Gli3 is a negative regulator of Tas1r3-expressing taste cells

Mouse taste receptor cells survive from 3–24 days, necessitating their regeneration throughout adulthood. In anterior tongue, sonic hedgehog (SHH), released by a subpopulation of basal taste cells, regulates transcription factors Gli2 and Gli3 in stem cells to control taste cell regeneration. Using single-cell RNA-Seq we found that Gli3 is highly expressed in Tas1r3-expressing taste receptor cells and Lgr5+ taste stem cells in posterior tongue. By PCR and immunohistochemistry we found that Gli3 was expressed in taste buds in all taste fields. Conditional knockout mice lacking Gli3 in the posterior tongue (Gli3CKO) had larger taste buds containing more taste cells than did control wild-type (Gli3WT) mice. In comparison to wild-type mice, Gli3CKO mice had more Lgr5+ and Tas1r3+ cells, but fewer type III cells. Similar changes were observed ex vivo in Gli3CKO taste organoids cultured from Lgr5+ taste stem cells. Further, the expression of several taste marker and Gli3 target genes was altered in Gli3CKO mice and/or organoids. Mirroring these changes, Gli3CKO mice had increased lick responses to sweet and umami stimuli, decreased lick responses to bitter and sour taste stimuli, and increased glossopharyngeal taste nerve responses to sweet and bitter compounds. Our results indicate that Gli3 is a suppressor of stem cell proliferation that affects the number and function of mature taste cells, especially Tas1r3+ cells, in adult posterior tongue. Our findings shed light on the role of the Shh pathway in adult taste cell regeneration and may help devise strategies for treating taste distortions from chemotherapy and aging.


Introduction
In mouse tongue taste buds are found in three types of papillae: anterior fungiform (FF), lateral foliate (FO), and posterior circumvallate (CV). The numerous FF papillae each contain a single taste bud, while the two FO and single CV papillae each contain hundreds of taste buds [1,2]. Each taste bud contains~50-100 mature receptor cells classified as type I, type II, or type III cells based on morphology and markers. These cells are further classified into functional subtypes that respond to basic taste qualities of sweet, bitter, umami, sour, and salt [3][4][5].
The role of Shh signaling in regulating taste papillae development and taste cell differentiation at the embryonic and adult stages has been well studied [19][20][21][22][23][24][25][26][27]. In embryos, SHH is a suppressor of taste placode formation in the FF papillae [17,28] while it promotes development of taste buds in CV papillae [29]. Yet, SHH overexpression in adult taste epithelium induces numerous ectopic FF taste buds but has no major effect in other taste fields [1,27]. SHH signals through the membrane-bound receptors PTCH1 and SMO to regulate the bifunctional transcription factors GLI2 and GLI3, the principal effectors of the pathway in adults [30][31][32][33][34]. In the absence of SHH signaling, GLI2 and GLI3 are C-terminally truncated to generate transcriptional repressors that are mostly sequestered in the cytoplasm [30,33,34]. SHH signaling prevents the proteolysis of GLI2 and GLI3 and promotes their localization to the nucleus, where they regulate the expression of numerous target genes [35][36][37].
The role of GLI3 in adult taste cell turnover has not been investigated to date. We generated single-cell RNA-Seq data from multiple taste cell subtypes from mouse CV papillae and found that Gli3 is highly expressed in green fluorescent protein (GFP) marked cells positive for Lgr5 (Lgr5-GFP marked taste stem cells) and in Tas1r3-GFP marked type II taste cells. These results were confirmed using reverse transcription PCR (RT-PCR), in situ hybridization, and immunohistochemistry. Conditional knockout of Gli3 (Gli3 CKO ) in CV and FO papillae increased taste bud size and the numbers of Tas1r3-and Lgr5-expressing taste cells relative to wild-type animals (Gli3 WT ). Similar changes were observed in Gli3 CKO taste organoids derived from Lgr5-GFP+ taste stem cells. In posterior tongue in vivo and in organoids these alterations were accompanied by changes in the expression of Tas1r3, Trpm5, Gnat3, and multiple Gli3 target genes. In line with changes in taste cell number and gene expression, Gli3 CKO mice showed increased lick and glossopharyngeal (GL) nerve responses to sweet and umami taste stimuli and decreased lick responses to bitter and sour taste stimuli. Our data indicate that Gli3 is a negative regulator of differentiation and/or survival of taste stem cells and Tas1r3+ type II taste cells that influences taste receptor cell composition and function.

