Patent Application
20220259595
The present invention relates to functional nucleic acid molecules comprising at least one target binding sequence comprising a sequence reverse complementary to a frataxin mRNA sequence; and a regulatory sequence comprising an RNA comprising a SINE B2 element or a functionally active fragment of a SINE B2 element or an internal ribosome entry site (IRES) sequence or an IRES derived sequence.
Friedreich's ataxia (FRDA) is a life-threatening monogenic disease with neuro- and cardio-degenerative progression. It represents the most frequent type of inherited ataxia, affecting more than 15,000 patients in Western countries. Patients typically show degeneration of large sensory neurons of the dorsal root ganglia, Betz pyramidal neurons of the cerebral cortex and lateral cortico-spinal and spinocerebellar tracts, as well as lesions in the dentate nucleus of the cerebellum. In addition, non-neurological degeneration causes hypertrophic cardiomyopathy and increased incidence of diabetes mellitus. Neurodegenerative motor symptoms typically appear before adolescence with progressive gait instability and loss of coordination, while the cardiac component of the disease causes premature mortality at a mean age of 40 years. Almost all FRDA patients carry an intronic homozygous expansion of natural GAA repeats located in the FXN gene. The human FXN locus contains normally from 10 to 66 GAA-triplet repeats within the first intron, whereas FRDA individuals have an hyperexpansion of such repeats, up to 1700 triplets. In a small percentage of cases, however, patients are compound heterozygotes for GAA expansion on one FXN allele and a second allele with a small insertion, deletion or point mutation in FXN open reading frame. Longer hyperexpansions result in a more severe phenotype with an earlier onset and faster progression. GAA repeat expansions impair FXN transcription by inducing the formation of triple helical DNA structures (sticky DNA), persistent DNA/RNA hybrids (R-loops) and specific epigenetic modifications. The FXN gene encodes for the precursor of frataxin, a small iron-binding protein, that is mainly, but not exclusively, confined inside the mitochondrial matrix, where it is converted into the functional mature form. Although its primary function is still debated, mature frataxin is a key component of the iron-sulfur cluster (ISC) biosynthetic apparatus, which provides the essential cofactor to all ISC-dependent enzymes of the cell. As a consequence of insufficient FXN expression, defective ISC biosynthesis triggers a series of vicious cycles leading to deregulated intracellular iron homeostasis, impaired mitochondrial electron transport chain and higher sensitivity to trigger oxidant- and stress-induced cell death. Currently, there are no therapies to treat the disease or prevent its progression.
The most promising approaches point to restore sufficient frataxin levels, mostly by enhancing FXN transcription. Among them, IFN-γ and dyclonine have been identified as encouraging candidates by drug repositioning programs. Synthetic histone deacetylase (HDAC) inhibitors have been described to increase FXN mRNA in FRDA-derived cells and in FRDA animal models. More recently, synthetic nucleic acids were successfully employed targeting GAA repeats, acting as R-loops inhibitors. Moreover, polyamide-based transcription factors capable of binding GAA microsatellite were developed. Interestingly, protein replacement therapy, based on TAT-frataxin delivery, and frataxin degradation prevention, by a class of ubiquitin-competing small molecules, have recently been proposed as potential treatments targeting the frataxin polypeptide. Finally, an effective gene replacement strategy in the FRDA mouse model opened new opportunities for gene therapy in the future.
However, recent data has proved that prolonged over-expression at non-physiological levels of frataxin affects the cellular metabolism, leading to a significant increase of oxidative stress and labile iron pool levels. These cellular alterations are similar to those observed when the gene is partly silenced, as occurs in FRDA patients. These results suggest that any long-term therapeutic intervention must finely tune frataxin protein levels within a physiological range.
In view of the above, there is a need for new therapeutic approaches for Friedreich's ataxia, in particular new therapies that do not increase frataxin protein beyond physiological levels. Furthermore, there is a need for new therapies that target frataxin expression in a highly gene-specific manner limiting side effects.
Recently, a novel functional class of antisense (AS) lncRNAs was identified, which increase translation of partially overlapping sense protein-coding mRNAs. These RNAs are also called SINEUPs, as they require a SINE B2 element to UP-regulate translation and are disclosed in WO 2012/133947.
