US20220372492A1

US20220372492A1 - Compounds for modulating fc-epsilon-ri-beta expression and uses thereof

Info

Publication number: US20220372492A1
Application number: US17/688,618
Authority: US
Inventors: Glenn P. Cruse; Dean D. Metcalfe
Original assignee: US Department of Health and Human Services; North Carolina State University
Current assignee: US Department of Health and Human Services; North Carolina State University
Priority date: 2016-02-01
Filing date: 2022-03-07
Publication date: 2022-11-24
Also published as: US20190062756A1; WO2017136435A1; US11268096B2

Abstract

Methods for treating diseases and conditions mediated by the high affinity IgE receptor (FcεRI). Antisense oligomers for modulating splicing of mRNA encoding the FcεRIβ protein, thereby down-regulating cell-surface expression of FcεRI, and uses of the antisense oligomers for inhibiting mast cell degranulation, cytokine release, migration, and proliferation.

Description

CROSS REFERENCE TO RELATED APPLICATION

This application is a divisional of U.S. patent application Ser. No. 16/052,130, filed Aug. 1, 2018 (now U.S. Pat. No. 11,268,096), which itself is a continuation of PCT International Patent Application Serial No. PCT/US2017/016042, filed Feb. 1, 2017, which itself claims the benefit of U.S. Provisional Patent Application Ser. No. 62/289,447, filed Feb. 1, 2016, each of which is incorporated herein by reference in its entirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing in ASCII text file (Name: 297_305_2_PCT_US_DIV_ST25.txt; Size: 169 kilobytes; and Date of Creation: Mar. 7, 2022) filed with the instant application is incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to the use of antisense oligonucleotides to modulate cell surface expression of FcεRIβ protein, thereby modulating IgE-mediated immune responses.

BACKGROUND

Asthma and related allergic diseases affect up to one in ten people in developed countries and about 10% of patients with asthma cannot be controlled with currently available approaches. Current therapies rely on damping the inflammatory response and relaxing the constricted airway smooth muscle cells with orally inhaled glucocorticosteroids and/or β adrenoreceptor agonists. But high doses of steroids are associated with undesirable side effects, and inhaled β-agonists increase the risk of death from asthma if not used in combination with glucocorticosteroids. Moreover, it has been suggested that β-agonists may promote the underlying inflammation that contributes to the airway remodeling observed in asthma patients. Other clinical approaches aimed at longer-term alleviation of symptoms include desensitization with incremental increases in the dose of allergen, or hypersensitization to induce immune tolerance. While such approaches have been beneficial for some patients, they have not been beneficial for all patients, and serious adverse side effects have been observed.
It is known that the FcεRIβ protein contributes to IgE-dependent mast cell signaling by trafficking the FcεRI receptor complex to the cell surface and amplifying FcεRI-induced signaling. The first transmembrane domain of FcεRIβ is required for trafficking the receptor complex, and the C-terminal immunoreceptor tyrosine-based activation motif (ITAM) amplifies signaling. While reports that polymorphisms in the MS4A2 gene were associated with the development of asthma raised interest in this area, studies into the functional consequences of mutations in the MS4A2 gene failed to affect the function of FcεRIβ. There remains a need for new and effective treatments for treating allergic diseases.
The invention utilizes new pathways and novel compounds for providing such treatments.

