Immune cell-specific genetic architecture of Alzheimer's disease revealed by multi-omics analysis for therapeutic target discovery and prioritization.
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- [1] § Materials and methods › MR using Sc-eQTL data ↔ analysispipeline_main.R, lines 133–189 · score 0.59 · inverse variance weighted, Wald ratio, MR, eQTL, colocalization, SNP
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The authors' code
R · 358 lines · 12 KB · Apache-2.0 · 1 match
- # Pipeline Overview: Single-cell MR Discovery, Replication, and Colocalization
- # ----------------------------
- # Step 1: Discovery Mendelian Randomization (MR)
- # ----------------------------
- ## 1.1 Load necessary libraries and data
- library(readxl)
- library(dplyr)
- library(TwoSampleMR)
- library(MRInstruments)
- library(writexl)
- # 1.1 Load raw single-cell eQTL data and format
- dataset1K1K_raw <- read_excel("file_path/dataset1K1K.xlsx")
- dataset1K1K <- dataset1K1K_raw %>%
- dplyr::filter(pvalue < 1e-5) %>%
- dplyr::mutate(
- se = abs(`rho correlation coefficient` / qnorm(pvalue/2)),
- beta = `rho correlation coefficient`,
- pval = pvalue,
- cell = `Cell type`,
- phenotype = `Gene ID`,
- effect_allele = `SNP assessed allele`
- ) %>%
- dplyr::select(cell, phenotype, SNP, effect_allele, beta, se, pval)
- # Save formatted dataset1K1K file for reuse
- write_xlsx(dataset1K1K, "file_path/dataset1K1K_formatted.xlsx")
- ## 1.2 Load and format outcome GWAS data
- outcome_df <- data.table::fread(file = "file_path/outcome.tsv", header = TRUE)
- outcome_df <- as.data.frame(outcome_df)
- outcome <- format_data(
- outcome_df,
- type = "outcome",
- snp_col = "SNP",
- beta_col = "beta",
- se_col = "standard_error",
- effect_allele_col = "effect_allele",
- other_allele_col = "other_allele",
- pval_col = "p_value"
- )
- # Save formatted outcome for reuse
- save(outcome, file = "file_path/outcome.RData")
- ## 1.3 Run MR for a cell type
- cell_type <- "B IN" # manual: set cell_type (`"B IN", "B Mem", "CD4 ET",
- #"CD4 NC", "CD4 SOX4", "CD8 ET", "CD8 NC", "CD8 S100B", "DC", "Mono C", "Mono NC",
- #"NK", "NK R", "Plasma")
- exp_df <- dataset1K1K %>%
- dplyr::filter(cell == cell_type)
- exp_obj <- format_data(
- exp_df,
- type = "exposure",
- snp_col = "SNP",
- beta_col = "beta",
- se_col = "se",
- effect_allele_col = "effect_allele",
- phenotype_col = "phenotype",
- pval_col = "pval"
- )
- har <- harmonise_data(exp_obj, outcome, action = 1)
- mr_res_cell_type <- mr(har) %>%
- dplyr::filter(method %in% c("Inverse variance weighted", "Wald ratio")) %>%
- dplyr::mutate(qval = p.adjust(pval, method = "BH")) %>%
- mutate(cell = cell_type)
- # (Repeat the above block for each cell type)
- # After running for all desired cell types, bind and save combined results:
- combined <- dplyr::bind_rows(mget(ls(pattern = "^mr_res_")))
- write_xlsx(combined, "file_path/discMR_outcome.xlsx")
- # ----------------------------
- # Step 2: Replication Mendelian Randomization (MR)
- # ----------------------------
- ## 2.1 Load previously formatted outcome for replication
- load("file_path/outcome.RData")
- ## 2.1 Load libraries and replication exposure dataset
- library(readr)
- library(readxl)
- library(dplyr)
- library(meta)
- library(genetics.binaRies)
- library(TwoSampleMR)
- scBloodNL_cell_type <- read_delim(
- "file_path/cell_type_expression_eQTLsFDR-ProbeLevel.txt", delim = "\t") %>%
- dplyr::filter(PValue < 1e-5) # manual: set cell_type ("B", "CD4", "CD8", "DC",
- #"Mono", "NK")
- ## 2.2 Identify significant genes from discovery MR
- discMR <- read_excel("file_path/discMR_outcome.xlsx")
- sig_genes <- discMR %>% filter(cell %in% cell_types, qval < 0.05) %>%
- pull(exposure) # manual: set cell_types ("B IN", "B Mem", "Plasma" for "B",
- #"CD4 ET", "CD4 NC", "CD4 SOX4" for "CD4", "CD8 ET", "CD8 NC", "CD8 S100B" for "CD8",
