TBX2 specifies and maintains inner hair and supporting cell fate in the Organ of Corti

Kaiser, Marina; Lüdtke, Timo H.; Deuper, Lena; Rudat, Carsten; Christoffels, Vincent M.; Kispert, Andreas; Trowe, Mark-Oliver

doi:10.1038/s41467-022-35214-4

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Published: 09 December 2022

TBX2 specifies and maintains inner hair and supporting cell fate in the Organ of Corti

Nature Communications volume 13, Article number: 7628 (2022) Cite this article

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Abstract

The auditory function of the mammalian cochlea relies on two types of mechanosensory hair cells and various non-sensory supporting cells. Recent studies identified the transcription factors INSM1 and IKZF2 as regulators of outer hair cell (OHC) fate. However, the transcriptional regulation of the differentiation of inner hair cells (IHCs) and their associated inner supporting cells (ISCs) has remained enigmatic. Here, we show that the expression of the transcription factor TBX2 is restricted to IHCs and ISCs from the onset of differentiation until adulthood and examine its function using conditional deletion and misexpression approaches in the mouse. We demonstrate that TBX2 acts in prosensory progenitors as a patterning factor by specifying the inner compartment of the sensory epithelium that subsequently gives rise to IHCs and ISCs. Hair cell-specific inactivation or misexpression causes transdifferentiation of hair cells indicating a cell-autonomous function of TBX2 in inducing and maintaining IHC fate.

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Introduction

Hearing relies on two types of highly specialized mechanosensory cells in the Organ of Corti, the sensory epithelium of the mammalian cochlea. Inner hair cells (IHCs) are the main sensory cells since they convert sound into auditory information; outer hair cells (OHCs) act as mechanical amplifiers that enhance sensitivity to sound and adjust frequency selectivity. IHCs and OHCs are not only functionally diverse, they also differ in size, shape, innervation, and number, and associate with distinct non-sensory supporting cells in separate compartments in the organ of Corti. A single row of large IHCs associates with two types of inner supporting cells (ISCs: inner phalangeal and inner border cells) in the inner compartment; smaller OHCs form three rows which are each supported by outer supporting cells (OSCs: Deiters’ cells) in the outer compartment. The two compartments are separated by two pillar cells that flank the fluid-filled tunnel of Corti^1,2 (Fig. 1a).

**Fig. 1: *Tbx2*/TBX2 expression is progressively confined to IHCs and ISCs during cochlear development.**

All hair and supporting cells arise from common SOX2⁺ prosensory progenitors in embryonic development³. Activation of the transcription factor ATOH1 in a subset of these progenitors triggers hair cell differentiation, while Notch-mediated lateral inhibition prevents upregulation of ATOH1 in surrounding prosensory cells which subsequently differentiate into supporting cells^4,5. Only at postnatal stages, hair cell differentiation is completed and IHCs and OHCs become functional⁶. Since mature cochlear hair cells cannot be regenerated⁷, their progressive loss due to age, excessive sound, or ototoxic drugs contributes to (age-related) deafness. Cell-based strategies may enable targeted regenerative therapies in the future but require the knowledge of factors driving hair cell diversification.

Recent work identified IKZF2 (Helios) and INSM1 as transcriptional regulators of OHC differentiation in the mouse^8,9. IKZF2 is expressed in OHCs starting from postnatal day (P) 4. It is required for OHC maturation and is sufficient to induce an OHC-like fate in IHCs⁸. INSM1 is transiently expressed in OHCs at fetal and early postnatal stages (embryonic day (E) 15.5 - P2)¹⁰. Loss of this factor leads to transdifferentiation of a subset of OHCs into IHC-like cells with concomitant derepression of a set of IHC-specific genes including the T-box transcription factor gene Tbx2⁹. Since TBX2 acts as a patterning and differentiation factor in many developmental contexts¹¹, including the anterior-ventral restriction of the neurogenic domain in the early otocyst¹², it presents a strong candidate for an as yet unknown regulator of IHC differentiation.

Here, we characterize the dynamic expression of Tbx2/TBX2 during cochlear development. Using conditional deletion and misexpression approaches, we analyse the function of Tbx2 in murine sensory cell development in a time-resolved manner. We show that prior to the onset of differentiation, TBX2 acts as a patterning factor for the inner compartment of the Organ of Corti from which IHCs and ISCs arise. At later stages TBX2 acts in a cell-autonomous manner to specify and maintain the IHC fate.

Results and discussion

TBX2 expression progressively restricts to IHCs and ISCs during cochlear development

To determine the expression pattern of Tbx2 mRNA and TBX2 protein during cochlear development, we performed mRNA in situ hybridization and (co-)immunofluorescence analyses from cochlear outgrowth (E12.5) to a stage when hair cells have reached full maturity (P21) (Fig. 1b–e). At E12.5 and E13.5, Tbx2 was widely expressed in the floor of the cochlear duct. Starting at E14.5, expression was excluded from the outer (lateral) region of the developing organ of Corti and was strongly upregulated in the inner (medial) region until E18.5. Weaker Tbx2 expression was detected in cells of the adjacent greater and lesser epithelial ridges (Fig. 1b). TBX2 protein followed the pattern of the mRNA. Regionalisation of TBX2 expression in the developing organ of Corti succeeded the specification of prosensory cells (marked by SOX2) at E12.5 and E13.5, coincided spatially and temporarily with the formation of CDH1⁺ outer and CDH2⁺ inner compartments at E14.5, and preceded the differentiation of hair cells (marked by MYO7A) at E15.5 (Fig. 1c). Co-immunofluorescence analysis using specific markers for all hair cells (MYO7A), IHCs (SLC17A8, also known as VGLUT3; CALB2), OHCs (BCL11B; SLC26A5, also known as PRESTIN; KCNQ4), Deiters’ and pillar cells (PROX1) revealed that TBX2 is confined to IHCs and ISCs at E18.5 and P21 (Fig. 1d, e). This expression profile is compatible with a role for TBX2 in establishing and/or maintaining hair and supporting cells in the inner compartment of the organ of Corti.