Gli3 is expressed in Tas1r3+ and Lgr5+ taste cells
To identify Gli-family transcription factors selectively expressed in subsets of adult taste cells, we analyzed single-cell RNA-Seq data generated from Lgr5-GFP+ stem, Tas1r3-GFP+ type II and Gad1-GFP+ type III taste cells isolated from respective GFP-transgenic mouse strains. The transcription factors Gli1 and Gli2 were expressed in all three types of cells, while Gli3 (and its upstream regulators Ptch1 and Smo) was highly expressed in both Lgr5-GFP+ and Tas1r3-GFP + but not in Gad1-GFP+ taste cells (S1 Table). RT-PCR showed that Gli3 was expressed in FF, FO and CV papillae taste tissue, as well as in lingual epithelium devoid of taste buds (Fig 1A). Using GFP+ taste cells purified by fluorescence-activated cell sorting (FACS) Gli3 was found in Lgr5-GFP+ and Tas1r3-GFP+ but not Gad1-GFP+ taste cells (Fig 1A). Quantification of Gli3 mRNA expression by quantitative PCR (qPCR) showed that it is expressed at high levels in Lgr5-GFP+ and Tas1r3-GFP+, but at only low levels in Gad1-GFP+ taste cells (Fig 1B). In situ hybridization using Gli3 antisense probes confirmed that it is expressed in taste cells in all three taste papillae (Fig 1C-1E), while the control sense probe produced only minimal background signal in taste cells (Fig 1F-1H). Indirect immunohistochemistry using an antibody generated against the N-terminus of GLI3 capable of detecting both the truncated and full-length forms of the protein revealed that it too is expressed in taste cells in all three taste papillae (Fig 1I-1K). The specificity of RNA probes (S1B and S1C Fig) and antibody (S1E Fig) were validated with the positive control jejunum tissue. Further, both reagents produced weak or no signal in CV papillae from Skn-1a knockout mice that lack all type II taste cells (S1D and S1F Fig); pre-incubation of GLI3 antibody with its immunogenic peptide confirmed specificity of the reagent (S1G Fig).
To confirm these results and identify other taste cell subtypes that express GLI3 we doublelabeled taste cells with the GLI3 antibody along with other antibodies or with GFP transgenes that mark specific types of taste cells. In both anterior and posterior tongue fields GLI3 was frequently co-expressed with Tas1r3-GFP, a marker for sweet and umami receptor-expressing type II cells (Fig 2A, 2D and 2G); less frequently with TRPM5, a marker for all type II cells ( Fig  2B, 2E and 2H); and at even lower frequency with Gnat3-GFP, a marker for another subset of type II cells (Fig 2C, 2F and 2I). Double-labeled immunohistochemistry with anti-GLI3 antibody plus an antibody against the type III taste cell markers CAR4 (S2A-S2C Fig)  Quantification showed that GLI3 was frequently expressed with TAS1R3 and TRPM5, but rarely or not at all with CAR4, 5HT or GLAST (S2 Table). Among TAS1R3+ cells,~92% expressed GLI3 in either CV or FO papillae. With TRPM5+ cells, 45-64% expressed GLI3, with a higher percentage in the CV papillae. For GNAT3+ cells 31-51% expressed GLI3, with a lower percentage in the FO vs. CV papillae taste cells. Only about 3% of CAR4+ and 1% of 5HT+ type III cells also expressed GLI3. While for GLAST+ type I cells, no GLI3+ cells were found among 88 CV and 64 FO papillae taste cells examined. Among the GLI3+ cells, nearly all (97-99%) also expressed TAS1R3 and/or TRPM5, but only 35-63% expressed GNAT3. In sum, GLI3 is expressed in type II cells, most often in the Tas1r3-GFP+ subset and less frequently in TRPM5+ or GNAT3+ subsets.

Selective ablation of Gli3 affects taste bud size and composition in vivo
As a key mediator of the Shh pathway that regulates the expression of a large number of genes [35,37], Gli3 may play a significant role in taste cell regeneration and survival. To test this, we generated a double-knockin mouse strain homozygous for the floxed Gli3 allele and also carrying the Lgr5-EGFP-IRES-CreERT2 allele. In this strain, administering the ERT2 ligand tamoxifen would ablate Gli3 in Lgr5+ stem cells in posterior tongue. Immunostaining with an antibody for KCNQ1, a marker for all taste cells, showed that in Gli3 conditional knockout (Gli3 CKO ) mice, the CV papillae taste buds were larger in size and contained more taste cells than did those of Gli3 WT mice (Fig 3A, 3B and 3I). Most of this may be accounted for by an increase in the number of TAS1R3+ type II cells, as the numbers of TRPM5+ and TAS1R3 + but not GNAT3+ and PKD2L1+ (a type III cell marker) cells increased dramatically in Gli3 CKO mice (Figs 3C-3H, 3J, S3A, S3E and S3I). Conversely, the numbers of CAR4+ type III cells decreased significantly in Gli3 CKO mice (S3B, S3F and S3I Fig). In agreement with this, qPCR showed that mRNAs expressing Tas1r3, Gna14 and Trpm5, but not Gnat3, Pkd2l1 or Snap25, increased in Gli3 CKO mice (Figs 3K and S3J). As expected, the number of GLI3+ cells and the amount of Gli3 mRNA decreased drastically, indicating that Gli3 deletion was successful. At the same time, GFP expression from the Gli3 locus was turned on in CV papillae tissue from Gli3 CKO mice, which supports this conclusion (S3C, S3D, S3G-S3J Fig

