Patent Application
20240352460
The instant application contains a Sequence Listing as an XML file entitled “P244115951US_CASEQ.xml” created on Jul. 3, 2024 and having a size of 64,445 bytes.
The present invention relates to the technical field of gene engineering, and more particularly, to snRNA targeting USH2A pre-mRNA and application thereof.
Usher syndromes are a class of genetic diseases, also known as deafness-retinitis pigmentosa syndromes, which are characterized by varying degrees of congenital sensorineural hearing loss and retinitis pigmentosa (RP)-induced progressive vision loss. Clinically, the Usher syndromes can be divided into three types: 1. Type I Usher syndrome, in which a patient suffers congenital heavily-severe sensorineural hearing loss in terms of hearing, vestibular response appearance in terms of vestibular response, and retinitis pigmentosa before puberty in terms of vision, and is then gradually blind, and genes associated with this type include MYO7A, CDH23, USH1C, PCHD15, etc.; 2. Type II Usher syndrome, in which a patient suffers congenital moderately severe sensorineural hearing loss in terms of hearing, normal vestibular response, and retinitis pigmentosa during puberty in terms of vision, and is then gradually blind, and genes associated with this type include USH2A, GPR98, WHRN, etc.; and 3. Type III Usher syndrome, in which a patient suffers progressive sensorineural hearing loss in terms of hearing, normal vestibular response, and retinitis pigmentosa at the end of puberty in terms of vision, and is then gradually blind, and genes associated with this type include CLRN1, etc. Type II Usher syndrome accounts for more than 50% of Usher syndromes, while USH2A gene mutation is the most common cause of Type II Usher syndrome, covering more than 50% of patients with Usher syndromes. At the same time, mutations in a USH2A gene are also one of the important causes of nonsyndromic retinitis pigmentosa (NSRP).
USH2A, which is localized at 1q41 and has a span of more than 800 kb in a genome, encodes a large transmembrane protein Usherin, is anchored to plasma membranes of retinal photoreceptors cells and inner ear hair cells, and thus is an essential component for cilia development and maintenance. In the retina, Usherin is an important part of a USH2 complex and is regarded to play a role in stabilizing the outer segments of photoreceptors. USH2A has two subtypes, and the main subtypes in retinal cells contain seventy-two Exons each having a coding region length of about 15.6 kb. An extracellular portion of a Usherin protein contains several repeating domains, including ten Laminin EGF-like (LE) domains and thirty-five Fibronectin type 3 (FN3) domains. A human USH2A Exon 13 has a length of 642 bp and encodes amino acids 723-936, which are four of ten LE domains in the Usherin protein.
Mutations in Exon 13, Exon 50, and Intron 40 of a USH2A gene cause Usher syndromes. To date, more than 1,000 pathogenic mutations have been identified throughout the USH2A gene, and Exon 13 is the most frequently mutated one in the USH2A gene, accounting for about 35%. Mutations in Exon 13 of the USH2A gene comprise c.2802T>G (p.Cys934Trp, the most frequent mutation in Chinese patients), c.2299delG (p.Glu767Serfs*21, the most frequent mutation in European and American patients), c.2276G>T (p.cys759phe, the most common mutation site in nonsyndromic RP), c.2522C>A (p.S841Y), c.2242C>T (p.Gln748X), c.2541C>A (C847X), c.2761delC (Leu921fs), as well as c.2776C>T (p.R926C), c.2209C>T, c.2310delA, c.2391_2392deITG, c.2431A>T, c.2431_2432delAA, c.2440C>T, c.2525dup, c.2610C>A, c.2755C>T, c.2176T>C, c.2236C>G, c.2296T>C, c.2332G>T, and c.2339 G>T (PMID: 31904091).
For Exon 13 of the USH2A gene, there are generally three common methods in the prior art. In the first method, Exon 13 is deleted directly by editing genomic DNA by a CRISPR/Cas system, or a site related to RNA splicing is destroyed. In the second method, key bases of the above splicing-related site are modified by using a single-base editor, which can also promote Exon skipping. In the third method, antisense oligonucleotides (AONs) are used to perform target interference on pre-mRNA splicing, which promotes the Exon skipping efficiency.
The present invention provides snRNA which targets USH2A pre-mRNA.
The present invention provides snRNA that targets the USH2A pre-mRNA. The snRNA comprises a recognition domain that is reversely complementary to the USH2A pre-mRNA sequence. The snRNA binds to the USH2A pre-mRNA to induce splicing skipping of Exon 13.
After investigating and researching USH2A, the inventors have found that, since a coding region of USH2A has a length of about 15.6 kb, such a large coding sequence is hardly packaged by conventional gene therapy delivery methods (e.g., recombinant lentivirus and recombinant adeno-associated virus), so it is difficult to directly deliver USH2A for treatment. However, Exon 12 of mouse USH2A is homologous to Exon 13 of human USH2A, both of which have a length of 642 bp, and the deletion of this Exon may not cause subsequent frameshift mutations. At the same time, the inventors have found that after knocking out Exon 12 of mouse USH2A, Usherin is still able to correctly locate and perform normal functions. Therefore, Exon 13 of human USH2A containing pathogenic mutations can be treated with a series of means to cause skipping.