TBX2 mediates differentiation of IHCs and ISCs from prosensory progenitors

To explore the functional significance of compartmentalisation of TBX2 expression in the early development of the organ of Corti, we inactivated and misexpressed Tbx2 in the prosensory domain at E12.5, using a tamoxifen-inducible Sox2^CreERT2 mouse line¹³ in combination with a loxP-flanked Tbx2 loss-of-function allele (Tbx2^fl)¹⁴ and a TBX2 misexpression allele which harbours a Cre-activatable TBX2-IRES-GFP expression cassette in the X-chromosomal Hprt locus (Hprt^TBX2)^15,16, respectively. Analysis of expression of a GFP reporter as well as of TBX2 protein confirmed efficient recombination and loss of TBX2 in the inner compartment of the organ of Corti in Sox2^CreERT2/+;Tbx2^fl/fl (Sox2-Tbx2LOF) embryos and ectopic TBX2 expression at physiological levels in the medial half of the outer compartment in Sox2^CreERT2/+;Hprt^TBX2/Y(+) (Sox2-TBX2ME) embryos as early as E14.5 (Supplementary Fig. 1).

We started the phenotypic characterization of hair and supporting cells in mutant cochleae at E18.5. In both Sox2-Tbx2LOF and Sox2-TBX2ME mutants the number of hair cells was preserved (Supplementary Fig. 2a) but they were misaligned in rows of four to five cells of width without a clear separation into one inner and three outer rows. In Sox2-Tbx2LOF embryos, expression of the IHC marker SLC17A8 was absent, while expression of the OHC marker BCL11B and the OHC regulator Insm1⁹ expanded to the innermost row of hair cells (Fig. 2a, b, Supplementary Fig. 2b). In contrast, in Sox2-TBX2ME cochleae the number of BCL11B⁺ OHCs was reduced while that of SLC17A8⁺ cells was increased paralleling the pattern of forced TBX2 expression (Fig. 2a, b, Supplementary Fig. 1f–h). In both transgenic conditions, a small number of hair cells lacked both SLC17A8 and BCL11B (Fig. 2a, b) indicating that these cells have not (yet) differentiated into one of the two hair cell subtypes.

**Fig. 2: *Tbx2* regulates the differentiation of cells in the inner compartment of the Organ of Corti.**

The pattern of supporting cells followed the hair cell changes. In Sox2-Tbx2LOF cochleae, pillar cells (marked by NGFR) were shifted to border the innermost hair cell row. Moreover, all supporting cells underneath the hair cells strongly expressed S100A1 (marks Deiters’ cells) and PROX1 (marks Deiters’ and pillar cells), indicating a gain of OSCs at the expense of ISCs. In Sox2-TBX2ME mutants, NGFR⁺ pillar cells intermingled with OHC rows. Expression of PROX1 and S100A1 was strongly reduced indicating a gain of ISCs at the expense of OSCs. Hair and supporting cell changes in Sox2-Tbx2LOF and Sox2-TBX2ME embryos were accompanied by a medial expansion and reduction, respectively, of the outer compartment marker CDH1 (Fig. 2c, Supplementary Fig. 2c), pointing to disturbed compartmentalization of the organ of Corti at this stage.

Histological and molecular analysis of mice at P21 and P17, respectively, revealed that the altered patterns of hair cell types observed at E18.5 were preserved in mature Sox2-Tbx2LOF and Sox2-TBX2ME cochleae. In Sox2-Tbx2LOF mice, all cochlear hair cells presented features of OHCs (smaller size, smaller nucleus, expression of KCNQ4 and SLC26A5). Importantly, these cells also expressed IKZF2, the key regulator of OHC maturation. In contrast, Sox2-TBX2ME cochleae exhibited an increased number of hair cells with characteristics of IHCs (larger size, large nucleus, expression of SLC17A8 and CALB2) while the number of (IKZF2⁺) OHCs was correspondingly decreased (Fig. 2d). Because IHCs and OHCs differ in their neural innervation, we stained for CALB2, which labels type I afferent neurons of the spiral ganglion that exclusively contact IHCs. In Sox2-Tbx2LOF cochleae, the number of CALB2⁺ afferent fibers innervating the OHC-like cells in the region of the former IHC compartment was strongly reduced. 23% (168 out of 763) of the OHCs and OHC-like cells were innervated. In Sox2-TBX2ME cochleae, 92% (195 out of 211) of the ectopic IHC-like cells were innervated by CALB2⁺ afferents (Fig. 2e).

Together these data show that in prosensory progenitors Tbx2 is both required and sufficient to regulate differentiation of ISCs and correctly innervated IHCs.

TBX2 patterns prosensory progenitors in an inner and an outer compartment

The disturbed compartmentalization in Sox2-Tbx2LOF mice may result from a mispatterning of prosensory progenitors or from a transdifferentiation of hair and supporting cells that have been correctly specified. To discriminate between these two possibilities, we performed transcriptional profiling by microarray analysis of control and mutant cochlear ducts at E14.5 when hair and supporting cell differentiation has not yet occurred. Significance Analysis of Microarrays (SAM) identified 36 upregulated and 90 downregulated genes in the mutant. Among the list of downregulated transcripts, some genes have been described to be expressed in cells of the inner compartment such as Pvalb¹⁷ and Fgf8¹⁸, Fabp7¹⁹, and Lfng²⁰ (Supplementary Table 1). In contrast, some of the upregulated genes were previously identified as markers of the outer compartment (Crhr1^21,22, Lgr6²³, Ctgf²⁴, and Fgfr3²⁵) (Fig. 3a, Supplementary Table 2) indicating an expansion of the outer at the expense of the inner compartment at onset of organ of Corti development.

