Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice.

Peripheral nerve injury-induced neuropathic pain is a chronic and debilitating condition characterized by mechanical hypersensitivity. We previously identified microglial activation via release of colony-stimulating factor 1 (CSF1) from injured sensory neurons as a mechanism contributing to nerve injury-induced pain. Here, we show that intrathecal administration of CSF1, even in the absence of injury, is sufficient to induce pain behavior, but only in male mice. Transcriptional profiling and morphologic analyses after intrathecal CSF1 showed robust immune activation in male but not female microglia. CSF1 also induced marked expansion of lymphocytes within the spinal cord meninges, with preferential expansion of regulatory T-cells (Tregs) in female mice. Consistent with the hypothesis that Tregs actively suppress microglial activation in females, Treg deficient (Foxp3DTR) female mice showed increased CSF1-induced microglial activation and pain hypersensitivity equivalent to males. We conclude that sexual dimorphism in the contribution of microglia to pain results from Treg-mediated suppression of microglial activation and pain hypersensitivity in female mice.

Introduction

Microglia are brain resident macrophages with essential roles in neural circuit function in physiology and disease (Priller and Prinz, 2019; Hammond et al., 2018; Vainchtein and Molofsky, 2020). Microglia respond in sexually dimorphic ways in a variety of contexts, including autism, stroke, neurodegenerative diseases, and interestingly in the microglial contribution to pain processing (Mogil, 2020; Villa et al., 2018; Weinhard et al., 2018; Sorge et al., 2011; Inyang et al., 2019; Rosen et al., 2019; Kodama and Gan, 2019; Guneykaya et al., 2018). For example, although male and female microglia are competent to induce pain (Yi et al., 2021), pharmacologic ablation or chemogenetic inhibition of microglia reverses peripheral nerve injury-induced mechanical hypersensitivity only in male mice (Sorge et al., 2015; Saika et al., 2020). In contrast, inhibition of microglia is sufficient to reverse injury-induced hypersensitivity in B- and T-cell deficient female mice (Sorge et al., 2015). Taken together, these data imply that there are sex-specific differences in how the innate and adaptive immune compartments interact to regulate neuropathic pain.

We previously identified microglial activation via release of the myeloid survival factor, colony-stimulating factor 1 (CSF1), from injured sensory neurons as a mechanism contributing to nerve injury-induced pain (Guan et al., 2016). Here, we show that intrathecal administration of CSF1 is sufficient to induce pain (mechanical hypersensitivity) in male, but not female mice. Transcriptomic profiling of dorsal horn microglia and morphologic analyses demonstrated that this sex-specific effect correlates with robust microglial activation in male but not female mice. Furthermore, intrathecal CSF1 markedly expanded lymphocytes and myeloid cells in the spinal cord meninges, and resulted in a preferential expansion of regulatory T-cells (Tregs), in female mice. Finally, we demonstrate that Treg depletion (FoxP3) in female mice promotes CSF1-induced microglial activation and is sufficient to induce CSF1-induced pain hypersensitivity equivalent to males. Our findings reveal novel cross-regulatory interactions between Tregs and spinal cord microglia that modulate a sex-specific pain phenotype.

Results

CSF1 is de novo expressed in injured sensory neurons (Guan et al., 2016), and in the spinal cord, parenchymal microglia are the only cells expressing CSF1 receptor (CSF1R). We first analyzed injury-induced mechanical hypersensitivity in female Avil mice (Adv-CSF1) in which CSF1 is specifically deleted from sensory neurons. We found that female Adv-CSF1 mice developed normal mechanical hypersensitivity after peripheral nerve injury (Figure 1—figure supplement Figure 1—figure supplement 1A, B), in contrast to male rats and mice, in which hypersensitivity was CSF1-dependent (Guan et al., 2016; Okubo et al., 2016). Thus, CSF1 is not required to induce mechanical hypersensitivity in females.

Figure 1—figure supplement 1.

CSF1 deletion in sensory neurons rescues pain in male but not female mice.

(A) Schematic and von Frey assay for Avil at day 7 after peripheral nerve injury. Dots represent individual mice, unpaired Student’s t-test. (B) Full-time course of data summarized in (A). (C) Mechanical hypersensitivity after high dose (30 ng) CSF1 (N=4 mice/group). (D) Flow cytometry plot for CD11b and CD45 highlighting male and female microglia in the naïve and CSF1 group. One representative mouse per condition is shown. N=5 mice per group. CSF1, colony-stimulating factor 1; SNI, spared nerve injury.

We next assessed whether selective administration of CSF1, via an intrathecal route, is sufficient to induce mechanical hypersensitivity. Three consecutive injections of CSF1 provoked profound mechanical hypersensitivity in male, but not in female mice (Figure 1A–C), even at very high doses (30 ng; Figure 1—figure supplement 1C). Furthermore, after intrathecal CSF1, male microglia acquired a robust amoeboid morphology, characterized by loss of ramification, but in females, microglia acquired a highly ramified morphology, consistent with a persistent homeostatic phenotype (Figure 1D–E). Fluorescence-activated cell sorting (FACS) analysis also revealed larger numbers of microglia in males and higher expression of cell surface activation markers, CD11b/CD45 (Figure 1F–H, Figure 1—figure supplement 1D). Taken together, these data demonstrate a male-specific impact and sufficiency of CSF1 for microglia activation and pain hypersensitivity.

Figure 1.

CSF1 induces pain hypersensitivity and microglial activation in male but not female mice.

(A) Schematic depicting 3 days of CSF1 intrathecal injection (i.t.) paradigm with von Frey assay. (B, C) Change in mechanical pain threshold in males and females after saline or CSF1 injection. N=5–7 mice per condition, repeated measures ANOVA. (D) Representative immunohistochemistry of lumbar spinal cord sections after 3 days of CSF1 i.t. injection. Insets indicate single microglia and binary images used for subsequent quantifications. Scale bar=50 µm. (E) Ramification calculated by Scholl analysis in males (blue, top) and females (red, bottom). N=3 mice/condition, 25 cells/group; dots represent individual microglia, Student’s t-test. (F) Representative flow cytometry plot demonstrating right-shift of the CD11b+/CD45+ population in lumbar spinal cord. Insets indicate microglia population gated on CD11b+CD45+Ly-6C−. (G) Microglial activation index calculated from flow-cytometry data as a sum of mean fluorescence intensity of CD11b and CD45 fluorescence intensity. Dots represent individual mice. One-way ANOVA with Tukey’s multiple comparisons. (H) Microglial numbers calculated by flow cytometry data. Dots represent individual mice. One-way ANOVA with Tukey’s multiple comparisons. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. CSF1, colony-stimulating factor 1.