At the same time, there is a small nuclearRNA (snRNA) in a cell, which is a main component of an RNA spliceosome in the post-transcriptional processing of eukaryotes and participates in the processing of mRNA precursors by binding to an snRNP protein. snRNA has a length of about 100-215 nucleotides in mammals, which are divided into seven categories, numbered U1-U7 because of its abundance of U. However, U7-snRNP does not participate in splicing but is a key factor in the unique 3′ end processing of a replication-dependent histone (RDH) pre-mRNA.
Therefore, the inventors replace a non-canonical Sm-binding site of U7-snRNA with a consensus sequence derived from major spliceosome U-snRNPs and change a histone-binding sequence of a 5′ region of U7-snRNA into a complementary sequence of a gene to be modified, which can induce splicing skipping of Exons by targeting the exons.
The inventors have found seven target regions and twenty-one target sites of U7-snRNP-induced splicing skipping through target screening to induce a splicing skipping effect of Exon 13 and also designed a recognition domain of U7-smOPT-snRNA to be reversely complementary to a splicing-skipping-related site of Exon 13 of USH2A pre-mRNA, thereby inducing the binding of U7-smOPT-snRNA to the splicing-skipping-related site of Exon 13 of USH2A pre-mRNA, and further inducing splicing skipping of Exon 13 of USH2A pre-mRNA. In some examples, Exon 12 is retained, such that the probabilities of double skipping (e.g., unexpected splicing skipping) of Exon 12 and Exon 13 are significantly reduced, which ensures safety while improving efficiency significantly.
In one example, the USH2A pre-mRNA sequence is selected from the following regions: Exon 13, Intron 12, or Intron 13 of USH2A.
In one example, the USH2A pre-mRNA sequence is selected from Exon 13 of USH2A and a region extending 50 bp to both sides.
In one example, the USH2A pre-mRNA sequence is selected from Exon 13 of USH2A and a region extending 20 bp to both sides.
In one example, the Exon 13 includes wild-type Exon 13 or Exon 13 containing mutations.
In one example, the mutations comprise at least one of the following mutation sites: c.2242C>T, c.2276G>T, c.2299delG, c.2522C>A, c.2541C>A, c.2761delC, c.2776C>T, c.2802T>G, c.2209C>T, c.2310delA, c.2391_2392deITG, c.2431A>T, c.2431_ 2432delAA, c.2440C>T, c.2525dup, c.2610C>A, c.2755C>T, c.2176T>C, c.2236C>G, c.2296T>C, and c.2332G>T.
In one example, the genomic location (corresponding to a GRch38 version of an NCBI database) region corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247142-216247185, Chr1: 216247130-216247161, Chr1: 216246616-216246649, Chr1: 216247213-216247246, Chr1: 216247204-216247232, Chr1: 216247187-216247220, and/or Chr1: 216247169-216247202.
In one example, the USH2A pre-mRNA sequence is selected from the following sequences: SEQ ID NOs: 1-7.
In one example, the genomic location region corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247223-216247246, Chr1: 216247218-216247241, Chr1: 216247213-216247236, Chr1: 216247209-216247232, Chr1: 216247204-216247227, Chr1: 216247197-216247220, Chr1: 216247191-216247214, Chr1: 216247187-216247210, Chr1: 216247179-216247202, Chr1: 216247174-216247197, Chr1: 216247169-216247192, Chr1: 216247162-216247185, Chr1: 216247155-216247178, Chr1: 216247147-216247168, Chr1: 216247147-216247173, Chr1: 216247142-216247165, Chr1: 216247138-216247161, Chr1: 216247130-216247153, Chr1: 216246626-216246649, Chr1: 216246622-216246645, and/or Chr1: 216246616-216246639.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 16 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 17 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 18 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 19 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 20 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 21 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 22 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 23 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 24 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 18-40 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is reversely complementary to a continuous sequence of at least 20-27 bp in the USH2A pre-mRNA sequence.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID NOs: 8-28.
In one example, the genomic location corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247213-216247236, Chr1: 216247209-216247232, Chr1: 216247204-216247227, Chr1: 216247197-216247220, Chr1: 216247191-216247214, Chr1: 216247187-216247210, Chr1: 216247179-216247202, Chr1: 216247174-216247197, and/or Chr1: 216247169-216247192.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID NOs: 10-18.
In one example, the genomic location corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247162-216247185, Chr1: 216247155-216247178, Chr1: 216247147-216247168, Chr1: 216247147-216247173, Chr1: 216247142-216247165, Chr1: 216247138-216247161, Chr1: 216247130-216247153, Chr1: 216246626-216246649, Chr1: 216246622-216246645, and/or Chr1: 216246616-216246639.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID NOs: 19-28.
In one example, the genomic location corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247213-216247236, Chr1: 216247209-216247232, Chr1: 216247204-216247227, Chr1: 216247197-216247220, Chr1: 216247191-216247214, Chr1: 216247187-216247210, Chr1: 216247179-216247202, Chr1: 216247174-216247197, Chr1: 216247169-216247192, Chr1: 216247162-216247185, Chr1: 216247155-216247178, Chr1: 216247147-216247168, Chr1: 216247147-216247173, Chr1: 216247142-216247165, and/or Chr1: 216247130-216247153.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID NOs: 10-23, or SEQ ID NO: 25.
In one example, the genomic location corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247213-216247236, Chr1: 216247209-216247232, Chr1: 216247204-216247227, Chr1: 216247197-216247220, Chr1: 216247191-216247214, Chr1: 216247187-216247210, Chr1: 216247179-216247202, Chr1: 216247174-216247197, Chr1: 216247169-216247192, Chr1: 216247162-216247185, Chr1: 216247147-216247168, Chr1: 216247147-216247173, Chr1: 216247142-216247165, and/or Chr1: 216247130-216247153.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID Nos: 10-19, SEQ ID NOs: 21-23, or SEQ ID NO: 25.
