Microbiota promote enhanced CD39 expression in γδ intraepithelial lymphocytes through the activation of TCR and IL-15 signaling

Alonso, Sara, Kaur, Harsimran, Jia, Luo, Nguyen, Mai Uyen, Laguerta, Alyssa, Fong, Andrew, Skariah, Neema, Argüello, Rafael J., Verzi, Michael Paul, & Swamy, Mahima. (2025). “Microbiota promote enhanced CD39 expression in γδ intraepithelial lymphocytes through the activation of TCR and IL-15 signaling.” Mucosal Immunology. https://doi.org/10.1016/j.mucimm.2025.07.005

Special immune cells called γδ intraepithelial lymphocytes (γδ IELs) constantly monitor the lining of the intestines. In this study, we looked at mice with a type of γδ IEL that grows more than usual and reacts strongly to certain gut bacteria. These cells also increase levels of a molecule called CD39, which is linked to immune regulation.

We found that signals from the T cell receptor and a molecule called IL-15 help the γδ IELs change from a naïve, immature state to a more mature, tissue-adapted state with high CD39. Activation of the T cell receptor and exposure to IL-15 both boost CD39 levels in these cells, but this increase only happens when the mice are exposed to their specific gut bacteria over time.

Interestingly, the CD39-high γδ IELs produce fewer inflammatory signals, which may explain why the intestines of these mice do not show signs of damage. Overall, our study reveals a new way that gut bacteria can influence the immune system, encouraging the growth of γδ IELs that help regulate inflammation rather than cause it.

Fig. 1 γδ^HYP mice exhibit an expansion of a CD39^hi population. (A) Immunofluorescence micrographs showing γδ IELs (green) in WT and γδ^HYP jejuna. Laminin is shown in magenta and F-actin in white. Scale bar = 30 μm. (B) Morphometric analysis of jejunal γδ IELs in WT and γδ^HYP mice. Bulk RNAseq was performed on sorted Vγ7 and Vγ1 IELs isolated from WT and γδ^HYP mice. n = 3–4. (C) GO terms of biological processes up and downregulated in γδ IELs (combined Vγ7 and Vγ1 IELs) from γδ^HYP mice compared to WT (gene sets < 1000 genes). (D) Heatmap of relative gene expression comparing WT vs γδ^HYP Vγ7 IELs and WT vs γδ^HYP Vγ1 IELs. Genes pertaining to cell cycle, nutrient and AA uptake, immune signaling, purinergic signaling and exhaustion, and effector molecules are shown. (E) Representative flow cytometry plots of CD39 expression in WT and γδ^HYP IELs. (F) Frequency of CD39^neg, CD39^int, and CD39^hi γδ IELs or (G) CD73⁺ γδ IELs in WT and γδ^HYP mice. All data shown as mean ± SEM from at least 2 independent experiments. Each data point represents an individual mouse. n = 3–6. Statistical analysis: (B,G) unpaired student’s t-test, (C,D) genes shown exhibit ± 1.5 fold change, DESeq2 adj p-value < 0.05, ‡ indicates significance only in γδ^HYP Vγ1 relative to WT, (F) two-way ANOVA with Tukey’s post hoc test. **P < 0.01, #P < 0.0001.