Selective ablation of Gli3 affects taste cell abundance ex vivo
Taste organoids cultured from single Lgr5-GFP+ cells faithfully recapitulate many features of taste cell development and function [38]. The effect of Gli3 ablation on the regenerative potential of Lgr5-GFP+ taste stem cells was tested in taste organoids derived from the doubleknockin (floxed Gli3 Lgr5-EGFP-IRES-CreERT2) mice by adding tamoxifen to the culture medium. Immunostaining of Gli3 CKO organoids showed that the proportion of TAS1R3+ cells increased significantly while that of CAR4+ cells decreased (the proportion of GNAT3+ cells remained unchanged) (Figs 4A-4E, S6A, S6B and S6I). Although not quantified, the proportion of NTPDase-expressing cells appeared largely unchanged (S6C-S6D Fig). Consistent with these results, qPCR of Gli3 CKO organoids showed that mRNAs expressing Tas1r3, Lgr5, Gna14 (I) Compared to control (Gli3 WT ) mice, the number of taste buds did not change in Gli3 CKO mice (t = 1.53, p>0.05), but the size (in μm 2 ) (t = 2.26, p<0.05) and the number of taste cells (t = 4.58, p<0.001) in taste buds increased. (J) Compared to Gli3 WT mice, the density of TRPM5+ (t = 9.44, p<0.0001) and T1R3+ (t = 8.94, p<0.0001) but not GNAT3+ (t = 1.49, p>0.05) taste receptor cells in Gli3 CKO mice increased. (K) qPCR showed that Trpm5 (t = 6.67, p<0.01), Tas1r3 (t = 12.28, p<0.001) and Gna14 (t = 13.42, p<0.0001) but not Gnat3 (t = 0.87, p>0.05) mRNA expression increased in CV taste buds from Gli3 CKO mice relative to those of Gli3 WT mice. Five control and Gli3 CKO mice each were used for analyses. and Gnat3 increased, while those of Pkd2l1 and Snap25 decreased, and that of Trpm5 and NTPDase2 remained unchanged (Figs 4F and S6J). Further, the expression of Shh target genes Gli1, Mycn, Jag2, and Ccnd2 decreased in Gli3 CKO organoids, while that of the upstream regulator Ptch1 increased dramatically (S6K Fig). As expected, in tamoxifen-treated Gli3 CKO organoids the numbers of GLI3-immunoreactive cells and the level of Gli3 mRNA decreased, while GFP expression from the Gli3 locus, indicative of successful Gli3 deletion, was turned on (S6E- S6J Fig). Collectively, these data suggest that Gli3 ablation in Lgr5+ taste stem/progenitor cells promote expansion or survival of Tas1r3+ cells and suppresses the differentiation of CAR4+ type III taste cells.

Selective ablation of Gli3 alters behavioral and taste nerve responses
In light of the profound changes in the proportion of taste cell subtypes and taste gene expression in tamoxifen-treated Gli3 CKO mice, we investigated the effect of Gli3 ablation on taste responses. In brief-access taste tests, Gli3 CKO mice showed altered behavioral responses to multiple taste qualities. Compared to Gli3 WT , the Gli3 CKO mice displayed increased preference for sucrose, sucralose and monosodium glutamate (Fig 5A-5C), increased aversion to denatonium benzoate and citric acid (Fig 5D and 5F), but no change in response to salt ( Fig 5E). Glossopharyngeal (GL) nerve recording revealed that compared to Gli3 WT the Gli3 CKO mice had increased nerve responses to sucrose, sucralose, and denatonium (Figs 6A, 6B, 6D and S7). However, the GL nerve responses to monosodium glutamate, citric acid, and NaCl were unchanged in Gli3 CKO vs. Gli3 WT mice (Figs 6E and S7). Furthermore, there were no significant differences in chorda tympani (CT) nerve responses of Gli3 CKO vs. Gli3 WT mice to most of the taste stimuli tested (S8 Fig), consistent with the mosaic expression of Lgr5-Cre in the FF papillae taste buds that are innervated by the CT nerve [39].