In one example, the genomic location corresponding to the USH2A pre-mRNA sequence is selected from Chr1: 216247218-216247241, Chr1: 216247187-216247210, Chr1: 216247147-216247168, Chr1: 216247147-216247173, Chr1: 216247142-216247165, and/or Chr1: 216247130-216247153.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID NO: 9, SEQ ID NO: 15, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, or SEQ ID NO: 25.
In one example, the recognition domain of the snRNA is selected from the following sequences: SEQ ID NO: 15, SEQ ID NO: 21, SEQ ID NO: 22, or SEQ ID NO: 23.
In one example, the snRNA is either U1-snRNA or U7-snRNA.
In one example, the U7-snRNA is chemically synthesized.
In one example, at least one nucleotide in the chemically synthesized U7-snRNA is chemically modified.
In one example, the chemical modification comprises at least one of 2′-O alkyl modification, 2′-O-methoxyl modification, or 2′-O-methoxyethyl modification.
In one example, the 2′-O alkyl modification is a 2′-O-methyl modification.
In one example, at least one nucleotide in the chemically synthesized U7-snRNA is linked by a phosphate bond, the phosphate bond comprises at least one of a phosphorothioate bond, a dithiophosphate bond, an alkyl phosphonate bond, an amide phosphate bond, a borane phosphate bond, or chirally linked phosphorus.
In one example, 6-80 nucleotides on both sides of the chemically synthesized U7-snRNA are chemically modified and linked by the phosphate bond.
In one example, 1-10 nucleotides on both sides of the chemically synthesized U7-snRNA are chemically modified and linked by the phosphate bond.
In one example, 3-40 bases on both sides of the chemically synthesized U7-snRNA are chemically modified and linked by the phosphate bond.
In one example, all nucleotides of the chemically synthesized U7-snRNA are linked by phosphorothioate bonds, and all are subjected to 2′-O-methoxyl modification.
In one example, three nucleotides on both sides of the chemically synthesized U7-snRNA are linked by phosphorothioate bonds, and subjected to 2′-O-methoxyl modification.
In one example, the first nucleotide at a 5′ end of the chemically synthesized U7-snRNA is adenylic acid.
In one example, the first nucleotide at a 5′ end of a recognition domain of the chemically synthesized U7-snRNA is adenylic acid.
In one example, there are 0-5 mismatched nucleotides in the reversely complementary pairing of the recognition domain of the chemically synthesized U7-snRNA and a target site.
In one example, there is 0-1 mismatched nucleotide in the reversely complementary pairing of the recognition domain of the chemically synthesized U7-snRNA and the target site.
In one example, the recognition domain of the chemically synthesized U7-snRNA has a sequence length greater than or equal to 16 bp.
In one example, the recognition domain of the chemically synthesized U7-snRNA has a sequence length of 18 bp-40 bp.
In one example, the recognition domain of the chemically synthesized U7-snRNA has a sequence length of 20 bp-27 bp.
In one example, the chemically synthesized U7-snRNA continues to extend by the sequence length of the recognition domain along a 5′ end or/and a 3′ end of a target sequence by reversely complementary pairing.
In one example, the extended sequence length of the recognition domain is less than or equal to 40 bp.
In one example, the snRNA comprises a sm sequence.
In one example, the sm sequence is a smOPT sequence, the smOPT sequence is shown in SEQ ID NO: 31.
In one example, the snRNA comprises a recognition domain, a smOPT sequence, and a U1-snRNA scaffold or U7-snRNA scaffold sequence; preferably, the U7-snRNA scaffold sequence is shown in SEQ ID NO: 49.
In one example, the snRNA further comprises a motif that recruits a splicing regulatory protein.
In one example, a free tail is introduced at the 5′ end of the U7-snRNA, the free tail sequence comprises the motif that recruits the splicing regulatory protein.
In one example, the splicing regulatory protein comprises at least one of hnRNPA1, SRSF1, RBM4, DAZAP1, or SR.
In one example, the free tail sequence comprises at least one hnRNPA1-binding motif.
In one example, the free tail sequence comprises two hnRNPA1-binding motifs.
The present invention further provides a nucleic acid comprising a nucleotide sequence coding the snRNA.
The present invention further provides a gene expression cassette. The gene expression cassette comprises the snRNA, and/or the nucleic acid.
The present invention further provides a vector. The vector comprises the snRNA, the nucleic acid, and/or the gene expression cassette.
In one example, the vector comprises a vector backbone and the snRNA, wherein the vector backbone comprises a promoter, a smOPT sequence, and an snRNA gene-specific 3′ box, the promoter is linked to the smOPT sequence through a Type IIs type restriction enzyme recognition site.
In one example, the vector is selected from pUC57, pAAV-CMV, lentivirus, or transposon.
In one example, the snRNA gene-specific 3′ box is a gene fragment with 28-131 bp epitaxial at a 3′ end of an snRNA gene.
In one example, the snRNA gene-specific 3′ box is a gene fragment with a length of 106 bp at the 3′ end of the snRNA gene.
The present invention further provides a virus particle. The virus particle comprises the snRNA, the nucleic acid, and/or the vector.
In one example, the virus particle is an AAV virus.