(A) Schematic and von Frey assay for Avil at day 7 after peripheral nerve injury. Dots represent individual mice, unpaired Student’s t-test. (B) Full-time course of data summarized in (A). (C) Mechanical hypersensitivity after high dose (30 ng) CSF1 (N=4 mice/group). (D) Flow cytometry plot for CD11b and CD45 highlighting male and female microglia in the naïve and CSF1 group. One representative mouse per condition is shown. N=5 mice per group. CSF1, colony-stimulating factor 1; SNI, spared nerve injury.

To determine whether there was a differential impact of CSF1 on male versus female microglia, we transcriptionally profiled flow-sorted microglia from the lumbar dorsal horn. Sex differences were modest at baseline (86 genes, pAdj<0.01), and CSF1 induced robust gene expression changes in both male and female microglia (Figure 2A, PC1, 56% of variance). However, CSF1 induced an 8.3-fold increase in differentially expressed genes (both upregulated and downregulated) in male microglia (Figure 2B, Supplementary file 1; adjusted p-value<0.01: males 1350 genes, females 165 genes). As CSF1 is an essential survival factor for microglia and myeloid cells, these sex-specific microglia responses to CSF1 were surprising. Neither the protein nor transcriptomic CSF1R levels differed between males and females (Figure 2—figure supplement 1A, B).

Figure 2.

CSF1 promotes immune activation in male but not female microglia.

(A) Principal component analysis of genes expressed by microglia isolated by flow cytometry from male and female mice after 3 days of saline or CSF1 i.t. Dots represent individual mice. (B) Number of differentially expressed genes (DEGs) per comparison (adjusted p-value<0.01). (C) Heatmap of DEGs in male and female microglia after CSF1 overlaid with microglia activation modules curated by Friedman et al., 2018. (D) Four-way plot depicting DEGs (adjusted p-values<0.01) that are male-specific (blue), female-specific (red), or male-female shared (green). Inset highlights gene ontology terms identified in the respective categories. CSF1, colony-stimulating factor 1; i.t., intrathecal injection.

(A) Histogram of CSF1R expression on microglia for each condition by flow cytometry. One representative trace per condition. Original data from n=3 mice per group. (B) CSF1R mRNA expression in microglia as determined by RNA sequencing. Each dot represents one mouse. N=4 mice/group. CSF1, colony-stimulating factor 1; FPKM, fragments per kilobase of transcript per million.

Figure 2—figure supplement 1.

Male and female microglia express equal levels of the CSF1 receptor.

(A) Histogram of CSF1R expression on microglia for each condition by flow cytometry. One representative trace per condition. Original data from n=3 mice per group. (B) CSF1R mRNA expression in microglia as determined by RNA sequencing. Each dot represents one mouse. N=4 mice/group. CSF1, colony-stimulating factor 1; FPKM, fragments per kilobase of transcript per million.

We next examined these gene expression changes in the context of published microglial transcriptomic data sets in homeostasis and disease (Friedman et al., 2018; Figure 2C). Both male and female microglia responded to CSF1 with a decrease in homeostatic gene expression and an increase in proliferative genes, which were more prominent in males than females. Most prominent in male microglia was a striking upregulation of pathology-associated microglial activation genes (Figure 2C; Neurodegeneration module) (Friedman et al., 2018; Keren-Shaul et al., 2017). Gene ontology (GO) enrichment analysis (Figure 2D) revealed that male microglia induced genes and GO terms that are linked to classical immune activation and recruitment pathways, including many (Itgax, Lpl, Ccl3, Cybb, Clec7a, and Ctsb) associated with the ‘disease associated microglia’ DAM phenotype identified in single-cell sequencing experiments (Butovsky and Weiner, 2018). Some of these genes, for example, Ctsb, have been linked to chronic pain (Sun et al., 2012). In addition, male microglia downregulated genes facilitating responsiveness to extracellular signals as well as some supportive functions, for example, extracellular matrix regulation (Figure 2D). Taken together, intrathecal CSF1 not only triggers pain hypersensitivity in male mice, but also induces robust transcriptomic changes associated with inflammatory activation in male but not female microglia.

Our findings suggest that other immune cells contribute to amplify or suppress the microglial response to CSF1. The CNS meninges have a rich population of immune cells that mirrors the composition of tissue resident immune cells in other organs (Alves de Lima et al., 2020; Figure 3B). Meningeal lymphocyte-derived cytokines also impact CNS function in both normal and pathologic settings (Liu et al., 2020; Pasciuto et al., 2020; Ribeiro et al., 2019). We examined the immune cell composition of spinal cord meninges using 11-parameter flow cytometry of dissociated meninges (Figure 3—figure supplement 1A-C, Figure 3A–C). As expected, intrathecal CSF1 expanded meningeal macrophages (Figure 3—figure supplement 1B), but we also observed a marked increase in lymphocytes, 6.5-fold in males and 9-fold in females (Figure 3—figure supplement 1C). Further examination of lymphocyte subsets demonstrated a similar increase of CD4+ FoxP3 T cells, CD8+ T cells, B cells, and ILC2 cells in male and female meninges, but also revealed a significantly greater expansion of regulatory T cells and natural killer (NK) cells in female mice (Figure 3B–C).

Figure 3.

Regulatory T-cells restrict microglial activation and pain behavior in female mice.

(A) Schematic of spinal cord meninges. (B) UMAP plot of lymphoid, non-myeloid cells (CD45+CD11b−) isolated from spinal cord meninges. Image is a pool of all samples colored by cell type specific markers as indicated. Bar graph shows fold-change in indicated populations in males and females after CSF1. Dots in bar graph: individual samples. N=5 mice per group. (C) Quantification of regulatory T-cells (Tregs; CD4+FoxP3+) from (B). (D) Principal component analysis (PCA) of microglial gene expression profiles in select conditions. Red=female, blue=male, green=Treg deficient female (FoxP3). Dots: individual mice. PCA consists of two experiments. The first experiment is depicted in Figure 2A and complemented with a second experiment consisting of WT females with CSF1 and Treg deficient females treated with CSF1. (E) Volcano plot depicting DEGs (adjusted p-values<0.05; green) between female Treg KO mice after CSF1 versus female mice after CSF1. N=4 mice per group. (F) Gene ontology terms for upregulated and downregulated genes from volcano plot in (E). (G) Schematic depicting the approach of using Rag1 KO mice (no T/B cells), antibody against CD4 (aCD4) to deplete T-cells and FoxP3 mice, in which Tregs are depleted using diphtheria toxin. (H, I) Change in mechanical hypersensitivity at day 3 after i.t. CSF1 in WT female mice (data from day 3, Figure 1B) or in females lacking regulatory T-cells (FoxP3). Dots: individual mice. (J) Change in mechanical hypersensitivity at day three after CSF1 i.t. in Rag1−. Dots: individual mice. (K) Change in mechanical hypersensitivity at day 3 after CSF1 in female mice injected with a CD4 blocking antibody 1 day prior to CSF1 injections. Dots: individual mice. In (I–K) unpaired two-tailed t-test and (C) one-way ANOVA with Tukey’s multiple testing correction. *p<0.05, **p<0.01, ****p<0.0001. DEG, differentially expressed gene; WT, wild-type.