Discussion
We used single cell transcriptomics to identify transcription factors selectively expressed in Tas1r3+ taste receptor cells, reasoning that they might play a role in the development and/or maintenance of these taste cells. Although the transcription factor Skn-1a is critical for the development of Tas1r3+ taste receptor cells, it plays this role in all type II taste cells [40]. We anticipated that other transcription factors would be expressed selectively in particular subsets of type II cells, e.g. Tas1r3+ sweet/umami cells or Tas2r+ bitter cells. By single cell transcriptomics we found that the transcription factor Gli3 and its upstream regulators Ptch1 and Smo were more highly expressed in Tas1r3+ taste cells and Lgr5+ stem cells than in Gad1+ type III Gli3-deficient mice exhibit increased behavioral responses to sweet, umami, and bitter tastants. Brief-access tests were used to measure behavioral responses to sweet (sucrose and sucralose, A and B), umami (monosodium glutamate [MSG], C), bitter (denatonium, D), salty (NaCl, E), and sour (citric acid, F) taste stimuli. Compared to Gli3 WT mice, Gli3 CKO mice display increased lick responses over a range of concentrations to the appetitive stimuli (sucrose, sucralose, and MSG) and decreased lick responses to the aversive stimuli (denatonium and citric acid). Lick ratios were calculated by dividing the number of licks to a taste solution by the number of licks to water in each test session. Data are means ± SEM Statistically significant differences were determined by repeated two-way ANOVA test cells. Conventional expression studies using PCR, in situ hybridization and immunohistochemistry confirmed that Gli3 was indeed expressed in taste cells. Using Skn-1a null mice lacking all type II cells we showed that Gli3 was expressed selectively in type II cells. By double immunohistochemistry we found that Gli3 was most highly expressed in Tas1r3+ taste cells vs. other types of type II cells (e.g. Trpm5+ or Gnat3+ type II cells), and not expressed in type I or III taste cells.
Gli1,2,3 are zinc finger-containing transcription factors that act via the Shh pathway to regulate organogenesis and self-renewal [41,42]. Gli2 and Gli3 are the main effectors of the Shh pathway in adults, with Gli2 acting mainly as a transcriptional activator and Gli3 as a repressor [33,34]. Overexpression of Gli2 leads to malformation of taste buds in FF papillae, while overexpression of a dominant negative Gli2 transgene or deletion of Gli2 in taste cell precursors results in loss of taste buds in both FF and CV papillae [19,43]. However, prior to our work the effects of manipulating Gli3 on adult taste cell regeneration were not known. To determine what role Gli3 might play in taste cells we turned to knockout mice. Conventional Gli3 null mice are embryonic/perinatal lethal [44,45]; therefore we generated conditional null mice in which Gli3 was selectively eliminated from taste stem cells using a transgene in which CRE-ERT2 was driven from the Lgr5 promoter. Conditional ablation of Gli3 from taste stem cells and their progeny in the posterior taste field led to altered taste bud morphology with numbers of Tas1r3 + taste cells, but not of Gnat3+ cells. These changes may be cell-autonomous and cause only an increase in taste bud size at the expense of the epithelial tissue within the taste papillae or cause an overall increase in the size of the taste papillae by affecting the fate of the neighboring nontaste epithelium by non-cell-autonomous mechanisms. We have not tested which of these two possibilities account for the changes in Gli3 CKO mice. The Gli3 CKO mice showed altered shortterm lick test responses to sweet, umami, and bitter tastants and diminished glossopharyngeal nerve responses to sweet and bitter. Although Lgr5-CRE-ERT2 is only expressed in a weak, mosaic pattern in FF papillae, we observed modest changes in CT nerve responses to sucralose and citric acid, indicating that Gli3 could play a role in the anterior taste field also. Definitively determining this will require experiments using a Cre driver that is strongly expressed in FF papillae.
The Shh pathway is active in all taste papillae [19,24,46,47], but its effect is context dependent. In the embryonic stage, Shh signaling suppresses the development of FF papillae, while it promotes taste bud development in CV papillae [20,28,29,48]. In adults, Shh expressing cells give rise to all subtypes of taste cells; pharmacological inhibition of Shh signaling inhibits taste cell turnover [21,24,47,49]. Further, overexpression of Shh in the lingual epithelium triggers the development of multiple ectopic FF taste buds [27]. SHH is secreted by a subpopulation of post-mitotic cells in the base of the taste buds, and SHH-responsive, putative stem cells are located around and outside the base of taste buds. Indeed, current evidence suggests that the Shh pathway is active in stem cells [19,23]; and is critical for the development of taste cells in all taste fields, as noted above. Lgr5 is a marker for posterior taste stem cells, but also a coreceptor in the Wnt signaling pathway [38,39]. Because we ablated Gli3 in posterior tongue using the Lgr5-CreERT2 driver and because the Shh pathway is downstream of Wnt [28,50] it is likely that we ablated Gli3 in taste stem cells before Shh signaling was turned on. Using the Lgr5-CreERT2 driver and tamoxifen, Gli3 was ablated from most but not all posterior field taste cells. The remaining Gli3+ cells may be progeny of the Lgr5+ cells where Gli3 deletion failed or long-lived taste cells generated prior to tamoxifen treatment.
In Gli3 CKO mice the numbers of type III cells did not change overall, but the Car4+ subset of type III cells decreased markedly. Notably, Gli3 is not expressed in type III cells, including Car4+ cells, so its effect on this cell type is most likely a consequence of Gli3 activity in the Lgr5 + stem cells themselves or in lineage-specific precursor cells that gave rise to Car4+ cells. It is possible that the lack of Gli3 inhibits the differentiation of Car4+ cells as it does not affect the expression of Car4.
CAR4 is thought to be necessary for amiloride-insensitive salt taste perception [51], but Gli3 CKO mice retained normal salt taste sensitivity. Conversely, Gli3 CKO mice had heightened sensitivity to all other primary taste qualities in brief-access tests and to bitter and sweet tastants in taste nerve responses. The magnitude of the changes in lick responses in particular are somewhat surprising because the anterior taste field is not affected in Gli3 CKO mice, and may mask the effect of changes in the posterior taste field. But it is possible that taste buds in the soft palate, which also are endoderm-derived and in the pharynx could show changes similar to those in CV and FO papillae in Gli3 CKO mice, although we have not tested this. Consistent with these observations, only those taste qualities that elicit stronger responses in the posterior taste field, namely sweet and bitter, show robust changes in Gli3 CKO mice. On the other hand, the behavioral and GL nerve responses to umami tastants did not change dramatically, although Gli3 CKO mice had a higher number of Tas1r3+ cells and expressed more Tas1r3 mRNA than did wild-type mice in CV papillae. This may reflect the low baseline umami taste sensitivity and expression level of the Tas1r1 subunit of the umami taste receptor in CV papillae [52,53]. In Gli3 CKO mice the number of bitter (Gnat3+) and sour (Pkd2l1+) receptor cells did not change, but the sensitivity to these tastants, especially to bitter, increased. This may be attributed at least in part to changes in innervation density or selective innervation of particular types of taste cell types, although we have not tested this. Another possibility is that the expression level of taste receptors or their downstream signaling/regulatory machinery changed in Gli3 CKO mice. Indeed, the expression of many taste marker genes, such as Tas1r3, Trpm5, Gnat3, Gna14, Snap25, Pkd2l1 and NTPDase2, is affected in Gli3 CKO mice and/or organoids.
In CV papillae and/or organoids derived from Gli3 CKO mice, we observed changes in mRNA expression of the Gli3 target genes Ccnd2, Mycn, and Jag2 and of the upstream regulator Ptch1. While these changes confirm that Gli3 deletion had the expected effects, they represent only a small subset of the thousands of Gli3 target genes. RNA-Seq analysis of Gli3 CKO taste cells may help identify many more genes affected by Gli3 deletion and help delineate the developmental pathways regulated by Gli3 in taste cells.
In this study we demonstrate the utility of organoids cultured from purified taste stem cells for studying taste system development. Being an ex vivo system, taste organoids are not influenced by signals from other tissues. Hence, the results of genetic or other manipulations can be interpreted in a more straightforward manner. Also, the role in the taste system of key genes and pathways can be readily studied in taste organoids without concern for lethal effects from knockouts in vivo. Further, large numbers of cultured taste cells can be obtained from organoids which will be useful for protein expression and biochemical studies. Indeed, the effect of Gli3 knockout in taste organoids largely parallels that observed in vivo, underlining the utility of this system.
What could be responsible for the increases in Lgr5+ and Tas1r3+ cells in Gli3 CKO mice? In other tissues, Shh signaling can drive either differentiation or maintenance of stem cells [54,55]. It is possible that Gli3 enhances taste stem cell maintenance and acts as a negative regulator of taste cell differentiation. Another possibility is that Gli3 promotes apoptosis of Tas1r3+ and/or Lgr5+ cells. In either case, our data support a critical role of Gli3 activity in both stem and type II sweet taste receptor cells. The continued expression of Gli3 in Tas1r3+ cells and the profound changes in the number of these cells and in sweet and bitter taste sensitivity in Gli3 conditional knockout mice are evidence for an additional role for Shh signaling and Gli3 in these mature taste cells. One way to tease apart the role of Shh signaling in stem and Tas1r3+ cells is by conditional ablation of Gli3 or other Shh pathway components using Tas1r3-or type II-specific Cre drivers (e.g. Skn-1a [40]).
The role of other signaling pathways in taste development can also be context dependent. The Wnt and Bmp signaling pathways are critical for the development of embryonic FF papillae, but play relatively minor roles in the CV papillae [17,28,[56][57][58], while the Fgf signaling pathway, much like the Shh pathway, plays opposite roles in embryonic CV and FF papillae development [2]. Such differences are not surprising given that developmentally the FF papillae originate from the ectoderm while the CV and FO papillae are derived from the endoderm [59]. Many of these pathways may play relatively subtle but significant roles in taste fields where they seem dispensable (similar to what we have shown for Gli3, and by extension the Shh pathway).
In summary, our results indicate that Gli3 is a suppressor of taste stem cell proliferation and affects the number and function of mature taste cells, especially of the Tas1r3+ subtype in posterior tongue. Our findings shed more light on adult taste cell regeneration and may help devise strategies for treating taste distortions caused by conditions such as chemotherapy and aging.

