Systematic alanine scanning of PAX8 paired domain reveals functional importance of the N-subdomain

in Journal of Molecular Endocrinology
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  • 1 Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
  • 2 Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan

Correspondence should be addressed to S Narumi: narumi-s@ncchd.go.jp

Thyroid-specific transcription factor PAX8 has an indispensable role in the thyroid gland development, which is evidenced by the facts that PAX8/Pax8 mutations cause congenital hypothyroidism in humans and mice. More than 90% of known PAX8 mutations were located in the paired domain, suggesting the central role of the domain in exerting the molecular function. Structure-function relationships of PAX8, as well as other PAX family transcription factors, have never been investigated in a systematic manner. Here, we conducted the first alanine scanning mutagenesis study, in which 132 alanine variants located in the paired domain of PAX8 were created and systematically evaluated in vitro. We found that 76 alanine variants (55%) were loss of function (LOF) variants (defined by <30% activity as compared with wild type PAX8). Importantly, the distribution of LOF variants were skewed, with more frequently observed in the N-subdomain (65% of the alanine variants in the N-subdomain) than in the C-subdomain (45%). Twelve out of 13 alanine variants in residues that have been affected in patients with congenital hypothyroidism were actually LOF, suggesting that the alanine scanning data can be used to evaluate the functional importance of mutated residues. Using our in vitro data, we tested the accuracy of seven computational algorithms for pathogenicity prediction, showing that they are sensitive but not specific to evaluate on the paired domain alanine variants. Collectively, our experiment-based data would help better understand the structure-function relationships of the paired domain, and would provide a unique resource for pathogenicity prediction of future PAX8 variants.

Abstract

Thyroid-specific transcription factor PAX8 has an indispensable role in the thyroid gland development, which is evidenced by the facts that PAX8/Pax8 mutations cause congenital hypothyroidism in humans and mice. More than 90% of known PAX8 mutations were located in the paired domain, suggesting the central role of the domain in exerting the molecular function. Structure-function relationships of PAX8, as well as other PAX family transcription factors, have never been investigated in a systematic manner. Here, we conducted the first alanine scanning mutagenesis study, in which 132 alanine variants located in the paired domain of PAX8 were created and systematically evaluated in vitro. We found that 76 alanine variants (55%) were loss of function (LOF) variants (defined by <30% activity as compared with wild type PAX8). Importantly, the distribution of LOF variants were skewed, with more frequently observed in the N-subdomain (65% of the alanine variants in the N-subdomain) than in the C-subdomain (45%). Twelve out of 13 alanine variants in residues that have been affected in patients with congenital hypothyroidism were actually LOF, suggesting that the alanine scanning data can be used to evaluate the functional importance of mutated residues. Using our in vitro data, we tested the accuracy of seven computational algorithms for pathogenicity prediction, showing that they are sensitive but not specific to evaluate on the paired domain alanine variants. Collectively, our experiment-based data would help better understand the structure-function relationships of the paired domain, and would provide a unique resource for pathogenicity prediction of future PAX8 variants.

Introduction

Organ-specific transcription factors play pivotal roles in organogenesis, organ growth and maintenance of organ functions. As for the thyroid gland, three thyroid-specific transcription factors (TTF), namely PAX8 (encoded by PAX8) (Plachov et al. 1990, Zannini et al. 1992), TTF-1 (encoded by NKX2-1) (Guazzi et al. 1990, Lazzaro et al. 1991), TTF-2 (encoded by FOXE1) (Zannini et al. 1997) and HEX (encoded by HHEX) (Crompton et al. 1992, Thomas et al. 1998), have been known to play such roles.