SUMMARY

Rather than the administration of β-agonists, glucocorticoids, or allergen to produce hypersensitization, the present invention relies on a different approach, namely altering cellular responses to IgE-directed antigens. This approach is based on the finding that the gene(s) at loci 11q12-q13 are strongly linked to allergy and asthma susceptibility, and the knowledge that the MS4A gene family is clustered around 11q12-q13. It is also known that the gene MS4A1, which encodes the protein CD20, and MS4A2, which encodes the FcεRIβ protein, are associated with activation and proliferation of B-cells and mast cells, respectively. Thus, these genes are considered candidates for the linkage of these genetic regions with allergy.
One aspect of this disclosure is an antisense oligomer comprising 10 to 50 linked nucleosides, wherein the antisense oligomer is targeted to a region of a pre-mRNA molecule encoding a FcεRIβ protein. The targeted region may comprise sequences involved in splicing of the FcεRIβ-encoding pre-mRNA such that hybridization of the antisense oligomer to the FcεRIβ-encoding pre-mRNA alters splicing of the pre-mRNA. Hybridization of the antisense oligomer to the FcεRIβ-encoding pre-mRNA may reduce cell surface expression of high affinity IgE receptor (FcεRI).
In one aspect, the targeted region comprises at least a portion of a polynucleotide sequence selected from the group consisting of an intron sequence, an exon sequence, a sequence comprising an intron/exon junction, a splice donor sequence, a slice acceptor sequence, a splice enhancer sequence, a splice branch point sequence, or a polypyrimidine tract. In this aspect, the targeted region of the pre-mRNA may comprise a polynucleotide sequence selected from an intron 2 sequence, an exon 3 sequence, a sequence comprising an intron 2/exon 3 junction, an exon 3 splice donor sequence, an exon 3 slice acceptor sequence, an exon 3 splice enhancer sequence, an exon 3 splice branch point sequence, or an exon 3 polypyrimidine tract.
These antisense oligomers may be targeted to regions of an FcεRIβ-encoding pre-mRNA transcribed from an MS4A2 gene (a “MS4A2 pre-mRNA”). The encoded FcεRIβ protein may be from any mammal, including a human, a mouse, a dog, a cat or a horse (e.g., the encoded FcεRIβ protein may be a human FcεRIβ protein, a murine FcεRIβ protein, a canine FcεRIβ protein, a feline FcεRIβ protein, and an equine FcεRIβ protein). In a preferred aspect, the MS4A2 pre-mRNA encodes a human FcεRIβ protein. The human FcεRIβ protein may comprise SEQ ID NO:2. The MS4A2 transcript comprises SEQ ID NO:1.
Hybridization of an antisense oligomer of this disclosure to an MS4A2 pre-mRNA may result in the production of a mature MS4A2 mRNA molecule lacking a portion, or all of exon 3, which encodes a transmembrane domain from an FcεRIβ protein. Hybridization of an antisense oligomer of this disclosure to an MS4A2 pre-mRNA results in production of an mRNA molecule encoding a truncated FcεRIβ protein. The truncated FcεRIβ protein may be t-FcεRIβ.
One aspect of this disclosure is an antisense oligomer comprising 10 to 50 linked nucleosides, wherein the 10 to 50 linked nucleosides comprise a targeting nucleic acid sequence sufficiently complementary to a target nucleic acid sequence in an FcεRIβ-encoding pre-mRNA, such that the oligomer specifically hybridizes to the target sequence. Hybridization of the antisense oligomer to the FcεRIβ-encoding pre-mRNA alters splicing of the pre-mRNA. Hybridization of the antisense oligomer to the FcεRIβ-encoding pre-mRNA may reduce cell surface expression of high affinity IgE receptor (FcεRI).
In one aspect, the targeting sequence in the antisense oligomer comprises at least 6 contiguous nucleobases fully complementary to at least 6 contiguous nucleobases in the target sequence. The targeting sequence in the antisense oligomer may be at least 80% complementary over its entire length to an equal length of contiguous nucleobases in the target sequence. The targeting sequence may comprise at least a portion of a polynucleotide sequence selected from an intron sequence, an exon sequence, a sequence comprising an intron/exon junction, a splice donor sequence, a slice acceptor sequence, a splice enhancer sequence, a splice branch point sequence, or a polypyrimidine tract. In one aspect, the polynucleotide sequence is selected from an intron 2 sequence, an exon 3 sequence, a sequence comprising an intron 2/exon 3 junction, an exon 3 splice donor sequence, an exon 3 slice acceptor sequence, an exon 3 splice enhancer sequence, an exon 3 splice branch point sequence, or an exon 3 polypyrimidine tract.
The target nucleic acid sequences may be in an FcεRIβ-encoding pre-mRNA transcribed from an MS4A2 gene. The encoded FcεRIβ protein may be from any mammal, including a human, a mouse, a dog, a cat, or a horse. In a preferred aspect, the MS4A2 pre-mRNA encodes a human FcεRIβ protein.
One aspect of this disclosure is an antisense oligomer comprising 10 to 50 linked nucleosides, wherein the 10 to 50 linked nucleosides comprises a nucleic acid sequence at least partially complementary to a target nucleic acid sequence in a pre-mRNA molecule, which encodes a protein comprising SEQ ID NO:2 or SEQ ID NO:4. The protein may be encoded by an MS4A2 transcript comprising SEQ ID NO:1. Hybridization of the antisense oligomer to the pre-mRNA may alter splicing of the pre-mRNA. Hybridization of the antisense oligomer to the pre-mRNA may reduce cell surface expression of high affinity IgE receptor (FcεRI).
In these aspects, the target sequence may comprise at least a portion of a polynucleotide sequence selected from the group consisting of SEQ ID NOs:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. The portion may be at least 10 contiguous nucleotides. The target sequence may comprise a sequence at least 90% identical to a sequence selected from the group consisting of SEQ ID NOs:11-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. The target sequence may comprise a sequence selected from SEQ ID NOs:11-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015.