In one example, a capsid protein of the AAV virus is a naturally derived variant based on naturally derived capsid protein.
In one example, the capsid protein of the AAV virus is derived from animals or plants.
In one example, the capsid protein of the AAV virus is selected from AAV1, AAV2, AAV3, AAV5, AAV6, AAV7, AAV8, AAV9, AAVrh8, AAVrh10, or AAVrh43.
In one example, the variant AAV virus based on the naturally derived capsid protein is an AAV virus obtained after directed evolution based on the naturally derived capsid protein or reasonable modification of amino acids/peptide fragments.
In one example, the variant AAV virus is selected from AAV2.5, AAV2i8, AAV-TT, AAV9.HR or CAM130.
In one example, when the AAV virus is AAV ITR, a serotype is consistent with a serotype of a Rep gene.
The present invention further provides a cell. The cell comprises the snRNA, the nucleic acid, the vector, and/or the virus particle.
The present invention further provides a pharmaceutical composition. The pharmaceutical composition comprises the snRNA, the nucleic acid, the vector, and/or the virus particle.
The present invention further provides a method for obtaining a Usherin protein with the deletion of an Exon 13 expression product, the method comprises contacting the USH2A pre-mRNA with the snRNA, the nucleic acid, the vector, the gene expression cassette, the viral particle, the cell, and/or the pharmaceutical composition.
In one example, the method is used in scientific research.
The present invention further provides an application of the method in the process of performing splicing skipping of Exon 13 in USH2A pre-mRNA, preparing mature USH2A mRNA with the deletion of Exon 13, obtaining a Usherin protein with the deletion of Exon 13, and/or inhibiting the expression and function of Exon 13 in USH2A pre-mRNA.
The present invention further provides an application of the snRNA, the nucleic acid, the vector, the gene expression cassette, the virus particle, or the cell in the preparation of a drug for the prevention and/or treatment of eye diseases and/or ear diseases.
In one example, the eye diseases are deafness-retinitis pigmentosa syndromes or non-syndromic retinitis pigmentosa diseases.
Compared with the prior art, the present invention has the following technical effects:
According to the snRNA of the present invention that targets the USH2A pre-mRNA, Exon 13 in the USH2A is selected as a target region to induce splicing skipping of Exon 13, so as to treat eye diseases and ear diseases with USH2A protein dysfunctions caused by the missense, frameshift, codon termination, nonsense mutation, synonymous mutation of Exon 13 in USH2A. Meanwhile, according to the U7-snRNA that targets USH2A, U7-snRNP which does not participate in splicing, but is a key factor for processing at a unique 3′ end of replication-dependent histone (RDH) pre-mRNA. In addition, the modified U7-snRNA is a unique working mechanism in which a non-canonical Sm-binding site of the U7-snRNA is replaced with a consensus sequence derived from major spliceosome U-snRNPs and a histone-binding sequence in a 5′ region of the U7-snRNA is changed to a complementary sequence of a gene to be modified. The splicing skipping of Exon 13 in the USH2A pre-mRNA is induced by binding snRNA that targets USH2A pre-mRNA.
To facilitate the understanding of the present invention, the present invention will be described more comprehensively with reference to the relevant drawings below. Preferred examples of the present invention are given in the drawings. However, the present invention may be implemented in many different forms and is not limited to the examples described herein. On the contrary, the purpose of providing these examples is to make the disclosure of the present invention more thorough and comprehensive.
Unless otherwise defined, all technical and scientific terms used in the present invention have the same meaning as commonly understood by a person of ordinary skill in the art. The terms used in the description of the present invention herein are only for the purpose of describing specific examples and are not intended to limit the present invention. The term “and/or” as used herein comprises any combinations of one or more related listed items. It should be noted that when a sequence is referred to as being “selected from” another sequence, it may be either another sequence or a sequence fragment within another sequence; when a genomic location region is “selected from” another genomic location region, its corresponding sequence may be directly a sequence corresponding to another gene location region or a sequence fragment corresponding to another gene location region; and the sequence comprises DNA or RNA.
the snRNA of the present invention is a main component of an RNA spliceosome in the post-transcriptional processing of eukaryotes and participates in the processing of mRNA precursors by binding to an snRNP protein.
The reagents, materials, and equipment used in this embodiment, unless otherwise specified, are commercially available sources; and unless otherwise specified, the experimental methods are all conventional experimental methods in the field.
Wild-type U7-snRNA comprises a stem-loop structure (scaffold), a U7-specific Sm sequence (AAUUUGUCUAG, SEQ ID NO: 61), and a recognition domain (complementary to histone pre-mRNA).
According to U7-snRNA in this example, based on a gene sequence (NCBI Reference Sequence: NR_024201.3) of mouse wild-type U7-snRNA on NCBI, a U7-specific sm sequence AATTTGTCTAG (SEQ ID NO: 30) was replaced with an optimized consensus sm sequence, i.e., smOPT: AATTTTTGGAG (SEQ ID NO: 31), an original recognition domain at a 5′ end of a smOPT sequence was replaced with a recognition domain that was reversely complementary to a specific target site of the USH2A pre-mRNA, and a U7 original stem-loop structure sequence is retained at a 3′ end of the smOPT sequence, as shown in
The specific operation process was as follows: firstly, a pUC57 vector (as shown in
2. Construction of U7-snRNA Vector that Targets Exon 13 in USH2A and Different Sites Near Exon 13
In this example, a total of twenty-one target sites were set for seven target regions of USH2A pre-mRNA, and the seven target regions of USH2A pre-mRNA were shown below.