PAX8 is a member of the PAX gene family, which is characterized by the presence of DNA-binding paired domain. In mice and humans, Pax8/PAX8 is expressed in the thyroid from prenatal period to adulthood (Plachov et al. 1990). In cultured cell lines, PAX8 directly regulates the transcription of thyroid-specific genes, such as thyroglobulin (Tg), thyroid peroxidase (TPO) (Di Palma et al. 2003) and sodium iodine symporter (Ohno et al. 1999). Genetically engineered Pax8-deficient mice show severe thyroid hypoplasia due to defective proliferation and survival of thyroid precursor cells (Mansouri et al. 1998), indicating the indispensable role of Pax8 in the early organogenesis. In humans, heterozygous PAX8 mutations cause congenital hypothyroidism (CH) with autosomal dominant inheritance. To date, 33 mutation-carrying families harboring a total of 23 distinct PAX8 mutations have been described (Macchia et al. 1998, Congdon et al. 2001, Komatsu et al. 2001, Vilain et al. 2001, de Sanctis et al. 2004, Meeus et al. 2004, Grasberger et al. 2005, Al Taji et al. 2007, Tonacchera et al. 2007, Di Palma et al. 2010, Jo et al. 2010, Narumi et al. 2010, 2011, 2012, Carvalho et al. 2013, Hermanns et al. 2013, Ramos et al. 2014, Zou et al. 2015, Lof et al. 2016, Srichomkwun et al. 2016, Liu et al. 2017). Clinical phenotypes of the mutation carriers are variable, ranging from overt CH with severe thyroid hypoplasia to subclinical hypothyroidism with a normal-sized thyroid (Supplementary Table 1, see section on supplementary data given at the end of this article).

Previously reported experimentally verified PAX8 mutations have been found exclusively in the paired domain, except for one truncating mutation (p.Thr277*) located outside the domain (de Sanctis et al. 2004). This fact implies the importance of the paired domain in exerting the molecular function of PAX8. Nonetheless, genetic variants located in functionally important domains do not necessarily result in loss of function (LOF) sufficient for disease onset. Hence, when a novel variant is found in a patient, it is necessary to presume its pathogenicity. To this end, a handful of computational algorithms, such as PolyPhen-2 (Adzhubei et al. 2010) and SIFT (Kumar et al. 2009), have been used. However, the accuracy of these in silico algorithms remains around about 70% (Thusberg et al. 2011), which is not reliable enough to be used in clinical genetic diagnosis. In this present study, systematic alanine scanning mutagenesis was performed to determine which residues are functionally important. Alanine substitution eliminates side chain interactions without altering main chain conformation, enabling to assess the contribution of specific residue on the function. We performed systematic alanine scanning mutagenesis that targeted all 132 non-alanine residues of the paired domain of PAX8, and assessed the effects of amino acid alterations in vitro. We also compared in silico algorithms’ accuracy using our in vitro dataset.

Materials and methods

Plasmids

We used simian virus 40 promoter-driven effector plasmids carrying human PAX8 cDNA that has been previously described (Narumi et al. 2010). We created a total of 132 alanine-substituted, the smallest chiral amino acid, variant PAX8 (Met1Ala to Gln137Ala; five alanine residues (Ala19, Ala38, Ala84, Ala104 and Ala113) were excluded) using PrimeSTAR Mutagenesis Basal Kit (Takara Bio Inc). We confirmed each alanine mutation substitution by direct sequencing. Alanine scanning enables quick determination of each individual amino acid’s contribution to the protein function. The transcriptional activities of PAX8 proteins (wild type (WT) or alanine variants) were assessed with firefly luciferase reporters that contain the promoter sequence of the human Tg gene corresponding to −284/+39 region (TG-luc) (Narumi et al. 2010), or the promoter sequence of the rat TPO gene corresponding to −1/+426 region (Tpo-luc) (Di Palma et al. 2003).

