Foundry120 atlas

Increased neutrophils in inflammatory bowel disease accelerate the accumulation of amyloid plaques in the mouse model of Alzheimer's disease

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Dataset overview

Participants None
Samples 8
Reuse readiness 6.0/10 evidence-backed score

Increased neutrophils in inflammatory bowel disease accelerate the accumulation of amyloid plaques in the mouse model of Alzheimer's disease.

Abstract

<h4>Background</h4>Alzheimer's disease (AD) is one of the neurodegenerative diseases and characterized by the appearance and accumulation of amyloid-β (Aβ) aggregates and phosphorylated tau with aging. The aggregation of Aβ, which is the main component of senile plaques, is closely associated with disease progression. App<sup>NL-G-F</sup> mice, a mouse model of AD, have three familial AD mutations in the amyloid-β precursor gene and exhibit age-dependent AD-like symptoms and pathology. Gut-brain interactions have attracted considerable attention and inflammatory bowel disease (IBD) has been associated with a higher risk of dementia, especially AD, in humans. However, the underlying mechanisms and the effects of intestinal inflammation on the brain in AD remain largely unknown. Therefore, we aimed to investigate the effects of intestinal inflammation on AD pathogenesis.<h4>Methods</h4>Wild-type and App<sup>NL-G-F</sup> mice at three months of age were fed with water containing 2% dextran sulfate sodium (DSS) to induce colitis. Immune cells in the brain were analyzed using single-cell RNA sequencing (scRNA-seq) analysis, and the aggregation of Aβ protein in the brain was analyzed via immunohistochemistry.<h4>Results</h4>An increase in aggregated Aβ was observed in the brains of App<sup>NL-G-F</sup> mice with acute intestinal inflammation. Detailed scRNA-seq analysis of immune cells in the brain showed that neutrophils in the brain increased after acute enteritis. Eliminating neutrophils by antibodies suppressed the accumulation of Aβ, which increased because of intestinal inflammation.<h4>Conclusion</h4>These results suggest that neutrophils infiltrate the AD brain parenchyma when acute colitis occurs, and this infiltration is significantly related to disease progression. Therefore, we propose that neutrophil-targeted therapies could reduce Aβ accumulation observed in early AD and prevent the increased risk of AD due to colitis.

Study facts

Organism
Mus musculus
Platform
Illumina NovaSeq 6000
Age group
paediatric
Disease groups
—
Anatomical sites
Brain

Data availability

  • Raw counts
  • Processed matrix

File types MTXTSV

Files and samples

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Raw counts are advertised
  • Processed matrices are advertised

Limitations

  • 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 single-cell RNA sequencing
Single-cell RNA sequencing (scRNA-seq)

Section Single-cell RNA sequencing (scRNA-seq), offset —

assay.library_chemistry Chromium Next GEM Single Cell 5' Reagent Kits v2
Libraries were prepared according to the protocol of the Chromuim Next GEM Single Cell 5' Reagent Kits v2

Section Library preparation and NGS, offset —

assay.platform Illumina NovaSeq 6000
Illumina NovaSeq 6000

Section —, offset —

assay.reference_genome Genome Reference Consortium Mouse Build 38 (mm10)
Feature barcode matrices were created from the FASTQ data by Cell Ranger Multi (mouse genome; Genome Reference Consortium Mouse Build 38, mm10)

Section Preprocessing, offset —

assay.sequencing_type scrna_seq
immune cells in their brains were analyzed by scRNA-seq analysis

Section Single-cell RNA sequencing (scRNA-seq), offset —

Cohort

FieldValueEvidence
cohort.age_group paediatric from source
GEO age characteristics: 16 weeks old; 16 weeks old; 16 weeks old; 16 weeks old; 16 weeks old; 16 weeks old; 16 weeks old; 16 weeks old

Section GEO family SOFT, offset —

cohort.treatment_exposure_documented True
The control groups received only water, the acute colitis groups received DSS (2%, w/v...) in their drinking water for one week, and the chronic colitis group received three cycles of alternating 2% DSS then only water

Section DSS exposure, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
Public on Dec 01 2022

Section —, offset —

data_assets.processed_matrix True
matrix.mtx.gz

Section —, offset —

data_assets.raw_counts True
matrix.mtx.gz

Section —, offset —

data_assets.raw_reads True
GSE214747_RAW.tar

Section —, offset —

Processing

FieldValueEvidence
processing.cell_type_annotation_method Manual annotation using previously reported marker genes
Each identified cluster was then manually annotated with marker genes that have been previously reported as marker genes for defining cell subsets

Section Data analysis, offset —

processing.normalization_method Seurat normalizeData with scale.factor = 10,000
Expression data were normalized with the normalizeData function (scale.factor = 10,000)

Section Data analysis, offset —

processing.quality_control_reported True
Cells with more than 5% of mitochondrial genes and cells with nFeature_RNA less than 200 were filtered out

Section Data analysis, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['Brain']
Brain

Section —, offset —

specimens.number_of_samples 8
"sample_count": 8

Section —, offset —