Foundry120 atlas

Particulate matter 10 exposure affects intestinal functionality in both inflamed 2D intestinal epithelial cell and 3D intestinal organoid models

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Dataset overview

Participants None
Samples None
Reuse readiness 5.0/10 evidence-backed score

Particulate matter 10 exposure affects intestinal functionality in both inflamed 2D intestinal epithelial cell and 3D intestinal organoid models.

Abstract

<h4>Background</h4>A growing body of evidence suggests that particulate matter (PM10) enters the gastrointestinal (GI) tract directly, causing the GI epithelial cells to function less efficiently, leading to inflammation and an imbalance in the gut microbiome. PM10 may, however, act as an exacerbation factor in patients with inflamed intestinal epithelium, which is associated with inflammatory bowel disease.<h4>Objective</h4>The purpose of this study was to dissect the pathology mechanism of PM10 exposure in inflamed intestines.<h4>Methods</h4>In this study, we established chronically inflamed intestinal epithelium models utilizing two-dimensional (2D) human intestinal epithelial cells (hIECs) and 3D human intestinal organoids (hIOs), which mimic <i>in vivo</i> cellular diversity and function, in order to examine the deleterious effects of PM10 in human intestine-like <i>in vitro</i> models.<h4>Results</h4>Inflamed 2D hIECs and 3D hIOs exhibited pathological features, such as inflammation, decreased intestinal markers, and defective epithelial barrier function. In addition, we found that PM10 exposure induced a more severe disturbance of peptide uptake in inflamed 2D hIECs and 3D hIOs than in control cells. This was due to the fact that it interferes with calcium signaling, protein digestion, and absorption pathways. The findings demonstrate that PM10-induced epithelial alterations contribute to the exacerbation of inflammatory disorders caused by the intestine.<h4>Conclusions</h4>According to our findings, 2D hIEC and 3D hIO models could be powerful <i>in vitro</i> platforms for the evaluation of the causal relationship between PM exposure and abnormal human intestinal functions.

Study facts

Organism
Homo sapiens
Platform
Illumina NextSeq1000
Age group
Disease groups
Anatomical sites

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised

Limitations

  • Not documented: feature/otu tables are advertised
  • Not documented: taxonomic tables 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.paired_end True
with a read length of 2 × 100 bases.

Section RNA-sequencing analysis, offset —

assay.platform Illumina NextSeq1000
We performed RNA-seq on an Illumina NextSeq1000 (Illumina) using the standard Illumina RNA-Seq protocol

Section RNA-sequencing analysis, offset —

assay.read_length 100
with a read length of 2 × 100 bases

Section RNA-sequencing analysis, offset —

Cohort

FieldValueEvidence
cohort.treatment_exposure_documented True
To generate inflamed 2D hIECs, 10, 50, and 100 ng/ml IFNγ and 10, 50, and 100 ng/ml TNFα were differentiated from days 4 to 14. PM10 was administered between days 7 and 14.

Section hPSC-derived 2D hIECs differentiation, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True from source
"isOpenAccess": "Y"

Section publication metadata, offset —

data_assets.pipeline_or_tool_versions True
Cutadapt v.3.7

Section RNA-sequencing analysis, offset —

data_assets.qc_or_negative_controls_reported True
In order to evaluate the sequence data, the NGSQCToolkit v.2.3.3 was used

Section RNA-sequencing analysis, offset —

data_assets.raw_reads True inferred
The original contributions presented in the study are publicly available. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227514 .

Section Data availability statement, offset —

Specimens

FieldValueEvidence
specimens.body_site small intestine
we differentiated hPSCs into 2D hIECs, which are relevant models for the human small intestine

Section Results — Establishment of in vitro 2D inflamed hIECs, offset 16880

specimens.inflamed_status_available True
RNA-seq analyses were performed on normal and inflamed hIECs with or without PM10 treatment.

Section RNA-sequencing analysis, offset —