ArticleNature communications2022
Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers, 4 of them syntheses that pooled it.
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Who cites it
93 citing papers in PubMed, 4 syntheses or guidelines pooled it, 115 citations in OpenAlex.
- Optimized summary-statistic-based single-cell eQTL meta-analysis.Scientific reports · 2025Pooled it
- Molecular exploration of host-pathogen interactions in severeFrontiers in medicine · 2025Pooled it
- Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data.Genome biology · 2023Pooled it
- Integration ofFrontiers in immunology · 2023Pooled it
- Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet.Nature communications · 2026Article
- Cell-type-specific genetic architecture reveals neuronal and immune contributions to neuropsychiatric disorders.Molecular psychiatry · 2026Article
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- A whole-blood cryopreservation method streamlines clinical sample collection for multimodal single-cell immune profiling in sepsis.JCI insight · 2026Article
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- Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencing.iScience · 2026Article
- A map of intra- and intercellular immune responses across diverse in vitro stimuli and inflammatory disease.Genome medicine · 2026Article
- Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.Cell genomics · 2026Review
- Hierarchical classification of immune cell transcriptomes at population-scale.bioRxiv : the preprint server for biology · 2026Article
- Longitudinal clinical proteomics reveals pneumonia type-specific protein biomarkers and autoantibodies.JCI insight · 2026Article
- Genetic survey of biomarkers at early and mid-pregnancy identifies pregnancy-specialized immune regulation.PLoS genetics · 2026Article
- Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics.Immune network · 2026Review
- Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Dissecting Immune Mechanisms Underlying Sarcopenia Using Multi-omics Approaches.Calcified tissue international · 2026Article
- Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients.Nature communications · 2026Article
- Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.Genome biology · 2026Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
Abstract
The host's gene expression and gene regulatory response to pathogen exposure can be influenced by a combination of the host's genetic background, the type of and exposure time to pathogens. Here we provide a detailed dissection of this using single-cell RNA-sequencing of 1.3M peripheral blood mononuclear cells from 120 individuals, longitudinally exposed to three different pathogens. These analyses indicate that cell-type-specificity is a more prominent factor than pathogen-specificity regarding contexts that affect how genetics influences gene expression (i.e., eQTL) and co-expression (i.e., co-expression QTL). In monocytes, the strongest responder to pathogen stimulations, 71.4% of the genetic variants whose effect on gene expression is influenced by pathogen exposure (i.e., response QTL) also affect the co-expression between genes. This indicates widespread, context-specific changes in gene expression level and its regulation that are driven by genetics. Pathway analysis on the CLEC12A gene that exemplifies cell-type-, exposure-time- and genetic-background-dependent co-expression interactions, shows enrichment of the interferon (IFN) pathway specifically at 3-h post-exposure in monocytes. Similar genetic background-dependent association between IFN activity and CLEC12A co-expression patterns is confirmed in systemic lupus erythematosus by in silico analysis, which implies that CLEC12A might be an IFN-regulated gene. Altogether, this study highlights the importance of context for gaining a better understanding of the mechanisms of gene regulation in health and disease.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.