Foundry120 atlas

← IBD single-cell transcriptomics

Gene expression profile at single cell level of patient-derived colon fibroblasts induced by different cytokine cocktails to become inflammation-associated fibroblasts (IAFs)

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Dataset overview

Participants None
Samples 8
Reuse readiness 6.7/10 evidence-backed score

Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling: IAFs disrupt colon epithelium via PGE2-EP4.

Dong Y, Johnson BA, Ruan L, Zeineldin M, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, et al. · bioRxiv : the preprint server for biology · 2023

Abstract

Inflammation-associated fibroblasts (IAFs) are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. In this study, we developed an <i>in vitro</i> model whereby human colon fibroblasts are induced to become IAFs by specific cytokines and recapitulate key features of IAFs <i>in vivo</i>. When co-cultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid swelling and barrier disruption due to swelling and rupture of individual epithelial cells. Epithelial cells co-cultured with IAFs also exhibit increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated through a paracrine pathway involving prostaglandin E2 (PGE2) and the PGE2 receptor EP4, leading to PKA-dependent activation of the CFTR chloride channel. Importantly, EP4-specific chemical inhibitors effectively prevented colonoid swelling and restored normal proliferation and genome stability of IAF-exposed epithelial cells. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a potential treatment to mitigate inflammation-associated epithelial injury.

doi:10.1101/2023.09.28.560060 ↗ PMID 37808771 ↗ PMC10557697 ↗

Study facts

Organism
Homo sapiens
Platform
10x Genomics Chromium Next GEM single cell 3’ HT reagent kit V3.1; Illumina NovaSeq 6000
Age group
adult
Disease groups
—
Anatomical sites
colon

Data availability

  • Processed matrix

File types TXT

Strengths & limitations for reuse

Strengths

  • Processed matrices are advertised
  • Cell metadata are advertised

Limitations

  • Not documented: raw counts 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
we performed single-cell RNA sequencing (scRNAseq)

Section Single Cell RNA sequencing of patient-derived fibroblast lines, offset —
assay.library_chemistry 10x Genomics single cell 3′ HT v3.1
loaded for single cell 3’ HT V3.1

Section —, offset —
assay.platform 10x Genomics Chromium Next GEM single cell 3’ HT reagent kit V3.1; Illumina NovaSeq 6000
the Chromium Next GEM single cell 3’ HT reagent kit V3.1 was used for sample preparation. After QC, sequencing was performed using a S4 flow cell in a NovaSeq 6000 system

Section Single Cell RNA sequencing of patient-derived fibroblast lines, offset —
assay.reference_genome GRCh38
Assembly: GRCh38

Section —, offset —
assay.sequencing_type scrna_seq
analyzed using scRNAseq

Section —, offset —

Cohort

FieldValueEvidence
cohort.age_group adult from source
GEO age characteristics: mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed; mixed

Section GEO family SOFT, offset —
cohort.crohns_disease_participants 4
2 CD non-stenotic samples, 2 CD stenotic samples

Section Results, offset —
cohort.non_ibd_controls 2
2 healthy controls

Section Results, offset —
cohort.treatment_exposure_documented True from source
GEO sample characteristics document treatment/therapy

Section GEO family SOFT, offset —
cohort.ulcerative_colitis_participants 2
2 UC samples

Section Results, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True
GSE237034_de-multiplexed_sample_information.txt.gz

Section —, offset —
data_assets.open_access True
Public on Jul 30 2023

Section —, offset —
data_assets.processed_matrix True
GSE237034_FibA_A01_sample_filtered_feature_bc_matrix.tar.gz

Section —, offset —

Processing

FieldValueEvidence
processing.cell_type_annotation_method Seurat reference mapping with anchor-based label transfer using a published UC atlas
Using a published reference mapping method, we compared single-cell gene expression profiles with a published UC atlas database

Section Single Cell RNA sequencing of patient-derived fibroblast lines, offset —
processing.normalization_method SCTransform
Seurat objects were normalized using SCTransform

Section Single Cell RNA sequencing of patient-derived fibroblast lines, offset —
processing.quality_control_reported True
After QC, sequencing was performed

Section Single Cell RNA sequencing of patient-derived fibroblast lines, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['colon']
colon

Section —, offset —
specimens.number_of_cells 60845
60,845 cells were recovered

Section Results, offset —
specimens.number_of_samples 8
obtained from 2 UC samples, 2 CD non-stenotic samples, 2 CD stenotic samples, and 2 healthy controls

Section Results, offset —
specimens.specimen_type resection
Fresh colonic tissue was harvested from patient specimens (CD, UC, and unaffected normal) within thirty minutes of surgical resection

Section Patient sample collection, offset —