Cell culture and transfection

HeLa cells were maintained in DMEM supplemented with 100 IU/mL penicillin, 100 µg/mL streptomycin and 10% fetal bovine serum. Transient transfection was performed with the Lipofectamine 3000 reagent (Thermo Fisher Scientific). Cells grown in 96-well plates with 70–80% confluence were transfected with 90 ng of each luciferase reporter (TG-luc or Tpo-luc) and 10 ng of each effector plasmid (empty vector, WT-PAX8 or alanine variant PAX8). Forty-eight hours after transfection, we measured luciferase activities using ONE-Glo Luciferase Assay System (Promega) according to the manufacture’s instruction. Luciferase activities were represented relative to the activity obtained by transfection of WT-PAX8 (set to 100%) and empty vector (set to 0%). Experiments were conducted in quadruplicate, and were repeated at least three times. The activity data were expressed as mean ± s.e.m. Based on the transactivating capacities, the following terms were defined: profound LOF, less than 10.0% activity; moderate LOF, 10.0–29.9% activity; minimal LOF, 30.0–69.9% activity; functionally neutral, 70.0–119.9% activity; hyperfunctioning, equal or more than 120% activity. We considered variants with profound LOF or moderate LOF as disease-causing variants (described as significant LOF).

Three-dimensional modeling

The three-dimensional modeling structure of PAX8-DNA complex has not been determined to date. Instead, we used crystal structure data of the PAX5-DNA complex to display the positions of the variants, considering the high protein sequence similarity (94% identical in the paired domain) between PAX8 and PAX5. The crystal structure data of PAX5-DNA complex was obtained from protein data bank (ID 1MDM; http://www.rcsb.org/pdb), and was used as a template to visualize the effects of alanine substitutions. The pictures were produced with PyMOL (http://www.pymol.org). Residues that were not identical between PAX8 and PAX5 were not shown. The effect of alanine substitution in the pairing region of PAX8 was shown as color-coded spheres: red, profound LOF; orange, moderate LOF; yellow, minimal LOF; gray, functionally neutral; and blue, hyperfunctioning. Presumed effects of alanine substitution were classified into five categories: (i) loss of hydrogen bond(s) to target DNA; (ii) loss of van der Waals contact(s) to target DNA; (iii) loss of hydrogen bond(s) within PAX8, (iv) loss of van der Waals contact(s) within PAX8; and (v) no recognizable effect on contact to target DNA or within PAX8 (‘free side chain’ residues). We used PyMOL to predict hydrogen bonds with a default setting van der Waals contacts were defined based on the distance (3.50 to 3.99 Å) between the Ala side chains to other carbon molecules (target DNA or other residues of PAX8).

Computational prediction of pathogenicity of PAX8 alanine variants

The pathogenicity of 132 alanine variants were assessed by following seven computational algorithms: FATHMM (Shihab et al. 2013), MutationAssessor (Reva et al. 2011), MutationTaster (Schwarz et al. 2010), PolyPhen-2 (Adzhubei et al. 2010), PROVEAN (Choi et al. 2012), SIFT (Kumar et al. 2009) and VEST-4 (Carter et al. 2013). The accuracy of computational prediction tools was assessed by ROC curves. In this study, a gold standard was defined by the results of in vitro functional assays, in which variants with significant LOF (i.e. transactivating capacity less than 30%) were considered to be deleterious.

Results

Transactivating capacities of alanine variants

PAX8 protein is made up of 450 amino acids comprising a paired domain of Gly9 to Gln137. To systematically assess the effect of amino acid substitutions in the paired domain and its N-terminal region (Met1 to Ser8), 132 non-alanine residues were substituted by alanine one by one, and transcriptional activities of each mutant were assessed with two luciferase reporters (TG-luc and Tpo-luc) (Supplementary Table 2). There was a significant correlation between the transactivating capacities for TG-luc and Tpo-luc among the 132 alanine variants (R² = 0.66, P < 0.001; Supplementary Fig. 1). Discordance in transactivating capacities between the two reporters was observed in only one alanine variant Val75Ala (TG-luc 65.8±12.3%, Tpo-luc 127.0 ± 17.2%). For simplicity, descriptions of transactivating capacities below are based on ones measured with TG-luc.