In these aspects, the targeting sequence may comprise at least 10 contiguous nucleobases fully complementary in sequence to at least 10 contiguous nucleobases in a sequence selected from SEQ ID NOs:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. The targeting sequence may comprise a sequence at least 80% complimentary to at least a portion of a sequence selected from SEQ ID NO:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. The targeting sequence may be at least 80% identical over the full length of a sequence selected from the group consisting of SEQ ID NOs:22-1006. The targeting sequence may also be selected from any one of SEQ ID NOs:22-1006.
These antisense oligomers may be an antisense RNA molecule, which may further comprise a modification selected from a nucleoside modification, an internucleoside modification, a sugar modification, a sugar-internucleoside linkage modification, and combinations thereof. Such modifications may increase resistance to degradation by a ribonuclease. A morpholino oligomer is an exemplary modified antisense oligomer.
Another aspect provides an expression vector that expresses an antisense oligomer of this disclosure, while another aspect is a pharmaceutical composition comprising an antisense oligomer of this disclosure.
One aspect of this disclosure is a method of modulating splicing of FcεRIβ mRNA in a cell by contacting the cell with an antisense oligomer, an expression vector, or a composition of this disclosure, thereby modulating splicing of the FcεRIβ mRNA. The amount of full-length FcεRIβ-encoding mRNA produced by the cell may be reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or at least 99%, or completely eliminated.
One aspect of this disclosure is a method of reducing cell surface expression of FcεRI in a cell, comprising contacting the cell with an antisense oligomer, an expression vector, or a composition of this disclosure, thereby reducing expression of FcεRI on the surface of the cell. The amount of FcεRI expressed on the cell surface may be reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or completely eliminated.
One aspect of this disclosure is a method of modulating FcεRI receptor complex-dependent degranulation in a mast cell, comprising contacting the mast cell with an antisense oligomer, an expression vector, or a composition of this disclosure, thereby modulating FcεRI receptor complex-dependent degranulation in the mast cell. FcεRI receptor complex-dependent degranulation may be reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or at least 99%, or completely eliminated.
One aspect of this disclosure is a method of modulating FcεRI receptor complex-dependent mast-cell migration, comprising contacting the mast cell with an antisense oligomer, an expression vector, or a composition of this disclosure, thereby modulating FcεRI receptor complex-dependent mast cell migration. FcεRI receptor complex-dependent mast cell migration activity may be reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or at least 99%, or completely eliminated.
One aspect of this disclosure is a method of modulating cytokine release, comprising contacting a cytokine-producing cell with an antisense oligomer, an expression vector, or a composition of this disclosure, thereby modulating cytokine release. The cytokine may be a vasoactive amine, a proteoglycan, a protease, a growth factor, a chemokine, a pro-inflammatory lipid mediator, a histamine, a serotonin, heparin, tryptase, chymase, TNFα, IL-1, IL-6, IL-8, IL-10, TNFα, VEGF, TGFβ, CCL2-4, a prostaglandin, and/or a leukotriene. The amount of at least one cytokine released may be reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or at least 99%, or completely eliminated. These methods may be performed on a cell in culture or in the body of an individual.
One aspect of this disclosure is a method of inhibiting an anaphylactic reaction in an individual by administering to the individual an antisense oligomer, an expression vector, or a composition of this disclosure.
One aspect of this disclosure is a method of treating an allergic condition in an individual, by administering an antisense oligomer, an expression vector, or a composition of this disclosure, to an individual in need of such treatment. The allergic condition treated may be asthma, atopic dermatitis, chronic rhinitis, chronic sinusitis, and/or allergic conjunctivitis.
One aspect of this disclosure is a method of reducing the incidence or severity of an allergic reaction in an individual, by administering an antisense oligomer, an expression vector, or a composition of this disclosure, to an individual chronically experiencing allergic reactions or at risk of having an allergic reaction.
One aspect of this disclosure is a method of treating an individual at risk of developing an anaphylactic reaction, by administering an antisense oligomer, an expression vector, or a composition of this disclosure, to the individual at risk of developing an anaphylactic reaction.
One aspect of this disclosure is a method of treating a mast cell-related disease in an individual, comprising administering an antisense oligomer, an expression vector, or a composition of this disclosure, to an individual in need of such treatment. The mast cell-related disease may be mastocytosis, or a mast cell tumor, including mastocytoma.
In these methods, the individual to whom the antisense oligomer, expression vector, or composition of this disclosure is administered may be a human, mouse, dog, cat, or horse.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B show the transfection efficiency and cytotoxicity of morpholino antisense oliogonucleotides (AONs). FIG. 1A is density plots of FITC positivity (X axis) versus propridium iodide positivity (Y axis) of mock treated control cells (top panels) and FITC morpholino AON transfected cells (lower panels). FIG. 1B shows the data from the panels in FIG. 1A displayed as histograms.