- #"DC" for "DC", "Mono C", "Mono NC" for "Mono", "NK", "NK R" for "NK")
- ## 2.3 Subset replication exposure and export for manual formatting
- subset_cell_type <- scBloodNL_cell_type %>% dplyr::filter(HGNCName %in% sig_genes)
- write_xlsx(subset_cell_type, "file_path/subset_cell_type.xlsx")
- # manual: keep required columns, format column names and add beta_i, se_i, beta_ii, se_ii and save
- rep_cell_type <- read_excel("file_path/subset_cell_type.xlsx")
- df1 <- rep_cell_type %>% dplyr::select(HGNCName, SNP, beta_i, se_i) %>%
- dplyr::mutate(obs = row_number())
- df2 <- rep_cell_type %>% dplyr::select(HGNCName, SNP, beta_ii, se_ii) %>%
- rename("beta_i" = "beta_ii", "se_i" = "se_ii") %>% dplyr::mutate(obs = row_number())
- meta_df <- bind_rows(df1, df2) %>% arrange(obs)
- ma_rep <- metagen(TE = beta_i, seTE = se_i, data = meta_df, common = TRUE,
- random = FALSE, sm = "MD", backtransf = FALSE, subgroup = obs)
- rep_cell_type <- bind_cols(rep_cell_type,
- data.frame(beta = ma_rep$TE.fixed.w, se = ma_rep$seTE.fixed.w))
- clumped <- ld_clump_local(
- tibble(rsid = rep_cell_type$SNP, pval = rep_cell_type$PValue),
- plink_bin = "file_path/plink_win64_20231211/plink.exe",
- bfile = "file_path/Eur_ldref/EUR",
- clump_r2 = 0.1, clump_p = 1, clump_kb = 10000
- )
- rep_cell_type <- rep_cell_type %>% dplyr::filter(SNP %in% clumped$rsid)
- ## 2.4 Format and run replication MR
- rep_cell_type <- format_data(
- rep_cell_type,
- type = "exposure",
- snp_col = "SNP",
- beta_col = "beta",
- se_col = "se",
- effect_allele_col = "effect_allele",
- phenotype_col = "HGNCName",
- pval_col = "PValue"
- )
- har_rep <- harmonise_data(rep_cell_type, outcome, action = 1)
- mr_cell_type <- mr(har_rep) %>%
- dplyr::filter(method %in% c("Inverse variance weighted", "Wald ratio")) %>%
- dplyr::mutate(qval = p.adjust(pval, method = "BH")) %>%
- mutate(cell = cell_type)
- # (Repeat the above block for each cell type)
- # After running for all desired cell types, bind and save combined results:
- combined <- dplyr::bind_rows(mget(ls(pattern = "^mr_")))
- write_xlsx(combined, "file_path/repMR_outcome.xlsx")
- # ----------------------------
- # Step 3: Colocalization Analysis
- # ----------------------------
- ## 3.1 Format outcome for colocalisation
- outcome_df <- data.table::fread(file = "file_path/outcome.tsv", header = TRUE) %>%
- dplyr::rename("snp" = "SNP", "se" = "standard_error", "pval" = "p_value") %>%
- dplyr::mutate(varbeta = se^2) %>%
- dplyr::select(snp, beta, varbeta, pval)
- outcome <- as.list(outcome_df)
- outcome$type <- "cc"
- outcome$s <- p #manual: add proportion of cases in outcome population
- ## 3.2 Subset eQTLs for finer cell and matching genes
- disc_hits <- read_excel("file_path/discMR_outcome.xlsx") %>%
- filter(cell == cell_type, qval < 0.05) # manual: set cell_type (`"B IN", "B Mem",
- #"CD4 ET", "CD4 NC", "CD4 SOX4", "CD8 ET", "CD8 NC", "CD8 S100B", "DC", "Mono C",
- #"Mono NC", "NK", "NK R", "Plasma")
- rep_hits <- read_excel("file_path/repMR_outcome.xlsx") %>%
- filter(cell == cell_type, qval < 0.05) # manual: set cell_types
- #("B" for "B IN","B Mem","Plasma","CD4" for "CD4 ET","CD4 NC","CD4 SOX4",
- # "CD8" for "CD8 ET","CD8 NC","CD8 S100B","DC" for "DC",
- # "Mono" for "Mono C","Mono NC","NK" for "NK","NK R")
- matching_genes <- intersect(disc_hits$exposure, rep_hits$exposure)
- dataset1K1K <- read_excel("file_path/dataset1K1K_formatted.xlsx", col_names = TRUE)
- eqtl_df <- dataset1K1K %>% filter(cell == cell_type, phenotype %in% matching_genes)
- # manual: set cell_type (`"B IN", "B Mem", #"CD4 ET", "CD4 NC", "CD4 SOX4", "CD8 ET",
- #"CD8 NC", "CD8 S100B", "DC", "Mono C", "Mono NC", "NK", "NK R", "Plasma")
- eqtl_df$varbeta <- eqtl_df$se^2
- eqtl_df$MAF <- MAF #MAF values of SNPs can be obtained from Ensembl
- eqtl_df <- eqtl_df %>%
