Patent Application
20190093098
This application contains a sequence listing in accordance with 37 C.F.R. 1.821-1.825. The sequence listing accompanying this application is hereby incorporated by reference in its entirety.
The present invention relates to a method and substances for targeted alteration of genetic information on the RNA level.
The nucleoside adenosine can be enzymatically desaminated. Inosine is created, and during a translation is read as guanosine. This nucleoside alteration is called A-to-I editing and may be used to insert individual point mutations into RNA to alter the resulting proteins in a targeted manner.
It is known of the naturally occurring hADARs (human adenosine deaminase acting on RNA) enzymes that they can desaminate adenosine and are highly promiscuous therein (5). Thus the enzyme hADAR2 can detect and edit thousands of different substrates, wherein nearly every double strand RNA having a length of more than 30 base pairs can act as a substrate. Nevertheless, only a very few substrates are edited highly selectively and efficiently (7). The reason for this seems to be the recognition of special sequences and secondary structures by the dsRBD (dsRNA binding domains). ADAR2 has two dsRBD (1 & 2) in the N-terminus. It was possible to demonstrate on model substrates, such as the GluR2 transcript, that the dsRBD1 & 2 each bind at different regions in the GluR2 transcript in defined modes (8,
Known from the prior art is a method for directing its enzyme activity, in a highly specific and RNA-dependent manner, to new substrates (1, 2, 4, 6, 9). The dsRBD-protein domains are replaced by a so-called SNAP tag to which a specially constructed guide RNA is covalently coupled. The aforesaid SNAP tag construct is activated by this specially constructed added guide RNA.
In another known method, an in-peptide is added to the natural hADAR2 and a BoxB motif is added to the guide RNA to enable the binding (3).
One major drawback of the methods known from the prior art is that they do not use the naturally occurring ADAR2 enzyme, but the enzyme variant modified with the SNAP tag or in-peptide. Another drawback is that the guide RNA includes chemically altered nucleotides, such as, e.g., benzylguanine (BG), that are not genetically codable. In these methods, therefore, the guide RNA must first be produced in vitro and may only be transfected to the cell afterwards.
The object of the present invention is to provide a method and substances with which it is possible to add point mutations in gene products (RNA) efficiently and reversibly without altering the coding gene.
This object is attained by provided specially constructed, genetically codable guide RNAs that are capable of recruiting endogenous editing enzymes in order to introduce in a targeted manner point mutations in selected RNAs.
Specifically, the inventive guide RNA includes at least the following nucleotides that are coupled to one another, listed from the 5′ end (
Therein, individual nucleotides of the segments A and G, B and F, or C and E pair to form a double helix and the nucleotides of segment D form a hairpin structure (
Segment A has in particular the length of four nucleotides and has the GUGG nucleotide sequence.
Segment B has in particular the length of four nucleotides and has the AAUA nucleotide sequence.
Segment C has in particular the length of nine nucleotides and has the GUAUAACAA sequence.
Segment E has in particular the length of nine nucleotides and has the UUGUUAUAG nucleotide sequence.
Segment F has in particular the length of four nucleotides and has the UAUC nucleotide sequence.
Segment G has in particular the length of four nucleotides and has the CCAC nucleotide sequence.
Segments H and I are designed such that they pair with the target mRNA and place the target base to be edited in an A:C mismatch pair.
The preferred guide RNAs are shown in the SEQ ID NO 1 through SEQ ID NO 7 sequences, which are given in the sequence listing.
In one special embodiment of the invention, the guide RNA is appended on the 3′ end for stabilizing additionally a hairpin structure, e.g. a BoxB motif.
The structure of the particularly preferred embodiment of the inventive guide RNA is illustrated in
The editing enzymes involved are primarily hADAR enzymes, in particular the hADAR2 and hADAR1 enzymes. Since the two enzymes are involved with different substrates and are expressed differently in body tissues, according to the invention specific tissues or cells may be targeted using the selection of the editing enzymes.