FIGS. 2A-2D show the effects of transfecting mouse and human mast cells with antisense oligonucleotides targeting exon 3 of the MS4A2 gene. Mouse BMMC and human mast cell lines were transfected with either 10 μM of standard control AON (non-matching 25mer morpholino AON) or 10 μM of 25mer morpholino AONs targeting FcεRIβ pre-mRNA. FIG. 2A shows qualitative RT-PCR of FcεRIβ mRNA from the transfected cells. FL-FcεRIβ=full length FcεRIβ transcript; t-FcεRIβ=exon 3 truncation. FIG. 2B shows flow cytometric analysis of surface FcεRIα expression in mouse (left panel) and human (right panel) mast cells 48 hours after transfection with either the standard control AON (Std Con AON—rightmost peak) or FcεRIβ AONs (center peak). The leftmost peak represents the isotype control. Data are representative of five experiments. FIG. 2C shows FcεRIα surface expression in cells transfected with various amounts of AONs. The graphs show the results from five experiments using moue BMMCs (left panel) and three experiments for LAD-2 cells (right panel). FIG. 2D shows a comparison of the efficiency of MS4A2 exon skipping in mouse and human cells using various doses of AONs.

FIGS. 3A-3C show the effect of FcεRIβ antisense oligonucleotides on degranulation on mast cells. FIG. 3A shows antigen-induced degranulation in mast cells transfected with varying amounts of FcεRIβ antisense oligonucleotides. Data are the mean±SEM from five experiments. *p<0.05, ****p<0.0001. FIG. 3B shows the percent degranulation of BMMCs in response to either antigen (DNP—left panel) or thapsigargin (right panel). FIG. 3C shows ratiometric calcium signaling of the cells as in (FIG. 3B). The arrowhead denotes the time of the stimulant addition. Example plots are representative of four experiments. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

FIGS. 4A and 4B show the effects of FcεRIβ antisense oligonucleotides on IgE-dependent degranulation in human mast cells. FIG. 4A shows that IgE-dependent LAD-2 cell degranulation is significantly reduced with FcεRIβ exon skipping, but FIG. 4B shows that thapsigargin-induced degranulation is unaffected. Data are the mean±SEM from seven experiments. *P<0.05, **P<0.01, ***P<0.001.