Profound LOF was observed in 46 alanine variants (35% of total alanine variants), while moderate LOF was observed in 30 alanine variants (23%) (Fig. 1A and B). Eight alanine variants (7%) were considered to be functionally neutral. One alanine variant (Glu67Ala) showed slightly elevated transactivating capacities (139 ± 7.9% activity relative to WT-PAX8).

Figure 1
Figure 1

Effects of alanine substitutions in paired domain of PAX8. (A) A schematic diagram showing the secondary structure of the paired domain (Gly9 to Gln137) of PAX8. Residues that caused profound loss of function (LOF), moderate LOF and minimal LOF were colored in red, orange and yellow, respectively. Residues with comparable activities with wild type and high activity were colored in gray and blue, respectively. Two β-sheets and six α-helices are showed as boxes. Bars indicate the locations of previously reported missense PAX8 mutations. (B, C, D and E) The three-dimensional structure of the DNA-binding paired domain and its target DNA (colored in silver), based on the crystal structure data of PAX5–DNA complex. An overall view indicating the three subdomains (B): N-subdomain (C), C-subdomain (D) and the linker polypeptide (E).

Citation: Journal of Molecular Endocrinology 62, 3; 10.1530/JME-18-0207

Structure-function relationships of the paired domain of PAX8

The paired domain consists of two β-sheets (β1 and β2) and six α-helices (α1 to α6) (Fig. 1A). Based on the crystal structure data, paired domains can be subdivided into three segments: N-terminal subdomain (β1, β2, α1 to α3), C-terminal subdomain (α4 to α6) and the linker polypeptide between the two subdomains (Fig. 1B). As for 66 alanine variants in the N-subdomain, 30 (45%) were profound LOF and 13 (20%) were moderate LOF (Fig. 1C). As for 50 alanine variants in the C-subdomain, nine (18%) were profound LOF and 14 (28%) were moderate LOF (Fig. 1D). The effects of alanine substitution in the linker polypeptide were generally modest, except for Gly77, Gly78 and Ser79 that contact with DNA at the bottom of minor groove (Fig. 1E).

Based on the crystal structure data, we classified the effects of the alanine substitution into five categories according to the presence or absence of contact(s) to the target DNA or within PAX8 (Table 1). Contacts to the target DNA, which were chiefly via hydrogen bonds, were found in twelve and five residues in N- and C-subdomains, respectively. About 70% of alanine substitutions of these residues caused significant LOF. Intramolecular contacts (hydrogen bonds or van der Waals contacts) were seen in 25 and 29 residues in N- and C-subdomains, respectively. About 60% of alanine substitutions of the residues caused significant LOF in both of the two domains. ‘Free side chain’ residues were observed in 16 and 11 residues in N- and C-subdomains, respectively. Eleven out of 16 ‘free side chain’ residues in N-subdomain caused, when mutated to alanine, significant LOF, while only three out of 11 did in C-subdomain (P = 0.036 by Fisher exact test).

Table 1

Structure-function relationships of the N-subdomain and C-subdomain.

Classification of the effectN-subdomainC-subdomainP valueb
Total (n)LOFa (n)%LOF (%)Total (n)LOFa (n)%LOF (%)
Loss of hydrogen bond(s) to DNA12108343750.47
Loss of van der Waals contact(s) to DNA000100NA
Loss of hydrogen bond(s) within PAX86350116550.38
Loss of van der Waals contact (within PAX8)1914741811610.20
No effect (‘free side chain’)161169113270.036

aSignificant LOF (i.e. relative activity <30% of wild type). b P values were calculated with Fisher exact test.

LOF, loss of function.

