{'fraction_non_alphanumeric': 0.030602879596168187, 'fraction_numerical': 0.02899673033901222, 'mean_word_length': 5.088178802165182, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
SMAD transcription factors are altered in cell models of HD and regulate HTT expression

Transcriptional dysregulation is observable in multiple animal and cell models of Huntington's disease, as well as in human blood and post-mortem caudate. This contributes to HD pathogenesis, although the exact mechanism by which this occurs is unknown. We therefore utilised a dynamic model in order to determine the differential effect of growth factor stimulation on gene expression, to highlight potential alterations in kinase signalling pathways that may be in part responsible for the transcriptional dysregulation observed in HD, and which may reveal new therapeutic targets. We demonstrate that cells expressing mutant huntingtin have a dysregulated transcriptional response to epidermal growth factor stimulation, and identify the transforming growth factor-beta pathway as a novel signalling pathway of interest that may regulate the expression of the Huntingtin (HTT) gene itself. The dysregulation of HTT expression may contribute to the altered transcriptional phenotype observed in HD.


Introduction
Huntington's Disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion within the first exon of the Huntingtin (HTT) gene, which gives rise to an expanded polyglutamine tract in the huntingtin (HTT) protein. HD is characterised by progressive motor abnormalities that manifest in the third to fourth decades of life, and is also commonly associated with cognitive impairments and psychiatric disturbances [1]. Neuronal dysfunction has been found to occur prior to both striatal atrophy and overt motor symptom onset [2,3]. It is therefore possible that cell death and degeneration in HD-affected neuronal cells follow an initial period of dysregulation of multiple cellular processes [4].
The regulation of kinase signalling is altered by, and in turn alters, gene expression: in HD aberrant regulation of multiple kinase signalling pathways has been shown [5]. The TGFβ pathway is a regulator of cell growth, proliferation and apoptosis, and is upstream of the core regulatory mothers against decapentaplegic-homolog (SMAD) family of transcription factors [6,7]. To date, the characterisation of TGFβ1 in association with HD has been limited, and has yielded contradictory results; TGFβ1 is reduced in the peripheral blood of asymptomatic HD patients, and is inversely correlated with CAG repeat length [8]. However, while YAC128 and R6/2 mice exhibit reduced TGFβ1 in the cortex, increased TGFβ1 has been observed in HD patient and R6/2 mouse plasma [9]. Increased TGFβ signalling has also been identified in the hippocampus of a transgenic rat model of HD and in the R6/2 mouse model, where it has an inverse effect on neural stem cell proliferation [10], and in the cortex of the Q175 mouse model [11]. The TGFβ pathway is upregulated in human HD induced pluripotent stem cells (hiPSCs) and restored to normal levels by replacement of the expanded CAG repeat with a CAG repeat of non-pathogenic length [12]. Further analysis of iPSC-derived neural progenitor cells (NPCs) carrying expanded CAG repeats showed increased levels of TGFβ1 and enhanced SMAD2 phosphorylation [11].
We investigated differential gene expression after epidermal growth factor (EGF) stimulation in the immortalised StHdh Q111 cell model of HD and identified TGFβ signalling as a dysregulated pathway. Further characterisation of this pathway in both the StHdh Q111 model and in hiPSCderived NPCs revealed dysregulation of SMAD expression, localisation and phosphorylation in cells carrying a CAG expansion, as well as evidence of direct regulation of Htt gene expression by Smad3 activation.