AS Uchl1, a lncRNA antisense to the mouse orthologue of human Uchl1/PARK5 gene, can be considered the representative member of this new class of lncRNAs, as it was found to increase UchL1 protein synthesis acting at a post-transcriptional level. AS Uchl1 activity depends on the combination of two functional domains: at the 5′ end, the overlapping region, indicated as “binding domain” or “target binding sequence”, dictates AS Uchl1 specificity towards Uchl1 mRNA; at the 3′ end, the non-overlapping region contains an embedded inverted SINE B2 element, which acts as “effector domain” (or “regulatory sequence”) and triggers translation up-regulation of bound target mRNA.
More than 30 antisense lncRNAs promote translation up-regulation of partially overlapping mRNAs. By replacing the binding domain, it is possible to re-direct AS Uchl1 activity towards a target mRNA of choice.
It is an object of the present invention to provide a functional nucleic acid molecule that increases the frataxin protein without overcoming physiological levels, targets frataxin expression in a highly gene-specific manner and limits side effects.
This object is achieved by means of the functional nucleic acid molecule as defined herein.
Other objects of the present invention are to provide a DNA molecule encoding the functional nucleic acid molecule, a composition, and uses as defined herein.
By “functional nucleic acid molecule” there is intended generally that the nucleic acid molecule is capable of enhancing the translation of a target mRNA of interest, in this particular case a frataxin mRNA.
By “frataxin mRNA sequence” there is intended an mRNA sequence of any length of at least 10 nucleotides comprised in the mRNA of the corresponding frataxin (FXN) gene. The FXN gene sequence is known in the art, for example see Gene ID: 2395 or Ensembl ID: ENSG00000165060. The FXN gene encodes the frataxin protein. The frataxin protein sequence is known in the art, for example see UniProt ID: Q16595.
The term “SINE” (Short Interspersed Nuclear Element) may be referred to as a non-LTR (long terminal repeat) retrotransposon, and is an interspersed repetitive sequence (a) which encodes a protein having neither reverse-transcription activity nor endonuclease activity or the like and (b) whose complete or incomplete copy sequences exist abundantly in genomes of living organisms.
The term “SINE B2 element” is defined in WO 2012/133947, where specific examples are also provided (see table starting on page 69 of the PCT publication). The term is intended to encompass both SINE B2 elements in direct orientation and in inverted orientation relative to the 5′ to 3′ orientation of the functional nucleic acid molecule. SINE B2 elements may be identified, for example, using programs like RepeatMask as published (Bedell et al. Bioinformatics. 2000 November; 16(11): 1040-1. MaskerAid: a performance enhancement to RepeatMasker). A sequence may be recognizable as a SINE B2 element by returning a hit in a Repbase database with respect to a consensus sequence of a SINE B2, with a Smith-Waterman (SW) score of over 225, which is the default cutoff in the RepeatMasker program. Generally a SINE B2 element is not less than 20 bp and not more than 400 bp. Preferably, the SINE B2 is derived from tRNA.
By the term “functionally active fragment of a SINE B2 element” there is intended a portion of sequence of a SINE B2 element that retains protein translation enhancing efficiency. This term also includes sequences which are mutated in one or more nucleotides with respect to the wild-type sequences, but retain protein translation enhancing efficiency. The term is intended to encompass both SINE B2 elements in direct orientation and in inverted orientation relative to the 5′ to 3′ orientation of the functional nucleic acid molecule.