(A) Flow cytometry gating strategy for spinal cord meningeal immune cells. (B, C) Quantification of myeloid and non-myeloid cells after three daily CSF1 i.t or saline injections. N=4–5 mice/group. Numbers: fold expansion in females after CSF1 over females with saline. (D) Schematic depicting the approach to deplete Tregs in combination with CSF1 injections. (E) Tregs in the SC meninges with and without depletion at day 3. Each dot represents one mouse. (F) Results of microglial sequencing, showing the upregulated ‘neurodegeneration’ related genes from per Friedman et al., 2018. Common genes are upregulated in male and female microglia after Treg depletion (red), as well as genes unique to Treg depletion in females (dark blue). (G) Change in mechanical hypersensitivity at day 3 after i.t. CSF1 in WT males and in males lacking regulatory T-cells (FoxP3). Dots: individual mice. (H) Schematic depicting depletion of CD4+ T-cells in combination with CSF1 injections. (I) CD4+ T-cells in the SC meninges after CSF1, with and without CD4+ depletion at day 3. Each dot represents one mouse. CSF1, colony-stimulating factor 1; i.t., intrathecal injection; WT, wild-type.

Representative immunohistochemistry of lumbar spinal cord sections for Iba1, CD45, and CD3 showing minimal to no T-cell infiltration 7 days after SNI. Scale bar=100 µm. SNI, spared nerve injury.

Figure 3—figure supplement 1.

Isolation and depletion of meningeal immune cells.

(A) Flow cytometry gating strategy for spinal cord meningeal immune cells. (B, C) Quantification of myeloid and non-myeloid cells after three daily CSF1 i.t or saline injections. N=4–5 mice/group. Numbers: fold expansion in females after CSF1 over females with saline. (D) Schematic depicting the approach to deplete Tregs in combination with CSF1 injections. (E) Tregs in the SC meninges with and without depletion at day 3. Each dot represents one mouse. (F) Results of microglial sequencing, showing the upregulated ‘neurodegeneration’ related genes from per Friedman et al., 2018. Common genes are upregulated in male and female microglia after Treg depletion (red), as well as genes unique to Treg depletion in females (dark blue). (G) Change in mechanical hypersensitivity at day 3 after i.t. CSF1 in WT males and in males lacking regulatory T-cells (FoxP3). Dots: individual mice. (H) Schematic depicting depletion of CD4+ T-cells in combination with CSF1 injections. (I) CD4+ T-cells in the SC meninges after CSF1, with and without CD4+ depletion at day 3. Each dot represents one mouse. CSF1, colony-stimulating factor 1; i.t., intrathecal injection; WT, wild-type.

As NK cells are traditionally considered pro-inflammatory including in the context of pain (Greisen et al., 1999; Das et al., 2018) and microglial activation (Garofalo et al., 2020), whereas Tregs are potent suppressors of inflammation, we next asked whether Tregs in females counter the CSF1-induced microglial activation and pain. To acutely deplete Tregs, we administered diphtheria toxin to FoxP3 mice (Sakaguchi et al., 2008; Ali et al., 2017; Da Costa et al., 2019; Kim et al., 2007; Figure 3—figure supplement 1D,E). From these mice, we transcriptionally profiled female microglia after CSF1 intrathecal injection in the control or Treg depleted setting (Figure 3D–F/Supplementary file 3). We found that female microglia expressed many of the male-specific CSF1 induced genes, including genes involved in immune activation and recruitment (Clec7a, Il1rn, Ccl3, Ccl4, and Ctsb; Figure 3E–F). We also observed alterations of genes that are unique to the Treg-depleted context (Figure 3—figure supplement 1F). We conclude that Treg depletion partly restores the pro-inflammatory microglial response to CSF1 in female mice.

Finally, we tested whether Tregs suppress CSF1-induced mechanical hypersensitivity in female mice. We depleted Tregs in FoxP3 mice by administering diphtheria toxin prior to CSF1 injection (Figure 3G). Compared to wild-type (WT) females, Treg depletion in females led to a 33% increase in mechanical hypersensitivity (Figure 3H–I; summarizes D3 timepoint from Figure 1A). This effect was phenocopied in Rag1 which lack T- and B-cells from birth but retain innate lymphocytes, such as NK cells (Figure 3J) and the findings are reminiscent of those reported in Rag1− female after peripheral nerve injury (Sorge et al., 2015). Of note, depleting Tregs in males did not alter their mechanical hypersensitivity (Figure 3—figure supplement 1G). Acute antibody blockade of CD4+ T-cells, which include both suppressive (Tregs) and inflammatory subsets (Th1/Th2), also phenocopied this increase in mechanical hypersensitivity (Figure 3K; Figure 3—figure supplement 1H-I). Taken together, we demonstrate that this difference reflects a suppressive effect of Tregs on the CSF1-mediated immune activation in female mice, rather than a direct pain-mediating effect of T-cells on dorsal horn pain circuitry.

Discussion

Our identification of a sex-specific interaction between spinal cord microglia and Tregs that mediates male/female differences in a model of neuropathic pain has several important implications. First, we defined the immune activation profile of CSF1 on microglia in vivo and demonstrated robust expansion of lymphocytes within the spinal cord meninges in response to CSF1. These results are consistent with a model in which one function of CSF1-stimulated myeloid cells is to recruit other immune cells that in turn release cytokines and chemokines to impact microglial function. However, the nature of this immune response is strikingly sex-specific. In males, the balance tips toward pro-inflammatory signaling. In females, Tregs suppress inflammatory activation and limit mechanical hypersensitivity development, despite expansion of the myeloid and lymphoid compartments. As intrathecal CSF1 induces mechanical hypersensitivity in Treg-depleted female mice, we concur that female microglia are indeed competent to contribute to pain hypersensitivity (Yi et al., 2021; Sorge et al., 2015). However, our results demonstrate that CSF1-mediated cross-talk between spinal cord microglia and lymphocytes can either amplify or suppress pain phenotypes.

Our findings also introduce spinal cord meninges as a potentially relevant source of immune cells that coordinate microglial responses in the setting of neuropathic pain. Importantly, in contrast with a previous report (Costigan et al., 2009), we rarely detected lymphocytes, including T-cells, in the spinal cord, even after nerve injury (Figure 3—figure supplement 2). However, we found that immune cells markedly expand within the spinal cord meninges, even when absent from the parenchyma. As lymphocytes act primarily via secreted cytokines, we suggest that release of meningeal-derived cytokines impacts microglial function as well as directly impacts nociceptors (Liu et al., 2014). Although our report focuses on the contribution of Tregs, we also detected a female-specific increase in meningeal NK cells in response to CSF1. NK cells are classically associated with pro-inflammatory responses, however, recent studies highlight their more diverse functions. These include instruction of anti-inflammatory astrocytes from meningeal NK cells (Sanmarco et al., 2021), beneficial effects after peripheral nerve injury (Davies et al., 2019), and a negative correlation between NK cells in the cerebrospinal fluid and mechanical pain sensitivity in chronic neuropathic pain patients (Lassen et al., 2021). The function of meningeal NK cells in CSF1-induced pain in mice remains to be determined.