**Fig. 3: *Tbx2* patterns prosensory progenitors in the developing organ of Corti.**

This notion was corroborated by in situ hybridization analysis of upregulated genes in E14.5 and E18.5 Sox2-Tbx2LOF cochleae. Rnf182, a gene expressed in OHCs of control animals at E18.5, was ectopically expressed in the entire developing organ of Corti at E14.5. Expression of Tectb was strongly enhanced in the inner compartment of the organ of Corti and in the adjacent greater epithelial ridge. Lgr6 and Ptpn5 were ectopically expressed in the inner compartment (Fig. 3b, c). Since Lgr6 marks pillar cells starting from E15.5²³, this points to a premature specification of this cell type. Together with loss of CDH2 expression in the inner compartment of the developing organ of Corti at E14.5 (Supplementary Fig. 3), these changes indicate that the inner compartment is not established in the prosensory region of Sox2-Tbx2LOF embryos.

We noted increased and/or ectopic expression of some candidate genes in the cochlear epithelium outside the organ of Corti in Sox2-Tbx2LOF embryos (Supplementary Fig. 4) pointing to a functional implication of TBX2 expression in the lesser and greater epithelial ridges.

Fgfr3 (fibroblast growth factor receptor 3) was the only deregulated gene, which exhibited a complementary pattern of expression to Tbx2 in the developing organ of Corti. Fgfr3 was expressed in the outer compartment of control cochleae. Its expression expanded into the inner compartment in Sox2-Tbx2LOF embryos and was medially reduced in Sox2-TBX2ME mutants. Concordantly, expression of Etv4 and Etv5, direct targets of FGF signaling²⁶, was medially expanded upon Tbx2-deletion and the Etv4/5-negative outer region was lost upon TBX2-misexpression (Fig. 3d, e).

Previous work implicated FGF signalling in multiple aspects of cell differentiation in the outer compartment of the organ of Corti^{25,27,28,29,30,31}. Notably, lineage tracing experiments in mouse demonstrated that OHCs, OSCs and pillar cells derive from FGFR3⁺ progenitors³², and deletion or inactivation of Fgfr3 resulted in disturbed maturation of pillar cells and reduced expression of the OHC-marker SLC26A5^18,33. This strongly suggests that Tbx2 establishes the inner compartment of the organ of Corti by preventing FGFR3-dependent FGF signalling in this region. Given numerous reports that TBX2 acts as a transcriptional repressor in a wide variety of developmental contexts³⁴, early compartmentalization of the organ of Corti may rely on direct repression of Fgfr3 expression by TBX2.

TBX2 maintains the fate of differentiating IHCs and ISCs

We next explored whether TBX2 is critical for maintaining the fate of cochlear hair and supporting cells. At E16.5, when these cell types are established at the base of the cochlear duct^9,10,18,35,they still express SOX2. We therefore administered a single pulse of tamoxifen at E16.5 to Sox2-Tbx2LOF embryos and analysed phenotypic changes at E18.5 (Fig. 4a–c). Since we did not obtain Sox2-TBX2ME embryos at this stage, we limited our analysis to the loss-of-function situation.

**Fig. 4: *Tbx2* maintains IHC and ISC fate by preventing transdifferentiation into OHCs and OSCs, respectively.**

In Sox2-Tbx2LOF cochleae, the total number of hair cells was unchanged (Supplementary Fig. 5a). Hair cells in the outer compartment of the organ of Corti were perfectly aligned and expressed the OHC marker BCL11B comparable to control. In contrast, hair cells of the inner compartment were misaligned, showed partly reduced expression of IHC markers SLC17A8 and S100A1, and to some extent ectopic expression of the OHC-marker BCL11B. NGFR⁺ pillar cells were intermingled with the innermost row of hair cells. Although the number of S100A1⁺ Deiters’ cells was unchanged, the PROX1⁺ OSC population expanded medially in Sox2-Tbx2LOF mutants. Expression of CDH1 was normal but CDH2 was strongly downregulated in the inner compartment (Fig. 4a–c).

Transcriptional profiling of E18.5 Sox2-Tbx2LOF cochlear ducts by microarray analysis identified 48 down- and 32 upregulated genes. Among the genes with reduced expression, we found candidates whose specific or enhanced expression in cells of the inner compartment was previously described: Fgf8¹⁸, Cabp2³⁶, Slc17a8³⁷ and Gabrg3³⁸ in IHCs, Fgf20²⁷ and Otol1³⁹ in ISCs, and Npy³² in inner pillar cells (Supplementary Table 3). In the list of upregulated genes, some genes have been described to be expressed in cells of the outer compartment: Pdzk1ip1³², Tal1²², Drd5⁴⁰, Insm2⁹, and Crhr1²¹ (Fig. 4d, Supplementary Table 4). Only very few candidates were detectable by RNA in situ hybridization in control and mutant embryos at E18.5. Trh, Il33 and Otol1 were expressed in the inner domain of the organ of Corti and were downregulated in the mutant (Supplementary Fig. 5b). Insm2 and Ccdc88 showed increased expression in OHCs but were not ectopically expressed in the innermost hair cell indicating non-cell-autonomous effects of Tbx2 loss in the outer compartment. Tectb was enhanced in the inner compartment and the greater epithelial ridge (Fig. 4e). Pdzk1ip1, Tal1 and Slc6a1 were expressed in Deiters’ cells in both control and mutant (Supplementary Fig. 5c). Together, marker analysis and transcriptional profiling suggest that in E18.5 Sox2-Tbx2LOF cochleae, hair and supporting cells of the inner compartment have undergone a partial fate shift.

