CD5⁺ fraction remains in the ILC3 gate after exclusion of T cells using CD3 and TCRβ

Besides its importance for ILC3s, RORγt is also involved in the development of T cells, mainly T_H17 and γδ T cells [13], [15]. However, most ILC3 and T cell subsets will subsequently downregulate the expression of RORγt [16]. By breeding a transgenic mouse expressing the Cre recombinase under the control of the RORc promoter (driving RORγt) to a ROSA26-stop^fl/fl eYFP reporter mouse yielding in RORc-eYFP mice, the fate of these YFP positive RORγt -dependent cells can be mapped [17].

Using leukocytes isolated both from lymphoid (spleen) and non-lymphoid organs (colon and lung), we compared different gating approaches for the efficiency in separating ILC3s and T cells. The gating strategy involved exclusion of doublets, dead cells and B220 expressing events from CD45⁺ leukocytes. In order to exclude T cells, CD3 and TCRβ positive events were negatively selected followed by gating on YFP expressing cells (Figure 1a). Similar gating approaches are used to characterize both murine and human ILCs but are often not depicted in any figure or involve gating out multiple lineage markers in one fluorescent channel [10], [18]–[20]. However, upon further scrutiny of the assumed ILC3s, we discovered a significant percentage of these cells to stain positive for CD5, a molecule described to inhibit the T and B cell receptor signaling and was historically used as a pan T cell marker. Whereas in the colon this frequency was relatively low with 43.9% CD5⁺ cells within the ILC3 gate, in spleen and lung it reached 78.2% and 68.9%, respectively (Figure 1b). Strikingly, in RORc-eYFP fate mapping mice deficient for RAG1 no expression of CD5 was detected, suggesting that the CD5⁺ cells obtained from non-RAG mice belong to the T cell lineage (Figure 1c). Notably, as CD5 is upregulated upon TCR engagement, it is highly expressed in activated TCR^low and CD3^low T cells, which will appear close to the ILC gate [21].

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Figure 1. Flow cytometric analysis of ILC3s using RORc-eYFP fatemap mice.

(a) Gating strategy for ILC3s in RORc-eYFP mice: after exclusion of doublets, live CD45⁺ B220⁻ CD3⁻ TCRβ⁻ YFP⁺ cells were selected. (b) The population gated in panel a contains a significant fraction of CD5⁺ cells both in spleen, lung and colon. (c) In RORc-eYFP-RAG^−/− mice all YFP⁺ CD45⁺ live cells stain negative for CD3, TCRβ and also CD5. Representative plots for n = 3 (mean +/− s.e.m.).

https://doi.org/10.1371/journal.pone.0094196.g001

CD5⁺ cells remaining within the CD3⁻ TCRβ⁻ ILC3 gate consist of αβ T cells

To determine the nature of the CD5 expressing CD3⁻ TCRβ⁻ cells, this population was purified by flow cytometric cell sorting from the spleen (Figure 1a and b). The mRNA levels for the constant region of the T cell receptor α and δ chain (TRAC and TRDC) were compared to that of CD5⁻ ILC3s, αβ and γδ T cells as well as monocytes. As a genetic control we used ILC3s derived from RORc-eYFP RAG1^−/− mice. Whereas CD3⁻ TCRβ⁻ CD5⁻ ILC3s showed minor expression of both TRAC and TRDC (probably reflecting inevitable contamination from the sort purification), purified αβ and γδ T cell populations as expected transcribed high levels of TRAC or TRDC, respectively (Figure 2). Strikingly, when analyzing TRAC and TRDC expression levels in CD3⁻ TCRβ⁻ CD5⁺ cells we detected high levels of TRAC, suggesting that this population indeed consisted mainly of αβ T cells.

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Figure 2. CD5⁺ positive cells within the ILC3 gate express high levels of TRAC.