FIGS. 5A-5F show the effects of AONs on IgE-dependent cell signaling, cytokine production and migration. FIG. 5A shows immunoblots from mouse BMMCs transfected with either standard control AON (left four lanes) or FcεRIβ AON (right four lanes) and stimulated with the indicated molecules. FIGS. 5B-5D show combined quantification of phosphorylation data for standard control AON (left bars) or the FcεRIβ AON (right bars) transfected BMMCs. FIG. 5E is ELISA data for GM-CSF release after 6 h. FIG. 5F shows BMMC migration with FcεRIβ AON treatment. Data are the mean±SEM from three (FIGS. 5B-5E) or four (FIG. 5F) experiments. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001

FIGS. 6A-6D show that transfection of FcεRIβ antisense oligonucleotides (AONs) eliminate the pro-survival effect of IgE. FIG. 6A shows a gating strategy for cell death and apoptosis flow cytometry. FIG. 6B shows that removal of IL-3 from BMMCs induces apoptosis and cell death. FcεRIα expression was eliminated with FcεRIβ AON (Bottom Left) compared with untreated cells (gray plots) and standard control AON (Top Left). Removal of IL-3-induced cell death in both standard control AON (Top Middle, light line compared with gray histogram) and FcεRIβ AON cells (Bottom Middle, light line compared with gray histogram). The addition of IgE to the cultures protected the standard control AON-treated BMMCs from cell death (Top Middle, dark line compared with gray histogram), but did not protect the FcεRIβ AON-treated BMMCs (Bottom Middle, dark line compared with gray histogram). Similar results were seen when examining apoptosis by gating out dead cells and plotting surface Annexin V staining (Right). Mast cells externalize Annexin V during exocytosis, and weakly Annexin V-positive cells likely represent constitutive exocytosis. Cumulative data from dead cells (FIG. 6C) or apoptotic cells (FIG. 6D) was assessed by flow cytometry. Data are the mean±SEM from three experiments. *P<0.05; **P<0.01; n.s., not significant.

FIGS. 7A-7C show the effect of transfection with FcεRIβ antisense oligonucleotides on BMM cell proliferation. FIG. 7A shows CellTrace Violet dilution proliferation assays of mouse BMMCs, in the presence of IL-3, transfected with either standard control AON (blue lines) or FcεRIβ AON (light lines). CellTrace Violet was loaded into the BMMCs and cells were transfected with AONs at day 0. On day 5 (top panels) and day 7 (bottom panels) after CellTrace Violet loading BMMCs were immunostained for surface FcεRIα. Confirmation of loss of surface FcεRI with FcεRIβ AON treatment was performed on all experiments (left panels). No significant difference in proliferation was observed between the standard control AON (dark lines) and the FcεRIβ AON (light lines) at either 5 (top right panel) or 7 days (bottom right panel). Proliferation of cells results in dilution of the CellTrace Violet dye and a left shift in fluorescence in divided cells. Immunostaining for surface FcεRI confirmed that FcεRIβ AON treatment was effective 5 days after transfection (top left panel). However, by 7 days post-transfection, FcεRIβ AON efficacy began to decline with evidence of a population of cells that were re-expressing FcεRI (bottom, left panel). FIG. 7B shows flow cytometry histograms of FcεRIβ AON treated BMMCs from (FIG. 7A) gated on surface FcεRIα expression as either FcεRI+(light lines) or FcεRI− (black lines) populations demonstrate that the proliferating cells in the FcεRIβ AON treated condition are the FcεRI+cell population. Data are representative of three experiments. FIG. 7C shows aggregate data from three experiments for proliferation at

days

5 and 7. Data are the mean±SEM.

FIGS. 8A and 8B show the effect of FcεRIβ antisense oligonucleotides on an anaphylactic allergic response. FIG. 8A shows the measurement of Evan's blue extravasation into the ears of mice treated with either standard control Vivo-morpholino AON (left two bars) or Vivo-morpholino FcεRIβ AON (right two bars) after challenge with antigen. Data are the mean±SEM from 13 mice for standard control AON and 14 mice for FcεRIβ AON combined from three experiments. *p<0.05. FIG. 8B shows the qualitative RT-PCR of total RNA isolated from skin tissue near the site of AON administration from mice after the PCA reaction. Example RT-PCR reactions demonstrate exon skipping in vivo. Data are representative of 5 mice for each condition.