Cellular models
StHdh Q7/7 , StHdh Q7/111 and StHdh Q111/111 immortalised embryonic striatal cells were a kind gift from Marcy MacDonald (Molecular Neurogenetics Unit, Massachusetts General Hospital, Massachusetts, USA). Cell lines were grown and maintained in high glucose Dulbecco's modified eagle medium (DMEM; Life Technologies), containing 1% penicillin-streptomycin solution, 1% 40 mg/ml Geneticin (both Life Technologies) and 10% fetal bovine serum (FBS; PAA), in a humid environment at 33°C with 5% CO 2. Q109 (heterozygous for a 109 CAG repeat expansion) and Q21 (wild-type, homozygous for 21 CAG repeats) hiPSC-derived lines were maintained at the NPC stage of differentiation, in order to best match the immortalised StHdh Q111 cell lines. NPCs were grown and maintained on Matrigel-coated plates (VWR) in Expansion media consisting of advanced DMEM F12, supplemented with 1% penicillin-streptomycin solution, 1% glutamine supplement (all Life Technologies), 10 μg/ml epidermal growth factor (EGF; Peprotech), 10 μg fibroblast growth factor (FGF; Peprotech) and 2% Neurobrew with vitamin A (Miltenyi). Cells were grown in a humid environment at 37°C with 5% CO2. Media was replaced daily, and cells were passaged upon reaching 90% confluence using Accutase (Life Technologies). Immunofluorescence was carried out on these cells with common NPC markers to confirm differentiation stage ( Supplementary Fig. 1).

Growth factor stimulation
Cells were serum starved overnight prior to treatment with EGF (Life Technologies). Following serum starvation, cells were incubated for 2 h with 100 ng/ml EGF, followed immediately by RNA extraction. Control cells were serum starved for the same period of time and processed in parallel with EGF treated cells.
In order to induce Smad phosphorylation, cells were serum starved overnight, then incubated with 100 ng/ml of either mouse (for StHdh Q111 cells) or human (for hiPSC-derived NPCs) TGFβ1 (NEB) for 30 min (for protein analysis) or for 2 h (for nucleic acid analysis).

RNA extraction
RNA was extracted from cells grown in 6-well plates using the phenol/chloroform method, precipitated in ethanol, and purified using RNeasy MinElute Cleanup kit (Qiagen) according to manufacturer's instructions.

Microarray and bioinformatics analysis
The microarray was kindly carried out by Cardiff University's Central Biotechnology Services (CBS), utilising the Affymetrix GeneChip Mouse Gene 1.0 ST array system.
Raw microarray data was analysed in Partek® Genomics Suite™, where it underwent quantile normalisation to log base 2 and median polish probeset summarisation. There was no adjustment for GC content or probe sequence, and robust multi-array average (RMA) background correction was applied. Gene expression data were analysed by a 2-way ANOVA containing a 'genotype x EGF' interaction term to identify genes for which EGF stimulation resulted in significantly different expression changes between the genotypes, plus individual contrasts to identify simple main effects, that is, genes for which EGF stimulation significantly changes expression in a particular genotype. The focus for the following stages of analysis was on the differences between StHdh Q7/7 and StHdh Q111/111 cell lines only, as this is where the PCA suggested the largest differences are likely to lie. The following lists of significantly differentially expressed genes were created from normalised data with the parameters described in Supplementary  Table 1. Individual gene lists for differentially expressed genes following EGF stimulation in StHdh Q7/7 and StHdh Q111/111 cells were created. As there were a large number of significant genes in the genoype x EGF interaction list, only the top 500 most significant genes were selected in order to focus on the genes with the strongest effect. These lists were put through pathway analyses using The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (http://david.abcc. ncifcrf.gov/; [13,14]). To widen the analysis beyond the regulation of transcription, all of the enriched functional terms from the DAVID analysis were subject to additional clustering to eliminate redundancy and to clarify visualization.
Clustering of terms showing significant enrichment from the DAVID analysis was performed as follows: Firstly, the terms were ranked in order of enrichment significance, with the most significant term first. For each term in turn, a measure of overlap was calculated between that term and the terms in each of the existing clusters. The measure of overlap used was the Jaccard index, calculated as the number of genes associated with both terms divided by the number of genes associated with either term. The term was assigned to the cluster with which it had the highest average Jaccard index, provided this was N50%. If the term did not have an average Jaccard index N50% with any existing cluster, it was placed in a new cluster. This process was repeated until the end of the list of terms was reached. The resulting clusters were visualised in Cytoscape [15].

qRTPCR
TaqMan (Life Technologies) qRTPCR technologies were utilised throughout this project using a two-step protocol. Extracted RNA was reverse transcribed to cDNA using the High Capacity RNA-to-cDNA kit (Life Technologies) according to manufacturer's instructions, prior to quantitative PCR utilising pre-designed TaqMan gene expression assays and Fast Advanced Master Mix (Life Technologies) according to manufacturer's instructions.