The twenty-one target sites were shown in the table below.
Similar to oligonucleotides, U7-snRNAs could also be chemically synthesized directly to produce RNA containing a recognition domain, smOPT, and a U7-snRNA scaffold. U7-snRNAs synthesized in vitro could be specifically modified to be tolerant to nuclease degradation or to increase the affinity for a target sequence.
In this example, U7-snRNA was chemically synthesized with 2′methoxy(2′-OME) modification and phosphorothioated modification at three bases at 5′ and 3′ ends, thereby increasing the nuclease resistance. Taking snRNA #16 and snRNA #15 as examples, the chemically synthesized snRNA sequences and modifications were as follows (* represented a phosphorothioated backbone, m represented 2′-methoxyl modification, an underline represented a recognition domain in reversely complementary pairing with the target sequence, and an italic represented a smOPT sequence):
Based on the sequence shown in SEQ ID NO: 33, thiophosphorylated backbone modification and methoxyl modification were added to the first three bases at the 5′ and 3′ ends in the modified sequence;
Based on the sequence shown in SEQ ID NO: 34, thiophosphorylated backbone modification and methoxyl modification were added to the first three bases at the 5′ and 3′ ends in the modified sequence.
A reporter vector was constructed to quantitatively evaluate the splicing skipping efficiency of Exon 13 in USH2A.
An RGleft-USH2A EXON13mut-RGright sequence (a 5′ end and a 3′ end were added to AgeI and EcoRI digestion sites, respectively) was acquired by whole gene synthesis; and a synthesized sequence was inserted between AgeI and EcoRI digestion sites of a pX601 vector by performing restriction enzyme AgeI and EcoRI digestion, electrophoresis, gel cutting and recovery, and binding on the synthesized sequence and a pX601 plasmid (Addgene, 61591), in order to replace a SaCas9 gene sequence of an original vector, thereby obtaining a reporter vector. Further, a purified reporter vector plasmid was obtained by transformation of E. coli competent cells, monoclonal screening, PCR and sequencing verification, and was stored at −20° C. for later use.
The reporter vector had a structure as follows: pCMV-RGleft-USH2A EXON13mut-RGright; RG represented a reporter gene; RGleft represented the first half of a 5′ end of the reporter gene without a reporting function; RGright represented the second half of a 3′ end of the reporter gene without a reporting function; and the tandem expression of RGleft and RGright could normally perform a complete reporter gene function. In this example, the reporter gene was a green fluorescent gene EGFP, and the vector had a structure of pCMV-EGFPleft-Exon13mut-EGFPright. EXON13mut represented USH2A Exon 13 containing a pathogenic mutation, as well as upstream and downstream intron sequences (the upstream intron sequence was a tandem gene sequence of 204 bp at a 5′ end and 490 bp at a 3′ end of Intron 12 in a human USH2A gene; and the downstream intron sequence was a tandem gene sequence of 703 bp at a 5′ end and 216 bp at a 3′ end of Intron 13 in human USH2A). The pathogenic mutations in the USH2A Exon 13 may comprise c.2802T>G, c.2299delG, c.2276G>T, c.2522C>A, c.2242C>T, c.2541C>A, c.2761delC or c.2776C>T, etc. In this example of the present invention, the pathogenic mutations of the USH2A Exon 13 in this example of the present invention were c.2802T>G, and c.2299delG. That is, the vector structures obtained were pCMV-EGFPleft-Exon13c.2802T-G-EGFPright (a map of the reporter vector was shown in
Detection method: 293T cells were inoculated into a 24-well plate in a certain amount so that the cell confluence reached about 80% after 24 h. Lipofectamine 2000 was selected to co-transfect 293 T cells (a vector mass ratio of 100 ng: 400 ng) with pCMV-EGFPleft-Exon13c.2802T>G-EGFPright and pUC57-U7-snRNA plasmid targeting USH2A pre-mRNA. 293T cells transfected with reporter plasmids alone and 293T cells co-transfected with reporter plasmids and pUC57-U7-con were respectively used as two negative controls, and 293T cells without any plasmid transfection were used as a blank control. The transfected cells continued to be cultured for 48-72 h, and trypsinized into single cells. A flow cytometer was then used to detect GFP-positive rates (i.e., proportions of cells in which Exon 13 in USH2A pre-mRNA was induced to splicing skipping) of different U7-snRNA groups and mean FITC intensity of GFP-positive cells (i.e., a mean level of splicing skipping of Exon 13 in USH2A pre-mRNA in GFP cells). A location of the U7-snRNA that targeted the target region 1 on the genome (a picture from left to right corresponded to a 5′ end to a 3′ end in the genome) was shown in
Experimental results: as shown in
Detection method: the same as in Example 4, a location of the U7-snRNA that targeted the target region 2 on a genome (a picture from left to right corresponded to a 5′ end to a 3′ end of the genome) was shown in
Experimental results: as shown in
Detection method: the same as in Example 4, a location of the U7-snRNA that targeted the target region 3 on a genome (a picture from left to right corresponded to a 5′ end to a 3′ end of the genome) was shown in
Experimental results: as shown in
In combination with the analysis of Examples 4, 5 and 6, it was found that although the prior art showed that the target regions 1, 2 and 3 were non-sensitive regions targeted by AON, that is, targeting this region could not induce/inefficiently induce splicing skipping of Exon 13, the snRNA targeting this region could significantly induce the skipping splicing of Exon 13. Thus, although both snRNA and AON could induce splicing skipping, they had different action mechanisms and different target site sensitivity (target sites in the target region to which they apply).