Animals
All animal experiments were performed in accordance with the National Institutes of Health guidelines for the care and use of animals in research and approved by the Institutional Animal Care and Use Committee at Monell Chemical Senses Center (protocols: #1163, #1151). 6-12-week old were used for all experiments. Animals were housed with a 12-h light/dark cycle and ad libitum access to food and water. The double-knockin mouse strain carrying a floxed Gli3 allele was a kind gift from Dr. Rolf Zeller, University of Basel (Basel, Switzerland) [60]. Lgr5-EGFP-IRES-CreERT2 knockin mice and Tas1r3-GFP and Gnat3-GFP transgenic mice were as previously described [61,62]. Glast1-EMTB-GFP was a kind gift from Dr. Eva Anton, University of North Carolina School of Medicine (Chapel Hill, NC) [63]. Skn-1a knockout mice were a kind gift from Dr. Ichiro Matsumoto, Monell Chemical Senses Center (Philadelphia, PA) [40]. For Cre activation, tamoxifen (Sigma-Aldrich, St. Louis, MO; cat. no. T-5648) was dissolved in corn oil (Sigma-Aldrich cat. no. C8267) to a stock concentration of 20 mg/ml and administrated by oral gavage for three weeks at a dose of 2 mg/20 g body weight. Mice were given 2-day breaks each week during treatment to recover from the drug. Tissue was harvested 4 weeks after completion of tamoxifen treatment.