At P21, almost all hair cells expressed OHC-specific markers (IKZF2, SLC26A5, KCNQ4) whereas expression of IHC-specific markers (CALB2, SLC17A8) was not detected (Fig. 4f, Supplementary Fig. 5d). Moreover, CALB2⁺ afferent fibers that normally innervate IHCs, were strongly reduced (Fig. 4g) indicating a complete conversion of IHCs to OHCs after an extended time interval. This shows that Tbx2 is required to maintain the fate of IHCs and ISCs after E16.5 by preventing their transdifferentiation into OHC and OSC, respectively.

To address whether FGFR3-mediated signalling contributes to the observed cytodifferentiation defects in Sox2-Tbx2LOF embryos, we analysed the expression of some FGF signalling components at E18.5. Hair cells of the inner row lacked expression of Fgf8 consistent with the loss of an IHC fate. Expression of Fgfr3 was medially expanded but did not translate into expression of the FGF targets Etv4 and Etv5 that mark pillar cells at this stage (Supplementary Fig. 5e). This precludes transcription-dependent effects of FGFR3 signalling as contributors of hair and supporting cell fate changes in this setting.

TBX2 cell-autonomously induces IHC fate in nascent hair cells

To manipulate Tbx2 function specifically in hair cells, we used an Atoh1-CreERT2 mouse line⁴¹ that mediates stochastic recombination in hair cells at low frequency after tamoxifen administration at E15.5 or at P0-1 (Supplementary Fig. 6). We first investigated the phenotypic consequences of manipulating Tbx2 expression by a single pulse of tamoxifen administration at E15.5, i.e., a stage when hair cells have just appeared. We found that the total number of MYO6⁺ hair cells and their separation in one inner and three outer rows was preserved in the cochlea of both Atoh1-CreERT2/+;Tbx2^fl/fl (Atoh1-Tbx2LOF) and Atoh1-CreERT2/+;Hprt^TBX2/+ (Atoh1-TBX2ME) mutants at E18.5 (Supplementary Fig. 7a, Fig. 5a). However, in the innermost hair cell row of Atoh1-Tbx2LOF cochleae the number of hair cells expressing the IHC marker SLC17A8 was decreased whereas the number of hair cells expressing the OHC-marker BCL11B, or none or both of these markers was increased (Fig. 5a, b, Supplementary Fig. 7b). In Atoh1-TBX2ME embryos, we detected a significantly increased number of SLC17A8⁺ and BCL11B/SLC17A8-double-negative hair cells in the outer compartment of the organ of Corti (Fig. 5a, c, Supplementary Fig. 7b).

Since we found a fate switch of supporting cells upon early loss or misexpression of Tbx2 in the prosensory domain, we investigated whether the subtype switch of individual hair cells leads to a corresponding switch of supporting cell fate by a non-cell autonomous mechanism (i.e., without altering Tbx2 expression in supporting cells). Immunofluorescence analysis on whole-mount preparations of E18.5 organs of Corti revealed gaps in the row of NGFR⁺ pillar cells in Atoh1-Tbx2LOF, but no alteration in Atoh1-TBX2ME mutants. Expression of the OSC marker PROX1 and the ISC marker GLAST was unaffected in both mutants (Supplementary Fig. 7c). This indicates that the proper formation of the tunnel of Corti is susceptible to the locally restricted loss of IHCs but that conversion of hair cells is not sufficient to induce the conversion of the underlying supporting cells as previously reported⁴².

Histological analysis at P21 revealed a normal structural appearance of the organ of Corti in Atoh1-Tbx2LOF mutants. However, hair cells located medially to pillar cells, i.e., in the inner row, expressed OHC markers (SLC26A5, KCNQ4) and the regulator of OHC-fate IKZF2 instead of IHC markers (SLC17A8, CALB2). In contrast, in Atoh1-TBX2ME embryos, we found ectopic IHC-like cells and supernumerary pillar cells in the outer compartment of the organ of Corti (Fig. 5d, Supplementary Fig. 8). OHC-like cells in the inner row of Atoh1-Tbx2LOF mutants appeared to be innervated by CALB2⁺ type I afferents (13 out of 13). In Atoh1-Tbx2ME cochleae 50% (9 out of 18) of the ectopic IHC-like cells were innervated (Fig. 5e). Together, these data show that TBX2 confers IHC fate cell-autonomously and independently from positional information to nascent hair cells.

Transdifferentiation of hair cells upon neonatal Tbx2 manipulation

We next inactivated or misexpressed Tbx2 using the Atoh1-CreERT2 mouse line and applying a single pulse of tamoxifen to breast feeding dams at P0-1. i.e., stage when differentiated IHCs and OHCs are established. Subsequently, the phenotypic consequences of manipulated Tbx2 expression were analyzed at P21. The total number of hair cells in the organ of Corti was preserved in both Atoh1-Tbx2LOF and Atoh1-TBX2ME mice (Supplementary Fig. 9a) but in the innermost hair cell row of Atoh1-Tbx2LOF cochleae the number of SLC17A8⁺ hair cells was decreased whereas the number of SLC26A5⁺ hair cells was increased (Fig. 6a, b). Conversely, in Atoh1-TBX2ME embryos, we detected a decreased number of SLC26A5⁺ and increased number of SLC17A8⁺ hair cells in the outer compartment of the organ of Corti (Fig. 6a, c). In contrast to the analysis at E18.5, we did not find any SLC26A5/SLC17A8-double-positive or -negative hair cells (Supplementary Fig. 9b, c) indicating that non-committed hair cells differentiate to a specific hair cell type after birth.

