Elucidating a normal function of huntingtin by functional and microarray analysis of huntingtin-null mouse embryonic fibroblasts

Background The polyglutamine expansion in huntingtin (Htt) protein is a cause of Huntington's disease (HD). Htt is an essential gene as deletion of the mouse Htt gene homolog (Hdh) is embryonic lethal in mice. Therefore, in addition to elucidating the mechanisms responsible for polyQ-mediated pathology, it is also important to understand the normal function of Htt protein for both basic biology and for HD. Results To systematically search for a mouse Htt function, we took advantage of the Hdh +/- and Hdh-floxed mice and generated four mouse embryonic fibroblast (MEF) cells lines which contain a single copy of the Hdh gene (Hdh-HET) and four MEF lines in which the Hdh gene was deleted (Hdh-KO). The function of Htt in calcium (Ca2+) signaling was analyzed in Ca2+ imaging experiments with generated cell lines. We found that the cytoplasmic Ca2+ spikes resulting from the activation of inositol 1,4,5-trisphosphate receptor (InsP3R) and the ensuing mitochondrial Ca2+ signals were suppressed in the Hdh-KO cells when compared to Hdh-HET cells. Furthermore, in experiments with permeabilized cells we found that the InsP3-sensitivity of Ca2+ mobilization from endoplasmic reticulum was reduced in Hdh-KO cells. These results indicated that Htt plays an important role in modulating InsP3R-mediated Ca2+ signaling. To further evaluate function of Htt, we performed genome-wide transcription profiling of generated Hdh-HET and Hdh-KO cells by microarray. Our results revealed that 106 unique transcripts were downregulated by more than two-fold with p < 0.05 and 173 unique transcripts were upregulated at least two-fold with p < 0.05 in Hdh-KO cells when compared to Hdh-HET cells. The microarray results were confirmed by quantitative real-time PCR for a number of affected transcripts. Several signaling pathways affected by Hdh gene deletion were identified from annotation of the microarray results. Conclusion Functional analysis of generated Htt-null MEF cells revealed that Htt plays a direct role in Ca2+ signaling by modulating InsP3R sensitivity to InsP3. The genome-wide transcriptional profiling of Htt-null cells yielded novel and unique information about the normal function of Htt in cells, which may contribute to our understanding and treatment of HD.


Background
Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder which is caused by polyglutamine (polyQ) expansion in the amino-terminus of huntingtin (Htt). Htt is a soluble protein of 3,144 amino acids that has no sequence homology with other proteins. Except for the extreme amino-terminus, with its adjacent polyQ region and proline-rich segments, the entire ~350-kD protein is predicted to be composed of 36 α-helical HEAT repeats. Increasing evidence indicates that Htt functions as a molecular scaffold that is able to organize a variety of signaling complexes [1,2]. Htt is expressed ubiquitously in humans and rodents, with the highest levels found in CNS neurons and the testes [3][4][5]. Intracellularly, Htt is associated with various organelles, including the nucleus, endoplasmic reticulum (ER) and Golgi complex [6][7][8]. This widespread subcellular localization does not facilitate the definition of its function. Hdh is evolutionary conserved -a single copy of the Htt gene is expressed in all vertebrates (from fish to humans) [9]. The Htt gene is also present in D. melanogaster genome, but absent in the C. elegans and S. cerevisiae genomes [9]. All vertebrate isoforms of Htt, but not Drosophila Htt, contain an amino-terminal polyQ region.
Complete knockout of the mouse Htt gene (Hdh) causes embryonic death before day 8.5 (E8.5, before gastrulation and the formation of the nervous system) [10][11][12]. After gastrulation, Htt becomes important for neurogenesismice carrying a <50% dose of wild-type Htt display profound malformations of the cortex and striatum [13]. Another study has shown that greatly reduced Htt levels are insufficient to support normal mouse development [14]. In addition to its function in development, Htt may play a role in the regulation of apoptosis, control of BDNF production, vesicular and mitochondrial transport, neuronal gene transcription, and synaptic transmission (reviewed in [9]). Despite all of these efforts and results, the exact function of Htt in cells still remains largely unknown.
In addition to answering an academic question concerning the normal function of Htt, knowledge of its function is important for understanding HD pathogenesis and for the treatment of Huntington's disease (HD). Although the HD mutation is considered to be a "gain of function" mutation, it has been suggested that the loss of normal Htt function might also contribute to the pathogenesis of HD [9]. Approaches that are based on reducing mutant Htt expression such as RNA interference [15] and the use of intrabodies [16,17] are currently considered to be promising strategies for HD treatment. It is likely that these agents will cause inactivation or impair normal function of both mutant and wild type Htt alleles. One can envision a therapy that combines such Htt-inactivat-ing agents with drugs that restore the function of targets and pathways downstream from wild-type Htt. However, because both normal Hdh function is not known and downstream pathways have not been identified, such a combined therapy approach is not feasible at the moment.
To systematically search for Htt's normal function, we used Hdh +/- [12] and Hdh-floxed mice [18] to generate immortalized mouse embryonic fibroblasts (MEF) which contain a single functional copy of Hdh gene (Hdh-HET) or lack Hdh completely (Hdh-KO). We compared inositol 1,4,5-trisphosphate receptor (InsP 3 R)-mediated Ca 2+ signals in these cells. We then performed a genome-wide gene transcription profiling of Hdh-HET and Hdh-KO MEF cells using microarrays to obtain novel, unique, and unbiased information about the normal function of Htt in fibroblasts, which may contribute to our understanding and treatment of HD.

