ArticlePLoS genetics2022
Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 87 citations in OpenAlex.
- Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes.Circulation. Genomic and precision medicine · 2023Pooled it
- Machine learning and statistical methods for molecular quantitative trait loci.Nature reviews. Genetics · 2026Review
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Cryopreservation alters contractile function of human induced pluripotent stem cell-derived cardiomyocytes.Scientific reports · 2026Article
- Single-Cell Multi-Omics Reveal Gene Regulatory Mechanisms Underlying Cardiac Embryonic Development.Genes · 2026Review
- The spatiotemporal dynamics of MAMs: mechanisms, pathologies, and therapeutic rewiring.Cellular & molecular biology letters · 2026Review
- Single cell transcriptomic landscape of adult and pediatric non-ischemic cardiomyopathy.Journal of molecular and cellular cardiology · 2026Review
- Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells.medRxiv : the preprint server for health sciences · 2026Article
- Transcriptome-wide association studies at cell-state level using single-cell eQTL data.Cell genomics · 2026Article
- Early multi-omic signatures and machine learning models predict cardiomyocyte differentiation efficiency and enable robust hPSC differentiation to cardiomyocytes.bioRxiv : the preprint server for biology · 2026Article
- distQTL: distribution quantitative trait loci identification by population-scale single-cell data.NAR genomics and bioinformatics · 2025Article
- Integrating Spatial Omics and Deep Learning: Toward Predictive Models of Cardiomyocyte Differentiation Efficiency.Bioengineering (Basel, Switzerland) · 2025Review
- distQTL: Distribution Quantitative Trait Loci Identification by Population-Scale Single-Cell Data.bioRxiv : the preprint server for biology · 2025Article
- Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components.American journal of human genetics · 2025Article
- Effect of iPS cell culture medium on the differentiation potential of induced cardiac tissues.Scientific reports · 2025Article
- Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells.G3 (Bethesda, Md.) · 2025Article
- Comparative transcriptomics of iPSC-derived cardiomyocytes in a high and a low altitude population.bioRxiv : the preprint server for biology · 2025Article
- Characterizing the Cellular Constituents of Proximal Airway Disease in Granulomatosis With Polyangiitis.Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2025Article
- Trans-eQTL hotspots shape complex traits by modulating cellular states.Cell genomics · 2025Article
- Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes.PLoS genetics · 2025Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.
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