**Fig. 6: Postnatal *Tbx2* inactivation or misexpression causes cell-autonomous transdifferentiation of hair cells.**

IHCs and OHCs differ in stereocilia bundle morphology. Whereas OHCs have shorter stereocilia that are arranged in V-shaped bundles, IHC stereocilia are longer and arranged in linear bundles. Co-staining of F-ACTIN and SLC17A8 demonstrated that upon loss of Tbx2 29% of the SLC17A8^- IHCs had stereocilia with bundle morphology resembling that of OHCs whereas 71% of these hair cells had no stereocilia at all (Fig. 6d, e). This indicates that Tbx2 is required to maintain IHC fate at postnatal stages, but that these Tbx2-deficient hair cells do not completely convert to OHCs. Upon misexpression of TBX2 87% of the SLC17A8⁺ OHCs (i.e., ectopic IHC-like cells) exhibited stereocilia with a bundle morphology resembling that of IHCs (Fig. 6f, g) indicating a robust conversion from OHC to IHC identity.

OHC-like cells in the inner row of Atoh1-Tbx2LOF cochleae were innervated by CALB2⁺ type I afferents (32 out of 32). In Atoh1-Tbx2ME cochleae, only 7% of the ectopic IHC-like cells (12 out of 162) were innervated by CALB2⁺ fibers indicating that innervation patterns of hair cells are stably established before birth (Fig. 6h). We conclude that neonatal Tbx2 inactivation or misexpression causes cell-autonomous transdifferentiation of hair cells, which however, maintain their initial innervation pattern.

While we were in the process of revising this manuscript, a study reported that embryonic and neonatal differentiating IHCs acquire phenotypic characteristics of OHCs when Tbx2 was conditionally deleted in these cells⁴³. Our study confirms that Tbx2 is required to prevent this fate switch but additionally uncovered that TBX2 is sufficient to induce complete OHC-to-IHC conversion upon ectopic activation during fetal stages, whereas a partial fate shift without proper innervation occurred when TBX2 was misexpressed postnatally.

Our study also found that the function of TBX2 as a differentiation factor is not limited to hair cells but extends to supporting cells. Moreover, we show that prior to cell differentiation TBX2 acts as a patterning factor by specifying the inner compartment of the organ of Corti, which subsequently gives rise to IHCs and ISCs. Our transcriptional profiling experiments suggest that Fgfr3 is a critical target of TBX2 during its early patterning function, while its latter role in differentiated IHCs is possibly mediated by repression of regulators of OHC fate such as IKZF2.

Together, the two studies defined that TBX2 sets up the transcriptional network driving inner hair and supporting cell fate in the Organ of Corti. This finding paves the way to further unravel the molecular circuits of cochlear hair and supporting cell differentiation and rationalizes therapeutic avenues in hair cell-related hearing disorders.

Methods

Ethics and animals

Up to four mice per cage were housed with ad libitum access to food and water under conditions of regulated temperature (22 °C) and humidity (50%) and a 12-h light/ dark cycle at the central animal laboratory of Hannover Medical School. The experiments were in accordance with the German Animal Welfare Legislation and approved by the local Institutional Animal Care and Research Advisory Committee and permitted by the Lower Saxony State Office for Consumer Protection and Food Safety (Permit Number: 33.12-42502-04-19/3081).

All mouse alleles employed in this study have previously been described and were maintained on an NMRI genetic background. A conditional floxed allele of Tbx2 [Tbx2^tm2.1Vmc, synonym: Tbx2^fl]¹⁴ was provided by Vincent Christoffels; an allele with insertion of the human TBX2 gene at the Hprt locus [Hprt^{tm2(CAG-TBX2,-EGFP)Akis}, synonym: Hprt^TBX2]¹⁵ was generated in house. The double fluorescent Cre reporter line Gt(ROSA)26Sor^{tm4(ACTB-tdTomato,-EGFP)Luo/J} [#007576, synonym: R26^mTmG]⁴⁴, the tamoxifen-inducible CreERT2 driver lines Sox2^CreERT2 [#017593, Sox2^{tm1(cre/ERT2)Hoch}]¹³ and Atoh1-CreERT2 [#007684, Tg(Atoh1-cre/Esr1*)14Fsh]⁴¹ were obtained from The Jackson Laboratory. The Hprt^TBX2 strain is available upon request from Andreas Kispert.

Embryos for Tbx2/TBX2 expression analyses were derived from matings of NMRI wild-type mice. For generation of loss-of-function mutants Sox2^CreERT2/+;Tbx2^fl/fl males were mated with Tbx2^fl/fl;R26^mTmG/mTmG females to obtain Sox2^CreERT2/+;Tbx2^fl/fl;R26^mTmG/+ (Sox2-Tbx2LOF) mice, and Atoh1-CreERT2/+;Tbx2^fl/fl males with Tbx2^fl/fl;R26^mTmG/mTmG females to obtain Atoh1-CreERT2/+;Tbx2^fl/fl;R26^mTmG/+ (Atoh1-Tbx2LOF) mice. For generation of misexpression mutants Sox2^CreERT2/+ males were mated with Hprt^TBX2/TBX2 females to obtain Sox2^CreERT2/+;Hprt^TBX2/Y(+) (Sox2-TBX2ME) mice, and Atoh1-CreERT2/+ males with Hprt^TBX2/TBX2 females to obtain Atoh1-CreERT2/+; Hprt^TBX2/Y(+) (Atoh1-TBX2ME) mice. For generation of mTmG-positive controls, Sox2^CreERT2/+ and Atoh1-CreERT2/+ males were mated with R26^mTmG/mTmG females to obtain Sox2^CreERT2/+;R26^mTmG/+ and Atoh1-CreERT2/+;R26^mTmG/+ mice, respectively. Cre-negative littermates or Sox2^CreERT2/+;R26^mTmG/+ and Atoh1-CreERT2/+;R26^mTmG/+ mice served as controls.