Generation of Hdh-HET and Hdh-KO MEF cell lines
To generate cell lines lacking Htt expression, we employed a conditional mutagenesis strategy based on the in vitro recombination of an Hdh(flox) allele in cultured fibroblasts that are also carrying either a wild-type (+) or null (standard knock-out) Hdh allele. The Hdh(flox/+) and Hdh(flox/-) fibroblasts were obtained from embryos derived from a cross between Hdh +/-and Hdh-floxed/ floxed mice (Fig 1). Primary fibroblasts were prepared and plated separately from each embryo as described in Methods. After two days in culture, the primary fibroblasts from all embryos with identical genotype (Hdh floxed/+ or Hdh floxed/-) were pooled together and transfected with a linearized SV40 plasmid. Transfected cells were then cultured for four to six weeks until immortalized Hdh floxed/+ and Hdh floxed/-mouse embryonic fibroblasts (MEFs) were obtained (Fig 1). To recombine the Hdh floxed allele, immortalized Hdh floxed/+ and Hdh floxed/ -MEFs were infected with Lenti-NLS-GFP-Cre virus encoding nuclear-targeted GFP-Cre fusion protein [19] (Fig 1). Using the procedure described above, we generated four Hdh-HET (lines 1,2,3,5) and four Hdh-KO (lines 11, 12, 16, 27) MEF cell lines. The expression of Htt in the generated MEF lines was assessed by Western blotting of whole cell lysates using anti-Htt monoclonal antibody. Quantification of Western blotting data verified similar levels of Htt expression in all 4 Hdh-HET lines (data not shown). Consistent with the genotype of the generated cells, we detected a protein of predicted size (~350 kD) in lysates from the Hdh-HET cells, but not in lysates from Hdh-KO lines (Fig 2). The same samples were probed with monoclonal antibodies against β-actin as a loading control ( Fig  2). Thus, we concluded that we successfully generated four Hdh-HET and four Hdh-KO MEF lines on similar Experimental procedure used to generate the Hdh-HET and Hdh-KO MEF cell lines genetic background. We reasoned that comparison of resulting MEF lines may reveal clues about normal function of Htt protein in cells.