Alanine substitution on the residues affected in CH patients

To date, a total of 16 distinct CH-causing missense PAX8 mutations affecting 13 residues have been described in the paired domain (Macchia et al. 1998, Congdon et al. 2001, Vilain et al. 2001, Meeus et al. 2004, Grasberger et al. 2005, Al Taji et al. 2007, Di Palma et al. 2010, Narumi et al. 2010, 2012, Carvalho et al. 2013, Hermanns et al. 2013, Ramos et al. 2014, Lof et al. 2016, Srichomkwun et al. 2016). Out of the 13 residues, 12 caused significant LOF when substituted with alanine (Table 2). The only exception was Gln40Ala (corresponding human mutation, Gln40Pro), which showed minimal LOF (61.0 ± 1.8% activity).

Table 2

Effects of alanine substitutions on 13 residues that have been affected in human CH patients.

Human mutationAlanine variantTG-luc activity of Ala variant (%)
Leu16ProLeu16Ala5.8 ± 1.5
Phe20SerPhe20Ala−0.4 ± 2.0
Pro25ArgPro25Ala21.2 ± 2.6
Arg31HisArg31Ala−0.9 ± 0.4
Arg31CysArg31Ala−0.9 ± 0.4
Gln40ProGln40Ala61.0 ± 1.8
Ile47ThrIle47Ala−1.9 ± 0.9
Ser48PheSer48Ala22.7 ± 4.2
Arg52ProArg52Ala0.9 ± 4.9
Ser54ArgSer54Ala−0.6 ± 0.9
Ser54GlySer54Ala−0.6 ± 0.9
Ser54CysSer54Ala−0.6 ± 0.9
His55GlnHis55Ala9.2 ± 1.8
Cys57TyrCys57Ala16.1 ± 6.7
Leu62ArgLeu62Arg−1.4 ± 0.9
Arg133GlnArg133Ala11.9 ± 4.1

Comparison of computational algorithms

With assuming in vitro transactivating capacities as a gold standard test, we compared accuracy of seven computational algorithms (FATHMM, MutationAssessor, MutationTaster, PolyPhen-2, PROVEAN, SIFT and VEST-4) in predicting the pathogenicity of 132 PAX8 alanine variants (Supplementary Table 2). The area under the ROC curve values of the seven algorithms were 0.65 ± 0.09 (mean ± s.d.) (Fig. 2). Highest area under the ROC curve was scored in MutationAssessor with 0.76. When default cut-off threshold was applied, all seven computational algorithms showed high sensitivity (0.95 ± 0.04) and very low specificity (0.14 ± 0.15). When optimal cut-off values based on the ROC curves were used, the sensitivity and specificity were 0.62 ± 0.21 and 0.63 ± 0.14, respectively (Supplementary Fig. 2A, B, C, D, E, F and G).

Figure 2
Figure 2

ROC curves of seven computational algorithms (FATHMM, MutationAssessor, MutationTaster, PolyPhen-2, PROVEAN, SIFT and VEST-4) are shown. For each of 132 PAX8 alanine variants, scores were obtained with the seven algorithms. With assuming in vitro transactivating capacities as a gold standard test, ROC curves were drawn.

Citation: Journal of Molecular Endocrinology 62, 3; 10.1530/JME-18-0207

Discussion

In this study, we conducted the first systematic alanine scanning mutagenesis targeting the paired domain of a PAX transcription factor. Our findings would provide unique insights into structure-function relationships of the paired domain of PAX8, and possibly other PAX gene family transcription factors, since amino acid sequences (and three-dimensional structures probably) are well conserved (Supplementary Fig. 3).

