlexW4318935146

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.