Western blotting
Protein lysates were extracted from StHdh Q111 and NPC lines using 10× Cell Lysis Buffer (NEB) according to manufacturer's instructions. 20 μg protein from each sample was resolved on a 4-12% Bis-Tris gel (Life Technologies) and electroblotted onto a PVDF membrane (Millipore). Blots were incubated for 30 min in 5% skimmed milk powder in PBS with 0.1% Tween (PBS-T), and were then incubated overnight at 4°C with the appropriate primary antibody. The next day, blots were washed with PBS-T, and incubated with the appropriate peroxidase secondary antibody (Vector Laboratories) for 1 h at room temperature. Bands were then detected using an enhanced chemiluminescent HRP substrate (SuperSignal West Dura Extended Duration Substrate; Fisher Scientific), and visualised after exposure onto Hyperfilm (Fisher Scientific) and processing through an Ecomax X-ray film processor. Processed blots were then stripped using Restore PLUS stripping buffer (Fisher Scientific), probed with additional antibodies and re-imaged. Blots were stripped and re-probed up to a maximum of 4 times before being discarded.

Immunofluorescence
Cells were grown on glass coverslips and fixed by incubation with 10% Formalin solution (Sigma Aldrich). They were then permeabilised with 0.1% Triton x-100 (Life Technologies) in PBS, and blocked with 1% (w/v) bovine serum albumin (BSA; Sigma Aldrich) in PBS. Cells were then incubated with the relevant primary antibody for 1 h in a humid environment at 37°C, followed by the appropriate AlexaFluor secondary antibody (LifeTechnologies) for 1 h in a humid environment at 37°C, while wrapped in foil. Coverslips were mounted onto glass microscope slides using ProLong Gold antifade reagent with DAPI (Life Technologies), and stored in the dark at 4°C for at least 24 h before visualization. Slides were imaged on a Leica DM6000B fluorescent microscope and nuclear/cytoplasmic mean pixel intensity ratios were calculated as previously described [16] 2.8. Antibodies See Supplementary Table 2.

Chromatin immunoprecipitation
ChIP was carried out using approximately 4 × 10 7 cells per condition, grown in multiple 15 cm dishes. Prior to chromatin preparation, DNA was crosslinked using formaldehyde and glycine. Chromatin preparation, digestion and immunoprecipitation were carried out using the SimpleChIP kit (NEB), according to manufacturer's instructions. The antibodies used for chromatin immunoprecipitation were anti-SMAD3 (1:50; NEB) and anti- Fig. 1. Functional annotation networks of differential gene expression following EGF stimulation. A. StHdh Q7/7 and StHdh Q111/111 DAVID functional annotations for differential gene expression following EGF stimulation, following our clustering algorithm and visualised together as pathway networks in Cytoscape. Node colour saturation is indicative of StHdh Q7/7 cluster p-value, and the width of node outlines indicates StHdh Q111/111 cluster p-values (thicker outlines correspond to smaller p-values). Node size positively correlates with the size of the gene set contributing to StHdh Q7/7 -associated nodes. Edge width positively correlates with the similarity coefficient between the two connected nodes. B. DAVID functional annotations following our clustering algorithm for the interaction term gene list, visualised as pathway networks in Cytoscape. Node colour saturation is indicative of cluster p-value, node size positively correlates with the size of the gene set contributing to the node. Edge width positively correlates with the similarity coefficient between the two connected nodes. phosphorylated SMAD3 (1:100; NEB). Histone H3 (1:50) and normal rabbit IgG (1 μg) were used as negative controls (provided in SimpleChIP kit). The resulting precipitated DNA was amplified using qPCR and primers against the 5′ end of the Htt gene, incorporating the SBE region. Both antibodies were compared against normal rabbit IgG. Purified DNA from the ChIP process was quantified by Sybr Green (Life Technologies) qPCR using the following conditions; a. initial denaturation 95°C 3 min, b. denaturation 95°C 15 s, c. anneal and extension 60°C 60 s, d. repeat b and c for a total of 40 cycles. qPCR primers were designed to incorporate the Smad binding element (SBE) in the 5′ upstream promoter region of the Htt gene, and were as follows; forward 5'CTGAGCGCCTTGGTTCCG-3′, reverse 5′-ATCAGCTTTTCCAGGG TTGC-3′. Table 1 Clustered functional annotations for genes differentially expressed between baseline and following EGF stimulation. Significant DAVID functional annotations following our clustering mechanism for A. genes differentially expressed in StHdh Q7/7 and StHdh Q111/111 cells between baseline and following EGF stimulation, and B. genes with a significant EGF x Genotype interaction.