For embryonic staging, the detection day of a vaginal plug was defined as embryonic day (E) 0.5. To induce recombination, 4 mg of tamoxifen (#T5648, Sigma-Aldrich) dissolved in corn oil (#C8267, Sigma-Aldrich) were orally applied to timed pregnant or breast-feeding dams in a single pulse at E12.5, E15.5, E16.5 or P0-1. From E15.5 onwards, 2 mg of progesterone (#P8783, Sigma-Aldrich) were additionally applied. Pregnant females and juvenile mice were euthanized by cervical dislocation, neonates were euthanized by decapitation. Embryos at E14.5, E16.5 and E18.5, neonates at P4 and juveniles at P17/21 were collected for analyses. Both sexes were interchangeably used with the exception of Sox2-TBX2ME mice, where we used male mice at embryonic stages and female mice at postnatal stages. The sample size was not predetermined by statistical methods. The experiments were not blinded due to the obvious phenotype. For all experiments, animals were assigned to groups based on their genotype.

Tissue collection and preparation

Embryos were dissected in phosphate-buffered saline (PBS) and decapitated. For organ of Corti whole-mount preparations, cochleae were isolated in PBS and non-sensory epithelia (stria vascularis, Reissner’s membrane) were removed. Embryonic heads and cochlear whole-mounts were then fixed overnight in 4% paraformaldehyde (PFA)/PBS (#A3813, AppliChem) at 4 °C, dehydrated through an ascending methanol series (diluted in PBS) and stored in absolute methanol at −20 °C until use.

For collection of older tissue (P21), inner ears were isolated in PBS after decapitation, fixed in 4% PFA overnight and decalcified for 2 days in 0.5 M EDTA/PBS (#A2937, AppliChem), pH7.4, at 4 °C. Whole organs of Corti were isolated from inner ears after decalcification and dissected into three pieces (basal, medial, apical). Inner ears and cochlear whole-mounts were then dehydrated and stored in absolute methanol at −20 °C until use.

Genotypes were determined by sorting of GFP-expressing tissues and by PCR on genomic DNA prepared from embryonic tissues or ear clips.

Histological analysis

Embryonic heads or postnatal inner ears were embedded in paraffin wax and sectioned to 5-µm. Sections were stained with Hematoxylin (#GHS332, Sigma-Aldrich) for 45 s, blued in 0.5% sodium-acetate for 1 min and counterstained with Eosin Y solution (#HT110132, Sigma-Aldrich) for 60-90 s.

Immunohistochemistry on sections

Detailed information on antibodies, including order number and working concentrations, can be found in Supplementary Table 5. Tissue was embedded in paraffin wax and sectioned to 5-µm, followed by deparaffinization in Roti-Histol (#6640, Roth) and rehydration in a descending ethanol/H₂O series. For embryonic sections (E14.5, E16.5, E18.5), epitope retrieval was accomplished with citrate-based antigen unmasking solution (#H-3300, Vector Laboratories) for 15 min at 100 °C. Postnatal tissue sections (P17/21) were subjected to heat-induced antigen retrieval 10 mM Tris-HCl/2 mM EDTA buffer, pH 9.0, for 90 min at 80 °C. Endogenous peroxidase activity was blocked by incubation in 3% H₂O₂/PBS (#AP121076.1211, AppliChem) for 15 min at room temperature (RT). All washing steps were performed using 0.1% Tween-20 in PBS (PBST). Samples were blocked with TNB Blocking Buffer (#FP1012, PerkinElmer) for 1 h. For antibodies generated in mice an additional IgG blocking step was performed using the M.O.M. Mouse Ig Blocking Reagent (#MKB-2213-1, Vector Laboratories). After blocking, sections were incubated with primary antibodies (diluted in TNB) overnight at 4 °C, followed by appropriate secondary and sometimes tertiary antibodies in TNB for 1 h at RT. Sections were counterstained with DAPI (0.1 µg/ml in PBST, #6335, Roth) for 10 min and mounted with Immunoselect Antifading Mounting Medium (#SCR-038447, Dianova).

For weakly expressed proteins, biotin-labelled secondary antibodies (1 h at RT) and the Tyramide Signal Amplification Kit (TSA, #NEL702001KT/NEL701001KT, PerkinElmer) were used for signal detection. HRP-conjugated streptavidin was diluted in TNB (1:100) and applied to sections for 30 min to 1 h at RT, whereas incubation with TSA reagent was performed for 10 to 15 min at RT in accordance with the manufacturer’s protocol.

For sequential double amplification, a 30 min 6% H₂O₂/PBS and an Avidin/Biotin block (15 min each, #SP-2001, Vector Laboratories) were performed in between the two amplification steps.

For sequential double labelling with two primary antibodies generated in the same host, masking of the first primary antibody was performed using the following unconjugated FAB fragments: goat-anti-rabbit FAB fragment (#111-007-003, Dianova), donkey-anti-mouse FAB fragment (#715-007-003, Dianova).