Figure 3—figure supplement 2.

T-cells are rarely detected 7 days post SNI.

Representative immunohistochemistry of lumbar spinal cord sections for Iba1, CD45, and CD3 showing minimal to no T-cell infiltration 7 days after SNI. Scale bar=100 µm. SNI, spared nerve injury.

In the setting of injury, inflammatory signaling at multiple access points (e.g., injury site, nerve, and DRG) activates nociceptive circuits (Yu et al., 2020). However, our finding that intrathecal activation of myeloid cells is sufficient to activate meningeal immunity raises the possibility that modulating the meninges is a potential therapeutic avenue of neuropathic pain management, by suppressing meningeal Treg expansion-mediated microglial activation or by the release of intrathecal immune modulators that override peripheral inflammatory cues. Given that human genetic analyses and other studies indicate a contribution of Tregs and their dominant cytokines in neuropathic and inflammatory pain models (Davoli-Ferreira et al., 2020; Fischer et al., 2019; Milligan et al., 2006; Eijkelkamp et al., 2016; Echeverry et al., 2009; Kringel et al., 2018), further investigations of Treg localization and impact on microglia will be relevant to understanding the generation and conceivably the treatment of nerve-injury-induced chronic pain.

Materials and methods

Mice

All mouse experiments were approved by UCSF Institutional Animal Care and Use Committee and conducted in accordance with the guidelines established by the Institutional Animal Care and Use Committee and Laboratory Animal Resource Center. All mice were between 8 and 14 weeks old when experiments were performed. Littermate controls were used for all experiments when feasible and all experiments were performed in male and female mice. WT (C57BL/6J) and Rag1 knockout (B6.129S7-Rag1tm1Mom/J; Stock no.: 002216) mice were purchased from The Jackson Laboratory. The following previously described strains were used and bred in house: Csf1 (Harris et al., 2012), Avil (Zurborg et al., 2011), and FoxP3 (B6.129(Cg)-Foxp3J) (Kim et al., 2007).

Injury, injections, and behavioral analysis

Spared Nerve Injury (SNI) was performed by ligation and transection of the sural and superficial peroneal branches of the sciatic nerve, leaving the tibial nerve intact (Shields and Eckert, 2003). CSF1 (Life Technologies; PMC2044) was injected intrathecally at low dose (15 ng) or high dose (30 ng) in a total volume of 5 µl for three times over 3 days (24 hr between injections). Behavioral analysis was done 2 hr after injections; mice were euthanized for analysis about 4 hr after the last injection. All Von Frey behavioral experiments were performed during the light cycle as previously reported (Guan et al., 2016) in a blinded manner. Intraperitoneal injection of anti-CD4 (250 µg) (InVivoPlus; Bio X Cell) and Diphtheria toxin (30 ng/g) (Sigma-Aldrich) were all in a volume of 200 µl per injection. Anti-CD4 was given 1 day prior to the start of CSF1 injections, and on day 2 of the CSF1 injections. Diphtheria toxin was given 2 days (two subsequent injections) before the start of the CSF1 injections, and on day 2 of the CSF1 injections.

Immunohistochemistry and analysis

Avertin-anesthetized mice were transcardially perfused with 1× phosphate-buffered saline (PBS) (~10 ml) followed by 4% (weight/volume) paraformaldehyde (PFA) diluted in PBS (~10 ml). Spinal cord tissue was dissected out and post-fixed in 4 % PFA for 4 hr and then transferred to a 30% sucrose solution overnight. Subsequently, spinal cords were sectioned coronally at 25 µm using a cryostat (Thermo Fisher Scientific). Spinal cord sections were incubated in a blocking solution consisting of 10% normal goat (Thermo Fisher Scientific) and 0.4% Triton (Sigma-Aldrich) diluted in 1× PBS. Primary antibodies included: rabbit anti-mouse Iba1 (WAKO, 1:2000); Alexa 647-coupled mouse anti-CD45 (BioLegend, 1:200); and hamster anti-CD3 (BD BioScience, 1:200). Antibodies were diluted in 10% normal goat with 0.4% Triton in PBS and incubated on a shaker overnight at 4oC. Secondary antibodies (Thermo Fisher Scientific, 1:1000) were diluted in 0.4% Triton in PBS and spinal cord sections were incubated on a shaker for 2 hr at room temperature. Spinal cord sections were mounted on coverslips with DAPI containing Fluoromount-G (Thermo Fisher Scientific). Slides were imaged on an LSM700 (Zeiss) confocal microscope using 63× objectives and z-stacks with a step size of 1 µm were collected. In Fiji (Schindelin et al., 2012) (ImageJ), maximum intensity images were generated and binary, thresholded images for morphology analysis were created. Subsequently, Scholl analysis (Ferreira et al., 2014) was done in Fiji (ImageJ) on microglia from the binary images with a step size of 2.5 µm.

Fluorescence-activated cell sorting of microglia

To isolate microglia, we followed a previously described method (Galatro et al., 2017). Briefly, lumbar dorsal horn spinal cords were mechanically dissociated in isolation medium (HBSS, 15 mM HEPES, 0.6% glucose, 1 mM EDTA pH 8.0) using a glass tissue homogenizer (VWR). Next, the suspension was filtered through a 70 µm filter and then pelleted at 300×g for 10 min at 4oC. The pellet was resuspended in 22% Percoll (GE Healthcare) and centrifuged at 900×g for 20 min (acceleration set to 4 and deceleration set to 1). The myelin free pelleted cells were then incubated in blocking solution consisting of anti-mouse CD16/32 antibody (eBioscience) for 5 min on ice, followed for 30 min in a mix of PE or PE/Cy7-conjugated anti-mouse CD11b (eBioscience), FITC or PE/Cy7-conjugated anti-mouse CD45 (eBioscience), and APC or APC/Cy7-conjugated anti-mouse Ly-6C (BioLegend) in isolation medium that did not contain phenol red. For flowcytometric analysis of CSF1R expressed by microglia, PE-conjugated anti-mouse CSF1R (BioLegend) was added. The cell suspension was centrifuged at 300×g for 10 min at 4oC and the pellet was incubated with DAPI (Sigma-Aldrich) before sorting. Microglia were sorted on a BD FACS Aria III and gated on forward/side scatter, live cells by DAPI, and CD11bhigh, CD45low, and Ly-6Cneg. After sorting, cells were spun down at 500×g, 4oC for 10 min and the pellet was lysed with RLT+ (Qiagen).