- rename("gene" = "phenotype", "snp" = "SNP", "position" = "Position")
- ## 3.3a Colocalization using coloc.abf
- library(coloc)
- # Get unique gene values
- unique_genes <- unique(eqtl_df$gene)
- # Initialize a list to store colocalization results
- results_list <- list()
- # Initialize an empty dataframe to store the posterior probabilities
- pp_df_abf <- data.frame(
- Gene = character(),
- PP_H0 = numeric(),
- PP_H1 = numeric(),
- PP_H2 = numeric(),
- PP_H3 = numeric(),
- PP_H4 = numeric(),
- stringsAsFactors = FALSE
- )
- for (gene in unique_genes) {
- # Subset dataframe for the current gene and convert to list
- gene_subset <- as.list(eqtl_df[eqtl_df$gene == gene, ])
- # Add scalars to the list
- gene_subset$type <- "quant"
- gene_subset$N <- s # manual: set sample size (CD4 NC=463528,
- #CD4 ET=61786, CD4 SOX4=4065, CD8 ET=205077, CD8 NC=133482, CD8 S100B=34528,
- #DC=8690, Plasma=3625, Mono C=38233, Mono NC=15166, B Mem=48023, B IN=82068,
- #NK=159820, NK R=9677)
- # Run colocalization analysis using coloc.abf()
- coloc_result <- coloc.abf(gene_subset, outcome, MAF = NULL,
- p1 = 1e-04, p2 = 1e-04, p12 = 1e-05)
- # Store the coloc_result for that gene in results_list
- results_list[[gene]] <- coloc_result
- # Check if the coloc_result object has row names
- if (length(rownames(coloc_result)) == 0) {
- print(paste("No colocalization results found for gene:", gene))
- } else {
- # Extract the posterior probabilities from the coloc_result object
- pp_h0 <- coloc_result$PP.H0.abf
- pp_h1 <- coloc_result$PP.H1.abf
- pp_h2 <- coloc_result$PP.H2.abf
- pp_h3 <- coloc_result$PP.H3.abf
- pp_h4 <- coloc_result$PP.H4.abf
- # Create a row for the current gene in the pp_df_abf dataframe
- gene_row <- data.frame(
- Gene = gene,
- PP_H0 = pp_h0,
- PP_H1 = pp_h1,
- PP_H2 = pp_h2,
- PP_H3 = pp_h3,
- PP_H4 = pp_h4,
- stringsAsFactors = FALSE
- )
- # Append the gene_row to the pp_df_abf dataframe
- pp_df_abf <- rbind(pp_df_abf, gene_row)
- }
- }
- pp_df_abf$cell <- cell_type
- pp_df_abf_cell_type <- pp_df_abf
- # After running for all desired cell types, bind and save combined results:
- combined <- dplyr::bind_rows(mget(ls(pattern = "^pp_df_abf_")))
- write_xlsx(combined, "file_path/colabf_outcome.xlsx")
- ## 3.3b Colocalization using coloc.susie for Gene IDs with >1 eQTL as IV
- remotes::install_github("chr1swallace/coloc")
- library(coloc)
- library(data.table)
- library(TwoSampleMR)
- # Identify overlapping SNPs with outcome
- eqtl_df <- eqtl_df %>% rename(SNP = snp)
- outcome <- data.table::fread(file = "file_path/outcome.tsv", header = TRUE)
- common_snps <- intersect(eqtl_df$SNP, outcome$SNP)
- outcome <- outcome[outcome$SNP %in% common_snps, ]
- # Mismatch correction
- # Identify allele mismatches and correct them
- mismatched_snps <- eqtl_df %>%
- inner_join(outcome, by = "SNP") %>%
- filter(effect_allele.x != effect_allele.y)
- if (nrow(mismatched_snps) > 0) {
- for (i in 1:nrow(mismatched_snps)) {
- snp <- mismatched_snps$SNP[i]
- # Update effect allele to match outcome and flip beta
- eqtl_df <- eqtl_df %>%
- mutate(
- effect_allele = ifelse(SNP == snp, outcome$effect_allele[outcome$SNP == snp], effect_allele),
- beta = ifelse(SNP == snp, -beta, beta)
- )
- cat("Corrected allele mismatch for SNP:", snp, "\n")
- }
- }
- # Write the list of common SNPs
- write.table(common_snps, "locus_snps.txt", row.names = FALSE, col.names = FALSE, quote = FALSE)
- system("file_path/plink_win64_20231211/plink.exe --bfile file_path/Eur_ldref/EUR --extract locus_snps.txt --keep-allele-order --out locus_ld --r square --write-snplist")
- # Read LD matrix and SNP names
- ld <- read.table("locus_ld.ld", header = FALSE)
- ldnames <- fread("locus_ld.snplist", header = FALSE)
- # Create LD matrix
- ld.mat <- matrix(as.vector(data.matrix(ld)), nrow = nrow(ldnames), ncol = nrow(ldnames))
- # Name rows and columns