Immunohistochemistry on cochlear whole-mount preparations

Cochlear whole-mounts were rehydrated in a descending methanol/PBS series. For the first permeabilization step, whole-mounts were treated with proteinase K (10 µg/ml, #RP102B, 7Bioscience) diluted in buffer for 2 min at RT. Digestion was stopped by washing in 0.2% glycine/PBS (#A1067, Applichem). For all following permeabilization or washing steps 0.3% Triton X-100 in PBS was used. Endogenous peroxidase activity was blocked by incubation in 3% H₂O₂/PBS for 15 min at RT. Samples were blocked with 20% heat-inactivated FCS in PBS-Triton for 1 h at RT, followed by an overnight incubation with primary antibodies, diluted in blocking solution, at 4 °C. Appropriate secondary and sometimes tertiary antibodies were applied to cochlear whole-mounts for 2 h at RT.

For detection of BCL11B, antigen retrieval was required prior to the blocking step. This was performed using 10 mM sodium citrate, pH 6 with 0.25% Triton X-100 for 30 min at 90 °C, followed by cooling down at RT for 30 min.

For visualization of NGFR (P75^NTR), a biotin-labelled secondary antibody (2 h at RT) and the TSA Kit were used. Cochlear whole-mounts were incubated with the staining reagent for 30 min at RT, followed by washing with PBS-Triton on ice and inactivation of the horseradish peroxidase by incubation in 6% H₂O₂/PBS for 30 min at RT.

For co-staining of SLC17A8 and F-actin, non-methanol treated cochlear whole-mounts were used and counterstained with Phalloidin-iFluor488 (#ab176753, abcam, 1:1500) for 1 h at RT.

If required, cochlear whole-mount preparations were counterstained with DAPI. All specimens were mounted in Immunoselect Antifading Mounting Medium (SCR-038447, Dianova).

Generation of antisense RNA in situ probes

In vitro transcription of digoxigenin-labelled-antisense RNA probes from DNA templates was performed using digoxigenin-labelling mix (#11277073910, Sigma) and T7/T3/SP6-RNA-Polymerases (#M0251/11031163001/M0207, NEB/Sigma-Aldrich).

For transcripts, for which no DNA template was available, primers pairs were designed using the MacVector software (version 16.0.8), modified with an additional T7-promoter sequence at the 5′ end of the reverse primer, and used for PCR based amplification of DNA templates from genomic DNA or cDNA. Accuracy of all probe templates was confirmed by sequencing.

Primer sequences used for amplification of DNA templates are listed in Supplementary Table 6.

RNA in situ hybridization

In situ hybridization analysis was performed on 10-µm paraffin sections following a standard procedure with digoxigenin-labelled antisense riboprobes⁴⁵. In brief, sections were deparaffinized, rehydrated in a descending ethanol/water series, and then treated with 10 µg/ml proteinase K (#RP102B, 7Bioscience) diluted in Tris-HCl buffer solution, pH 7.4, for 7 min at 37 °C. Followed by a 5 min incubation in 0.2% glycine/PBS, and re-fixation in 4% PFA/0.2% glutaraldehyde for 20 min at RT. Hybridization with digoxigenin-labelled riboprobes was performed overnight at 70 °C. After two 30 min washing steps in saline sodium citrate/formamide at 65 °C and a blocking step at RT, sections were incubated with sheep-anti-digoxigenin Fab fragments conjugated with alkaline phosphatase (1:4000, #11093274910, Roche) for 2 h at RT. Staining reaction was developed using the BM Purple AP substrate precipitating solution (#11442074001, Sigma Aldrich) to localize bound anti-digoxigenin antibody.

Microarray analysis of cochlear ducts

For the E14.5 microarray analysis, whole cochlear ducts were isolated in Leibovitz’s L15 Medium (#F1315, Biochrom) and the spiral ganglion was removed. For the E18.5 microarray analysis, cochlear ducts were isolated in Leibovitz’s L15 Medium and dissected into two halves. The spiral ligament and the spiral ganglia were removed from the basal half and the remaining sensory tissue was collected for analysis. Immediately after dissection/isolation the tissue was frozen using dry ice and stored at −80 °C until use.

For the E14.5 microarray analysis, four independent sex-sorted pools per genotype, each containing 23–27 cochlear ducts, were collected from Sox2-Tbx2LOF mutants and cre-negative controls after a single pulse of tamoxifen at E12.5. For the E18.5 microarray analysis four independent sex-sorted pools per genotype, each containing 16–20 organs of Corti from the basal half of the cochlear duct, were collected from Sox2-Tbx2LOF mutants and cre-negative controls after a single pulse of tamoxifen at E16.5. After total RNA extraction using the peqGOLD RNAPure reagent (#732-3312, Peqlab) according to the manufacturer’s instructions, samples were sent to the Research Core Unit Transcriptomics of Hannover Medical School where they were hybridized to Agilent Whole Mouse Genome Oligo v2 (4x44K) Microarrays (#G4846A, Agilent Technologies) in a dual-colour mode.

Deregulated genes were determined with the software Significance Analysis of Microarrays 5.0 (SAM, Stanford University, CA, USA)⁴⁶. For the analysis normalized expression data was assessed by two class unpaired comparison with t-statistics (n = 4). The value of k for the k-nearest-neighbor algorithm was set to 10 (default), the number of permutations was 100 (default). For the significance cut-off we used a minimum fold change of 1.5 and values for delta (1.39 for E14.5, 1.15 for E18.5) that resulted in an estimated false discovery rate (FDR) of zero.