Isolation of spinal cord meningeal cells

Single-cell suspensions were prepared by digesting dissected spinal cord meninges with Liberase TM (0.208 WU/ml) and DNase I (40 ug/ml) in 1.0 ml cRPMI (RPMI supplemented with 110% (vol/vol) fetal bovine serum (FBS), 1% (vol/vol) Hepes, 1% (vol/vol) Sodium Pyruvate, 1% (vol/vol) penicillin-streptomycin) for 30–40 min at 37°C, 220 RPM. Digested samples were then passed over a 70 µm cell strainer and any remaining tissue pieces macerated with a plunger. Cell strainers were additionally flushed with FACS wash buffer (FWB, PBS w/o Mg2+ and Ca2+ supplemented with 3% FBS and 0.05% NaN3). Single-cell suspensions were washed and resuspended in FWB.

Flow cytometry of spinal cord meningeal cells

To exclude dead cells from the analysis, single-cell suspensions were stained with a fixable viability dye (Zombie NIR, BioLegend), followed by staining for surface antigens with a combination of the following fluorescence-conjugated mAbs: Brilliant Violet 421-conjugated anti-Thy1.2 (53-2.1) (BioLegend), PEDazzle594-conjugated anti-CD19 (6D5) (BioLegend), Brilliant Violet 605-conjugated anti-CD11b (M1/70) (Thermo Fisher Scientific), Brilliant Violet 711-conjugated anti-CD4 (RM4-5) (BioLegend), Brilliant Violet 785-conjugated anti-CD8a (53-6.7) (BioLegend), Brilliant Violet 650-conjugated anti-NK1.1 (PK136) (BioLegend), Alexa Fluor 700-conjugated anti-CD3 (17A2) (BioLegend), and BUV395-conjugated anti-CD45 (30-F11) (BD Biosciences). Cells were then fixed and permeabilized using the Foxp3/Transcription Factor Staining Buffer Set (eBioscience), followed by staining for intracellular antigens using the following mAbs (all from eBioscience): AF488-conjugated anti-FoxP3 (FJK-16s) and PE-conjugated anti-Gata3 (TWAJ). Samples were acquired on a Fortessa (BD Biosciences) and analyzed with FlowJo 10 software (BD Biosciences).

RNA sequencing of microglia

RNA from RLT+ lysed microglia was isolated using the RNeasy Plus Micro Kit (Qiagen) and quality and concentration were assessed with the Agilent RNA 6000 Pico Kit on a Bioanalyzer (Agilent). For samples from male and female microglia collected from the saline or CSF1 injection data sets, cDNA and libraries were generated using the Ovation RNA-Seq System V2 Kit (NuGen). For samples from female Treg knockout or WT microglia collected from the CSF1 injection data set, cDNA and libraries were generated using the Trio RNA-Seq Kit (NuGen). Quality was determined with the Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent) and concentrations were measured on Qubit (Thermo Fisher Scientific) with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Libraries were pooled and RNA sequencing was performed on an Illumina HiSeq 4000 with single-end 50 (SE50) sequencing. Between 40 and 60 million reads were sequenced per sample.

RNA sequencing Analysis

Quality of reads was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and all samples passed quality control. Subsequently, reads were aligned to mm10 (GRCm38; retrieved from Ensembl) using STAR (version 2.5.4b) (Dobin et al., 2013) without FilterMultimapNmax one so as to only keep reads that map one time to the reference genome. Uniquely mapped reads were counted using HTSeq (version 0.9.0) (Anders et al., 2015) and the DESeq2 package (version 1.24.0) (Love et al., 2014) in R was used to normalize the raw counts and perform differential gene expression analysis (using the apeglm method [Zhu et al., 2019] for effect size shrinkage). One CSF1-treated WT female sample was subsequently removed from the analysis as its counts significantly deviated from the rest. Specifically, its gene expression pattern resembled severe injury, potentially due to damage to the spinal cord during the mouse experimental procedures. Batch correction was done using the Limma package (Ritchie et al., 2015) in R. Volcano plot was generated using the EnhancedVolcano package (version 1.2.0), and the heatmap using ComplexHeatmap (Gu et al., 2016) in R. Metascape was used for GO analysis (Zhou et al., 2019). FPKM values were generated using Cufflinks (version 2.2.1) (Trapnell et al., 2010).

Statistical analysis

For most statistical analyses, we used Graphpad Prism 8. Figure legends identify the specific statistical test used and additional details are provided in Table 1. RNA-sequencing data were analyzed in R as described in Materials and methods section.

Table 1.

Statistical reporting.

Figure	N	Statistical test	Exact p-value	95% confidence interval
Figure 1b	Male mice saline=3, male mice CSF1=6	two-way ANOVA, repeated measures, Sidak’s multiple comparison	Treatment=0.0009	D1=34.46–75.46; D3=34.13–75.13; D5=8.754–49.75
Figure 1c	Female mice saline=5, female mice CSF1=5	Two-way ANOVA, repeated measures, Sidak’s multiple comparison	Treatment=0.1890	D1 = −30.41 to 10.58; D3=−28.58 to 12.41; D5=−30.13 to 10.86
Figure 1e	25 cells/group from 3 mice/condition	Unpaired t-test, two-tailed	Males<0.0001; females=0.0184	Males=−309 to –195.1; females=16.78–174.6
Figure 1g	Control males=10 mice, CSF1 males=9 mice, control females=10 mice, CSF1 females=10 mice	Ordinary one-way ANOVA, Tukey’s multiple comparisons	Males<0.0001; females=0.0034; male vs. female CSF1=0.0002	Males=−31.11 to –17.53; females=−15.81 to –2.591; male vs. female CSF1=4.976–18.56
Figure 1h	Male saline=7, male CSF1=9, female saline=10, female CSF1=10	Ordinary one-way ANOVA, Tukey’s multiple comparisons	Males<0.0001; females=0.0677	Males=−55.56 to –20.86; females=−30.01 to 77.82
Figure 1—figure supplement 1a.	Female WT=6, female KO=5, male wt=9, male KO=7	Unpaired students t-test for each sex	Females=0.2424; males< 0.0001	Females=−11.33–39.37; males=62.83–114.3
Figure 1—figure supplement 1b.	female WT = 6, female KO = 5, male WT = 3, male KO = 2	N/A	N/A	N/A
Figure 1—figure supplement 1c.	4 mice/group	Unpaired two-tailed t-test (each time point vs. baseline)	D1=0.2238; D2=0.1794	D1=−0.2804 to 0.0804; D2=−0.2232 to 0.05217
Figure 2—figure supplement 1b.	4 mice/group	Two-way ANOVA	Interraction=0.2397, sex=0.3858, treatment=0.0501
Figure 3b	5 mice/group	Unpaired t-test between males and females for each cell type
Figure 3c	Control=4 mice/sex, CSF1=5 mice/sex	One-way ANOVA, Tukey’s multiple comparison test	Males=0.5422; females=0.0229	Males=−595.9 to 215.9; females=−870.4 to –58.58
Figure 3h	5 mice/group	Unpaired two-tailed t-test	0.22	–5.987 to 22.16
Figure 3i	WT=9 mice, FoxP3DTR=10	Unpaired two-tailed t-test	0.01	–54.72 to –10.71
Figure 3j	4 mice/group	Unpaired two-tailed t-test	0.04	–65.47 to –1.634
Figure 3k	10 mice/group	Unpaired two-tailed t-test	0.01	–29.61 to –5.255
Figure 3—figure supplement 1b.	Saline=4 mice/group, CSF1=5 mice/group	One-way ANOVA, Tukey’s multiple comparison test	Males=0.4533; females=0.0111	Males=−67049 to 21037; females=−100227 to –12141
Figure 3—figure supplement 1c.	Saline=4 mice/group, CSF1=5 mice/group	One-way ANOVA, Tukey’s multiple comparison test	Males=0.4797; females=0.0198	Males=−10975 to 3602; females=−15820 to –1244
Figure 3—figure supplement 1e.	No DT=2, DT=4	N/A	N/A	N/A
Figure 3—figure supplement 1g.	5 mice/group	unpaired two tailed t-test	0.2622	–14.75 to 23.55
Figure 3—figure supplement 1i.	5 mice/group	Unpaired two-tailed t-test	0	–515 to –238.9

