Foundry120 atlas

← IBD single-cell transcriptomics

Gene expression profile at single cell level of periheral blood mono-nucleus cells (PBMC) in response to bacterial protein (PFOR) stimulation

Download from source ↗

Dataset overview

Participants None
Samples 2
Reuse readiness 5.7/10 evidence-backed score

Pyruvate: Ferredoxin oxidoreductase is involved in IgA-related microbiota dysbiosis and intestinal inflammation.

Wang K, Guo Y, Liu Y, Cui X, Gu X, Li L, Li Y, Li M. · Frontiers in immunology · 2022

Abstract

<h4>Introduction</h4>Inflammatory bowel diseases (IBDs) are associated with both immune abnormalities and dysbiosis, characterized by a loss of Faecalibacterium prausnitzii (F. prausnitzii). However, the reason for F. prausnitzii deficiency remains unclear.<h4>Methods</h4>16S rDNA seque-ncing and IgA enzyme-linked immunosorbent assay (ELISA) were applied to identify bacterial community and IgA changes in ulcerative colitis (UC) patients. Forced immunization with F. prausnitzii in rabbits was conducted. To screen for potential IgA-reactive proteins in F. prausnitzii lysates, we performed western blotting and mass spectrometry analyses. Pyruvate: ferredoxin oxidoreductase (PFOR) was cloned and purified, then the immunoreactivity of PFOR was verified in peripheral blood mononuclear cells (PBMCs) through PCR, ELISpot assay and single-cell sequencing (scRNA-seq). Finally, the UC fecal dysbiosis was re-analyzed in the context of the phylogenetic tree of PFOR.<h4>Results</h4>F. prausnitzii was underrepresented in UC patients with elevated F. prausnitzii-reactive IgA in the fecal supernatant. Forced immunization with F. prausnitzii in rabbits led to high interferon-γ (IFN-γ) transcription in the colon, along with beta diversity disturbance and intestinal inflammation. PFOR was identified as an IgA-binding antigen of F. prausnitzii and the immunoreactivity was validated in PBMCs, which showed elevated expression of inflammatory cytokines. The scRNA-seq revealed enhanced signals in both T regulatory cells (Tregs) and monocytes after PFOR incubation. Furthermore, phylogenetic analysis revealed that PFOR was a common but conserved protein among the gut bacteria.<h4>Discussion</h4>Our results collectively suggest that PFOR is a bioactive protein in the immune system and may contribute to host-microbial crosstalk. Conserved but bioactive microbial proteins, such as PFOR, warrant more attention in future host-microbial interaction studies.

doi:10.3389/fimmu.2022.1040774 ↗ PMID 36569858 ↗ PMC9782971 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina HiSeq X Ten
Age group
—
Disease groups
—
Anatomical sites
peripheral blood

Data availability

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

File types MTXTSV

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised

Limitations

  • Not documented: raw counts are advertised
  • Not documented: processed matrices 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 10× Genomics droplet-based 3′-end scRNA-seq
Bulk PCR amplification was then performed to establish a library for 3’-end sequencing.

Section Single-cell RNA sequencing and data analysis, offset —
assay.library_chemistry 10× Genomics droplet capture
scRNA-seq of 10× Genomics based on droplet capture technology

Section Single-cell RNA sequencing and data analysis, offset —
assay.platform Illumina HiSeq X Ten
"instrument_model": {"HiSeq X Ten": 2}

Section sample_values_with_sample_counts, offset —
assay.reference_genome GRCh38
align the reads to the human reference genome (GRCh38)

Section sample_values_with_sample_counts, offset —
assay.sequencing_type scrna_seq
scRNA-seq of 10× Genomics based on droplet capture technology

Section Single-cell RNA sequencing and data analysis, 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.open_access True
Public on Dec 01 2022

Section series, offset —
data_assets.raw_reads True
GSE217868_RAW.tar

Section —, offset —

Processing

FieldValueEvidence
processing.batch_correction_reported True
The R package Seurat was used to remove batch effects

Section Single-cell RNA sequencing and data analysis, offset —
processing.cell_type_annotation_method scCATCH with manual correction based on marker genes
The cell types were automatically annotated via scCATCH and manually corrected according to their marker genes.

Section Single-cell RNA sequencing and data analysis, offset —
processing.normalization_method Seurat
The R package Seurat was used to remove batch effects and perform normalization

Section Single-cell RNA sequencing and data analysis, offset —
processing.quality_control_reported True
After quality control and filtering by multiple criteria

Section The effects of PFOR on PBMCs revealed by single-cell sequencing, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['peripheral blood']
peripheral blood cells

Section sample_values_with_sample_counts, offset —
specimens.number_of_cells 16006 inferred
transcriptomes of 9235 and 6771 cells from the PFOR- and control-stimulated PBMCs were acquired

Section The effects of PFOR on PBMCs revealed by single-cell sequencing, offset —
specimens.number_of_samples 2
"sample_count": 2

Section sample_count, offset —