Foundry120 atlas

← IBD single-cell transcriptomics

Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis

Download from source ↗

Dataset overview

Participants 8
Samples 12
Reuse readiness 7.6/10 evidence-backed score

Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis.

Du J, Zhang J, Wang L, Wang X, Zhao Y, Lu J, Fan T, Niu M, et al. · Nature communications · 2023

Abstract

Ulcerative colitis is a chronic inflammatory bowel disorder with cellular heterogeneity. To understand the composition and spatial changes of the ulcerative colitis ecosystem, here we use imaging mass cytometry and single-cell RNA sequencing to depict the single-cell landscape of the human colon ecosystem. We find tissue topological changes featured with macrophage disappearance reaction in the ulcerative colitis region, occurring only for tissue-resident macrophages. Reactive oxygen species levels are higher in the ulcerative colitis region, but reactive oxygen species scavenging enzyme SOD2 is barely detected in resident macrophages, resulting in distinct reactive oxygen species vulnerability for inflammatory macrophages and resident macrophages. Inflammatory macrophages replace resident macrophages and cause a spatial shift of TNF production during ulcerative colitis via a cytokine production network formed with T and B cells. Our study suggests components of a mechanism for the observed macrophage disappearance reaction of resident macrophages, providing mechanistic hints for macrophage disappearance reaction in other inflammation or infection situations.

doi:10.1038/s41467-023-39173-2 ↗ PMID 37344477 ↗ PMC10284839 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina NextSeq 500
Age group
—
Disease groups
—
Anatomical sites
inflamed colon region, normal ascending colon, healthy control colon

Data availability

  • Raw counts
  • Processed matrix
  • Analysis code

File types MTXTSV

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Analysis code is available
  • Participant mapping is available
  • Participant counts are documented

Limitations

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

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

Assay

FieldValueEvidence
assay.assay_type 10x Genomics droplet-based single-cell RNA sequencing
The single cells were loaded into Chromium microfluidic chips with v3 chemistry, then barcoded with a 10× Chromium Controller

Section Methods—Single-cell RNA-seq library construction, offset —
assay.library_chemistry Chromium Single Cell v3 reagent kit
sequencing libraries were constructed with reagents from a Chromium Single Cell v3 reagent kit

Section Methods—Single-cell RNA-seq library construction, offset —
assay.platform Illumina NextSeq 500
"instrument_model": "Illumina NextSeq 500"

Section —, offset —
assay.reference_genome GRCh38
Assembly: GRCh38

Section —, offset —
assay.sequencing_type scrna_seq
UC-self control,rep2,scRNA_seq

Section —, offset —

Cohort

FieldValueEvidence
cohort.non_ibd_controls 4
Four healthy control subjects and 4 UC patients were enrolled

Section Methods—Single-cell RNA-seq library construction, offset —
cohort.study_design cross_sectional inferred
For each of the 4 patients, 1 pinch biopsy specimen was collected from the inflamed colon region as the UC group, and 1 pinch biopsy specimen from the normal ascending colon of patients served as self-control

Section Methods—Single-cell RNA-seq library construction, offset —
cohort.total_participants 8
Four healthy control subjects and 4 UC patients were enrolled

Section Methods—Single-cell RNA-seq library construction, offset —
cohort.ulcerative_colitis_participants 4
Four healthy control subjects and 4 UC patients were enrolled

Section Methods—Single-cell RNA-seq library construction, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
All the codes related to the analysis are publicly available at https://github.com/shaoweinuaa/NC2022_Ulcerative_colitis .

Section Code availability, offset —
data_assets.open_access True
"isOpenAccess": "Y"

Section —, offset —
data_assets.participant_metadata True
"individual": "p1"

Section —, offset —
data_assets.processed_matrix True
Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

Section —, offset —
data_assets.raw_counts True
barcodes.tsv, features.tsv, matrix.mtx

Section —, offset —

Processing

FieldValueEvidence
processing.batch_correction_reported True
Batch effects across different individuals were removed by firstly identifying anchors using the FindIntegrationAnchors() function, followed by IntegrateData()

Section Methods—Single-cell RNA-seq analysis, offset —
processing.cell_type_annotation_method Seurat clustering and marker-based annotation
These genes were used for cluster annotation together with known lineage-specific markers.

Section Methods—Single-cell RNA-seq analysis, offset —
processing.quality_control_reported True
Cells with fewer than 200 and above 6000 detected genes were filtered out, as well as cells with a high proportion of mitochondrial gene counts per cell (>25%).

Section Methods—Single-cell RNA-seq analysis, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['inflamed colon region', 'normal ascending colon', 'healthy control colon']
Inflamed colon region; Normal ascending colon; Healthy control colon

Section —, offset —
specimens.inflamed_status_available True
"sample group": "UC"

Section —, offset —
specimens.number_of_cells 42952
42,952 single cells were captured with high sequencing quality

Section Results—scRNA-seq analysis confirms MDR of the UC ecosystem, offset —
specimens.number_of_samples 12
"n_samples": 12

Section —, offset —
specimens.participant_to_sample_mapping_available True
"individual": "p1"

Section —, offset —
specimens.specimen_type biopsy
4 pinch biopsy specimens from the healthy volunteers served as healthy control (HC group)

Section Methods—Single-cell RNA-seq library construction, offset —