It is possible to repair individual point mutations, such as, for instance, those that lead to premature stop signals, by means of a nucleotide exchange attained in this manner.
The nucleotide exchange may be attained at one or at a plurality of positions of the target RNA, so that even multi-genetic diseases may be treated with the inventive method.
According to the invention, therapy-relevant guide RNAs are attained either using individual administrations to the patient, e.g., are administered to the affected organs or cells, or they may be continuously expressed using installation in the cells or organs of the patient. The therapeutic guide RNA may be transferred, e.g., virally, as stabilized mRNA, or genetically coded. The desired point mutations may be switched tissue-specific, inducible, or reversible. Likewise, the degree of editing may be set according to need and may be adjusted depending on specific circumstances and therapy goals, so that editing may be attained to a degree between 0 and 100%.
Since in mammals the ADAR deaminases are strongly expressed especially in neurons, the inventive method may be employed for treating neurological diseases that are caused, for example, by individual point mutations. The intrinsically present ADARs could be recruited for corrective RNA editing using a single administration or ectopic expression of small artificial guide RNAs.
It is a major advantage of the inventive method that endogenous editing enzymes, i.e., the cell's own editing enzymes, are used to introduce targeted point mutations to the RNA. Only the short guide RNA, which is used according to the invention for recruiting endogenous editing enzymes, must be artificially produced for each special problem and expressed ectopically. Because of this, the targeted alteration of proteins on the translational level is particularly simple, so that it is possible to correct point mutations causing disease. In contrast to the prior art, with the inventive method it is not necessary to express an additional, exogenous protein, which is highly advantageous, especially for medical applications. Efficiency is also higher and there are fewer adverse secondary effects because only one construct has to be transferred to the target tissue, rather than two or more.
The method is particularly simple and advantageous due to the codability of the constructs used, because there is no synthesis of chemically stabilized guide RNAs: the guide RNA is coded on a plasmid, transfected into the cell, and formed by the cell itself.
Additional advantages, features, and potential applications of the invention shall be described in the following using the exemplary embodiments described below, and referring to the figures.
In the figures, the broken line represents the constructed inventive guide RNA, while the solid line represents the target mRNA to be edited; the asterisk marks the nucleotide to be edited in the target mRNA.
HEK 293T cells were used for transfecting the guide RNA according to the invention. For each experiment, 1.75*10≡cells were prepared in a 24-well plate format on the day prior to the transfection. Plasmids that are specific for human cell lines were used for the experiments. Lipofectamine™ 2000 (Invitrogen) was used as the transfection reagent.
W58X is a mutation in the “TGG” codon and leads to the “TAG” stop codon. The guide RNAs constructed for this exemplary embodiment are illustrated in
Both examination by microscope and RNA isolation were used to evaluate whether the editing of the W58X GFP mRNA took place.
Successful editing was evidenced by microscope using fluorescent GFP signal within the cells. The editing result is considered positive if the W58X GFP is edited and therefore corrected. Therefore fluorescent cells seen by microscope denote successful editing.
The cells transfected with the aforesaid plasmids were analyzed in the fluorescence microscope in numerous independent experiments and fluorescent cells were observed, suggesting successful editing. In addition, a positive control, in which the plasmid for the correct wild type GFP was transfected instead of the plasmid for W58X GFP, was analyzed. As expected, fluorescent cells were observed by microscope for the positive control.
The same experiments were conducted as a negative control, wherein either the plasmid that codes for the guide RNA or the plasmid that codes for the ADAR2 enzyme was omitted. There was no GFP in the fluorescence microscope, i.e., no positive editing was detectable. Nor was any editing detected in the sequencing of these RNA isolation specimens, which suggests the specificity of this method.