Isolation of lingual epithelium
Mice were sacrificed by CO 2 asphyxiation, and the tongues excised. An enzyme mixture (0.5 ml) consisting of dispase II (2 mg/ml; Roche, Mannheim, Germany; cat. no. 04942078001) and collagenase A (1 mg/ml; Roche cat. no. 10103578001) in Ca 2+ -free Tyrode's solution (145 mM NaCl, 5 mM KCl, 10 mM HEPES, 5 mM NaHCO 3 , 10 mM pyruvate, 10 mM glucose) was injected under the lingual epithelium, which was then incubated for 15 min at 37˚C. Lingual epithelia were peeled gently from the underlying muscle tissue and used for single-cell RNA--Seq, FACS sorting, or RNA isolation.

Single-cell RNA-Seq analysis
Single cell RNA-Seq was done as described [64]. GFP-expressing cells that were not physically attached to any other cell or cell fragment were picked irrespective of their shape individually from single cell preparations of CV papillae of Tas1r3-GFP (type II, sweet and umami receptor cells, n = 9), Lgr5-GFP (stem cells, n = 5), and Gad1-GFP type III, sour and high salt receptor cells, n = 11) transgenic mice. Two rounds of single-cell mRNA amplification were done using the TargetAmp 2-Round aRNA Amplification Kit 2.0 (Epicentre, Madison, WI). The antisense RNA generated from single cells was converted to Illumina sequencing libraries using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswitch, MA) and sequenced using the Illumina HiSeq 2000 platform. Sequencing reads were mapped to the mouse genome (version mm10, p4) using the STAR aligner [65] using Gencode M7 as splice junction database (https://www.gencodegenes.org/mouse_releases/7.html). The reads mapping to genes were counted using the featureCounts package [66] with Gencode M7 as reference. Data normalization and differential expression analysis were done using the DESeq2 package in R [67]. We obtained 30-70 million reads per library, of which 70-90% could be aligned to the mouse genome. On average, 10,184 genes were expressed per cell above an arbitrary cutoff of 10 reads per gene after normalization.

Fluorescence-activated cell sorting
GFP-fluorescent Tas1r3+, Gad1+, and Lgr5+ taste cells were isolated by FACS from male mice of these respective genotypes. The region of the lingual epithelium containing the CV papillae from four to five mice was excised and pooled, minced into small pieces, incubated with trypsin (0.25% in PBS) for 10-25 min at 37˚C, and mechanically dissociated into single cells using heat-pulled Pasteur pipettes. Cell suspensions were filtered using 70-μm cell strainers (BD Biosciences, Bedford, MA; cat. no. 352350) and then with 35-μm cell strainers (BD Biosciences cat. no. 352235). Cells were sorted into culture medium for organoid culture or Trizol LS (Thermo Fisher cat. no. 10296010) for RNA isolation using a BD FACS Aria II SORP FACS machine (Flow Cytometry and Cells Sorting Resource Laboratory, University of Pennsylvania), according to the enhanced green fluorescent GFP (EGFP) or GFP signal (excitation, 488 nm; emission, 530 nm).

PCR and qPCR
Total RNA was isolated from freshly dissected taste papillae, nontaste control epithelium from the ventral surface of the tongue, and taste organoids using the PureLink mini kit with on-column DNA digestion using PureLink DNase (Thermo Fisher cat. no. 12185010) and converted into cDNA using Super Script VILO kit (Thermo Fisher cat. no. 11755050). RNA from FACSsorted cells was isolated using the Trizol LS kit, and cDNA was synthesized using Ovation qPCR System (NuGEN, San Carlos, CA; cat. no. 2210-24). End-point PCR and qPCR were done as described [68]. Initially the expression of Gli3 was plotted as the logarithm of the ratio between its cycle threshold value and that of Gapdh. Subsequently, all qPCR results were normalized using the ΔΔCt method with Bact as reference.

Tissue preparation
Adult male mice were euthanized by CO 2 asphyxiation, and taste-papillae-containing portions of the tongue were quickly removed and briefly rinsed in ice-cold PBS. For in situ hybridization, tissues were freshly frozen in Tissue-Tek O.C.T. mounting media (Sakura Finetek, Torrance, CA; cat no. 4583) using a 100% ethanol dry ice bath and sectioned within 1 h after dissection. For immunohistochemistry, tissues were fixed for 1 h at 4˚C in 4% paraformaldehyde in 1× PBS and cryoprotected in 20% sucrose in 1× PBS overnight at 4˚C before embedding in O.C.T. Sections (10 μm thickness, coronal for FF and CV papillae, horizontal for FOL papillae) were prepared using a CM3050S cryostat (Leica Microsystems) and applied on precoated Fisherbrand Superfrost microscope slides (Fisher Scientific, Hampton, NH, Cat no 12-550-123). Sections were dried at 40˚C for 20 min and immediately used for in situ hybridization or stored at −80˚C for immunostaining.

In situ hybridization
Standard in situ hybridization methods were used as described. Fresh tissue sections with taste papillae were incubated with hybridization of 0.3 μg/ml Gli3 probe (GenBank NM_00813, 1809-2427 bp). Antisense and sense RNA probes were used at equivalent concentrations and run in parallel in the same experiment to ensure equivalent conditions. For each experiment, a positive control hybridization using Tas1r3 probe was done. In addition, in situ hybridization experiments were done on positive control tissues to confirm the quality and specificity of the RNA probes.