The terms “internal ribosome entry site (IRES) sequence” and “internal ribosome entry site (IRES) derived sequence” are defined in WO 2019/058304. IRES sequences recruit the 40S ribosomal subunit and promote cap-independent translation of a subset of protein coding mRNAs. IRES sequences are generally found in the 5′ untranslated region of cellular mRNAs coding for stress-response genes, thus stimulating their translation in cis. It will be understood by the term “IRES derived sequence” there is intended a sequence of nucleic acid with a homology to an IRES sequence so as to retain the functional activity thereof, i.e. a translation enhancing activity. In particular, the IRES derived sequence can be obtained from a naturally occurring IRES sequence by genetic engineering or chemical modification, e.g. by isolating a specific sequence of the IRES sequence which remains functional, or mutating/deleting/introducing one or more nucleotides in the IRES sequence, or replacing one or more nucleotides in the IRES sequence with structurally modified nucleotides or analogs. More in particular, the skilled in the art would know that an IRES derived sequence is a nucleotide sequence capable of promoting translation of a second cistron in a bicistronic construct. Typically, a dual luciferase (Firefly luciferase, Renilla Luciferase) encoding plasmid is used for experimental tests. A major database exists, namely IRESite, for the annotation of nucleotide sequences that have been experimentally validated as IRES, using dual reporter or bicistronic assays (http://iresite.org/IRESite_web.php). Within the IRESite, a web-based tool is available to search for sequence-based and structure-based similarities between a query sequence of interest and the entirety of annotated and experimentally validated IRES sequences within the database. The output of the program is a probability score for any nucleotide sequence to be able to act as IRES in a validation experiment with bicistronic constructs. Additional sequence-based and structure-based web-based browsing tools are available to suggest, with a numerical predicting value, the IRES activity potentials of any given nucleotide sequence (http://rna.informatik.uni-freiburg.de/; http://regrna.mbc.nctu.edu.tw/index1.php).
By the term “miniSINEUP” there is intended a nucleic acid molecule consisting of a binding domain (complementary sequence to target mRNA), a spacer sequence, and any SINE or SINE-derived sequence or IRES-derived sequence as the effector domain (Zucchelli et al., Front Cell Neurosci., 9: 174, 2015).
By the term “microSINEUP” there is intended a nucleic acid molecule consisting of a binding domain (complementary sequence to target mRNA), a spacer sequence, and a functionally active fragment of the SINE or SINE-derived sequence or IRES-derived sequence. For example, the functionally active fragment may be a 77 bp sequence corresponding to nucleotides 44 to 120 of the 167 bp SINE B2 element in AS Uchl1.
Polypeptide or polynucleotide sequences are said to be the same as or “identical” to other polypeptide or polynucleotide sequences, if they share 100% sequence identity over their entire length. Residues in sequences are numbered from left to right, i.e. from N- to C-terminus for polypeptides; from 5′ to 3′ terminus for polynucleotides.
For the purposes of comparing two closely-related polynucleotide sequences, the “% sequence identity” between a first nucleotide sequence and a second nucleotide sequence may be calculated using NCBI BLAST, using standard settings for nucleotide sequences (BLASTN). For the purposes of comparing two closely-related polypeptide sequences, the “% sequence identity” between a first polypeptide sequence and a second polypeptide sequence may be calculated using NCBI BLAST, using standard settings for polypeptide sequences (BLASTP). A “difference” between sequences refers to an insertion, deletion or substitution of a single nucleotide in a position of the second sequence, compared to the first sequence. Two sequences can contain one, two or more such differences. Insertions, deletions or substitutions in a second sequence which is otherwise identical (100% sequence identity) to a first sequence result in reduced % sequence identity.
A functional nucleic acid molecule of the present invention comprises at least one target binding sequence comprising a sequence reverse complementary to a frataxin mRNA sequence and at least one regulatory sequence comprising an RNA comprising a SINE B2 element or a functionally active fragment of a SINE B2 element or an internal ribosome entry site (IRES) sequence or an IRES derived sequence.
The functional nucleic acid molecules of the invention are able to modulate protein translation of the mRNA target however, compared to other methods, the modulation is not the result of modifying the target gene and therefore does not include the risks associated with genome editing. Furthermore, the functional nucleic acid molecules are highly specific to the target, reducing any off-target side effects.
Regulatory Sequences
In one embodiment, the regulatory sequence has protein translation enhancing efficiency. The increase of the protein translation efficiency indicates that the efficiency is increased as compared to a case where the functional nucleic acid molecule according to the present invention is not present in a system. In one embodiment, expression of the protein encoded by the target mRNA is increased by at least 1.5 fold, such as at least 2 fold. In a further embodiment, expression of the protein encoded by the target mRNA is increased between 1.2 to 3 fold, such as between 1.5 and 2.2 fold.