In the analysis of the isolated RNA, first there was reverse transcription to cDNA, which was multiplied then by PCR (polymerase chain reaction) so that sequencing could then be performed. The ratio of adenine to guanine in the sequencing traces at this target position provided information about how strong the editing was. In the experiment, compared to negative controls, the ratio of adenine to guanine in the cells transfected with the aforesaid plasmids was considerably higher, which suggests successful editing. When using the plasmid that codes for the guide RNA with the SEQ ID no. 1, conduct of part a) of the experiment demonstrated an editing yield of 58%, and with the guide RNA with the SEQ ID no. 3 demonstrated an editing yield of 38%. In the conduct of part b) of the experiment, the guide RNA with SEQ ID no. 1 demonstrated an editing yield of 42% and the guide RNA with SEQ ID no. 3 demonstrated an editing yield of 58%.
The PINK1 gene is linked to Parkinson's disease. In this exemplary embodiment, the so-called R407Q mutation was edited in the “CAG” codon.
The cells were cotransfected with the following plasmids:
The editing was analyzed by means of RNA isolation. Editing in the cells transfected with all of the aforesaid plasmids reached 35-40% at the target position. In the other exemplary embodiment, the W437X mutation was edited in the “TAG” codon. In this way a disease-relevant phenotype (loss of mitophagy) could be repaired.
The cells were cotransfected with the following plasmids:
The editing was analyzed by means of RNA isolation. Editing in the cells transfected with all of the aforesaid plasmids reached 30% at the target position. In addition, a PINK1 functionality assay was performed in HeLa cells and the loss-of-function phenotype could only be restored (microscopic analysis) if hADAR2 and the guide RNA were transfected. Restoration of mitophagy in HeLa cells could be demonstrated using the microscope.
The so-called W417X mutation was edited in the “TAG” codon in this exemplary embodiment.
The cells were transfected with the following plasmids:
The editing of the W417X luciferase mRNA was analyzed by means of RNA isolation. Editing in the cells transfected with all of the aforesaid plasmids reached 48% at the target position. In the negative control, the plasmid having the specific guide RNA was omitted during the transfection. There was no editing in the negative control, which suggests the exclusivity of the guide RNA in the editing.
This gene is linked to ALS (amyotrophic lateral sclerosis), a fatal neuro-degenerative disorder. The mutation of this gene is called R521H and includes a “CAC” codon, while the functional FUS has a “CGC” codon.
This gene was edited in the PCR reaction vessel. To this end, 350 nM purified ADAR2 protein, 125 nM specific 16 nt long guide RNA, and 25 nM of the mutated R521H FUS mRNA was used. The sequencer result demonstrated that 51% of the adenosines were successfully edited to inosine.
Six different genes (β-actin, GAPDH, GPI, GUSB, VCP, RAB7A) that are expressed endogenously at different strengths were edited. These were not disease-relevant mutations that have been addressed, but instead depict the attainability of naturally expressed mRNAs. The following cells were used for transfection:
a) standard HEK293T cells (as above) and
b) HEK cells having inducible ADAR2 protein expression (genomically integrated ADAR2). This integrated cell line, in which ADAR2 is induced, has approx. 20-times lower expression of the protein than the cells in the foregoing examples that express ADAR2 after transfection at 300 ng plasmid each. In this example, therefore, the intracellular concentrations of the ADAR2 proteins thus correspond more to those found in a natural cell.
The guide RNA structures of the flexible part H+I for the specific target genes are provided in Table 2.
a) The cells were cotransfected with the following plasmids:
The editing was analyzed by means of RNA isolation. The ratio of adenine to guanine in the cells transfected with these plasmids was considerably higher than in the negative controls, suggesting successful editing.
b) The cells were cotransfected with the following plasmid and hADAR2 expression was induced with doxycycline:
The editing was analyzed by means of RNA isolation. The ratio of adenine to guanine in the cells transfected with these plasmids was considerably higher than in the negative controls, suggesting successful editing.
| Number | Date | Country | Kind |
|---|---|---|---|
| 102015012522.2 | Sep 2015 | DE | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/DE2016/000309 | 8/9/2016 | WO | 00 |