Intracellular calcium signaling in Hdh-HET and Hdh-KO MEF cell lines
Previous studies have implicated impaired calcium signaling in the pathogenesis of HD [20][21][22]. The Htt directly binds to the inositol 1,4,5-trisposphate receptor (InsP 3 R), an intracellular Ca 2+ release channel [23,24]. The expression of mutated Htt has been shown to affect the InsP 3 R activity [23] and mitochondrial Ca 2+ signals and bioenergetics [25][26][27][28][29][30]. Since Htt and mutated Htt directly targets both ER and mitochondrial sites, it is possible that Htt may have some relevance for the physical and local Ca 2+ coupling between ER and mitochondria [31,32]. To test this idea and to determine a role played by Htt in intracellular Ca 2+ signaling, we performed a series of cytosolic and mitochondrial Ca 2+ imaging experiments with generated MEF lines. Two Hdh-HET (HET1 and HET 5) and two Hdh-KO MEF cell lines (KO12 and KO27) (Fig 2) were selected for Ca 2+ imaging studies.
In these experiments Hdh-HET and Hdh-KO MEF cell lines were challenged by ATP, an agonist of InsP 3 signaling pathway in fibroblasts. Before stimulation with ATP the incubation medium was switched to a Ca 2+ free buffer to prevent Ca 2+ entry. The cytosolic [Ca 2+ ] c and mitochondrial [Ca 2+ ] m levels were monitored simultaneously as described in Methods. We found that pre-stimulation [Ca 2+ ] c was higher in the Hdh-HET cells (HET1, 183 ± 11 nM (n = 42) and HET5 139 ± 9 nM (n = 33)) than that in the Hdh-KO cells (KO12, 102 ± 12 nM (n = 15) and KO27, 106 ± 6 nM (n = 48), p < 0.003). Stimulation with a suboptimal dose of ATP ( (Fig 3). The ATP-induced [Ca 2+ ] c spikes were closely followed by a [Ca 2+ ] m elevation in the Hdh-HET cells, whereas the [Ca 2+ ] m rise was modest in the Hdh-KO cells (Fig 3). Thus, the ATP-induced intracellular Ca 2+ mobilization was suppressed and desensitized in the Hdh-KO cells. Figure 3 has also showed that the [Ca 2+ ] c signal was effectively propagated to the mitochondria in the Hdh-HET cells but less Ca 2+ was transferred into the mitochondria in the Hdh-KO cells. To determine whether this resulted from the attenuated ER Ca 2+ mobilization or from impaired ER-mitochondrial Ca 2+ coupling, the [Ca 2+ ] m rise was plotted against the [Ca 2+ ] c increase for each cell., The relationship between [Ca 2+ ] c elevations and the ensuing [Ca 2+ ] m signals was similar in both the Hdh-HET and in the Hdh-KO cells (not shown). This result indicated that the local coupling between ER and mitochondria is maintained in the Hdh-KO cells.
The attenuated ATP-induced [Ca 2+ ] c signal in the Hdh-KO cells could be due to reduced InsP 3 generation, due to reduced sensitivity of InsP 3 R or due to depleted ER Ca 2+ pool. To discriminate between these possibilities the InsP 3 -induced Ca 2+ mobilization was quantified in suspensions of permeabilized MEF cells. The steady state [Ca 2+ ] c was similar in both Hdh-HET and in Hdh-KO cells (Fig 4A, HET1, n = 12; HET5, n = 12; KO12, n = 13; KO27, n = 10 measurements). The Ca 2+ pool size for both the ER and the ionophore-sensitive compartment was larger in Cytoplasmic and mitochondrial Ca 2+ signals in Hdh-HET and Hdh-KO cells the Hdh-KO than in the control cells (Fig 4A), whereas the uncoupler-sensitive mitochondrial compartment showed no difference (n = 3; not shown). Sequential application of a suboptimal and optimal InsP 3 revealed lesser InsP 3sensitivity in the Hdh-KO cells than in the HET cells ( Fig  4B, 4C, p < 0.01). However, the InsP 3 sensitive fraction of the ER was approximately 75% in both control and Hdh-HET cells (Fig 4D). Furthermore, neither the passive Ca 2+ buffering nor the mitochondrial Ca 2+ uptake was altered in the cells lacking the Hdh (Fig 4E, 4F). Collectively, the data obtained in permeabilized cells suggest that the InsP 3 sensitivity of the InsP 3 receptor is attenuated in the Hdhdeficient cells, providing a mechanism to underlie the suppression of the InsP 3 -linked [Ca 2+ ] c signaling in the Hdh-KO cells. The effect of Hdh on the InsP 3 sensitivity is likely to be mediated by direct association between Htt and InsP 3 R [23,24].

Microarray analysis of transcripts expressed in Hdh-KO and Hdh-HET MEFs
The results described in the previous section suggested that Htt plays a direct role in Ca 2+ signaling by modulating InsP 3 R function. Many studies suggested that Htt also plays a major role in control of gene transcription [33,34]. To uncover potential gene expression changes we performed genome-wide transcription profiling of Hdh-HET and Hdh-KO MEF cells. Using the procedures described in Methods, we isolated total RNA from Hdh-HET MEF lines 1, 2 (in duplicate), 3, and 5 (in duplicate) and from Hdh-KO MEF lines 11, 12, 16 (in duplicate), 27 (in duplicate). The resulting 12 samples were provided to the UT Southwestern Microarray Core Facility (MCF) for genome-wide expression profiling using Sentrix Mouse-6 Expression Bead Chips (Illumina) (see Methods for details).
All 12 arrays produced highly reproducible and consistent gene expression data. The microarray results have been deposited in NCBIs Gene Expression Omnibus (GEO), and are accessible through GEO Series accession number GSE11139 [35]. Cluster analysis of the over-all gene expression data from the 12 samples demonstrated that all six Hdh-HET samples and all six Hdh-KO samples were clustered together, forming two clearly distinct groups ( Fig 5). We also found that the duplicate samples (HET5.1 and HET5.2, HET2.1 and HET2.2, KO16.1 and KO16.2, and KO 27.1 and KO27.2) were most similar to each other when compared to other samples (Fig 5), as should be expected. Thus, we concluded that we obtained a high quality dataset of transcripts expressed in Hdh-HET and Hdh-KO MEF lines.
In the next level of analysis, we combined all results obtained in six arrays with the Hdh-HET samples (HET group) and in six arrays with the Hdh-KO samples (KO group). Using Illumina BeadStudio software, we per-formed a statistical analysis to identify the differentially expressed genes between the Hdh-KO and Hdh-HET groups. We found that from 45992 probes existing on the Mouse-6 BeadChips arrays, 14,065 probes were present (with detection p-value < 0.01) in at least one of these two groups. Statistical analysis (t-test) has identified 821 transcripts that were significantly different between Hdh-HET and Hdh-KO groups (p < 0.05) (Fig 6). Among these 821 targets, 455 were up-regulated in the KO group and 366 were down-regulated (Fig 6). Thus, we concluded that inactivation of Hdh expression has a very significant effect on the transcriptional profile of MEF cells. The average signal intensities for each probe in Hdh-HET and Hdh-KO groups are included in the Excel format for the 821 differentially expressed targets (Additional files 1 and 2).

Analysis and annotation of microarray data
In the annotation of microarray data, we focused on 279 unique genes whose expression differed by at least 2-fold between Hdh-HET and Hdh-KO groups. From these genes 173 genes (104 of which are annotated) were up-regulated and 106 genes (65 of which were annotated) were down-regulated in Hdh-KO cells when compared to Hdh-HET cells. In order to extract biological information from these genes, we performed annotation of the array results using the Ingenuity Pathway Analysis platform [36] and the GoStat software [37]. We found that several significant GO categories can be pulled from the data: developmental process (35), nervous system development and function (19), lipid metabolism (18), glucosamine metabolic process (2), transcription regulator activity (5), cellular_component:plasma membrane (16), regulation of cellular process (29), endocytosis (2), mitochondrion (3), extracellular matrix (2), cytoskeleton (5), others (33), indicating the possible disruption of several functional pathways in the absence of Htt (Additional files 1 and 2). We have not observed significant changes in gene expression levels of most proteins involved in Ca 2+ signaling pathways (Additional files 1 and 2), indicating that Ca 2+ signaling changes observed in our functional experiments (Figs 2, 3, 4) are likely to be due to post-translational effects, such as for example changes in InsP 3 R gating properties.

Confirmation of gene expression with real-time PCR
In order to confirm our microarray results, we performed quantitative real-time PCR (qPCR) analysis for several of the candidate genes. For these experiments we choose three genes that were significantly down-regulated in Hdh-KO MEFs (Hdh, Sox-2, Tcf2) and three genes that were significantly up-regulated in Hdh-KO MEFs (Cart1, Esm1, Pitx2) (Additional files 1 and 2). We observed a good correlation between averaged microarray results and qPCR data for all six genes evaluated (Table 1). Moreover, we observed a good correlation between microarray and Ca 2+ handling by Hdh-HET and Hdh-KO cells qPCR data for results obtained with cDNA samples from individual Hdh-HET and Hdh-KO MEF cell lines (Fig 7).

Comparison with gene expression profiling of Hdh-null ES cells
When our paper was in preparation, another group independently reported genome-wide expression profiling of Hdh-null embryonic stem (ES) cells [38]. It is of interest to compare our findings with Hdh-KO MEF cells with results obtained for Hdh-null ES cells. Strehlow at al (2007) reported that expression of 16 known transcripts was significantly affected in Hdh-null ES cells when compared to wild type ES cells. The affected transcripts were divided into several classes of interest: protein degradation (5), extracellular matrix (4), cell division (4), and patterning/development (3) [38]. To compare these data with our results, we attempted to locate the genes highlighted by the study by Strehlow at al (2007) among the genes which expression differs at p < 0.05 between Hdh-KO and Hdh-HET MEF cells in our experiments. We determined that two of the three genes in the patterning/development category (Otx2 and Pem) do not present in MEF cell lines, Leftb/Lefty is present in MEF cell lines, but did not show a significant difference between HET and KO MEFs. All five genes in the protein degradation category are present in MEF cell lines but did not show significant difference in our experiments. We found that Adam23 is not present in MEF cell lines. B3galt6, col4a1 and clo4a2 are present in MEF cells, but did not show significant difference. We further found that one out of four genes in cell division category (Ccdc5) is also significantly affected in our experiments. Ccdc5 is up-regulated in both Hdh-null ES cells and in Hdh-KO MEF cells. Plk1 is also strongly upregulated (8.7-fold) in Hdh-null ES cells [38] but did not show significant difference in Hdh-KO MEF cells in Cluster analysis of microarray data Figure 5 Cluster analysis of microarray data. Using the Illumina BeadStudio 1.5 software package, each of 12 arrays was treated as an independent experiment and cluster analysis was performed on the microarray hybridization results.
Altered gene expression between Hdh-HET and Hdh-KO groups Figure 6 Altered gene expression between Hdh-HET and Hdh-KO groups. Cluster analysis of the 821 differentially expressed genes between Hdh-HET and Hdh-KO (p < 0.05). The genes were selected by comparing 6 HET samples with 6 KO samples using t-test with computing false discovery rate. The genes with p value <0.05 were selected and Hierarchical cluster analysis were performed using Cluster and TreeView http://rana.lbl.gov/EisenSoftware.htm. Each column represents a sample and each row represents a gene. The colorgram depicts high (red) and low (green) relative levels of gene expression in each sample. our experiments. Aurkc is not present in MEF cells, while Pttg1 is present but did not show significant difference.

Strehlow at al (2007) induced neuronal differentiation of
Hdh-null ES cells by application of retinoic acid and performed microarray analysis of the in vitro differentiated neurons at 6, 8, and 10 days post-differentiation [38]. The expression of transcripts in the number of categories was different between Hdh-null and wild type in vitro differentiated neurons [38]. Changes in only a few genes have been consistently observed in the two studies (Table 2).

Figure 7
Correlation between microarray and qPCR results. The results of the microarray and qPCR analyses are compared for 3 genes downregulated (Hdh, Tcf2, Sox2) and 3 genes upregulated (Cart1, Esm1, Pitx2) in Hdh-KO cells. The microarray and qPCR results are shown for RNA extracted from 6 Hdh-KO samples (blue) and 6 Hdh-HET samples (red).

Discussion
Despite the importance of understanding the normal function of Htt for both basic biology and for HD, its function remains largely unknown [9,34]. The generation of Hdh-null MEF cell lines described in our study provides a new and unbiased approach to search for novel Htt functions.
Thus, in the first series of experiments we evaluated InsP 3 R-mediated Ca 2+ cytosolic and mitochondrial Ca 2+ signals in Hdh-null MEF cells. As a result of these experiments we found that InsP 3 R sensitivity to stimulation by InsP 3 was reduced in the absence of Hdh (Figs 3 and 4). We further found that Htt appears to be dispensable for ER-mitochondrial Ca 2+ coupling (data not shown). Thus the altered InsP 3 R-induced cytoplasmic and mitochondrial calcium signaling in the Hdh-null MEF cells may result from the lack of Hdh by itself and does not necessarily require a secondary change in gene regulation.

2: Comparison of gene expression changes in Hdh-KO MEF and differentiated Hdh-null ES cells. The genes are classified into functional categories (groups) based on GO classification as explained by Strehlow at al (2007). The number of genes affected in differentiated Hdh-null ES cells is shown. The number of these genes present among the genes affected in our experiments with Hdh-KO MEF cells is also shown. The official gene symbols, accession numbers, Diff scores and fold changes are shown for all overlapping genes. The positive Diff score corresponds to the genes upregulated in Hdh-KO MEG cells, the negative Diff score corresponds to the genes downregulated in Hdh-KO MEF cells. The genes which expression is affected in the opposite direction when Hdh-null ES and
Hdh-KO MEF data are compared are shown in italic. Interestingly, a large number of Ca 2+ -related genes, such as CACNA2D3 (calcium channel, voltage-dependent, alpha2/delta subunit 3), ITPR1 (inositol 1,4,5-trisphosphate receptor 1), HOMER1 (homer homolog 1), ATP2A2 (ATPase, Ca 2+ transporting, cardiac muscle, slow twitch 2), DRD2 (dopamine receptor 2), PRKCB1 (protein kinase C beta 1), PDE1B (phosphodiesterase 1B, Ca 2+ -calmodulin dependent), ATP2B2 (ATPase, Ca 2+ transporting, plasma membrane 2), CAMK2B (calcium/calmodulindependent protein kinase II, beta), PLCB1 (phospholipase C, beta 1), RGS4 (regulator of G-protein signaling 4), and CAMK2A (calcium/calmodulin-dependent protein kinase II alpha), have been recently reported to be consistently and significantly downregulated in a striatal region of symptomatic human HD patients and aging HD mouse models [39]. These results are in agreement with the "Ca 2+ hypothesis of HD" [22] and with a direct role of Htt in intracellular Ca 2+ signaling supported by our experiments.

Gene groups
Many studies suggested that Htt also plays a major role in control of gene transcription [33,34]. To search for changes in gene transcription resulting from deletion of Htt gene, we performed a genome-wide comparison of transcription profiles in MEF cells expressing a single copy of Hdh (Hdh-HET cells) and in MEF cells which lack Hdh expression (Hdh-KO cells). To minimize sources of variability, the Hdh-HET and Hdh-KO MEF cells were generated in parallel experiments and on identical genetic background. From our annotation analysis, we found that a large group of affected genes play a role in embryonic development (Additional file 1). This result was not unexpected because Htt is essential for embryonic development, and complete inactivation of Htt expression in knock-out mice causes early embryonic lethality [10][11][12].
The functions of these genes may provide additional clues about the mechanism responsible for embryonic lethality in Hdh knockout mice, for example there are some similar phenotypic manifestations between Hdh nullizygous embryos and knockout mutants lacking fibroblast growth factor receptor1(fgfr1) [12]. Interestingly, we found fgfrl1 message is downregulated approximately 2-fold in Hdh-KO MEF cells when compared to Hdh-HET cells (Additional files 1 and 2).
After gastrulation, Htt is important for neurogenesismice carrying a <50% dose of wild-type Htt display profound malformations of the cortex and striatum [13]. The neuronal inactivation of Htt during mid-to late gestation, for example, leads to neurological abnormalities and progressive degeneration (apoptotic cells in the hippocampus, cortex and striatum, and a lack of axons) [18]. Our analysis revealed a number of genes involved in nervous system development and function which were affected in Hdh-KO MEF cell lines (Additional file 1), and this list should also provide useful information to guide further studies of Htt's normal function in the nervous system. For example, Sox-2 expression was absent from Hdh-KO MEFs. Sox (Sry-related HMG box) genes encode transcription factors regulating crucial developmental decisions in different systems. Sox2 is expressed in, and is essential for, totipotent inner cell mass stem cells and other early multipotent cell lineages, and its ablation causes early embryonic lethality [40]. In many different species, Sox2 is a marker of the nervous system from the beginning of its development, it maintains a stem-cell like state and actively inhibits neuronal differentiation, Sox2 deficiency causes neurodegeneration and impaired neurogenesis in the adult mouse brain. Does the absence of Sox-2 play some role in the early embryonic lethality and neurodegeneration in Hdh knock-out mice and conditional knock-out mice respectively? Further studies are required to answer these questions. Sox-11 is another sox family gene which changes dramatically in Hdh-KO MEF cell lines (increases about 10-fold, see Additional files 1 and 2). The widespread expression of sox-11 in both the central and peripheral nervous system suggests that sox-11 plays a general role in neuronal development, and its changes in Hdh-KO cells merit further investigation.
Another group of genes whose expression was significantly affected in Hdh-KO MEF cells are the genes related to lipid metabolism. It has been reported in another microarray analysis using clonal striata-derived cells, that genes involved in lipid metabolism were affected after expressing different N-terminal 548-amino-acid Htt fragments [41]. Moreover, recent biochemical data indicated that Htt binds to caveolin and plays a direct role in cholesterol metabolism [42]. All these data suggested that Htt plays an important role in lipid metabolism, which may be affected by HD mutation. Indeed, RXRG (Retinoic acid receptor RXR-gamma) and RBP4 (retinol binding protein 4) are consistently downregulated in a striatal region of symptomatic human HD patients and aging HD mouse models [39].
From our analysis we also found calcium channel voltagedependent alpha2/delta subunit 1 (Cacna2d1) was downregulated about 2 fold (Additional files 1 and 2), interestingly the same CACNA2D1 protein has been recently identified as novel Htt-binding partner in unbiased massspectroscopy screen [24]. A closely related alpha2/delta subunit 3 (Cacna2d3) was reported on the 3 rd place on the list of the genes which are consistently and significantly downregulated in a striatal region of symptomatic human HD patients and aging HD mouse models [39]. As discussed above, these results indicate that Htt may play a role in regulation of Ca 2+ channel activity and Ca 2+ signaling in cells, consistent with Ca 2+ hypothesis of HD [22,43].

Conclusion
In conclusion, we generated four Hdh-HET and four Hdh-KO MEF cell lines and performed functional analysis of these cells by Ca 2+ imaging methods and genome-wide transcription profiling of these cell lines using a microarray approach. Our results indicated that Htt plays a direct role in intracellular Ca 2+ signaling by directly modulating

Generation of Hdh-HET and Hdh-KO MEF cell lines
Generation and characterization of the Hdh +/-and Hdhfloxed mice have been described previously [12,18]. E13.5 embryos obtained from a cross between the Hdh-floxed and Hdh +/-mice were first eviscerated and decapitated, and then the carcasses were finely minced using scissors. The tissue obtained from each embryo was digested with 0.25% Trypsin-EDTA at 37°C for 10 min, washed once with 10% FBS in DMEM, and the cell suspensions from each embryo were plated separately in 10% FBS-DMEM culture medium in order to obtain cultures of primary fibroblasts. Following plating of the cells, the genotype of each embryo was determined by PCR [12,18]. After two days in culture, the primary fibroblasts from each genotype (Hdh floxed/+ and Hdh floxed/-) were pooled together. The pooled cells were then plated on six-well tissue culture plates, grown to 60-80% confluence and transfected with SV40-Large T-antigen plasmid in pcDNA3-Zeo vector (linearized with PvuI) using the Fugene  nm, 380 nm excitation and 500 nm emission for fura2FF and 540 nm excitation and 580 nm emission for TMRE. Calibration of the fura fluorescence was carried out at the end of each measurement as described previously [45]. Experiments were with at least five different cell preparations in multiple parallels. Significance of differences from the relevant controls was calculated by ANOVA.

Microarray analysis
Total RNA was isolated from fibroblast cultures using the TRIZOL reagent according to manufacturer's instructions (Invitrogen). Briefly, the MEF cells were grown to 60-80% confluence in T25 tissue culture flask, the culture medium was aspired and 1 ml of TRIZOL reagent was added to each flask. The cells were incubated with TRIZOL at room temperature for 5 min. The resulting lysates were collected from each flask, mixed with 0.2 ml of chloroform and centrifuged at 12,000 × g for 15 min at 4°C. The supernatants were collected, mixed with an equal volume of 70% ethanol at room temperature and immediately transferred to RNAeasy mini spin columns for RNA purification according to the manufacturer's (Qiagen) instructions. The final RNA samples were eluted from the RNeasy mini spin columns in 30 μl of DEPC-treated water. Using the procedures described above, we isolated total RNA from Hdh-HET MEF lines 1, 2 (in duplicate), 3, and 5 (in duplicate), and from Hdh-KO MEF lines 11, 12, 16 (in duplicate), 27 (in duplicate). The resulting 12 samples were submitted to the UT Southwestern Microarray Core Facility for microarray analysis. Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer's directions starting with ~200 ng total RNA. Samples were purified using the RNeasy kit (Qiagen, Valencia, CA). Hybridization to the Sentrix Mouse-6 Expression Bead-Chip (Illumina, Inc., San Diego, CA), washing and scanning were performed according to the Illumina BeadStation 500× manual (revision C). Two BeadChips were used, each one containing 6 arrays. For each chip, three HET and three KO samples were analyzed to minimize the effects of chip-to-chip variability. Arrays were scanned with an Illumina Bead array Reader confocal scanner and the data was analyzed using Illumina's Bead-Studio software(Version 3). The raw data was background subtracted and normalized using "cubic spline" method in the software. The detection p values were computed using a dynamically constructed normal model based on the intensities of 700 negative controls. For differential analysis, the six arrays in HET group were compared with the six arrays in KO group using t-test with computing false discovery rate algorithm. The genes with p value <0.05 were considered differentially expressed and subject for further analysis.

Quantitative Real Time PCR
Quantitative real time (qRT)-PCR was performed using an Applied Biosystems Prism 7900HT sequence detection system using SYBR green chemistry. Briefly, total RNA was treated with DNase I (RNase-free, Roche Molecular Biochemicals), and reverse-transcribed with random hexamers using SuperScript II reverse transcriptase (Invitrogen) to generate cDNA as previously described [46]. Primers were designed using Primer Express Software (Perk-inElmer Life Sciences) and validated by analysis of template titration and dissociation curves. Each qRT-PCR contained (final volume of 10 μl) 25 ng of reverse-transcribed RNA, each primer at 150 nM, and 5 μl of 2× SYBR Green PCR Master Mix (Applied Biosystems), and each sample was analyzed in triplicate. Results were evaluated by the comparative C T method (User Bulletin No. 2, Perk-inElmer Life Sciences) using cyclophilin as the invariant control gene.