A Node
StHdh

Statistical analyses
For qRTPCR analyses, delta-Ct values were subject to a 2-way ANOVA, followed by post-hoc Tukey HSD tests. Western blots were semi-quantitatively analysed using densitometry analysis in ImageJ. The resulting measurements were normalised to measurements of αtubulin, and subject to the appropriate ANOVA and post-hoc Tukey tests. ChIP qPCR data was analysed using the fold-enrichment method; Ct values were normalised to the 2% input control, and the resulting fold-change as compared to the IgG control was determined. The resulting data was subject to a 2-way ANOVA and post-hoc Tukey tests.

Differential gene expression implicates TGFβ signalling pathways in mutant HTT carrying cells
We detected substantial differences in gene expression between StHdh Q7/7 , StHdh Q7/111 and StHdh Q111/111 cell lines in response to EGF treatment ( Supplementary Fig. 2, Supplementary Table 3) with genotype being the main source of variation, and stimulation with EGF the second largest source. There was also a mHTT/HTT gene dosage effect on expression. As there were substantial differences in gene expression profiles between StHdh Q7/7 and StHdh Q111/111 cells at baseline, we compared the extent of gene expression changes following EGF treatment within each cell line, rather than directly comparing levels of gene expression between the two genotypes.
Similar GO terms were implicated following EGF stimulation in both StHdh Q7/7 and StHdh Q111/111 cell lines (Supplementary Table 4). Although some pathways were associated with developmental processes, the majority of the most significant pathways were related to transcription and transcriptional control. The Transcription and Positive Regulation of Transcription pathways were also amongst the most significant pathways derived from genes showing differential effects of EGF stimulation between cell lines.
We clustered our DAVID pathway analysis outputs to simplify pathway enrichments without compromising the diversity of terms by eliminating terms with overlapping genes (see Section 2, Methods). Clustered nodes were then visualised as a network of functional categories using Cytoscape ( Fig. 1;(15)). The Regulation of Transcription, DNAdependent node contained the largest number of differentially expressed genes in both genotypes and was significantly enriched (p = 8.13 × 10 12 ). A comparison between StHdh Q7/7 and StHdh Q111/111 EGF-stimulated networks indicated minimal overlap between pathway nodes for each genotype (Fig. 1), although Positive Regulation of Developmental Processes, Rhythmic Processes and MAPK Signalling were significant for both cell lines ( Table 1).
The same clustering was applied to a list of genes with a significant interaction between the effect of growth factor stimulation and genotype ( Fig. 1; Table 1). At the centre of the network is a large Phosphoprotein node consisting of 228 genes. The next two largest nodes are Transcription Regulation and Alternative Splicing, which each share 66% of their gene set with the larger Phosphoprotein node. TGFβ Signalling was a significantly enriched term resulting from the investigation of differentially expressed genes between StHdh Q7/7 and StHdh Q111/111 cells following EGF stimulation ( Fig. 1; Table 1). Regulatory genes within this pathway, such as Smad3 and Smad7, were also present within the larger, and more central Phosphoprotein node. We therefore followed this up and investigated TGFβ signalling in HD cell models.

Alterations in TGFβ signalling
One of the inhibitory members of the TGFβ signalling family, Smad6, was identified and validated as a gene of interest (Supplementary Table  3). Both the activating Smad3 and inhibitory Smad7 exhibited similar patterns of expression to the microarray data, as detected by qRTPCR, and the effect of genotype on their expression at baseline was validated ( Supplementary Fig. 3).
Altered expression of additional members of the TGFβ signalling pathway, such as Smads 1, 2, 5, and TGFβ receptors, was also observed in StHdh Q111/111 cells within the microarray data, supporting the hypothesis that this pathway is dysregulated in these cells (Table 2).