Immunostaining
Immunostaining of taste buds was done as described. The antibodies used in this study and their concentrations are listed in S4 Table. For serotonin detection, mice were injected with 5-HT (Sigma-Aldrich cat. no. H9523) and sacrificed after 2 h. Species-specific secondary antibodies (S4 Table) were used to visualize specific taste cell markers and GLI3.

Imaging
Bright-field images were generated using a Nikon DXM 1200C digital camera attached to a Nikon Eclipse 80i microscope and captured using Nikon NIS-Element F 3.00 software. Acquisition parameters were held constant for images with both antisense and sense probes. Fluorescent images were captured with the TCS SP2 Spectral Confocal Microscope (Leica Microsystems Wetzlar, Germany) using UV, Ar, GeNe, and HeNe lasers and appropriate excitation spectra. Scanware software (Leica Microsystems) was used to acquire z-series stacks captured at a step size of 2-3 μm. Acquisition parameters (i.e., gain, offset, PMT settings) were held constant for experiments with antibodies and for controls without antibodies. Digital images were cropped and arranged using Photoshop CS (Adobe Systems). Fluorescence images within a figure were adjusted for brightness and contrast for background standardization.

Counting taste cells and taste buds
Quantitative measurements were carried out to determine the percentage of singly and doubly labeled type II and type III taste cells that co-expressed GLI3 and taste marker proteins.
Confocal images from two to four sections from CV and FO papillae in each mouse were used for counting. To avoid counting the same cells more than once, sections separated from each other by at least 40 μm were chosen. Nuclear staining with DAPI was used to help distinguish individual taste cells. Only cells with entire cell bodies and nuclei visible were used for counting. GLI3-positive and taste-marker-labeled taste cells were counted in respective single-channel images, and the double-positive cells were counted using overlaid images.
KCNQ1 antibody staining was used to visualize taste buds for determination of taste bud size and taste cell number. Measurement of taste bud size was conducted as previously described [70]. Five Gli3 CKO and Gli3 WT mice were used for counting taste cell number. We found, on average, 10 taste buds per trench and 20 cells in each taste bud section. Only taste buds with typical morphology (with clear taste pore and the base of taste bud reaching the basement membrane) were used for analysis. Serial sections from similar regions of the tissue from each mouse were used to minimize location difference in taste bud number and size. The average number of nuclei in each taste bud was used as a proxy for the number of taste cells. For measuring the number of taste buds, all KCNQ1+ taste buds were counted, regardless of the morphology of taste bud. Double immunostaining was conducted using KCNQ1 antibody and respective taste cell marker antibodies to quantify the number of T1R3+, TRPM5+, GNAT3+, PKD2L1+, and CAR4+ taste cells per total taste cells per section. To quantify the percentage of taste cell subtypes in taste organoids with a clear single organoid profile from Gli3 CKO mice, single and double immunostaining was performed using specific taste cell markers or Gli3 antibody. Nuclear staining with DAPI was used to help distinguish individual taste cells. Only cells with entire cell bodies and nuclei visible were used for counting.

Brief-access tests
Brief access tests were conducted using the Davis MS-160 mouse gustometer (Dilog Instruments, Tallahassee, FL) as described [71]. The following taste compounds were tested: sucrose (30, 100, 300, 1000 mM), sucralose (1, 3, 10, 30 mM), monosodium glutamate (MSG; 30, 100, 300, 100 mM), denatonium (0.3, 1, 3, 10 mM), citric acid (1, 3, 10, 30 mM), and NaCl (30, 100, 300, 600 mM). Mice were water-and food-restricted (1 g food and 1.5 mL water) for 23.5 h before test sessions for appetitive taste compounds (sucrose, sucralose, and MSG). For the aversive taste compounds (citric acid, denatonium, and NaCl), mice were water-deprived for 22.5 h before testing. In each test session, four different concentrations of each taste compound and water control were presented in a random order for 5 s after first lick, and the shutter reopened after a 7.5-s interval. The total test session time was 20 min. An additional 1-s "washout period" with water was interposed between each trial in sessions testing aversive tastants. Gli3 CKO and Gli3 WT mice were tested at the same time in parallel. Each mouse was tested with all the compounds. After each session mice were allowed to recover for 48 h with free access to food and water. Body weight of the mice was monitored daily, and only mice at or over 85% their initial body weight were used. The ratio of taste stimulus to water licks was calculated by dividing the number of licks for taste compounds by the number of licks for water presented in the parallel test session. Lick ratios > 1 indicate preference behavior to the taste compound, and lick ratios < 1 indicate avoidance behavior to the taste compound. With bitter and sour stimuli it appears that lick responses show a ceiling effect (maximum aversion) at higher concentrations. Thus, strain differences could only be seen at the lower concentrations.