Meanwhile, as shown in
Detection method: the same as in Example 4, a location of the U7-snRNA that targeted the target region 4 on a genome (a picture from left to right corresponded to a 5′ end to a 3′ end of the genome) was shown in
Experimental results: as shown in
Detection method: the same as in Example 4, a location of the U7-snRNA that targeted the target region 5 on a genome (a picture from left to right corresponded to a 5′ end to a 3′ end of the genome) was shown in
Experimental results: as shown in
Detection method: the same as in Example 4, a location of the U7-snRNA that targeted the target region 6 on a genome (a picture from left to right corresponds to a 5′ end to a 3′ end of the genome) was shown in
Experimental results: as shown in
Detection method: the same as in Example 4, a location of the U7-snRNA that targeted the target region 5 on a genome (a picture from left to right corresponded to a 5′ end to a 3′ end of the genome) was shown in
Experimental results: as shown in
Verification method: the same as in Example 4.
Experimental results: the mean FITC intensities of GFP-positive cells induced by U7-snRNA in different regions were shown in
Although proportions of cells (GFP %) that target the same region (the proportion of cells with induced splicing skipping) were similar, levels of mRNAs and their proteins (mean FITC intensity) for splicing skipping were obtained by induction of snRNA that targeted different targets in the same region in the same cell were different.
The target region 2 not only obtained a higher proportion of cells that induced splicing skipping (GFP %), but levels of mRNAs and their proteins (mean FITC intensity) for splicing skipping were obtained by induction in the same cell were higher.
However, target site #2 and its adjacent sites #1 and #3 with high efficiency of AON-induced splicing skipping in the prior art had lower levels of mRNAs and their proteins for splicing skipping by induction in the same cell in the snRNA system. In the prior art, the AON efficiency of the target region 3 was higher than that of the region 2, but in the snRNA system, the efficiency of the target region 2 was higher than that of the region 3. Thus, although both snRNA and AON could induce splicing skipping, they had different action mechanisms and different target site sensitivities. In combination with the analysis of the results of Example 12, since the efficiency of snRNA #24 was similar to that of snRNA #2 and AON1, it could be inferred that snRNA #3-#11 had better good effects than snRNA #2, snRNA #24 and AON1.
Detection method: 293 T cells were inoculated into a 24-well plate in a certain amount so that the cell confluence reached about 80% after 24 h. Lipofectamine 2000 was used to co-transfect 293 T cells (a vector mass ratio of 100 ng: 400 ng) with pCMV-EGFPleft-Exon13c.2802T>G-EGFPright and U7-snRNA plasmids of different targets respectively. 293 T cells transfected with reporter plasmids alone and 293 T cells co-transfected with reporter plasmids and pUC57-U7 Scramble were used as two negative controls. 293 T cells co- transfected with reporter plasmids and 10 pmol antisense oligonucleotide AON1 (5′-MA*MG*MC*MU*MG*MG*MA*MA*MU*MU*MA*MU*3′, “M” for 2′-O-methoxyl modification, and “*” for thiophosphorylation, SEQ ID NO: 62) were used a positive control. 293 T cells without any plasmid transfection were used as a blank control. The transfected cells were cultured for 48-72 h, and trypsinized into single cells, and a flow cytometer was then used to detect GFP-positive rates and mean FITC intensity of different snRNAs.
Experimental results: as shown in
Human host cells were inoculated into a 24-well plate at 6×105 cells/well. In this example, the human retinal nerve cells selected in this example were WERI-Rb-1 cells (a retinal nerve cell line). WERI cells which were transfected with 100 pmol U7-snRNA #1, snRNA #4, snRNA #8, snRNA #10 and snRNA #14 synthesized in vitro by using Lipofectamine 2000 were transfected with antisense oligonucleotide AON1 (5′-MA*MG*MC*MU*MU*MC*MG*MG*MA*MG*MA*MU*MU*MA*MU*MA*MU*MC*-3′, “M” for 2′-O-methoxy modification, and “*” for thiophosphorylation, SEQ ID NO: 62) and AON2 (5′-MU*MG*MA*MU*MC*MA*MC*MU*MA*MA*MG*MC*MC*MU*MA*MA*MA*MA*-3′, “M” for 2′-O-methoxyl modification, and “*” for thiophosphorylation, SEQ ID NO: 63) in the same dose (100 pmol), were used as blank controls. 1 μg of transfected EGFP plasmids were used as a negative control, and WERI cells without any plasmid transfection were used as a blank control. The transfected cells were cultured for 72 h, and RNA was then extracted from cells in each experimental group, and reversely transcribed to obtain cDNA. An RT-PCR experiment was performed by primers AGCCTTTCCGCCAAGGTGATC (SEQ ID NO: 37) and CACAACGTTGCCCAGCAATGG (SEQ ID NO: 38). Whether mature USH2A mRNA had Exon 13 was detected. Electrophoresis results were shown in
Experimental results: in WERI cells that endogenously expressed a Usherin protein, the effect of chemically synthesized U7-snRNA to induce splicing skipping of Exon 13 in USH2A pre-mRNA was compared with an AON technical solution. The RT-PCR test data and analysis results showed that an AON single-skipping band was weaker than the snRNA, and there were more obvious double-skipping bands under the AON single-skipping band. It could thus be seen that the effects of a chemically synthesized U7-snRNA experimental group 1 and a U7-snRNA experimental group 2 to induce single splicing skipping of Exon 13 were significantly better than those of the technical solutions of AON1 and AON2. In addition, rt-PCR electrophoresis bands were further quantitatively analyzed by ImageJ software. The proportions of USH2A mRNA in double skipping of Exon 12 and Exon 13 to USH2A mRNA in total skipping (a sum of USH2A mRNAs of Exon 13, Exon 12, and Exon 13 in single skipping) were analyzed. The results showed that the proportions of U7-snRNA that induced double splicing skipping of Exon 12 and Exon 13 were very low and lower than those of AON1 and AON2. Therefore, it was determined that U7-snRNA significantly improved the efficiency of single splicing skipping of Exon 13 while ensuring a USH2A mRNA by-product with low double-skipping.