In one embodiment, the regulatory sequence is located 3′ of the target binding sequence. The regulatory sequence may be in a direct or inverted orientation relative to the 5′ to 3′ orientation of the functional nucleic acid molecule. Reference to “direct” refers to the situation in which the regulatory sequence is embedded (inserted) with the same 5′ to 3′ orientation as the functional nucleic acid molecule. Instead, “inverted” refers to the situation in which the regulatory sequence is 3′ to 5′ oriented relative to the functional nucleic acid molecule.
Preferably, the at least one regulatory sequence comprises a sequence with at least 75% sequence identity, preferably at least 90% sequence identity, more preferably at least 95% sequence identity, even more preferably 100% sequence identity with a sequence selected from the group consisting of SEQ ID NO: 1-82. In one embodiment, the at least one regulatory sequence consists of a sequence with at least 75% sequence identity, preferably at least 90% sequence identity, more preferably at least 95% sequence identity, even more preferably 100% sequence identity with a sequence selected from the group consisting of SEQ ID NO: 1-82.
In one embodiment, the regulatory sequence comprises a SINE B2 element or a functionally active fragment of a SINE B2 element. The SINE B2 element is preferably in an inverted orientation relative to the 5′ to 3′ orientation of the functional nucleic acid molecule, i.e. an inverted SINE B2 element. As mentioned in the definitions section, inverted SINE B2 elements are disclosed and exemplified in WO 2012/133947.
Preferably, the at least one regulatory sequence comprises a sequence with at least 75% sequence identity, preferably 90% sequence identity, more preferably 95% sequence identity, even more preferably 100% sequence identity with a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:51.
SEQ ID NO:1 (the inverted SINE B2 element in AS Uchl1) and SEQ ID NO:2 (the 77 nucleotide variant of the inverted SINE B2 element in AS Uchl1 that includes nucleotides 44 to 120) are particularly preferred.
Other inverted SINE B2 elements and functionally active fragments of inverted SINE B2 elements are SEQ ID NO:3 to SEQ ID NO:51. Experimental data showing the protein translation enhancing efficiency of these sequences is not explicitly shown in the present patent application, but is disclosed in a previous patent application in the name of the same applicant. SEQ ID NO:3 to SEQ ID NO:51 can therefore be used as regulatory sequences in molecules according to the present invention.
SEQ ID NO:3 to SEQ ID NO:6, SEQ ID NO:8 to SEQ ID NO:11, SEQ ID NO:18, SEQ ID NO:43 to SEQ ID NO:51 are functionally active fragments of inverted SINE B2 transposable element derived from AS Uchl1. The use of functional fragments reduces the size of the regulatory sequence which is advantageous if used in an expression vector (e.g. viral vectors which may be size-limited) because this provides more space for the target sequence and/or expression elements.
SEQ ID NO:7 is a full length 183 nt inverted SINE B2 transposable element derived from AS Uchl1. SEQ ID NO:12 to SEQ ID NO:17, SEQ ID NO:19 and SEQ ID NO:20, SEQ ID NO:39 to SEQ ID NO:42 are mutated functionally active fragments of inverted SINE B2 transposable element derived from AS Uchl1.
SEQ ID NO:21 to SEQ ID NO:25 and SEQ ID NO:28 to SEQ ID NO:38 are different SINE B2 transposable elements. SEQ ID NO:26 and SEQ ID NO:27 are sequences in which multiple inverted SINE B2 transposable element have been inserted.
Alternatively, the regulatory sequence comprises an IRES sequence or an IRES derived sequence. Therefore, in one embodiment, the regulatory sequence comprises an IRES sequence or an IRES derived sequence. Said sequence enhances translation of the target mRNA sequence.
Several IRESs having sequences ranging from 48 to 576 nucleotides have been tested with success, e.g. human Hepatitis C Virus (HCV) IRESs (e.g. SEQ ID NO: 53 and 54), human poliovirus IRESs (e.g. SEQ ID NO: 55 and 56), human encephalomyocarditis (EMCV) virus (e.g. SEQ ID NO: 57 and 58), human cricket paralysis (CrPV) virus (e.g. SEQ ID NO: 59 and 60), human Apaf-1 (e.g. SEQ ID NO: 61 and 62), human ELG-1 (e.g. SEQ ID NO: 63 and 64), human c-MYC (e.g. SEQ ID NO: 65-68), human dystrophin (DMD) (e.g. SEQ ID NO: 69 and 70).
