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← IBD spatial transcriptomics

The role of DPF2 in mouse radiation-induced intestinal injury by spatial transcriptome

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Dataset overview

Participants None
Samples 2
Reuse readiness 5.9/10 evidence-backed score

The SWI/SNF chromatin-remodeling subunit DPF2 regulates macrophage inflammation in intestinal injury via the CACNA1D-mediated MAPK pathway.

Ji M, Liang H, Dong S, Guo Y, Lin Y, Zhang H, Wang Y, Lei Z, et al. · Proceedings of the National Academy of Sciences of the United States of America · 2025

Abstract

The immune system plays a pivotal role in pathogenesis of intestinal injury and subsequent regenerative processes, particularly macrophages, orchestrate the inflammatory response and tissue repair. Here, we identified that loss of double PHD fingers 2 (DPF2) enhances intestinal regeneration and reduces inflammation. Using a combination of mouse genetics, single cell RNA sequencing, and spatial transcriptomics, we found that <i>Dpf2</i> loss in macrophage modulates inflammatory polarization, thus protecting against intestinal injury. Mechanistically, <i>Dpf2</i> deficiency leads to loss of H3K27ac and H3K4me1 marks at <i>Cacna1d</i> enhancer, impairing <i>Cacna1d</i> messenger RNA (mRNA) expression and reducing intracellular calcium. Consequently, loss of <i>Dpf2</i> attenuates mitogen-activated protein kinases signaling activity, promoting an anti-inflammatory macrophage polarization. Finally, through analysis of clinical inflammatory bowel disease (IBD) single cell RNA and spatial transcriptome data, patient-derived organoids and clinical samples, we validated a positive correlation between DPF2, CACNA1D, and intestinal inflammation. Our findings establish an essential role for DPF2 in facilitating CACNA1D expression in macrophages to regulate intestinal inflammation and regeneration.

doi:10.1073/pnas.2518762122 ↗ PMID 41223220 ↗ PMC12646317 ↗

Study facts

Organism
Mus musculus
Platform
Spatial Transcriptomics
Age group
—
Disease groups
—
Anatomical sites
intestine

Data availability

  • Raw counts
  • Processed matrix
  • Spatial coordinates
  • Histology images
  • Analysis code

File types MTXPNGTSV

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates are advertised
  • Histology images are advertised
  • Analysis code is available

Limitations

  • 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.platform Spatial Transcriptomics
Library strategy: Spatial Transcriptomics

Section samples[WTIR].data_processing, offset —
assay.reference_genome GRCm38
Sequences were aligned to GRCm38 genome.

Section samples[WTIR].data_processing, offset —
assay.resolution spot
at least 50,000 reads per sopt(100μm)

Section samples[WTIR].extract_protocol, offset —
assay.segmentation_method BSTMatrix/BSTViewer built-in tissue recognition tool
The two images were aligned and the built-in tissue recognition tool was used to extract spots covered by tissue.

Section samples[WTIR].extract_protocol, offset —
assay.sequencing_based True from source
GEO assay type/library strategy: OTHER

Section GEO family SOFT, offset —

Cohort

FieldValueEvidence
cohort.treatment_exposure_documented True from source
GEO sample characteristics document treatment/therapy

Section GEO family SOFT, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8816nnn/GSM8816652/suppl/GSM8816652_wtirbarcodes.tsv.gz

Section GEO family SOFT, offset —
data_assets.file_manifest True from source
Supplementary files enumerated in family SOFT (ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8816nnn/GSM8816652/suppl/GSM8816652_wtirbarcodes.tsv.gz)

Section GEO family SOFT, offset —
data_assets.histology_images True from source
GEO deposit evidence: PNG in GEO suppfile types

Section GEO record summary, offset —
data_assets.open_access True
Public on Oct 07 2025

Section series.series_status, offset —
data_assets.processed_matrix True
matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

Section samples[WTIR].supplementary_files, offset —
data_assets.raw_counts True from source
GEO deposit evidence: MTX in GEO suppfile types

Section GEO record summary, offset —
data_assets.spatial_coordinates True
barcodes_pos.tsv.gz: list of spatial barcodes and the coordinates specifying spots

Section samples[WTIR].data_processing, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['intestine'] from source
GEO sample source names: intestine

Section GEO family SOFT, offset —
specimens.number_of_samples 2 computed
2 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method Fresh frozen, OCT embedded
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat

Section samples[WTIR].extract_protocol, offset —