ArticleImmunogenetics2017
Identification of innate lymphoid cells in single-cell RNA-Seq data.
Article in Immunogenetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 19 citations in OpenAlex.
- Trained Immunity and Its Potential Implications in the Etiopathogenesis of Hidradenitis Suppurativa: A New Paradigm in Chronic Inflammation?Experimental dermatology · 2025Review
- Understanding vertebrate immunity through comparative immunology.Nature reviews. Immunology · 2025Review
- Immune in myocardial ischemia/reperfusion injury: potential mechanisms and therapeutic strategies.Frontiers in immunology · 2025Review
- Deciphering the Role of Innate Lymphoid Cells Group 3 in the Gut Microenvironment: A Narrative Review of Their Novel Contributions to Autoimmune Disease Pathogenesis.Journal of inflammation research · 2025Review
- Dissecting and Visualizing the Functional Diversity of Cardiac Macrophages.Circulation research · 2024Review
- (Multi-) omics studies of ILC2s in inflammation and metabolic diseases.Frontiers in cell and developmental biology · 2024Review
- Innate lymphoid cells-Underexplored guardians of immunity.PLoS pathogens · 2023Article
- Strategies for optimizing CITE-seq for human islets and other tissues.Frontiers in immunology · 2023Article
- Adipose tissue aging is regulated by an altered immune system.Frontiers in immunology · 2023Review
- ILC2-mediated immune crosstalk in chronic (vascular) inflammation.Frontiers in immunology · 2023Review
- A cardioimmunologist's toolkit: genetic tools to dissect immune cells in cardiac disease.Nature reviews. Cardiology · 2022Review
- The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression.Nature communications · 2022Article
- Sprouty2 limits intestinal tuft and goblet cell numbers through GSK3β-mediated restriction of epithelial IL-33.Nature communications · 2021Article
- The impact of single-cell RNA sequencing on understanding the functional organization of the immune system.Briefings in functional genomics · 2018Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Innate lymphoid cells (ILCs) consist of natural killer (NK) cells and non-cytotoxic ILCs that are broadly classified into ILC1, ILC2, and ILC3 subtypes. These cells recently emerged as important early effectors of innate immunity for their roles in tissue homeostasis and inflammation. Over the last few years, ILCs have been extensively studied in mouse and human at the functional and molecular level, including gene expression profiling. However, sorting ILCs with flow cytometry for gene expression analysis is a delicate and time-consuming process. Here we propose and validate a novel framework for studying ILCs at the transcriptomic level using single-cell RNA-Seq data. Our approach combines unsupervised clustering and a new cell type classifier trained on mouse ILC gene expression data. We show that this approach can accurately identify different ILCs, especially ILC2 cells, in human lymphocyte single-cell RNA-Seq data. Our new model relies only on genes conserved across vertebrates, thereby making it in principle applicable in any vertebrate species. Considering the rapid increase in throughput of single-cell RNA-Seq technology, our work provides a computational framework for studying ILC2 cells in single-cell transcriptomic data and may help exploring their conservation in distant vertebrate species.
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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.