In addition, U7-snRNA #14 had a target site close to an AON site with a very high probability of double splicing skipping of Exon 12 and Exon 13 in the prior art, however, the probability of double splicing skipping of exons after U7-snRNA #14 treatment was very low. It was further proved that U7-snRNA could significantly reduce the double-skipping probability of Exon 12 and Exon 13 while inducing splicing skipping of Exon 13.
1. Construction of U7-snRNA Linked with the hnRNP A1-binding Motif
According to a pre-transcriptional DNA sequence corresponding to a gRNA sequence in the table, the corresponding Oligo DNAs were synthesized respectively. An Oligo DNA sense strand was a reverse complementary sequence (a DNA sequence corresponding to a recognition domain of a sequence) target sequence, and 5′ plus CCGCAATATGATAGGGACTTAGGGTG (SEQ ID NO: 39); and an antisense strand was a target sequence 5′ plus AATT and 3′ plus CACCCTAAGTCCCTATCATATT (SEQ ID NO: 40). For example, a recognition domain sequence of snRNA #14 was ACACUGGCAGGGCUCAUCCA (SEQ ID NO: 41); the synthesized Oligo DNA sense strand was
CCGCAATATGATAGGGACTTAGGGTG
ACACUGGCAGGGCUCACAUCCA,
and an antisense strand was
an underline indicated a DNA double-stranded sequence corresponding to the recognition domain sequence; and a bold italic indicated a DNA double-stranded sequence corresponding to a binding motif “UAGGGU” of a hnRNP A1 protein.
A sense strand and an antisense strand of the synthesized Oligo DNA were mixed according to an annealing reaction system (a total reaction volume 20 μl: Oligo-F (100 μM) 2 μl+Oligo-R (100 μM) 2 μl+10×NEB Cutter smart buffer 2 μl+deionized water 16 μl), incubated at 95° C. for 5 min, then placed on ice, and cooled and annealed to form a double-stranded DNA with sticky ends. The double-stranded DNA was diluted in 100 folds, then 1 μl of the double-stranded DNA was taken, digested with 10 ng of BsaI, and linked with a recovered linearized pUC57-U7-snRNA backbone plasmid. Further, a U7-snRNA vector which contained a hnRNP A1-binding motif and was used for inducing splicing skipping of USH2A Exon 13 was obtained by conversion of competent Escherichia coli cells, monoclonal screening, PCR and sequencing verification, and the vector was named pUC57-U7-hnRNP A1-snRNA #. The plasmids were purified and stored at −20° C. for later use.
U7-hnRNP A1-snRNA could also be chemically synthesized and modified according to the methods described in Example 2 and Example 4. Taking snRNA #14 as an example, the chemically synthesized U7-hnRNP A1-snRNA sequences and modifications were as follows (* represented a phosphorothioate backbone, m represented 2′-methoxyl modification, an underline represented a recognition domain in reversely complementary pairing with the target sequence, an italic represented a smOPT sequence, and a bold indicated hnRNP A1 protein-binding motif):
Based on the sequence shown in SEQ ID NO: 44, thiophosphorylated backbone modification and methoxyl modification were added to the first three bases at the 5′ and 3′ ends in the modified sequence.
2. Detection of the Efficiency of U7-snRNA Linked with a hnRNP A1-binding Motif to Induce Splicing Skipping of USH2A Exon 13 in Reporter Cells
Detection method: 293 T cells were inoculated into a 24-well plate in a certain amount so that the cell confluence reached about 80% after 24 h. Lipofectamine 2000 was used to co-transfect 293 T cells (a vector mass ratio of 100 ng: 400 ng) and pCMV-EGFPleft-Exon13c.2802T>G-EGFPright respectively with pUC57-U7-hnRNP A1-snRNA plasmids and pUC57-U7-snRNA plasmids. 293T cells transfected with reporter plasmids alone and 293T cells co-transfected with reporter plasmids and pUC57-U7 Scramble were used as two negative controls. 293T cells without any plasmid transfection were used as a blank control. The transfected cells were continuously cultured for 48-72 h, and trypsinized into single cells, and a flow cytometer was then used to detect the efficiency of splicing skipping induced by different snRNA groups.
Experimental results: as shown in
In this example, a free tail was introduced at the 5′ end of the U7-snRNA. The free tail sequence comprised a binding motif “UAGGGU” of a hnRNP A1 protein. The free tail sequence is preferably “UAUGA UAGGGA CU UAGGGU G” (SEQ ID NO: 45), which could recruit the hnRNP A1 protein, and promote the splicing skipping of USH2A Exon 13, but did not increase double skipping of Exon 12 and Exon 13, affect its targeting specificity, and cause or increase off-target effects.