Such sequences have been disclosed, defined and exemplified in WO 2019/058304. Preferably, such sequences have 75% sequence identity, preferably 90% sequence identity, more preferably 95% sequence identity, even more preferably 100% sequence identity to any of SEQ ID NO:53 to SEQ ID NO:82. More preferably, such sequences have 75% sequence identity, preferably 90% sequence identity, more preferably 95% sequence identity, even more preferably 100% sequence identity to any of SEQ ID NO:53 to SEQ ID NO:70.
Target Binding Sequences
In WO 2012/133947 it was already shown that the target binding sequence needs to have only about 60% similarity with a sequence reverse complementary to the target mRNA. As a matter of fact, the target binding sequence can even display a large number of mismatches and retain activity.
The target binding sequence comprises a sequence which is sufficient in length to bind to the frataxin mRNA transcript. Therefore, the target binding sequence may be at least 10 nucleotides long, such as at least 14 nucleotides long, such as least 18 nucleotides long. Furthermore, the target binding sequence may be less than 250 nucleotides long, preferably less than 200 nucleotides long, less than 150 nucleotides long, less than 100 nucleotides long, less than 80 nucleotides long, less than 60 nucleotides long or less than 50 nucleotides long. In one embodiment, the target binding sequence is between 4 and 50 nucleotides in length, such as between 18 and 44 nucleotides long.
The target binding sequence may be designed to hybridise with the 5′-untranslated region (5′ UTR) of the frataxin mRNA sequence. In one embodiment, the sequence is reverse complementary to 0 to 50 nucleotides, such as 0 to 40, 0 to 21 or 0 to 14 nucleotides of the 5′ UTR. Alternatively, or in combination, the target binding sequence may be designed to hybridise to the coding sequence (CDS) of the frataxin mRNA sequence. In one embodiment, the sequence is reverse complementary to 0 to 40 nucleotides, such as 0 to 32, 0 to 18 or 0 to 4 nucleotides of the CDS.
The target binding sequence may be designed to hybridise to a region upstream of an AUG site (start codon), such as a start codon within the CDS, of the frataxin mRNA sequence. In one embodiment, the sequence is reverse complementary to 0 to 80 nucleotides, such as 0 to 70 or 0 to 40 nucleotides of the AUG site. Alternatively, or in combination, the target binding sequence may be designed to hybridise to the frataxin mRNA sequence downstream of said AUG site. In one embodiment, the sequence is reverse complementary to 0 to 40 nucleotides, such as 0 to 4 nucleotides of the frataxin mRNA sequence downstream of said AUG site.
Preferably, the at least one target binding sequence is at least 10 nucleotides long and comprises, from 3′ to 5′:
Of course in case 1) the coding sequence starts on the first AUG site (M1) of the mRNA. In case 2), the preferred AUG site is that corresponding to methionine 76 (M76) in exon 2.
More preferably, the at least one target binding sequence is at least 14 nucleotides long and comprises, from 3′ to 5′:
In one embodiment, the functional nucleic acid molecule comprises a sequence with at least 75% sequence identity, preferably at least 90% sequence identity, more preferably at least 95% sequence identity, even more preferably 100% sequence identity to any of SEQ ID NO: 83-98. In a further embodiment, the functional nucleic acid molecule consists of a sequence with at least 75% sequence identity, preferably at least 90% sequence identity, more preferably at least 95% sequence identity, even more preferably 100% sequence identity to any of SEQ ID NO: 83-98.
Structural Features
The functional nucleic acid molecule preferably comprises more than one regulatory sequence, which can be the same sequence repeated more than once, or a different regulatory sequence (i.e. a different SINE B2 element/functionally active fragment of a SINE B2 element/an IRES sequence/an IRES derived sequence).