Characterisation of SMAD expression and activity in StHdh Q111 and hiPS-derived neural progenitor cells
In order to characterise the TGFβ signalling pathway, we used TGFβ1 as a stimulus.
There was little effect of TGFβ1 stimulation on the expression of Smads 1,2,4 and 5 in mouse StHdh Q111 cell lines or in the human iPSC-derived NPCs, although multiple alterations in expression were seen between StHdh Q7/7 , StHdh Q7/111 and StHdh Q111/111 cells both prior to, and following TGFβ1 stimulation, which most commonly exhibited a trend towards increased expression in mHtt-carrying cell lines (Fig. 2). Smad3 expression was significantly higher in StHdh Q111/111 cells at baseline, compared with both StHdh Q7/7 (p b 0.001) and StHdh Q7/111 cells (p b 0.05), whereas significantly higher levels of SMAD3 expression were observed in the human Q21 iPSC-derived NPCs compared to the human Q109 iPSC-derived NPCs (p b 0.05). The expression of Smad6 and Smad7 were both altered by TGFβ1 stimulation in both mouse StHdh Q111 and human NPC lines (Fig. 2); there was increased expression of Smad6 when homozygous Q 111 alleles were present in the absence of TGFβ1, and in StHdh Q7/111 cells in the presence of TGFβ1. Human Q21 and Q109 cells also exhibited increased SMAD6 expression in response to TGFβ1. TGFβ1 stimulation increased Smad7 expression in all mouse cell lines independent of genotype, and the most substantial effect of TGFβ1 in the human iPSC lines was on SMAD7 expression. Despite the Q109 NPC line being heterozygote for the mHTT expansion, the expression of SMAD7 mirrors that observed in the homozygous StHdh Q111/111 line. Similar to the StHdh Q7/7 cells, there was a significant effect of TGFβ1 in control Q21 cells (p b 0.05), however this effect was suppressed in Q109 cells, which expressed significantly less SMAD7 compared to Q21 cells following growth factor stimulation (p b 0.05).

Aberrant localisation of SMAD proteins in mouse StHdh Q111 and human NPC lines
The regulation of gene expression by SMAD transcription factors following activation of the TGFβ pathway involves cytoplasmic-nuclear shuttling where activated phospho-SMAD/co-SMAD complexes form transcriptional complexes and recruit DNA binding partners [7]. The subcellular localisation of both total and phosphorylated Smads 2 and 3 were therefore assayed by immunofluorescence. Typically, treatment with TGFβ1 initiated increased nuclear localisation of total and phosphorylated Smads 2 and 3 in all cell lines (Figs. 3-5). However, the presence of mHTT appeared to alter the extent of the nuclear accumulation of the Smads at both baseline, and following TGFβ1 stimulation.
There was little Smad2 accumulation in cell nuclei at baseline in StHdh Q7/7 and Q21 cells (Figs. 3; 5), however following TGFβ1 stimulation its localization was almost exclusively nuclear, which is also apparent in the nuclear/cytoplasmic (N/C) mean pixel intensity (MPI) ratios calculated for these cells (Figs. 3C; 5C). Both StHdh Q7/111 and StHdh Q111/111 cell lines had increased nuclear Smad2 at baseline compared with StHdh Q7/7 cells. Although there was movement into cell nuclei following TGFβ1 stimulation, the accumulation of Smad2 was not as exclusively nuclear as in StHdh Q7/7 cells, but remained in the area immediately surrounding the nucleus (Fig. 3). In contrast, despite several individual cells exhibiting high levels of nuclear SMAD2 in Q109 cells, there was very little effect of TGFβ1 on overall SMAD2 subcellular localisation. Phosphorylated Smad2 was primarily cytoplasmic at baseline in StHdh Q7/7 and Q21 cells, although its nuclear presence increased with mHtt gene dosage. There was movement of phosphorylated Smad2 into the nucleus in all three StHdh Q111 lines and both NPC lines following TGFβ1 stimulation (Figs. 3; 5).
Nuclear over-accumulation of phosphorylated Smad3 was less apparent in StHdh Q111/111 cells following TGFβ1 stimulation (Fig. 4), and there was high variability between cells as some individual cells failed to accumulate nuclear phosphorylated Smad3 to the same extent as other cells in the same frame and as in StHdh Q7/7 cells (Fig. 4). In both NPC lines, phosphorylated SMAD3 was initially more nuclear at baseline than total SMAD3, and while it increased in the nuclei of Q21 cells, this effect was less clear in Q109 cells; although this again appeared to be due to high variability between individual cells (Fig. 5).