Three segments (N-subdomain, linker polypeptide and C-subdomain) were recognizable in the paired domain of PAX8. Among 76 alanine variants with significant LOF, 43, 10 and 23 were located in the N-subdomain, linker polypeptide and C-subdomain, respectively. Relatively severe effects of alanine substitutions on the N-subdomain indicate the functional importance of the subdomain. The assumption agrees well with the following three facts: (i) the N-subdomain is better conserved among PAX family genes than the C-subdomain (Supplementary Fig. 3); (ii) vast majority of CH-causing PAX8 mutations have been observed in the N-subdomain (Fig. 1A and Supplementary Table 3); (iii) similarly, mutations have been preferentially observed in the N-subdomain in PAX3 defect (Waardenburg syndrome), PAX6 defect (Aniridia) and PAX9 defect (oligodontia or hypodontia), while mutations show broader distribution in PAX2 defect (renal coloboma syndrome) (Supplementary Table 3) (Schimmenti 2011). We could recognize two structural/functional differences between N- and C-subdomains. One is the number of contacts between PAX8 and the target DNA (12 contacts in N-subdomain; five contacts in C-subdomain). N-subdomain is expected to bind to the target DNA more tightly. The other difference is related to ‘free side chain’ residues. Among 16 ‘free side chain’ residues in N-subdomain, 69% caused, when mutated to alanine, significant LOF, while only 27% in C-subdomain. Relatively severe effects of alanine substitutions on ‘free side chain’ residues in N-subdomain imply the yet unknown function(s) of these residues. One possible explanation is interaction(s) between the PAX8 protein and other transcription factor(s). PAX5, a closely related transcription factor of PAX8, is known to bind to Ets by its N-subdomain to form a complex. PAX8 might have such partner molecule(s), although none have been identified so far.

Alanine substitutions of 13 residues that have been affected in human CH patients caused significant LOF, except for Gln40. This failure in prediction is probably explained by the nature of substitutions: Gln to Ala change affects the side chain only, while Gln to Pro change affects both the main chain and the side chain. We suppose that alanine scanning-based data will be a useful resource for pathogenicity prediction of future novel PAX8 variants, although the nature of amino acid substitution should also be considered.

In this study, we showed that widely used computational algorithms have two clear deficits in pathogenicity prediction of PAX8 variants. First, area under the ROC curve values of the algorithms were generally low, indicating insufficient performance of them. Among the seven tested algorithms, MutationAssessor worked best. Second, default cut-off thresholds for prediction were set inappropriately low in all seven algorithms. This would result in false positive results. We stress that caution for ‘overdiagnosis’ is needed when clinicians interpret the results of computational algorithms with default cut-off thresholds.

In summary, we report alanine scanning mutagenesis that targeted all 132 non-alanine residues of the paired domain of PAX8. Our works not only contribute to better understanding of the structure-function relationships of the paired domain, but also provide a unique resource for evaluating the pathogenicity of novel PAX8 variants identified in future CH patients.

Supplementary data

This is linked to the online version of the paper at https://doi.org/10.1530/JME-18-0207.

Declaration of interest

The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

Funding

This work was supported by JSPS KAKENHI (Grant Number 15K09630) from the Japan Society for the Promotion of Science.

Acknowledgements

The authors would like to thank Mariastella Zannini for providing us the Tpo-luc construct. We thank Professor Hiroyuki Ida of Department of Pediatrics, Jikei University School of Medicine, for fruitful discussion.

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  • View in gallery

    Effects of alanine substitutions in paired domain of PAX8. (A) A schematic diagram showing the secondary structure of the paired domain (Gly9 to Gln137) of PAX8. Residues that caused profound loss of function (LOF), moderate LOF and minimal LOF were colored in red, orange and yellow, respectively. Residues with comparable activities with wild type and high activity were colored in gray and blue, respectively. Two β-sheets and six α-helices are showed as boxes. Bars indicate the locations of previously reported missense PAX8 mutations. (B, C, D and E) The three-dimensional structure of the DNA-binding paired domain and its target DNA (colored in silver), based on the crystal structure data of PAX5–DNA complex. An overall view indicating the three subdomains (B): N-subdomain (C), C-subdomain (D) and the linker polypeptide (E).

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    ROC curves of seven computational algorithms (FATHMM, MutationAssessor, MutationTaster, PolyPhen-2, PROVEAN, SIFT and VEST-4) are shown. For each of 132 PAX8 alanine variants, scores were obtained with the seven algorithms. With assuming in vitro transactivating capacities as a gold standard test, ROC curves were drawn.