Image acquisition and analysis

Sections were photographed using the Leica DM5000 microscope with a Leica DFC300FX digital camera and Leica Firecam for Mac 1.9 software or the Leica DM6000 microscope with a Leica DFC350FX digital camera and Leica Application Suite X (3.0.1) software. Images of cochlear whole-mounts were acquired using the confocal laser scanning microscope Leica TCS SP8 and HC PL APO 20x/0.75 IMM, 40×/1.10 WATER, 63×/1.40 OIL CS2 objectives and Leica LAS X 3.5.5 software. Images were processed using Leica LAS X 3.0.1 (3D-reconstructions), FIJI/ImageJ 2.3.0 and Adobe Photoshop CS4.

Quantifications and statistical analysis

Quantification of specific cell types on cochlear whole-mounts at E18.5 occurred in two steps. First, a 500 µm-long region of the organ of Corti at the mid-basal level of the cochlear duct was defined. Second, MYO6⁺ cells were counted within this area (approx. 260 cells per sample) and each and every hair cell was analysed for expression of BCL11B and/or SLC17A8. For analysis at P21, we defined 400-500 µm-long regions at the basal level of the organ of Corti and MYO6⁺ hair cells were analysed for expression of SLC25A6 and SLC17A8. Measurements and cell counts were performed using FIJI/ImageJ 2.3.0 (NIH) and Adobe Photoshop CS4 software. Cell counts were normalized to a length of 100 µm of cochlea in Microsoft Excel 16.16.27.

Statistical analyses were performed using GraphPad Prism7 and JASP (version 0.13.1). Normal distribution of data was tested using the D’Agostino & Pearson and Shapiro-Wilk normality test (normal distribution if p-values ≥ 0.05) and Q-Q-plots. Equality of variances was assessed by performing the F- and Levene’s test (equal variances if p-values ≥ 0.05). For comparison of two groups with normal distribution (parametric) and equal variances we used the unpaired two-tailed t-test. For comparison of two groups with normal distribution and unequal variances we used the two-tailed Welch’s t-test. For comparison of two groups with nonparametric distribution we used the two-tailed Mann-Whitney U test. Results were expressed as mean ± SD. A p-value < 0.05 was considered statistically significant.

For the quantification of type I afferent innervation of ectopic OHCs and ectopic IHCs in Atoh1-Tbx2LOF and Atoh1-TBX2ME cochleae, respectively, at P21, apical regions of the organ of Corti were stained for CALB2, which is strongly expressed in Type I afferents and IHCs and weakly in OHCs. Weak-CALB2-positive ectopic OHCs or strong-CALB2-positive ectopic IHCs were counted in single or multiple non-overlapping maximum-intensity-projection-images of the organ of Corti per individuum each covering a length of 246 µm (summing up to regions with lengths of 246 to 738 µm). Then the overall-percentage of these cells, that were innervated with CALB2-positive afferents, was determined. Due to low recombination in P21 Atoh1-Tbx2ME (Tamoxifen at E15.5) mutants, all CALB2⁺ ectopic IHCs in the entire apical region were counted.

For the quantification of the stereocilia phenotypes of ectopic OHCs and IHCs in Atoh1-Tbx2LOF and Atoh1-TBX2ME cochleae at P21, all SLC17A8-positive (ectopic) IHCs and SLC17A8-negative (ectopic) OHCs were analysed in single or multiple non-overlapping z-stacks of the organ of Corti per individuum each covering a length of 74 µm. We counted the cells of a given cell type according to their stereocilia phenotype and calculated the (weighted) percentages. For several mutants, OHC stereocilia were not included in the z-stacks, and therefore neglected for the cell counts.

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

Data availability

All relevant data in this study are available within the article, Supplementary Data or Source Data. Microarray data have been deposited in Gene Expression Omnibus under the accession numbers GSE180500 and GSE180501. Source data are provided with this paper.

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Acknowledgements

The monoclonal antibody against CDH2 (clone: MNCD2) developed by Takeichi, M./Matsunami, H. was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH and maintained at The University of Iowa, Department of Biology, Iowa City, IA 52242. We thank the Research Core Unit Transcriptomics of Hannover Medical School for microarray analysis, and Achim Gossler for critical reading of the manuscript. This work was supported by the German Research Council (Deutsche Forschungsgemeinschaft) [DFG TR1325/1-1 to M.-O.T.].

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Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
Marina Kaiser, Timo H. Lüdtke, Lena Deuper, Carsten Rudat, Andreas Kispert & Mark-Oliver Trowe
Medical Biology, Amsterdam Reproduction & Development, Amsterdam University Medical Centers, Amsterdam, The Netherlands
Vincent M. Christoffels

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Marina Kaiser
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Timo H. Lüdtke
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Lena Deuper
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Carsten Rudat
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Vincent M. Christoffels
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Contributions

Conceptualization: A.K., M.-O.T., M.K.; Formal analysis: M.K., A.K., M.-O.T.; Investigation: M.K., T.H.L., L.D., C.R., M.-O.T.; Resources: V.M.C.; Data curation: M.K., M.-O.T.; Writing—original draft: M.K., A.K., M.-O.T.; Writing—review & editing: M.K., T.H.L., V.M.C., A.K., M.-O.T.; Visualization: M.K., M.-O.T.; Supervision: A.K., M.-O.T.; Project administration: M.-O.T.; Funding acquisition: M.-O.T.

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Correspondence to Andreas Kispert or Mark-Oliver Trowe.

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Kaiser, M., Lüdtke, T.H., Deuper, L. et al. TBX2 specifies and maintains inner hair and supporting cell fate in the Organ of Corti. Nat Commun 13, 7628 (2022). https://doi.org/10.1038/s41467-022-35214-4

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Received: 21 October 2022
Accepted: 21 November 2022
Published: 09 December 2022
DOI: https://doi.org/10.1038/s41467-022-35214-4

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