- colnames(ld.mat) <- ldnames$V1
- rownames(ld.mat) <- ldnames$V1
- # Prepare Dataset1 from eqtl_df
- Dataset1 <- list(
- beta = eqtl_df$beta,
- varbeta = eqtl_df$se^2,
- snp = eqtl_df$SNP,
- type = "quant",
- MAF = eqtl_df$MAF,
- N = s, # manual: set sample size (CD4 NC=463528,
- #CD4 ET=61786, CD4 SOX4=4065, CD8 ET=205077, CD8 NC=133482, CD8 S100B=34528,
- #DC=8690, Plasma=3625, Mono C=38233, Mono NC=15166, B Mem=48023, B IN=82068,
- #NK=159820, NK R=9677)
- LD = ld.mat
- )
- # Prepare Dataset2 from outcome_sub
- Dataset2 <- list(
- beta = outcome$beta,
- varbeta = outcome$se^2,
- snp = outcome$SNP,
- type = "cc",
- N = s, # manual: set sample size
- LD = ld.mat
- )
- # Run SuSiE fine-mapping on both traits
- S1 <- runsusie(Dataset1)
- S2 <- runsusie(Dataset2)
- # Perform coloc.susie
- susie_res <- coloc.susie(S1, S2)
- # Extract rsid and PP.H4.abf
- susie_df <- data.frame(
- rsid = susie_res$summary$hit1,
- PP_H4_abf = susie_res$summary$`PP.H4.abf`,
- stringsAsFactors = FALSE
- )
- susie_df$cell <- cell_type
- susie_df_cell_type <- susie_df
- # After running for all desired cell types, bind and save combined results:
- combined <- dplyr::bind_rows(mget(ls(pattern = "^susie_df_")))
- write_xlsx(combined, "file_path/colsus_outcome.xlsx")
analysispipeline_main.R at commit 1d96949, under Apache-2.0 · at the source
Overview
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122 P. R. China
- MOE Medical Basic Research Innovation Center for Gut Microbiota and Chronic Diseases, School of Medicine, Jiangnan University, Wuxi, Jiangsu China
- Department of Pathology, Affiliated Hospital of Jiangnan University, Wuxi, 214122 China
Abstract
Alzheimer’s disease (AD) is a multifactorial neurodegenerative condition in which accumulating genetic and molecular evidence implicates dysregulation of peripheral immune processes in disease pathogenesis. Nevertheless, the contribution of distinct peripheral immune cell subsets and associated gene regulatory landscapes to AD risk remains incompletely defined. To address this gap, we integrated single-cell expression quantitative trait loci (sc‑eQTL) data from the OneK1K cohort with AD GWAS summary statistics. We systematically interrogated immune cell-specific genes for their contributions to AD risk by integrating genetic causal inference with Bayesian colocalization analyses, and identified 24 eGenes that passed both the MR significance threshold (P < 0.05) and the criterion for strong shared genetic signals (PP.H4 > 0.8). Notable candidates included GATS, HLA-DOB, HLA-DQA1, PM20D1, and others, with each gene demonstrating a cell-type-specific association restricted to its corresponding immune cell type, such as monocytes, CD8 + T cells, or B cells. Independent peripheral blood single-cell transcriptomic data further supported disease-associated shifts in cell-type-specific expression patterns in AD. Phenome-wide association studies (PheWAS) indicated limited associations with off-target traits, indicating a favorable safety profile for therapeutic intervention, with the exceptions of B4GALNT3, PM20D1, and CNN2. Integration of immune gene targets with pharmacological databases yielded three candidate compound, including NSC321521 (targeting HLA-DQA1), phenoxybenzamine (targeting GSTP1), and rimexolone (targeting BIN1). Among these compounds, Predicted blood-brain barrier permeability was observed only for phenoxybenzamine and rimexolone, with docking studies indicating stable interactions, such as those between NSC321521 and HLA-DQA1, phenoxybenzamine and GSTP1, and rimexolone and BIN1. This integrative approach highlights key immune‑cell‑specific genes involved in AD and proposes repurposable drugs with central nervous system potential, paving the way for more targeted immunomodulatory strategies in AD.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.