SMAD phosphorylation is inhibited in cell models of HD
SMAD protein expression and phosphorylation were determined in mouse StHdh and human iPSC-derived NPC lines by western blot. There was a reduction in total Smad2 detection in both StHdh Q7/7 (p b 0.01) and StHdh Q7/111 (p b 0.05) cells following TGFβ1 stimulation, but no effect in the StHdh Q111/111 line (Fig. 6a); the reason for this reduction is unclear, although may be a result of induction of the ubiquitinproteasome system [17], or a technical artefact resulting from increased Smad2 phosphorylation and therefore potentially reduced specificity of the total Smad2 antibody. There was also no effect of genotype on the level of total SMAD2 detected in the human NPCs (Fig. 6b). For all three StHdh lines, there was a clear phosphorylation response in Smad2 following a 30 min treatment with TGFβ1 (Fig. 6A), which was similar in extent in both StHdh Q7/7 and StHdh Q7/111 cell lines (both p b 0.001), but did not reach significance in StHdh Q111/111 cells. As a result, following TGFβ1 stimulation, the level of phosphorylated Smad2 in StHdh Q111/111 cells was significantly lower compared to both StHdh Q7/7 (p b 0.05) and StHdh Q7/111 (p b 0.001) cells. The same pattern is present in the phosphorylated/total Smad2 ratio in human cells (Fig.  6b). Similar to StHdh lines, SMAD2 did exhibit some phosphorylation following TGFβ1 stimulation, although this response was not as pronounced as in the immortalised mouse cell line. However, there was a trend towards lower levels of phosphorylated SMAD2 in Q109 cells, and a significantly suppressed response following TGFβ1 stimulation (p b 0.05). The same pattern of effect was also apparent in the phosphorylated/total SMAD2 ratio (Fig. 6b).
There was no apparent effect of either genotype or TGFβ1 stimulation on the level of total Smad3 protein expression in either the mouse StHdh cells or in the human NPC lines (Fig. 6). Similar to the effect on Smad2, there was a substantial effect of TGFβ1 stimulation on the phosphorylation of all three cell lines (StHdh Q7/7 p b 0.01, StHdh Q7/111 p b 0.001, StHdh Q111/111 p b 0.05; Fig. 6). However, there was only a modest phosphorylation response in the human NPC lines, and significantly less phosphorylated SMAD3 in Q109 cells at both baseline (p b 0.001) and following TGFβ1 stimulation compared to Q21 NPCs (Fig. 6). Calculation of the phosphorylated/total Smad3 ratio demonstrates that there is a an increased phosphorylation response in StHdh Q7/111 cells compared to both StHdh Q7/7 (p b 0.01) and StHdh Q111/111 (p b 0.05) lines, and that the same phosphorylation response is suppressed in StHdh Q111/111 cells (p b 0.05; Fig. 6. Similar to the StHdh Q111/111 cells, the level of phosphorylated SMAD3 in Q109 cells remains significantly lower at both baseline and following TGFβ1 stimulation compared to Q21 cells following calculation of the phosphorylated/total SMAD3 ratio (both p b 0.001; Fig. 6).