The at least one target binding sequence and the at least one regulatory sequence are preferably connected by at least one spacer/linker sequence. In case of multiple sequences, several spacer/linker sequences can be inserted in-between the sequences. SEQ ID NO:52 is a non-limiting example of the spacer/linker sequence.
The functional nucleic acid molecule of the present invention is preferably a circular molecule. This conformation leads to a much more stable molecule that is degraded with greater difficulty within the cell (exonucleases cannot degrade circular molecules) and therefore remains active for a longer time.
Furthermore, the functional nucleic acid molecule may optionally comprise a non-coding 3′ tail sequence, which e.g. includes restriction sites useful for cloning the molecule in appropriate plasmids.
It should be noted that the functional nucleic acid molecules can enhance translation of the target gene of interest with no effects on mRNA quantities of the target gene. Therefore they can successfully be used as molecular tools to validate gene function in cells as well as to implement the pipelines of recombinant protein production.
DNA Molecules and Vectors
According to a further aspect of the invention, there is provided a DNA molecule encoding any of the above disclosed functional nucleic acid molecules. According to a further aspect of the invention, there is provided an expression vector comprising the above said DNA molecule.
Exemplary expression vectors are known in the art and may include, for example, plasmid vectors, viral vectors (for example adenovirus, adeno-associated virus, retrovirus or lentivirus vectors), phage vectors, cosmid vectors and the like. The choice of expression vector may be dependent upon the type of host cell to be used and the purpose of use. In particular the following plasmids have been used for efficient expression of functional nucleic acid molecules.
Mammalian Expression Plasmids:
Viral Vectors:
It should be noted that any promoter may be used in the vector and will work just as well as those mentioned above.
Compositions
The present invention also relates to compositions comprising the above said functional nucleic acid molecules or the above said DNA molecules. Any compositions are included allowing to deliver the above said functional nucleic acid molecules by viral vectors (AAV, lentivirus and the like) and non-viral vectors (nanoparticles, lipid particles and the like).
According to a further aspect of the invention, there is provided the functional nucleic acid molecule, DNA molecule, expression vector or the composition as defined herein for use as a medicament.
It will be understood that the functional nucleic acid molecules of the invention find use in increasing the level of frataxin protein within a cell. Therefore, the above said functional nucleic acid molecules, DNA molecules and/or compositions may be used as medicaments, preferably for treating Friedreich's ataxia and in particular promoting the recovery of disease-associated mitochondrial defects.
Friedreich's ataxia is a rare genetic disorder caused by an insufficient quantity of frataxin protein. The main root of the pathology is the impaired transcription of the FXN gene as a result of GAA repeat expansion. As shown in the Examples provided herein, the functional nucleic acid molecules were able to rescue the physiological translation of frataxin even in patient cells with a mRNA deficit (e.g. see
According to a further aspect of the invention, there is provided the use of the functional nucleic acid molecule (or DNA molecule, expression vector or composition) as defined herein for the manufacture of a medicament for the treatment of Friedreich's ataxia.
Methods
According to a further aspect of the invention, there is provided a method for enhancing protein translation of FXN mRNA in a cell comprising administering the functional nucleic acid molecule, DNA molecule, expression vector or composition as defined herein to the cell. Preferably the cell is a mammalian cell, such as a human or a mouse cell.
According to a further aspect of the invention, there is provided a method for increasing the protein synthesis efficiency of frataxin in a cell comprising administering the functional nucleic acid molecule, DNA molecule, expression vector or composition as defined herein to the cell.
The methods described herein may comprise transfecting into a cell the functional nucleic acid molecule, DNA molecule or expression vector as defined herein. The functional nucleic acid molecule, DNA molecule or expression vector may be administered to target cells using methods known in the art and include, for example, microinjection, lipofection, electroporation, using calcium phosphate, self-infection by the vector or transduction of a virus.
The target cell to be treated may comprise a reduced amount of frataxin. In one embodiment, the level of frataxin in the cell is lower than the level of frataxin in a normal cell (i.e. a cell comprising a normal phenotype with functional copies of the FXN gene). For example, the level of frataxin in the cell may be less than 70% of the level of frataxin in a normal cell, such as less than 60% or less than 50% of the level of frataxin in a normal cell. In a further embodiment, the level of frataxin in the cell is about 50% of the level of frataxin in a normal cell.