In the interests of transparency, eLife publishes the most substantive revision requests and the accompanying author responses.

Acceptance summary:

This manuscript is of broad relevance to the research areas of pain and neuroimmunology, and is of particular interest for its investigation of sex differences in pain sensation. The data support the major conclusions, and highlight a previously unappreciated role for specific types of immune cells residing in the spinal cord envelope and how they can influence the nervous system by acting on microglia within the spinal cord.

Decision letter after peer review:

Thank you for submitting your article "Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Kate Wassum as the Senior Editor. The following individuals involved in review of your submission have agreed to reveal their identity: Claire E Le Pichon (Reviewer #1); Long-Jun Wu (Reviewer #3).

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission. We are pleased to say that all agree this is an interesting and exciting study that would be suitable for eLife after a few revisions. The consensus is that some additional information should be added to help clarify a few important details. Specifically, the reviewers ask for evidence relating to the role of Treg in microglia-mediated pain control in males and that you discuss how meningeal Treg remotely communicate with microglia in the parenchyma of spinal cord. Ideally, these answers would be given through the inclusion of new data, or where not possible, at least discussed. Please refer to the specific reviewers' comments for details. We look forward to reading your revised manuscript when it is ready.

Reviewer #1:

The authors start with the discovery of a sex difference in intrathecally injected (i.t.) CSF1-induced pain behavior. Females do not develop the hypersensitivity observed in males after this treatment. The authors then go after the mechanism that would explain this sex difference and focus on one facet of how this occurs (a sex-specific role of regulatory T cells).

In previous work (Guan et al. 2016), the same authors had investigated the mechanism(s) underlying pain sensitivity following nerve injury. They had shown that nerve injury causes upregulation of the cytokine Csf1 in sensory neurons and a microglial response in the spinal cord, and that deletion of this gene in these neurons prevents the microglial activation and the pain behavior. They hypothesized that CSF1 from sensory neurons is secreted at their spinal terminals where microglia expressing the CSF1 receptor (Csf1r) engage in signaling that ultimately results in pain hypersensitivity behavior. They also showed the sufficiency of CSF1 to produce at least transient pain behavior by i.t. injection of CSF1 protein in the absence of a nerve injury. However all this was performed only in male mice.

In the current study, the authors reproduce this data in males and discover an intriguing sex difference. In females, i.t. CSF1 (in the absence of nerve injury) does not cause microglial activation nor pain hypersensitivity as it does in males. An advance over their previous study is a more in-depth characterization of the nature of the microglial activation, using transcriptional profiling and morphological analysis. By both these readouts, the microglia are significantly less activated in females. The authors hypothesize this dampening of microglial activation in females results from regulation of microglia by other immune cells residing in the meninges. The authors investigate the lymphocyte composition in the spinal cord meninges after i.t. CSF1 and observe that regulatory T cells (Treg) increase to a greater extent in females than males, along with other changes in lymphocyte populations that are differentially altered by sex. They ask whether Tregs are responsible for dampening the microglial activation in females. Remarkably, Treg depletion by multiple methods results in females now resembling males, with an increased microglial activation and pain behavior following i.t. CSF1.

Overall, this data in this study convincingly supports the major conclusions that (1) the immune response to i.t. CSF1 differs between sexes, and (2) meningeal lymphocytes play important roles in regulating microglial function. The methods employed are well suited to test the authors' hypotheses, and the authors consistently use multiple methods to converge on a given result (e.g. microglial activation in Figures 1 and 2 or Treg depletion in Figure 3G-K) which makes the data very convincing overall. The microglial profiling by sex is of high interest and provides a resource for the community to mine and to dig deeper into how the microglial activation might alter von Frey reflexive behavior.

The follow-up investigation of how this microglial activation may be repressed in females is only partial. It is restricted just to the role of Tregs and only in female mice, which may provide an incomplete picture of the mechanisms involved. However, it is nevertheless convincing as an investigation of one aspect of meningeal lymphocyte-dependent regulation of microglial function that then impacts neural circuits and behavior.

In summary, this well-written and -presented study opens up many interesting questions and directions for future work in the pain field and more broadly for other neurological conditions investigating the influence of meningeal lymphocytes on parenchymal inflammation that may be differentially regulated by sex.

Comments for the authors:

One useful control would be to actually show independent data for the citation of reference 32 (Costigan et al) that "lymphocytes including T cells are only rarely detected in the spinal cord, even after nerve injury". Demonstrating this would help solidify the authors' novel finding that lymphocytes do not infiltrate the parenchyma, but rather signal from the meninges.

Another recommendation is an experiment that would clarify to what extent the i.t. CSF1 mirrors CSF1 upregulation in the context of SNI (and therefore validity for neuropathic pain). The authors could examine SNI-induced meningeal lymphocyte composition. One hypothesis for how i.t. CSF1 and SNI may differ mechanistically is the exact location of CSF1 release (parenchymal vs meningeal) and thus which CSF1R-expressing myeloid cells it is able to act on. In other words – does CSF1 originating from neurons actually cause meningeal lymphocyte proliferation? (In Figure S3 the authors show that myeloid cells increase in the meninges after i.t. CSF1.)

An acknowledgement of the complexity of the many differences shown in Figure 3B would be a welcome addition before focusing on the Tregs.

Along similar lines, is it possible the CSF-1 dependent increase in NK cells in females shown in Figure 3B might influence microglial function despite the pro-inflammatory role that is cited (line 189-190)?