Gustatory nerve recording
The same sets of mice used for behavioral tests were used for electrophysiological recording of taste responses. Whole-nerve responses to tastants were recorded from the chorda tympani (CT) or the glossopharyngeal (GL) nerves as described [72]. Mice were anesthetized by an intraperitoneal injection (10 ml/kg, with 2.5 ml/kg further doses as necessary) of a mixture of ketamine (4.28 mg/ml), xylazine (0.86 mg/ml), and acepromazine (0.14 mg/ml). Under anesthesia, the trachea of each mouse was cannulated, and the mouse was then fixed in the supine position with a head holder to allow dissection of the CT or the GL nerve. The right CT nerve was dissected free from surrounding tissues after removal of the pterygoid muscle and cut at the point of its entry to the tympanic bulla. The right GL nerve from a different animal was exposed, dissected free from underlying tissues and cut near its entrance to the posterior lacerated foramen. All chemicals were used at~24˚C. The entire nerve was placed on the Ag-AgCl electrode. An indifferent electrode was placed in nearby tissue. For taste stimulation of fungiform papillae (FP), the anterior half of the tongue was enclosed in a flow chamber made of silicone rubber. For taste stimulation of the CV, an incision was made on each side of the animal's face from the corner of the mouth to just above the angle of the jaw, and the papillae were exposed and their trenches opened by slight tension applied through a small suture sewn in the tip of the tongue. For taste stimulation of fungiform papillae (FP), the anterior half of the tongue was enclosed in a flow chamber made of silicone rubber. Taste solutions were delivered to each part of the tongue by gravity flow for 30 s (CT) or 60 s (GL) at the same flow rate as the distilled water used for rinse (~0.1 ml/s). The following taste compounds were tested: sucrose (100, 300, 1000 mM), sucralose (3, 10, 30 mM), MSG (30, 100, 300 mM), denatonium (1, 3, 10 mM), citric acid (3, 10, 30 mM), and NaCl (30, 100, 300 mM). Neural responses resulting from chemical stimulations of the tongue were fed into an amplifier (K-1; Iyodenshikagaku, Nagoya, Japan) and monitored on an oscilloscope and an audio monitor. The whole-nerve responses were integrated with a time constant of 1.0 s, recorded using software (PowerLab 4/30; AD Instruments, Bella Vista, Australia), and analyzed using LabChart Pro software (AD Instruments). Nerve response magnitudes were measured at 5, 10, 15, 20, and 25 s after stimulus onset for the CT nerve and at 5, 10, 20, 30, and 40 s for the GL nerve. The stability of each preparation was monitored by the periodic application of 0.1 M NH 4 Cl. A recording was considered to be stable when the 0.1 M NH 4 Cl response magnitudes at the beginning and end of each stimulation series deviated by no more than 15%. Only responses from stable recordings were used for data analysis. At the end of the experiment, animals were killed by injecting an overdose of the anesthetic. The response values were averaged and normalized to responses to 100 mM NH 4 Cl to account for mouse-tomouse variations in absolute responses. In Glossopharyngeal nerve recordings (S7 Fig), the responses appear not to return to baseline for some of the highest concentrations of stimuli because it is difficult and takes much time to wash them out completely from the CV cleft. Subsequent recordings were only done after repeated washings to make sure the previous response return to baseline. All data were compared as normalized units.

Statistical analyses
Prism (GraphPad Software) was used for statistical analyses, including calculation of mean values, standard errors, and unpaired t-tests of cell counts and qPCR data. Data from taste behavioral tests and gustatory nerve recording were compiled using Microsoft Excel. For statistical analyses of behavioral and nerve responses, two-way ANOVA and post hoc t-tests were used to evaluate the difference between genotype (Gli3 CKO and Gli3 WT mice) and concentration using OriginPro (OriginLab). p-Values < 0.05 were considered significant. (B-D) qPCR shows increased expression of Lgr5 mRNA in FACS-purified Lgr5-GFP taste cells (t = 4.14, p<0.05) (B) and in CV papillae from Gli3 CKO mice (t = 3.58, p<0.05) (C). As expected, Gli3 expression in FACS-purified Lgr5-GFP cells was markedly reduced (t = 12.77, p<0.0001) (B). The expression of the Gli3 target genes Gli1 Ccnd2, and Mycn did not change significantly, while that of the target gene Jag2 (t = 2.88, p<0.05) decreased in CV papillae from Gli3 CKO mice. Among the upstream regulators of Gli3, expression of Ptch1 (t = 9.00, p<0.001) increased while that of Smo did not change significantly (D). Data are means + SEM. The response values were normalized to responses to 100mM NH 4 Cl bracketing the stimuli at beginning and end of the recording period. Abbreviations: Suc, sucrose; Sucra, sucralose; DB, denatonium benzoate; MSG, monosodium glutamate; NaCl, Sodium chloride; NH 4 Cl, Ammonium chloride. (B) Exemplar traces of responses to indicated taste stimuli. Shaded boxes indicate the response in Gli3 WT (blue) and the increase in response in Gli3 CKO above that in Gli3 WT mice (pink). All recordings shown are cut from continuous recordings from the same Gli3 WT or Gli3 CKO animal. Some responses to do not return to baseline immediately after the end of stimulation, but subsequent recordings were done only after repeated washout of stimuli to ensure the responses did indeed return to baseline (see Methods). Horizontal bars at the bottom of the traces in A and B indicate duration of taste stimulation (60 sec). (TIF)  Table. Co-expression of GLI3 with taste marker genes. Mouse taste cells from CV and FO papillae were doubly stained for GLI3 and taste cell markers CAR4, 5-HT or TRPM5, or singly stained for GLI3 in sections from Tas1r3-GFP, TRPM5, Gnat3-GFP or Glast1-GFP transgenic mice. Singly and doubly labeled cells were counted to determine co-expression.