Foundry120 atlas

← IBD single-cell transcriptomics

CD16+ CD163+ monocytes traffic to sites of inflammation in NEC

Download from source ↗

Dataset overview

Participants None
Samples 6
Reuse readiness 5.6/10 evidence-backed score

CD16+CD163+ monocytes traffic to sites of inflammation during necrotizing enterocolitis in premature infants.

Olaloye OO, Liu P, Toothaker JM, McCourt BT, McCourt CC, Xiao J, Prochaska E, Shaffer S, et al. · The Journal of experimental medicine · 2021

Abstract

Necrotizing enterocolitis (NEC) is a severe gastrointestinal complication of prematurity. Using suspension and imaging mass cytometry coupled with single-cell RNA sequencing, we demonstrate severe inflammation in patients with NEC. NEC mucosa could be subtyped by an influx of three distinct neutrophil phenotypes (immature, newly emigrated, and aged). Furthermore, CD16+CD163+ monocytes/Mϕ, correlated with newly emigrated neutrophils, were specifically enriched in NEC mucosa, found adjacent to the blood vessels, and increased in circulation of infants with surgical NEC, suggesting trafficking from the periphery to areas of inflammation. NEC-specific monocytes/Mϕ transcribed inflammatory genes, including TREM1, IL1A, IL1B, and calprotectin, and neutrophil recruitment genes IL8, CXCL1, CXCL2, CXCL5 and had enrichment of gene sets in pathways involved in chemotaxis, migration, phagocytosis, and reactive oxygen species generation. In summary, we identify a novel subtype of inflammatory monocytes/Mϕ associated with NEC that should be further evaluated as a potential biomarker of surgical NEC and a target for the development of NEC-specific therapeutics.

doi:10.1084/jem.20200344 ↗ PMID 34269788 ↗ PMC8289692 ↗

Study facts

Organism
Homo sapiens
Platform
10x Genomics Chromium
Age group
paediatric
Disease groups
—
Anatomical sites
small intestine

Data availability

  • Processed matrix

File types H5ADH5SEURATRDATA

Strengths & limitations for reuse

Strengths

  • Processed matrices are advertised

Limitations

  • Not documented: raw counts are advertised
  • Not documented: cell metadata are advertised
  • Not documented: participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.assay_type single-cell RNA sequencing
scRNA-seq was performed on a subset of small intestinal mucosa

Section Results, offset —
assay.library_chemistry 3′ GEM libraries
3' GEM libraries from 10X Medgenome kit

Section —, offset —
assay.platform 10x Genomics Chromium
using the 10× Genomics Chromium platform

Section scRNA-seq: 10X, offset —
assay.sequencing_type scrna_seq
3' Single cell RNA sequencing

Section —, offset —

Cohort

FieldValueEvidence
cohort.age_group paediatric from source
GEO age characteristics: 21 weeks; 21 weeks; 37 weeks; 36 weeks; 31 weeks; 39 weeks

Section GEO family SOFT, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
Public on Jun 15 2021

Section —, offset —
data_assets.processed_matrix True
GSE178088_cluster3.h5ad.gz

Section —, offset —

Processing

FieldValueEvidence
processing.batch_correction_reported True
The cells from different samples were integrated to minimize the batch effect.

Section scRNA-seq: Data analysis, offset —
processing.cell_type_annotation_method canonical gene expression
Clusters were identified based on canonical gene expression

Section scRNA-seq: Data analysis, offset —
processing.normalization_method LogNormalize
The data were normalized using the “LogNormalize” method.

Section scRNA-seq: Data analysis, offset —
processing.quality_control_reported True
Cells with mitochondria reads >25% or samples where the number of genes was <200 or >7,000 were filtered out.

Section scRNA-seq: Data analysis, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['small intestine']
3' Single cell RNA sequencing of viably cryoprserved human small intestinal tissue samples after live/dead selection.

Section series, offset —
specimens.inflamed_status_available True
"diagnosis": "necrotizing enterocolitis"

Section —, offset —
specimens.number_of_samples 6
"n_samples": 6

Section —, offset —