SMAD3 associates with the HTT promoter
A Smad binding element (SBE) consensus sequence was identified in the upstream promoter region of both mouse Htt and human HTT (Supplementary Fig. 4). Chromatin immunoprecipitation (ChIP) was therefore carried out in order to determine whether Smad TFs bind to the Htt promoter in StHdh Q111 cells.
ChIP was carried out using antibodies against both Smad3 and phosphorylated Smad3, as we observed a consistent dysregulation of its phosphorylation and subcellular localisation in both StHdh and iPSC-derived NPC lines. Htt promoter DNA was immunoprecipitated with the total Smad3 antibody, but there were no differences between genotypes (Fig. 7). However, the antibody against phosphorylated Smad3 pulled down substantial levels of Htt promoter sequence in both baseline and TGFβ1 stimulated StHdh Q7/7 cells (Fig. 7). In StHdh Q7/111 and StHdh Q111/111 cell lines, significantly less Htt DNA was immunoprecipitated; in StHdh Q111/111 cells at baseline, the amount of Htt detected in the precipitated DNA was significantly higher than in the IgG control, although not in StHdh Q7/111 cells. TGFβ1 stimulation increased the level of immunoprecipitated Htt in StHdh Q7/111 and StHdh Q111/111 cells (Fig. 7). We therefore examined whether HTT expression was regulated by SMAD3 activation by using a specific inhibitor of Smad 2 and 3 phosphorylation; SB525334.
Validation of the effects of SB525334 on Smad activation was carried out in both StHdh and NPC lines using western blot and immunofluorescence . There was a trend towards a TGFβ1induced increase in Htt expression in StHdh Q7/7 cells, which was blocked by inhibition with SB525334 (Fig. 8). In contrast, while SB525334 inhibition of Smads 2 and 3 reduced Htt expression in StHdh Q7/111 and StHdh Q111/111 cells, the effect was less marked due to a lack of effect of TGFβ1 alone.
The expression of HTT in Q21 and Q109 cells following SB525334 treatment was also determined by qRTPCR (Fig. 8). HTT expression was consistently higher in Q21 compared with the Q109 cells and TGFβ1 elicited a trend towards increased HTT expression in Q21 cells, which was prevented by treatment with SB525334. There was no observable effect of SB525334 on the expression of HTT in Q109 cells, although this is likely due to the absence of an initial effect of TGFβ1.