In a further embodiment, the cell is FXN haploinsufficient, i.e. wherein the presence of a variant allele in a heterozygous combination results in the amount of product generated by the single wild-type gene is not sufficient for complete or normal function. Generally, haploinsufficiency is a condition that arises when the normal phenotype requires the protein product of both alleles, and reduction to 50% or less of gene function results in an abnormal phenotype.
Methods of the invention result in increased levels of frataxin in a cell and therefore find use, for example, in methods of treatment for diseases which are associated with FXN defects (i.e. reduced frataxin levels and/or loss-of-function mutations of the FXN gene). Methods of the invention find particular use in diseases caused by a quantitative decrease in the predetermined, normal protein level. Methods of the invention can be performed in vitro, ex vivo or in vivo.
According to a further aspect of the invention, there is provided a method of treating Friedreich's ataxia comprising administering a therapeutically effective amount of the functional nucleic acid molecule, DNA molecule, expression vector or composition as defined herein.
It will be understood that the embodiments described herein may be applied to all aspects of the invention, i.e. the embodiment described for the functional nucleic acid molecules may equally apply to the claimed methods and so forth.
The invention will now be illustrated with reference to the following non-limiting examples.
This example shows how the regulatory sequences and the target binding sequences of the functional nucleic acid according to the invention have been designed.
In particular,
The sequences used in the examples are as follows.
This example shows that synthetic SINEUPs increase endogenous frataxin protein level in human cells in vitro. In particular, HEK 293T/17 cells (ATCC Cat. No. CRL-11268) were transfected with empty vector (ctrl) and SINEUP-FXN variants and harvested 48 hours post transfection. Empty vector (ctrl) and miniSINEUP-FXN −40/+4 M1-AUG were taken as negative and positive controls respectively. HEK 293T/17 cells were used to screen the activity of SINEUP-FXN because they endogenously express frataxin.
This example shows SINEUP effect on FXN knockdown HEK293T/17 cells. Silencing of FXN by shFXN (sh, Short Hairpin) in HEK 293T/17 cells. Cells were co-transfected with shCTRUSINEUP ctrl (empty vectors), shFXN/SINEUP ctrl and shFXN/SINEUP-FXN −40/+0 M1-AUG. shCTRL/SINEUP and shFXN/SINEUP were taken as negative and positive silencing controls respectively. 48 hours post transfection, whole cell lysates were analysed by Western blotting with anti-FXN and anti-β-actin antibodies (
This example shows that miniSINEUPs increase endogenous frataxin protein level in human cells in vitro.
In particular
This example shows that miniSINEUPs increase endogenous frataxin protein level in SH-SY5Y cells in vitro.
In
This example shows the binding domain's specificity: a selective increase of frataxin protein expression in vitro is demonstrated. In
This example shows effector domain optimization. microSINEUPs increase endogenous frataxin protein level in HEK 293T/17 cells in vitro. HEK 293T/17 cells were transfected with empty vector (ctrl), miniSINEUP-FXN −40/+0 M1-AUG and microSINEUP-FXN variants (−40/+0; −14/+0 M1-AUG). Cells were harvested 48 hours post transfection. Empty vector (ctrl) and miniSINEUP-FXN −40/+0 M1-AUG were taken as negative control and positive controls respectively. In
This example shows miniSINEUPs lentiviral transduction optimization. In particular,
This example shows lentiviral infection of HEK293T/17 cells. In
This example shows increased endogenous FXN protein expression in FRDA-derived fibroblasts. GM04078 cells (patients' primary fibroblasts) showed an intermediate phenotype carrying a hyper-expansion of about 541 repeats on one allele and 420 repeats on the other one. In
In
In
This example shows that AAV9-miniSINEUPs increase endogenous frataxin protein level in HEK 293T/17 cells in vitro. In
This example shows protein rescue of FRDA-derived lymphoblasts which carry the pathogenic expansion of GAA repeats and show reduced levels of the protein when compared to controls. GM16214 cells (patients' primary lymphoblasts) were stably transfected with empty vector (ctrl) and miniSINEUP-FXN variants. Ctrl, −40/+0 M1-AUG and −40/+4 M76-AUG stable clones were obtained from at least 15 days of G418 selection. Untransfected GM16214 cells and ctrl clone were taken as negative controls, while GM16215 cells (primary lymphoblasts derived from the healthy heterozygous patient's mother) were taken as positive control. In
This example shows the phenotypic rescue of FRDA-derived lymphoblasts. Frataxin-deficient cells are primarily affected by defective iron-sulfur cluster biosynthesis. Accordingly, insufficient frataxin levels trigger a typical loss in the activity of aconitases, two different ISC-dependent enzymes located in mitochondrial and cytosolic compartments. To assess the functional impact of SINEUPs, aconitase activity was chosen as a functional readout of restoring frataxin physiological levels for FRDA stable transfectants. Citrate synthase assay is used as an internal control.