A control experiment depleting Tregs in males is not included so it would be helpful to hear from the authors about why this may or may not have helped their study. From Figure 3B, Tregs do increase in males, although not to the same extent as in females. Similarly, would it be possible to induce Treg proliferation in males and test whether this now renders them female-like? A comment on the feasibility of these experiments would be appreciated, especially since the authors allude to conceptually similar strategies to potentially tune pain up or down (lines 257-259).

Reviewer #2:

The concept of crosstalk between spinal cord microglia and meningeal lymphocytes to control the sense of pain is intriguing and trendy in the field. The phenotypes they show in gender difference and Treg dependent pain control in females are stunning. This is a well-written and enjoyable manuscript for readers.

It will be reader's interest to know whether Tregs play a role in pain control only in females or also alleviate male's mechanical hypersensitivity at certain level. Although depletion of Treg in females recapitulates mechanical hypersensitivity induced by CSF1 in males, evidence suggests Treg may also play a role in males. For example, in figures 3 and 4, males show an increased Treg population after CSF1 injection compared to the saline control. In figure 3D, the PCA shows that microglial gene expression profiles in Treg depleted, CSF1 treated females are closer to "basal levels (saline treated)" in males, but are distant from "CSF1 treated" male microglia. The authors should include the male CSF1 treated, Treg depleted dataset to support the idea that Treg's effect is gender biased.

Reviewer #3:

In this study, Kuhn et al. investigated the sexual dimorphism in the contribution of microglia to chronic pain in mice. The study nicely extended their previous work on microglial CSF1 signaling in pain to sex dependence. Here, the authors started with an interesting phenomenon that CSF1 induced pain in female but not male mice. They further showed that CSF1 induced more immune activation in male than female mice. More interestingly, the study described CSF1-mediated cross talk between spinal cord microglia and lymphocytes from spinal cord meninges, and Treg can suppress the pain phenotype in female mice. Overall, the study is well designed and performed using multidisciplinary approaches, including behavioral test, FACs, RNAseq, and DTR mediated Treg ablation. Although it is relatively brief and lacks detailed mechanistic exploration, the results are exciting to understand an intriguing cellular mechanism of sex differences in neuropathic pain.

Reviewer #1:

[…] Comments for the authors:

One useful control would be to actually show independent data for the citation of reference 32 (Costigan et al) that "lymphocytes including T cells are only rarely detected in the spinal cord, even after nerve injury". Demonstrating this would help solidify the authors' novel finding that lymphocytes do not infiltrate the parenchyma, but rather signal from the meninges.

To validate the absence of substantial T cell infiltration upon sciatic nerve injury, we performed SNI in male and female mice. Seven days post injury, we only occasionally observed a CD3+ T cell in the lumbar region of the dorsal spinal cord. We added these data as Supplementary Figure 4 to the manuscript.

Another recommendation is an experiment that would clarify to what extent the i.t. CSF1 mirrors CSF1 upregulation in the context of SNI (and therefore validity for neuropathic pain). The authors could examine SNI-induced meningeal lymphocyte composition. One hypothesis for how i.t. CSF1 and SNI may differ mechanistically is the exact location of CSF1 release (parenchymal vs meningeal) and thus which CSF1R-expressing myeloid cells it is able to act on. In other words – does CSF1 originating from neurons actually cause meningeal lymphocyte proliferation? (In Figure S3 the authors show that myeloid cells increase in the meninges after i.t. CSF1.)

For a variety of reasons, we cannot provide information as to changes in meningeal Tregs after sciatic nerve injury. Even after intrathecal CSF1 we are detecting very few Tregs in the spinal cord meninges (Figures 3B,C). In contrast to intrathecal injections, sciatic nerve injury would induce a much more localized effect limited to the ipsilateral lumbar spinal cord making it very unlikely that we could detect a change in Tregs with a reasonable number of animals after SNI. For this reason, we respectfully request that this experiment not be required for the revision.

An acknowledgement of the complexity of the many differences shown in Figure 3B would be a welcome addition before focusing on the Tregs.

We modified the text to address this question.

Along similar lines, is it possible the CSF-1 dependent increase in NK cells in females shown in Figure 3B might influence microglial function despite the pro-inflammatory role that is cited (line 189-190)?

We added a short paragraph about NK cells to the discussion.

A control experiment depleting Tregs in males is not included so it would be helpful to hear from the authors about why this may or may not have helped their study.

To address this question, we repeated the experiment originally performed in females and now examined male mice. In contrast to female mice, ablation of Tregs using diphtheria toxin in Foxp3-DTR male mice did not alter mechanical withdrawal thresholds in response to intrathecal CSF1 (Suppl. Figure 3G). We conclude that Tregs do not modulate intrathecal CSF1-induced pain behavior in male mice.

From Figure 3B, Tregs do increase in males, although not to the same extent as in females. Similarly, would it be possible to induce Treg proliferation in males and test whether this now renders them female-like? A comment on the feasibility of these experiments would be appreciated, especially since the authors allude to conceptually similar strategies to potentially tune pain up or down (lines 257-259).

To induce Treg proliferation in spinal cord meninges of male mice, we injected i.p. and i.t. a combination of IL2/IL2RA antibodies, a well-established system to drive Treg proliferation. Unfortunately, injection of IL2/IL2RA alone resulted in a significant drop in mechanical thresholds compared to saline-treated mice. Intrathecal CSF1 after IL2/IL2RA treatment did not induce an additional drop in pain thresholds. Although this experiment might suggest that Tregs can inhibit CSF1-induced pain in male mice, we cannot draw this conclusion due to the lower pain thresholds in the IL2/IL2RA treated mice.

Inducing Treg proliferation with IL2/IL2RA alters mechanical withdrawal thresholds in male mice.

(A:) Schematic showing the timeline to increase Treg proliferation in mice prior to intrathecal CSF1 injections. (B:) Change in mechanical withdrawal threshold in male control and IL2/IL2RA injected mice before and after 3 days of CSF1 i.t. All thresholds are normalized to baseline thresholds prior to IL2/IL2RA treatment.

Reviewer #2:

[…] It will be reader's interest to know whether Tregs play a role in pain control only in females or also alleviate male's mechanical hypersensitivity at certain level. Although depletion of Treg in females recapitulates mechanical hypersensitivity induced by CSF1 in males, evidence suggests Treg may also play a role in males. For example, in figures 3 and 4, males show an increased Treg population after CSF1 injection compared to the saline control. In figure 3D, the PCA shows that microglial gene expression profiles in Treg depleted, CSF1 treated females are closer to "basal levels (saline treated)" in males, but are distant from "CSF1 treated" male microglia. The authors should include the male CSF1 treated, Treg depleted dataset to support the idea that Treg's effect is gender biased.