Discussion
By investigating differential gene expression between StHdh Q7/7 and StHdh Q111/111 cell lines using microarray analysis, we identified TGFβ  signalling as a significantly altered signalling pathway, despite using EGF as a stimulus. This is not surprising, as substantial crosstalk between EGF and TGFβ pathways has previously been identified [18][19][20][21]; for example, while SMAD7 is an inhibitor of SMAD signalling by competitive interaction with the TGFβ type 1 receptor [22] and by interfering with SMAD-SMAD interactions [7], it is also responsive to EGF stimulation in order to act as a negative regulator of this pathway [23]. Another significantly differentially expressed gene identified from our microarray analysis, Spry2, is also known to mediate the crosstalk between these two pathways; its activation is increased by stimulation of the EGF  receptor (EGFR), where it then propagates the signal by preventing degradation of the EGFR. TGFβ suppresses the transcription of Spry2, degrading its protein and suppressing EGFR activation [24]. Enhancement of the TGFβ signalling pathway would therefore be consistent with a suppressed response to EGF, which we observe in StHdh Q111/111 cells both in these microarray data, and in our previously published work [16].
The genes that were identified as having a stronger transcriptional response in StHdh Q111/111 cells encode a diverse range of functions, predominantly cellular survival and proliferation. However, the majority of genes on these lists are known to be responsive to TGFβ1 stimulation, and several have direct associations with SMAD transcription factors (TFs). For example, the HMGA2 protein regulates a feed forward mechanism of gene transcription via a direct interaction with SMADs 3 and 4 [25]. Irf2bp2 encodes a muscle enriched TF [26] that has been found to be a TGFβ responsive gene [27], as are Cdc42ep3 and Gadd45g [28][29][30].
Our identification of TGFβ signalling as a significantly altered pathway in a cell model of HD is consistent with a recent RNA-seq analysis of HD patient iPSC-derived NPCs, where TGFβ signalling was one of the most significantly dysregulated pathways [11], and targets of SMAD3 were over-represented within genes differentially expressed between HD-NPCs and their isogenic controls [11].
In order to further characterise the TGFβ signalling pathway, we focused on the regulation of SMAD TFs in the mouse StHdh Q111 model and in human iPSC-derived NPCs. The most consistent observation was for suppressed expression of the inhibitory SMAD, SMAD7, in response to TGFβ1 stimulation in StHdh Q111/111 and in Q109 NPCs, which would be suggestive of reduced inhibition of TGFβ signalling. However, as the remaining expression data and protein characterisation data do not indicate a substantial increase in TGFβ signalling activity, the lack of SMAD7 responsiveness may be a compensatory mechanism in these cells attempting to enhance kinase signalling and mediate transcriptional regulation.
Immunofluorescence analysis of StHdh Q7/7 cells and Q21 NPCs demonstrates that stimulation with TGFβ1 is activating SMAD TFs by inducing phosphorylation of SMADs 2 and 3 and their nuclear localisation, which is required for SMAD-regulated transcriptional activity. This translocation is altered in cells containing a CAG expansion. In particular, Smad2 exhibits increased nuclear localisation in StHdh Q7/111 and StHdh Q111/111 cells, and phosphorylated SMAD2 is predominantly nuclear in Q109 NPCs prior to TGFβ1 stimulation. This is consistent with the increased SMAD2 phosphorylation identified in other HD patient-derived NPCs [11]. Altered localisation and phosphorylation of SMAD3 is also observed in both cell lines, although it is more consistent with a generalised dysregulation and disordered response to TGFβ1, than nuclear accumulation in particular. As we do not observe an augmented phosphorylation response in CAG-repeat expansion cell lines in response to TGFβ1 by western blot, it is possible that the increased nuclear localisation of these factors, combined with suppressed SMAD7 expression and inhibition, may be a compensatory mechanism to retain higher TGFβ pathway activity in an otherwise detrimental environment.
An attempt to increase TGFβ signalling may be indicative of a protective response in these cells; increasing TGFβ1 in cellular growth media was found to reduce the activity of caspases 3 and 7 [11], and increased expression of TGFβ1 has been associated with  neuroprotection, astrogliosis and alleviation of neuroinflammation [31,32], whereas its knockdown promoted neuronal loss in rats following traumatic brain injury [32]. However, as microglia and astrocytes both express TGFβ1 and are inextricably involved in these neuroprotective processes [31][32][33][34], the culture of neuronal-like cells in isolation from these other neural cell types will not be fully sufficient for the elucidation of the potential neuroprotective effects of increased TGFβ1 in models of HD.
In addition to characterising the altered regulation of SMAD TFs in StHdh Q111 cells and iPSC-derived NPCs, we demonstrate that a SMAD binding element is present within the HTT promoter region, and SMAD3 can bind directly to the Htt promoter in StHdh Q111 cells, suggesting that SMAD3 activity may directly regulate the expression of Htt. This was supported by the increased expression of HTT in both StHdh Q7/7 and Q21 cells following TGFβ1 stimulation, and the suppression of this effect when SMAD activation was inhibited with the compound SB525334. The increased expression of HTT following TGFβ1 stimulation was not present in cells with an expanded CAG repeat, which is consistent with the reduced affinity of phosphorylated SMAD3 for the Htt promoter in StHdh Q7/111 and StHdh Q111/111 cells. As TGFβ is required for neurogenesis [35], as well as for midbrain dopaminergic neuronal development [36], and HTT has also been implicated in the regulation of neurogenesis [37,38] and is essential for embryonic development [39], it is possible that TGFβ signalling may be directly regulating HTT expression in order for these processes to occur.

Conclusions
• We implicate dysregulation of the TGFβ signalling pathway in mouse and human cell models of HD, consistent with recent RNA-seq data from hiPSC-derived NPCs [11]. • Characterisation of the downstream SMADs within this pathway uncovered widespread dysregulation, which may indicate a compensatory, neuroprotective response to the CAG expansion. • Finally, we demonstrate that SMAD3 binds to the HTT promoter, and that HTT expression can be regulated by SMAD3 activation in the absence of the CAG expansion. • This may have implications for neurogenesis and striatal development. TGFβ signalling is therefore a possible target for disease modification and could prove to be a useful biomarker for disease progression.