In this example, the U7-snRNA gene that target-induced splicing skipping of Exon 13 in USH2A pre-mRNA was inserted into and replaced an intermediate gene sequence of two ITR domains in a pAAV-CMV vector, thereby constructing a pAAV-U7-snRNA vector, together with AAV packaging plasmids, i.e., a serotype pRC plasmid (containing a Rep gene of AAV2 and respective Cap genes of each serotype) and a pHelper plasmid (a vector plasmid containing E2A, E4 and VA genes of adenovirus), were co-transfected into a host cell, and packaged to obtain an AAV-U7-snRNA virus that targeted splicing skipping of Exon 13 in USH2A pre-mRNA. The specific operation was as follows:
U7-snRNA gene expression cassette (without a recognition domain) (SEQ ID NO:46):
According to the methods of Example 1 and Example 6, a corresponding Oligo DNA sense strand and antisense strand were respectively synthesized according to pre-transcriptional DNA sequences corresponding to the snRNA recognition domain sequences in Table 1, and sticky ends similar to those cleaved by Type IIs restriction enzyme recognition sites were added to both ends. A recognition domain double-stranded DNA with sticky ends was formed by annealing. T4 ligase was linked into a linearized pAAV-U7-snRNA backbone plasmid recovered by the corresponding Type type II restriction enzyme digestion to form pAAV-U7-snRNA plasmids that induced splicing skipping by a specific site that targeted Exon 13 in USH2A pre-mRNA. The pAAV-U7-snRNA plasmids were named according to snRNA numbers corresponding to the recognition domain sequences as pAAV-U7-snRNA #3, pAAV-U7-snRNA #14, pAAV-U7-snRNA #16, etc.
A pAAV-U7-snRNA plasmid vector was obtained by inserting a target gene (a U7-snRNA gene expression cassette that target-induced splicing skipping of Exon 13 in USH2A pre-mRNA) into and replaced a gene sequence between AAV2-ITR domains of the PAAV-CMV plasmid. According to the instructions and standard cell operation procedures, the AAV-U7-snRNA virus that target-induced splicing skipping of Exon 13 in USH2A pre-mRNA was obtained.
24 h before transfection, HEK293/293T cells were inoculated into a 100 mm cell culture dish with a medium of 10% FBS DMEM medium and transfected at the confluence of 80%-90%. 3 h before transfection, an old medium was discarded and replaced with a fresh medium. At the time of transfection, a pAAV-U7-snRNA plasmid, a pRC plasmid, a pHelper plasmid, and a PEI (polyethylenimine) transfection reagent was prepared at the same time according to a system in the table below and added dropwise to a culture dish. After the PEI transfection mixture was added, the dish was shaken slightly to evenly distribute the transfection reagent, and the medium was cultured in a 37° C., 5% CO2 incubator.
24 h after transfection, a DMEM medium with fresh 2% FBS was replaced. 48-72 h after transfection, AAV virus-containing cells were collected, washed, and centrifuged, and a cell pellet was collected, and vortexed and oscillated to break. Subsequently, 0.5 mL of AAV Extraction Solution A was added to the cell pellet according to the kit instructions, and the cell pellet was fully suspended by vortexing for 15 seconds, stewed at room temperature for 5 min, and then vortexed and oscillated for 15 seconds, centrifuged under 2,000-14,000 g for 10 min at 4° C. to remove cell debris. A supernatant was collected into a new sterile centrifuge tube, added with 50 μL of AAV Extraction Solution B, and aspirated and mixed well by using a pipette to obtain AAV-U7-snRNA virus solutions with different recognition domains. A part of the solutions was taken and detected for viral titer by qPCR, and stored at 80° C. for later use.
Since an AAV2-ITR domain of the inserted AAV-U7-snRNA plasmid and its inserted target gene fragment should be less than 4.7 kb, by inserting a plurality of U7-snRNA gene expression cassettes (5′-mouse U7 promoter-recognition domain-smOPT sequence, snRNA gene-specific 3′box-3′), the expression of U7-snRNA could be increased with the same number of AAV virus particles. The gene sequence had a length of about 450 bp, and the pAAV-U7-snRNA plasmid preferably carried 1-10 U7-snRNA gene expression cassettes, and the plurality of U7-snRNA gene expression cassettes in the pAAV-U7-snRNA plasmid could have the same recognition domain.
Various technical features of the foregoing examples may be randomly combined. To make the description concise, not all possible combinations of the technical features in the foregoing examples are described. However, the combinations of these technical features shall be considered as falling within the scope recorded by this description provided that no conflict exists.
The above-mentioned embodiments only express several embodiments of the present invention, and the description is relatively specific and detailed, but it should not be understood as a limitation to the patent scope of the present invention. It should be pointed out that for those of ordinary skill in the art, without departing from the concept of the present invention, several modifications and improvements can be made, and these all fall within the protection scope of the present invention. Therefore, the protection scope of the patent of the present invention should be subject to the appended claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 202210003448.3 | Jan 2022 | CN | national |
The present application is a continuation application of International Application No. PCT/CN2022/140599, filed on Dec. 21, 2022, which claims priority of the Chinese Patent Application No. 202210003448.3 filed on Jan. 4, 2022, the contents of which are incorporated herein by reference in their entireties.
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/CN2022/140599 | Dec 2022 | WO |
| Child | 18764207 | US |