Normalized fold expression for TRAC and TRDC comparing CD5⁺ and CD5⁻ cells within the ILC3 gate (“CD5⁺ ILC3s”, pregated on CD45⁺ B220⁻ CD11b⁻ CD3⁻ TCRβ⁻ YFP⁺ cells), αβ and γδ T cells, monocytes (Mono) purified from RORc-eYFP mice and ILC3s derived from RORc-eYFP RAG1^−/− mice (ILC3s RAG1^−/−). Results are presented relative to those obtained from ILC3s of RORc-eYFP RAG1^−/− mice (mean +/− s.e.m.).

https://doi.org/10.1371/journal.pone.0094196.g002

Mouse strains

RORc-CRE and ROSA-stop^fl/fl-eYFP mice, provided by Andreas Diefenbach, were bred to obtain RORc-eYFP fate mapping animals. Both strains were crossed to RAG1^−/− mice, purchased from the Jackson Laboratory. Animals were between the ages of 6 to 16 weeks and kept under specific pathogen free conditions. All animal experiments were approved by the Swiss Cantonal Veterinary Office (license 147/2012, Zurich, Switzerland).

Cell isolation

Mice were euthanized using CO₂ inhalation and perfused with 40 ml cold PBS. Spleen, colon and lung were excised and processed as described below. Spleens were homogenized by mechanical disruption and filtered through a 70 µm mesh, followed by lysis of erythrocytes. Lungs were cut into small pieces, followed by 60 min of digestion at 37°C with 1 mg/ml Collagenase D (Roche) and 0.5 mg/ml DNAse (Sigma) in IMDM containing 25 mM HEPES and 2% fetal calve serum (FCS). Remaining pieces of tissue were homogenized using syringes and 18 gauge needles, followed by filtration through a 70 µm mesh. Colons were separated form the mesenteric fat. Luminal mucus was removed mechanically followed by incubation in Ca²⁺ Mg²⁺ lacking HBSS containing 2% of FCS, 1 mM DTT and 1.35 mM EDTA for 15 min at 37°C. After further incubation in HBSS complemented with EDTA for 30 min at 37°C the colons were cut and digested using 0.4 mg/ml collagenase IV (Sigma Aldrich) for 45 min at 37°C. The samples were then homogenized using a syringe with an 18 gauge needle and filtered through a 70 µm cell strainer.

Flow cytometry

All flourochrome-conjugated antibodies used were obtained either from BD, BioLegend or eBioscience, and stainings were performed according to standard procedures for 20 minutes at 4°C. In all stainings, dead cells were excluded using an Aqua Live/Dead fixable staining reagent (Invitrogen), and doublets were excluded by FSC-A vs FSC-H gating. Analysis was performed using a LSR II Fortessa (special order research product, BD) with four laser lines (405 nm, 488 nm, 561 nm and 640 nm). Cell sorting experiments were carried out using a FACSAria III (BD). Data analysis was done using FlowJo V9.x (Treestar).

mRNA extraction and quantitative real time PCR

Purified cells were resuspended in Trizol (Invitrogen) and kept at -80°C. RNA was extracted using the PureLink RNA Micro Kit (Invitrogen) according to the manufactures. RNA concentration was determined using a spectrophotometer (NanoDrop). Subsequent cDNA synthesis was performed using Superscript II rerverse transcriptase (Invitrogen) and oligo (dt) primers (PeproTech). Quantitative analysis was conducted using a SYBR Green master mix (Roche), TRAC and TRDC specific primers (see below) and measured by the C1000 Touch thermal cycler (BioRad). mRNA levels were determined by the cycle threshold values and normalized to the expression of the Pol2 gene. Primers were designed using CLC Workbench: TRAC: ACAAGCTTCACCTGCCAA forward, GCTTTTCTCAGTCAACGTGG reverse; TRDC: TAGTCTCCTCATGTCAGCCC reverse, CTACGACTGCTGTTTGCCA forward. Statistical significance was determined using the BioRad CFX Manager 3.0.