To better understand the role of Tregs in regulating CSF1-induced pain in male mice, we depleted Tregs in Foxp3-DTR male mice with diphtheria toxin, prior to intrathecal CSF1 injections. In contrast to female mice, we did not observe a difference in mechanical withdrawal thresholds between control and Treg depleted male mice (Suppl. Figure 3G), indicating that Treg depletion in males is not sufficient to alter pain thresholds in this model, even though we detected an increase in meningeal Tregs in response to CSF1. Based on this experiment, we believe that an additional microglia RNASeq gene expression analysis from Treg depleted male mice is unlikely to reveal key insights into sex specific pain signaling. For this reason, we hope that this experiment is not a requirement for the revision.

Key resources table

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Gene (Mus musculus)	Csf1	MGI	MGI:1339753NCBI Gene: 12,977
Gene (M. musculus)	Foxp3	MGI	MGI:1891436NCBI Gene: 20,371
Gene (M. musculus)	Avil	MGI	MGI:1333798NCBI Gene: 11,567
Strain, strain background (M. musculus, male and female)	C57BL/6 J	The Jackson Laboratory	RRID:IMSR_JAX:000664
Strain, strain background (M. musculus, male and female)	B6.129S7-Rag1tm1Mom/J	The Jackson Laboratory	RRID:IMSR_JAX:002216
Strain, strain background (M. musculus, male and female)	B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J	The Jackson Laboratory	RRID:IMSR_JAX:016958
Strain, strain background (M. musculus, male and female)	AvilCre	Zurborg et al., 2011
Strain, strain background (M. musculus, male and female)	Csf1fl/fl	Harris et al., 2012
Peptide, recombinant protein	CSF1(M. musculus)	Thermo Fisher Scientific	Cat: #PMC2044	15 ng or 30 ng in 5 µl (i.t.)
Peptide, recombinant protein	Diphtheria Toxin(Corynebacterium diphtheriae)	Sigma-Aldrich	Cat: #D0564	30 ng/g in 200 µl (i.p.)
Antibody	Monoclonal rat anti-mouse CD4Clone: GK1.5	Bio X Cell	Cat: #BE0003-1	250 µg in 200 µl (i.p.)
Antibody	Polyclonal Rabbit anti-mouse Iba1	WAKO	Cat: #019-19741	IF: (1:2000)
Antibody	Monoclonal Alexa 647-coupled rat anti-mouse CD45(clone 30-F11)	BioLegend	Cat: #103123	IF: (1:200)
Antibody	Monoclonal hamster anti-mouse CD3 (clone 145-2C11)	BD Bioscience	Cat: #553058	IF: (1:200)
Antibody	Monoclonal PE anti-mouse CD11b (clone M01/70)	eBioscience	Cat: #12-0112-81	FACS (1:200)
Antibody	Monoclonal PE/Cy7 anti-mouse CD11b (clone M01/70)	eBioscience	Cat: #25-0112-81	FACS (1:200)
Antibody	Monoclonal Brilliant Violet 605-conjugated anti-CD11b (M1/70)	Thermo Fisher Scientific	Cat: #BDB563015	FACS (1:400)
Antibody	Monoclonal FITC anti-mouse CD45 (clone 30-F11)	eBioscience	Cat: #11-0451-81	FACS (1:200)
Antibody	Monoclonal BUV395 anti-mouse CD45 (clone 30-F11)	BD Biosciences	Cat: #564279	FACS (1:400)
Antibody	Monoclonal PE/Cy7 anti-mouse CD45 (clone 30-F11)	eBioscience	Cat: #25-0451-82	FACS (1:200)
Antibody	Monoclonal APC anti-mouse Ly-6C (clone HK1.4)	BioLegend	Cat: #128016	FACS (1:150)
Antibody	Monoclonal APC/Cy7 anti-mouse Ly-6C (clone HK1.4)	BioLegend	Cat: #128025	FACS (1:150)
Antibody	Monoclonal PE anti-mouse CSF1R (clone AFS98)	BioLegend	Cat: #135505	FACS (1:100)
Antibody	Monoclonal Brilliant Violet 421-conjugated anti-Thy1.2 (clone 53-2.1)	BioLegend	Cat: #140327	FACS (1:400)
Antibody	Monoclonal PEDazzle594-conjugated anti-CD19 (6D5)	BioLegend	Cat: #115553	FACS (1:400)
Antibody	Monoclonal Brilliant Violet 711-conjugated anti-CD4 (RM4-5)	BioLegend	Cat: #100549	FACS (1:200)
Antibody	Monoclonal Brilliant Violet 785-conjugated anti-CD8a (53-6.7)	BioLegend	Cat: #100749	FACS (1:200)
Antibody	Monoclonal Brilliant Violet 650-conjugated anti-NK1.1 (PK136)	BioLegend	Cat: #108735	FACS (1:400)
Antibody	Monoclonal Alexa Fluor 700-conjugated anti-CD3 (17A2)	BioLegend	Cat: #100215	FACS (1:200)
Antibody	Monoclonal AF488-conjugated anti-FoxP3 (FJK-16s)	eBioscience	Cat: #53-5773-82	FACS (1:200)
Antibody	Monoclonal PE-conjugated anti-Gata3 (TWAJ)	eBioscience	Cat: #12-9966-42	FACS (1:100)
Antibody	Monoclonal anti-mouse CD16/32 antibody	eBioscience	Cat: #14-0161-82	FACS (1:200)
Commercial assay or kit	Foxp3/Transcription Factor Staining Buffer Set	eBioscience (Thermo Fisher Scientific)	Cat. no.: 00-5523-00
Commercial assay or kit	RNeasy Plus Micro Kit	Qiagen	Cat. no./ID: 74034
Commercial assay or kit	Agilent RNA 6000 Pico Kit	Agilent	Part no.: 5067-1513
Commercial assay or kit	Ovation RNA-Seq System V2 Kit	NuGen	Part no.: 7102
Commercial assay or kit	Trio RNA-Seq Kit	NuGen	Part no.: 0506
Commercial assay or kit	Qubit dsDNA HS Assay Kit	Thermo Fisher Scientific	Cat no.: Q32851
Software, algorithm	Fiji (ImageJ)	Schindelin et al., 2012	RRID:SCR_002285
Software, algorithm	FastQC	Babraham Institute	RRID:SCR_011106
Software, algorithm	STAR(version 2.5.4b)	Dobin et al., 2013
Software, algorithm	HTSeq(version 0.9.0)	Anders et al., 2015	RRID:SCR_005514
Software, algorithm	DESeq2(version 1.24.0)	Love et al., 2014	RRID:SCR_015687
Software, algorithm	Limma	Ritchie et al., 2015	RRID:SCR_010943
Software, algorithm	Metascape	Zhou et al., 2019	RRID:SCR_016620
Other	Zombie NIR(fixable viability dye)	BioLegend	Cat: #423105	FACS1:1000
Other	DAPI	Sigma-Aldrich	Cat: #9542	1:1000
Other	RLT+	Qiagen	Cat: # 1053393