The effect of miniSINEUP-FXN expression in vitro on aconitase activity was measured on whole cells lysates. Untransfected GM16214 cells and ctrl clones were taken as negative controls, while GM16215 cells (primary lymphoblasts derived from the healthy heterozygous patient's mother) were taken as positive control, as previously shown for other experiments. GM16214 cells expressing miniSINEUP-FXN show restored activity of endogenous aconitase as compared to GM16215 positive control. Activity of citrate synthase, the Krebs cycle enzyme catalysing the preceding step respect to aconitase, but lacking ISC, did not show significant fluctuations in assayed extracts. Aconitase (
This example shows analysis of off-target effects. To predict putative off-targets, the Basic Local Alignment Search Tool (BLAST) of Ensembl genome browser was used to align the binding domain sequences to the human mRNA dataset. Results were filtered for match orientation while non-functional genes (pseudogenes and patch chromosomes) were removed. Potential off-target mRNAs were identified for their 100% identity to SINEUP-FXNs within the 5′UTRs of STX1B, FAM49A and CBX3 genes with length ranging from 13 to 20 nucleotides. All complementary sequences were distant from the translation initiation site of the target mRNA. Unconventional positions of target binding sites were also identified for TUBGCP5 (CDS) and for SH3GLB2, EIF4E and DISC1 (3′UTRs).
HEK 293T/17 cells were transfected with empty vector (ctrl) and miniSINEUP-FXN variants (−40/+0; −14/+0 and −14/+4 M1-AUG or −40/+4 M76-AUG) and harvested 48 hours post transfection. Empty vector (ctrl) was taken as negative control. Whole cell lysates were analysed by western blotting. Average fold changes of both target and off-targets for each binding domain are shown. First, band intensity was normalized to the relative β-actin band. Then, fold change values were calculated normalizing to control cells (ctrl). The mean FXN fold changes are plotted as the mean±S.E.M. (n≥4); ns, P>0.05; *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001 (one-way ANOVA followed by Dunnett's post-test). Off-targets fold changes are plotted as the mean±SEM (n=3) and p values are calculated by unpaired t-test with Welch's correction. ns, P>0.05. As shown in
The above disclosed examples show that a number of antisense long non-coding SINEUP RNAs targeting human FXN mRNA are capable to up-regulate frataxin protein to physiological amounts acting at post-transcriptional level. FXN-specific SINEUPs promote the recovery of disease-associated mitochondrial defects in FRDA-derived cells. SINEUPs are feasibly the first gene-specific therapeutic approach to activate FXN translation in FRDA.
In detail:
The present invention therefore provides functional nucleic acids that are able to increase endogenous frataxin protein levels within physiological range and restore mitochondrial activity in FRDA patients' cells representing a new therapeutic strategy for this untreatable disease. By restoring physiological levels of frataxin, the molecules according to the invention limit potential side effects due to exaggerated overexpression of frataxin proteins by more conventional gene therapy approaches. In addition, by taking advantage of RNA base pairing between the binding domain and FRX mRNA, the molecules according to the invention limit potential side effects present when a small molecule approach is used to treat FRDA patients.
| Number | Date | Country | Kind |
|---|---|---|---|
| 102019000011490 | Jul 2019 | IT | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2020/069519 | 7/10/2020 | WO |
