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Nat Immunol. 2015 Mar;16(3):306-17. doi: 10.1038/ni.3094. Epub 2015 Jan 26.

Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets.

Author information

1
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
2
Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, USA.
3
Merck Research Laboratories, Palo Alto, California, USA.
4
Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.
5
Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.
6
Computer Science Department, Stanford University, Stanford, California, USA.
7
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
8
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, USA.
9
Division of Immunology, Department of Microbiology &Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.
10
Department of Microbiology &Immunology, University of California San Francisco, San Francisco, California, USA.
11
Icahn Medical Institute, Mount Sinai Hospital, New York, New York, USA.
12
Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA and Department of Cancer Immunology, Genentech, San Francisco, California, USA.
13
Department of Medicine, Boston University, Boston, Massachusetts, USA.
14
Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA.
15
Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA.
16
Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
17
Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

Abstract

The recognized diversity of innate lymphoid cells (ILCs) is rapidly expanding. Three ILC classes have emerged, ILC1, ILC2 and ILC3, with ILC1 and ILC3 including several subsets. The classification of some subsets is unclear, and it remains controversial whether natural killer (NK) cells and ILC1 cells are distinct cell types. To address these issues, we analyzed gene expression in ILCs and NK cells from mouse small intestine, spleen and liver, as part of the Immunological Genome Project. The results showed unique gene-expression patterns for some ILCs and overlapping patterns for ILC1 cells and NK cells, whereas other ILC subsets remained indistinguishable. We identified a transcriptional program shared by small intestine ILCs and a core ILC signature. We revealed and discuss transcripts that suggest previously unknown functions and developmental paths for ILCs.

PMID:
25621825
PMCID:
PMC4372143
DOI:
10.1038/ni.3094
[Indexed for MEDLINE]
Free PMC Article

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