DeepVasc-Lab/3-step_sceQTLMR
1d9694953d43eb94dc6efd2dc945851b3937ef15, 16 June 2025Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
3 files
- analysispipeline_main.R, R, 358 lines, 1 match
- LICENSE, License, 201 lines
- README.md, Text, 35 lines
Code availability
This article does not have its own special program; the calculation scripts refers to https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 1 script, each with its path and the digest of its content;
- 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- geo:GSE196830, at NCBI GEO; found in the text, “GWAS summary statistics”
Data availability
All data used to support the findings of this study are included within the article, and raw data are available from the corresponding author.
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 2, 28 September 2026
- Funding: added National Natural Science Foundation of China: 82401671, 81601121, 82571630, BK20231050, BK20211238; China Postdoctoral Science Foundation: 2020M651491; Government of Jiangsu Province; Jiangnan University; Fundamental Research Funds for the Central Universities: JUSRP123070
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 2 keywords, 6 MeSH terms, 67 references.
Cite
This paper
Gao, T.-l., Geng, S., Chen, J., Yang, L., Nie, Y.-j., Yu, H., & Chai, G.-s. (2026). Immune cell-specific genetic architecture of Alzheimer's disease revealed by multi-omics analysis for therapeutic target discovery and prioritization. Translational psychiatry, 16(1), 449. https://
BibTeX
@article{gao2026immune,
author = {Gao, Tian-long and Geng, Shan and Chen, Jia and Yang, Liu and Nie, Yun-juan and Yu, Haitao and Chai, Gao-shang},
title = {{Immune cell-specific genetic architecture of Alzheimer's disease revealed by multi-omics analysis for therapeutic target discovery and prioritization}},
journal = {Translational psychiatry},
year = {2026},
month = jun,
volume = {16},
number = {1},
pages = {449},
publisher = {Nature Publishing Group},
issn = {2158-3188},
doi = {10.1038/
url = {https://
pmid = {42331779},
pmcid = {PMC13538538}
}
RIS
TY - JOUR
AU - Gao, Tian-long
AU - Geng, Shan
AU - Chen, Jia
AU - Yang, Liu
AU - Nie, Yun-juan
AU - Yu, Haitao
AU - Chai, Gao-shang
TI - Immune cell-specific genetic architecture of Alzheimer's disease revealed by multi-omics analysis for therapeutic target discovery and prioritization
T2 - Translational psychiatry
J2 - Transl Psychiatry
PY - 2026
DA - 2026/
VL - 16
IS - 1
SP - 449
SN - 2158-3188
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1038/
"type": "article-journal",
"title": "Immune cell-specific genetic architecture of Alzheimer's disease revealed by multi-omics analysis for therapeutic target discovery and prioritization",
"container-title": "Translational psychiatry",
"author": [
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"family": "Gao",
"given": "Tian-long"
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{
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"given": "Jia"
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{
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"given": "Haitao"
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"given": "Gao-shang"
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"container-title-short":
"volume": "16",
"issue": "1",
"page": "449",
"DOI": "10.1038/
"PMID": "42331779",
"PMCID": "PMC13538538",
"ISSN": "2158-3188",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2026,
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]
}
}
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H3K9bhb ameliorates synaptic plasticity and cognition in Alzheimer's disease. Journal: Experimental & molecular medicineIn common: Alzheimer's / dementia, cellular / molecular, 1 reference, author Gao-shang Chai
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