Gate Lab at Northwestern University
10.5281/zenodo.10472192
The peripheral immune system in Alzheimer’s disease (AD) has not been thoroughly studied with modern sequencing methods. To investigate epigenetic and transcriptional alterations to the AD peripheral immune system, we used single cell sequencing strategies, including assay for transposase-accessible chromatin and RNA sequencing. We reveal a striking amount of open chromatin in peripheral immune cells in AD. In CD8 T cells, we uncover a cis-regulatory DNA element co-accessible with the CXC motif chemokine receptor 3 gene promoter. In monocytes, we identify a novel AD-specific RELA transcription factor binding site adjacent to an open chromatin region in the nuclear factor kappa B subunit 2 gene. We also demonstrate apolipoprotein E genotype-dependent epigenetic changes in monocytes. Surprisingly, we also identify differentially accessible chromatin regions in genes associated with sporadic AD risk. Our findings provide novel insights into the complex relationship between epigenetics and genetic risk factors in AD peripheral immunity.
This repository contains code used to process and analyze scRNA+TCR+BCRseq and scATACseq data from the Epigenetic dysregulation in Alzheimer’s disease peripheral immunity study. Preprocessing scripts are numbered to specify execution order and corresponding scripts for figure panels are listed below.
All R dependencies are listed in the renv.lock file. Upon opening the ad_apoe_pub.Rproj file in Rstudio, the renv package should automatically download and activate. Afterwards, the user can run renv::restore() to download all necessary packages for the study.
The RNA+BCR+TCR dataset can be viewed and analyzed interactively in our modified ShinyCell app.
Raw RNA+BCR+TCR .fastq files and gene expression matrices can be downloaded from GSE226602. Raw ATAC .fastq files and peak matrices can be downloaded from GSE226267.
For any comments/questions about the study please refer to the Gate Lab website for contact information.
All scripts in code folder.
B: ATAC_preprocessing/2-ATAC_archr_umap.R + RNA_preprocessing/2-RNA_seurat_preprocessing.R
Figure 2. Epigenetic dysregulation in AD peripheral immunity and concordance with differential gene expression.
A: ATAC_DA/ATAC_LR+DESeq2_overlap_barplot.R + ATAC_DA/ATAC_LR+DESeq2_overlap.R
B: ATAC_preprocessing/ATAC_DAR_peak_type_composition.R + ATAC_preprocessing/ATAC_DAR_up_down_composition.R
D: RNA_DE/RNA_MAST+edgeR_overlap_barplot.R + RNA_DE/RNA_MAST+edgeR_overlap.R
E: RNA+ATAC_analysis/RNA+ATAC_DAR+DEG_barplot_upset.R
A: RNA+ATAC_analysis/RNA+ATAC_DAR+DEG_overlap_scatter.R
B: ATAC_TF_analysis/ATAC_TF_enrichment_scatter.R
C-D: ATAC_TF_analysis/maxATAC/ATAC_ADvsHC_Monocytes_NFKB2.R
Figure 4. Cis-regulatory sequences correlate with quantity of transcription of CXCR3 in CD8 T cells, which home to the AD brain.
A: RNA+ATAC_analysis/RNA+ATAC_correlation/ATAC_cicero_summary.R
B: RNA+ATAC_analysis/RNA+ATAC_correlation/RNA+ATAC_cre-linked-gene+DEG_overlap.R
C: RNA+ATAC_analysis/RNA+ATAC_correlation/RNA+ATAC_CXCR3_correlation.R
A: RNA+ATAC_analysis/RNA+ATAC_DAR+DEG_ADvsHC_in_APOE_heatmap_upset.R
B: RNA+ATAC_analysis/RNA+ATAC_DAR+DEG_ADvsHC_heatmap.R
C: RNA+ATAC_analysis/RNA+ATAC_DAR+DEG_overlap_scatter.R
D: Misc/ATAC_coverage_plot.R
E: ATAC_TF_analysis/ATAC_TF_enrichment_scatter.R
A-D: ATAC_DA/ATAC_DAR_AD_risk_gene_overlap.R (coverage plots merged with heatmaps in Illustrator)
E: Misc/ATAC_coverage_plot.R
F: TCR_analysis/umap-clonal.R
G: RNA_DE/volcano.R
Misc/demographics/demographic_table.Rmd
A: Misc/demographics/demographic_plots_optimized.R
B: Misc/revisions/biomarker_boxplots.R
C-E: ATAC_preprocessing/1-ATAC_archr_preprocessing.R
F: ATAC_preprocessing/3-ATAC_archr_label_transfer.R
G: ATAC_preprocessing/1-ATAC_archr_preprocessing.R
H-J: Misc/revisions/neuron_figures.R
A: RNA_preprocessing/4-RNA_celltype_annotation.R
B-D: RNA_preprocessing/2-RNA_seurat_preprocessing.R
E: RNA_preprocessing/1-RNA_soupx.R (visual made with Prism)
F: RNA_preprocessing/5-seurat_rna_celltypemarkers_heatmap.R
G: RNA_preprocessing/3-RNA_integration_dim_reduc.R + Misc/revisions/neuron_figures.R
I: Misc/revisions/figures-cell_num_boxplots.R
Supplemental Figure 3 (Related to Figure 3). Transcription factor footprinting and TFBS analysis in monocytes.
A: ATAC_TF_analysis/ATAC_footprinting.R
B: ATAC_TF_analysis/maxATAC/ATAC_ADvsHC_Monocytes_32bp_barplot_wholegenome.R
Supplemental Figure 5 (Related to Figure 4). A cis-regulatory sequence correlates with quantity of transcription of ABCA1 in monocytes.
A: RNA+ATAC_analysis/RNA+ATAC_correlation/RNA+ATAC_cre-linked-gene+DEG_overlap.R
B: RNA+ATAC_analysis/RNA+ATAC_correlation/RNA+ATAC_ABCA1_correlation.R
Supplemental Figure 7 (Related to Figure 6). APOE genotype-dependent dysregulation of clonally expanded T cells in AD.
A: ATAC_DA/ATAC_DAR_AD_risk_gene_overlap.R (coverage plots merged with heatmaps in Illustrator)
B: TCR_analysis/tcr-clonal_DE_ADvsHC_within_APOE_genotype.R
C: RNA+ATAC_analysis/RNA+ATAC_DAR+DEG_overlap_scatter.R
D: Misc/ATAC_coverage_plot.R
Supplemental Figure 8 (Related to Figure 6). Clonally expanded CD8+ TCM cells are transcriptionally altered in AD.
A: RNA_DE/RNA_DEG_APOE_heatmap.R
B: RNA_DE/volcano.R
C: TCR_analysis/tcr-clonal_DE_APOEvsAPOE.R
D: RNA_DE/volcano.R
Supplemental Table 1. Demographic table containing blood and CSF biomarker measurements of all patients stratified by APOE genotype.
Misc/demographics/demographic_table.Rmd
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent