Abstract
Huntington’s disease (HD) is a multi-tissue failure disorder for which there is no cure. We have previously shown an effective therapeutic approach limited mainly to the central nervous system, based on a synthetic zinc finger (ZF) transcription repressor gene therapy, but it would be important to target other tissues as well. In this study, we identify a novel minimal HSP90AB1 promoter region that can efficiently control expression not only in the CNS but also in other affected HD tissues. This promoter-enhancer is effective in driving expression of ZF therapeutic molecules in both HD skeletal muscles and the heart, in the symptomatic R6/1 mouse model. Moreover, for the first time we show that ZF molecules repressing mutant HTT reverse transcriptional pathological remodelling in HD hearts. We conclude that this HSP90AB1 minimal promoter may be used to target multiple HD organs with therapeutic genes. The new promoter has the potential to be added to the portfolio of gene therapy promoters, for use where ubiquitous expression is needed.
Introduction
The zinc finger transcription factor (ZF-TF) platform is a broadly-applicable technology to silence lethal mutations at their source-at the DNA level Figure 1. We have previously shown its application in Huntington’s disease (HD), where a ZF synthetic construct effectively and selectively repressed the expanded CAG sequence within the mutant Huntingin allele, which is the source of HD (; ). Unlike CRISPR nuclease approaches, synthetic TFs are inherently safer because they do not cut DNA, which leads to permanent effects (; ; ). Furthermore, non-replicating, non-integrating vectors such as recombinant adeno-associated viruses (rAAVs) have now improved efficiency and safety, as well as providing clinically practical delivery routes, including intravenous injection ().
FIGURE 1
Huntington’s disease is a fatal neurodegenerative disorder for which there is currently no effective therapy (
Advances in synthetic gene regulation show promise in efficient delivery of artificial transcription factors (TFs) on recombinant AAV viruses, by direct injection. Our previous study showed that an endogenous promoter, based on a neuronal specific enolase (NSE) promoter-enhancer, was sufficient for stable long-term expression of a synthetic ZF targeting a mutant (but not wild type) Htt allele (
Results
We have previously shown that synthetic ZF transcription factors efficiently silenced mutant HTT transcripts in either specific brain regions (
To find a candidate ubiquitous endogenous promoter, we mined new endogenous promoters-enhancers in the literature. For instance, a recent RNA-seq study explored gene expression in the striatum and cortex, in WT and R6/2 mice, and found many genes consistently-upregulated in all four sample types (
We started with a preliminary analysis in silico for alternative promoter candidates and found 8 that are in the top 20 most-expressed genes in all conditions in Vashishtha et al. (
Out of this list, we selected the ubiquitous gene promoter Hsp90ab1 (hereafter abbreviated as HSP90) because the gene product is reported as being strongly expressed in a large variety of cell types in various organisms (see NCBI Gene ID: 15516). This gene promoter belongs to heat shock protein HSP90: the Hsp90beta isoform is constitutively expressed, whereas the Hsp90alpha isoforms is expressed under stress. As the promoter/enhancer had not been characterised, we set out to test a potential region in the mouse promoter (NCBI 15516 NC_000083.6). This region shares homology with the counterpart human promoter. Because we were constrained by the 1810bp packaging limit of our AAV-ZF vector, we selected a region of 1.7k upstream of the TSS, plus 95bp of the transcript, while remaining under the 1810bp AAV packaging limit. Flanking NheI sites were added for cloning into AAV vector (See Supplementary Figure S1). We therefore selected this promoter for vectorisation in AAV for studies of expression in mice.
In the first set of experiments, we validated the expression of our previous anti-mutant Huntingtin zinc finger, mZF-KRAB (
FIGURE 2

Long-term effects of bilateral intraventricular injection of AAV expressing mZF-KRAB zinc finger under the HSP90 promoter. (A) Zinc finger expression over time. mZF-KRAB transcript levels from whole brains were assayed by qRT-PCR at 3, 6, 12, and 24 weeks after viral (or PBS control) injections, in WT or R6/1 neonates. (B) Zinc finger repression of mutant Huntingtin in R6/1 mice. mut HTT (exon 1) expression levels in the whole brain samples from the various treatments were compared to transcript levels in PBS controls, by qRT-PCR. (C) Verification of lack of cross-reactivity of mZF-KRAB with short WT HTT alleles. WT HTT (exon 1) expression levels were quantified in the same treatment samples as above. All transcript levels were normalized to three housekeeping genes (see Supplementary Figure S2). Error bars are S.E.M (n = 4). **p < 0.01, ***p < 0.001, n.s. = not significant.
Next, we examined the mZF-KRAB expression in the specific brain regions 6 weeks post a single bilateral intraventricular injection of AAV2/9-ZF into neonatal R6/1 mice. We found mZF-KRAB mRNA to be detectable in all examined brain regions: Figure 3A) cortex, Figure 3B) cerebellum, Figure 3C) striatum, Figure 3D) hippocampus. Consequently, we detected a significant reduction of mutant Htt transcripts but not wild-type Htt on average by 60% in all studied brain regions Figure 3. That indicates that the ZF repressed the mutant but not wild-type allele, as expected, under expression with the HSP90 promoter. All transcript levels were normalised to a previously selected (
FIGURE 3

Effects of bilateral intraventricular injection of AAV expressing mZF-KRAB under the HSP90 promoter in specific brain regions 6 weeks post an injection. Unchanged expression WT HTT transcripts, as well the repression of mutant Huntingtin mut-Exon1, by targeted zinc finger expression. mZF-KRAB (ZFP) transcript levels are from dissected brain regions of the R6/1 mice, treated with either AAV2/9 (carrying mZF-KRAB under the HSP90 promoter) or PBS (control). The specific brain regions are: (A) cortex, (B) cerebellum, (C) striatum, (D) hippocampus. All transcript levels were normalized to three housekeeping genes see Supplementary Figure S3. Error bars are S.E.M (n = 4). ***p < 0.001.
We next studied whether the HSP90 promoter can efficiently drive expression of the mZF-KRAB mRNA in the CNS of symptomatic (3 months of age) R6/1 mice. For this purpose, we changed delivery route and we injected AAV2/9, carrying mZF-KRAB under the HSP90 promoter, into the lower lumbar part of the spine. We found mZF-KRAB mRNA in the whole brain of wild-type and R6/1 mice 6 weeks post a single intrathecal injection Figure 4B. As a result of mZF-KRAB expression, we detected a significant reduction of mutant Htt transcripts (approximately 40%) in whole brains of R6/1 mice Figure 4A, while wild-type Htt mRNA remained unchanged in both R6/1 mice and their wild-type littermates. This indicates that the zinc finger maintained allele-selective repression under this new promoter and delivery route. The transcripts were normalised to a specific panel of housekeeping genes Figure 4C. Overall, we concluded that our novel minimal HSP90 promoter efficiently drives expression of the therapeutic mZF-KRAB in the R6/1 mouse model during both early postnatal life, as well in the fully symptomatic mice.
FIGURE 4

Effects of intrathecal injection of AAV expressing mZF-KRAB under the HSP90 promoter. Three month old wild-type and R6/1 mice were treated either with PBS or with AAV2/9 carrying mZF-KRAB under the HSP90 promoter. (A) Unchanged expression WT HTT transcripts as well the repression of mutant Huntingtin mut-Exon1 by the zinc finger (ZFP) expression. mZF-KRAB transcript levels are from whole brains of the WT and R6/1 mice. (B) mZF-KRAB transcript levels in the whole brain of wild-type and R6/1 mice. All transcript levels were normalized to three housekeeping genes: (C) Raw crossing threshold (Ct) data for a panel of housekeeping genes. The following gene transcripts were used: Ubc (Ubiquitin C, 22190), Atp5b (ATP synthase subunit, 11947) and Rpl13a (Ribosomal protein L13a, 22121). Error bars are ±SEM (n = 6). **p < 0.01, ***p < 0.001.
Next, we validated the expression of the mZF-KRAB mRNA driven by HSP90 promoter in HD skeletal muscles. For this purpose, we injected AAV2/9 carrying mZF-KRAB under the HSP90 control directly into tibialis anterior (TA) muscles of 3-month old R6/1 mice (early-symptomatic stage) and their wild-type littermates. In order to verify the mZF-KRAB mRNA expression, we used two cohorts of mice and analysed those tissues at 3 weeks Figures 5A–D and at 6 weeks Figures 5E–H post single injection. We found mZF-KRAB transcripts to be expressed at both time-points (three and 6 weeks post single injection) Figures 5B,F. Already at 3 weeks post injection, the mutant Htt transcripts were significantly reduced by 60% as a consequence of the mZF-KRAB expression Figure 5A. Similar levels of mutant Htt transcript reduction were detected at 6 weeks post single injection Figure 5E. There was no reduction of wild-type Htt mRNA at both time-points, indicating allele-selective repression Figures 5A,E. We also monitored for any potential inflammatory response to the mZF-KRAB in TA muscles by quantification of Tnf-alpha (Tumor Necrosis Factor alpha) transcript levels. We did not detect any increase in the Tnf-alpha mRNA levels in TA muscles expressing mZF-KRAB at both time points Figures 5C,G. All transcript levels were normalised to a set of previously identified housekeeping genes Figures 5D,H. Our data indicate that the HSP90 promoter efficiently drives expression of the mZF-KRAB therapeutic molecule in the TA muscles of both wild-type and R6/1 mice.
FIGURE 5

Effects of intramuscular injection of AAV expressing mZF-KRAB under the HSP90 promoter. Tibialis anterior (TA) muscles of the 3 month old wild-type and R6/1 mice were injected with either PBS or with AAV2/9, carrying mZF-KRAB under the HSP90 promoter, and the tissue was harvested either 3 weeks (A–D) or 6 weeks (E–H) post single injection. The unchanged expression of WT HTT transcripts as well the repression of mutant Huntingtin mut-Exon1 in TA was apparent either 3 weeks (A) or 6 weeks (E) post single intramuscular injection. There was an apparent expression of the zinc finger mZF-KRAB transcript in the TA muscles of WT and R6/1 mice at both time-points at 3 weeks (B) and 6 weeks (F). Tnf-alpha (Tumor necrosis factor alpha transcript levels remained unchanged in the TA muscle expressing mZF-KRAB transcripts either 3 weeks (C) or 6 weeks (G) post single intramuscular injection. All transcript levels were normalized to three housekeeping genes: Raw crossing threshold (Ct) data for a panel of housekeeping genes are presented for the following gene transcripts: Ywhaz (Phospholipase A2, 22631), Atp5b (ATP synthase subunit, 11947) and Rpl13a (Ribosomal protein L13a, 22121). Error bars are ±SEM (n = 12). **p < 0.01, ***p < 0.001.
HD-related cardiomyopathy has been described as a relatively late pathological event in HD mouse models (
FIGURE 6

Effects of intrajugular vein injection of AAV expressing mZF-KRAB under HSP90 promoter in the HD heart. Transcript levels of wild type Htt remained unchanged while mutant exon-1 Htt transcript levels were significantly reduced with zinc finger in the hearts of R6/1mice, in comparison to R6/1 injected with PBS or wild-type mice injected with mZF-KRAB only (A). There was an apparent expression of the zinc finger mZF-KRAB transcript in the hearts of both WT and R6/1 mice at 6 weeks post single injection (B). All transcript levels were normalized to three housekeeping genes (C): Raw crossing threshold (Ct) data for a panel of housekeeping genes are presented for the following gene transcripts: Cyc1 (Cytochrome c-1, 66445), Atcb (Actin, beta, cytoplasmic, 11461), Gapdh (Glyceraldehydes-3-phosphate dehydrogenase, 14433) (D). A number of biomarkers of the HD pathology in the heart have been significantly reversed: Anf (atrial natriuretic factor), Bnp (brain natriuretic protein), members of the four-and-a-half LIM family Fhl1 and Fhl2, S100A4S100 calcium binding protein A4). Error bars are ±SEM (n = 6). **p < 0.01, ***p < 0.001.
Discussion
Gene locus silencing technology is based on the activity of synthetic zinc finger (ZF) molecules that can act as selective repressors to target virtually any gene sequence, resulting in a broad therapeutic potential. Due to their relative small size, these active ZF molecules can be delivered to various tissues and cells with adeno associated viruses (AAV) and their expression can be regulated by either tropism of the AAV or a cell-selective promoter (
Allele-selectivity by HTT-repressing ZFs is based on the properties of zinc fingers that bind longer target sequences preferentially because of avidity and co-operativity effects. For illustration, distributions of mutant Huntingtin in human populations have modal values of ∼15 CAG repeats for wild-type alleles and ∼42 for the longer mutant alleles. Thus, the mutant target provides many more overlapping opportunities for a ZFP to bind, increasing the avidity of the interaction. Moreover, it is well-known that zinc fingers unwind the DNA helix slightly when they bind (
In vivo, specifically targetting mutant HTT in the CNS led to an amelioration of a number of molecular and neurological phenotypes in HD mouse models and became a valid therapeutic strategy for Huntington’s disease (
One of the prominent pathological features in HD is transcriptional deregulation that has been described as an early and progressive event (
Next, we used the more clinically-relevant intrathecal route to deliver ZF molecules, under the control of HSP90 promoter, into the CNS of symptomatic R6/1 mice. We found that 6 weeks after a single injection, there was a significant reduction of mutant HTT mRNAs in the whole brain, indicative of active ZF therapeutics being present. Hence, we concluded that this new HSP90 promoter can efficiently drive expression of ZF molecules even with intrathecal delivery into symptomatic R6/1 mice.
Since malfunction of skeletal muscles is a major pathological feature of HD (
In summary, our study offers a novel asset, an HSP90 (HSP90AB1) promoter-enhancer, to be used for the efficient expression of therapeutic molecules in various somatic tissues. The use of this promoter can be extended beyond the HD therapeutic area whenever there is a need to apply therapeutic molecules in a ubiquitous manner.
Materials and methods
Mouse maintenance and genotyping
The R6/1 mouse line was purchased from Jackson Laboratories (US) and was bred and genotyped as previously described (
AAV production
AAV2/9 mZF–KRAB, containing a HSP90 promoter were used in this study were produced at the Centre for Animal Biotechnology and Gene Therapy of the Universitat Autonoma of Barcelona, as described previously (
Mouse surgery—AAV delivery routes
Free hand intraventricular AAV injections in neonates were performed as previously described (
The protocol for Intrathecal injections (IT) was adopted from (
Direct intra-muscular injections (IM) were performed accordingly to the previously published protocol (
In order to express the zinc finger transcripts in the HD heart, intra-jugular injections (IJ) were performed according to the previously published protocol (
A summary of all delivery routes including time-lines can be found in the Supplementary Figure S4.
RNA extraction and taqman real-time PCR expression analysis
Total RNA from eye tissues was extracted with the mini-RNA kit (Qiagen, United Kingdom), according to the manufacturer’s instructions. The reverse transcription reaction was performed using MMLV superscript reverse transcriptase (Invitrogen, United States) and random hexamers (Sigma, United States), as described in earlier studies (
Statistical analysis
Values were presented as mean ± SEM. Statistical analysis was performed using paired Student t tests (Excel) or One-Way Anova SPSS (IBM). A p-value of 0.05 was considered as a significant difference.
Statements
Data availability statement
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
Ethics statement
The animal study was reviewed and approved by Home Office, UK and the Animal Welfare and Ethical Review Body of Imperial College London.
Author contributions
MM and MI contributed to conception and design of the study. MM performed experimental work and the statistical analysis. MM and MI analysed data. MM and MI wrote the first draft of the manuscript. All authors contributed to manuscript revision, read, and approved the submitted version.
Funding
This work was supported by Imperial/ICR/NIHR BRC/NHS Confidence in Concept (iCiC) and DT-prime grant schemes. MI was funded by Investigator award no WT102944 from the Wellcome Trust United Kingdom.
Conflict of interest
The authors declare that they have filed a previous patent on this topic (WO2017077329).
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmolb.2023.1175407/full#supplementary-material
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Summary
Keywords
Huntington’s disease, mouse models, gene therapy, promoter, aav, zinc finger therapeutics
Citation
Mielcarek M and Isalan M (2023) A minimal region of the HSP90AB1 promoter is suitable for ubiquitous expression in different somatic tissues with applicability for gene therapy. Front. Mol. Biosci. 10:1175407. doi: 10.3389/fmolb.2023.1175407
Received
27 February 2023
Accepted
03 April 2023
Published
17 April 2023
Volume
10 - 2023
Edited by
Mahendra Pratap Kashyap, University of Alabama at Birmingham, United States
Reviewed by
Katarzyna Gaweda-Walerych, Mossakowski Medical Research Institute, Polish Academy of Sciences, Poland
Cleo Smeets, AstraZeneca, Sweden
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Copyright
© 2023 Mielcarek and Isalan.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Mark Isalan, m.isalan@imperial.ac.uk
Disclaimer
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.