DETAILED DESCRIPTION

Disclosed herein are novel methods for treating atopic diseases, including methods for treating diseases and syndromes mediated by the high-affinity Fc-epsilon receptor (FcεRI). The invention is based on the inventors' discovery of a novel, truncated isoform of the FcεRIβ protein (t-FcεRIβ), which lacks the first and second membrane-spanning regions, and the mRNA transcript for which is truncated in exon 3 (Cruse, et al., FASEB J., 2010 October; 24(10):4047-4057). This truncated FcεRIβ protein does not traffic to the plasma membrane, resulting in reduced expression of FcεRI on the plasma membrane. The finding of t-FcεRIβ, and its related effects, led to the discovery of selective editing of the FcεRIβ mRNA transcript, using antisense technology, to produce t-FcεRIβ, results in decreased cell-surface expression of the FcεRIβ protein. This in turn leads to a decrease in symptoms resulting from IgE-mediated diseases. Thus, methods and compounds of this disclosure are useful for treating FcεRI-mediated diseases by down-regulating cell-surface expression of FcεRI.
Antisense technology has been demonstrated to be an effective method of modifying the expression levels of gene products (see, for example, U.S. Pat. Nos. 8,765,703, 8,946,183, and U.S. Patent Publication No. 2015/0376615, which are incorporated herein by reference in their entirety). Antisense technology works by interfering with known steps in the normal processing of mRNA. Briefly, RNA molecules are transcribed from genomic DNA in the nucleus of the cell. These newly synthesized mRNA molecules, called primary mRNA or pre-mRNA, must be processed prior to transport to the cytoplasm for translation into protein at the ribosome. Such processing includes the addition of a 5′ methylated cap and the addition of a poly(A) tail to the 3′end of the mRNA.
Maturation of 90-95% of mammalian mRNAs then occurs with splicing of the mRNA. Introns (or intervening sequences) are regions of a primary transcript (or the DNA encoding it) that are not included in the coding sequence of the mature mRNA. Exons (expressed sequences) are regions of a primary transcript (or the DNA encoding it) that remain in the mature mRNA when it reaches the cytoplasm. During the splicing process, exons in the pre-mRNA molecule are spliced together to form the mature mRNA sequence. Splice junctions, also referred to as splice sites, are utilized by cellular apparatus to determine which sequences are removed and where the ends to be joined start and stop. Sequences on the 5′ side of the junction are called the 5′ splice site, or splice donor site, whereas sequences on the 3′ side the junction are referred to as the 3′ splice site, or the splice acceptor site. In splicing, the 3′ end of an upstream exon is joined to the 5′ end of the downstream exon. Thus, the un-spliced RNA (or pre-mRNA) has an exon/intron junction at the 5′ end of an intron and an intron/exon junction at the 3′ end of an intron. After the intron is removed, the exons are contiguous at what is sometimes referred to as the exon/exon junction or boundary in the mature mRNA. Cryptic splice sites are those which are less often used but may be used when the usual splice site is blocked or unavailable. The use of different combinations of exons by the cell can result in multiple mRNA transcripts from a single gene.
In one application of antisense technology, an antisense oligonucleotide (AON) binds to a mRNA molecule transcribed from a gene of interest and inactivates (“turns off”) the mRNA by increasing its degradation or by preventing translation or translocation of the mRNA by steric hindrance. The end result is that expression of the corresponding gene (i.e., final production of the protein encoded by the corresponding gene) is prevented.
Alternatively, antisense technology can be used to affect splicing of a gene transcript. In this application, the antisense oligonucleotide binds to a pre-spliced RNA molecule (pre-messenger RNA or pre-mRNA) and re-directs the cellular splicing apparatus, thereby resulting in modification of the exon content of the spliced mRNA molecule. Thus, the overall sequence of a protein encoded by the modified mRNA differs from a protein translated from mRNA, the splicing of which was not altered (i.e., the full length, wild-type protein). The protein that is translated from the altered mRNA may be truncated and/or it may be missing critical sequences required for proper function. Typically, the compounds used to affect splicing are, or contain, oligonucleotides having a base sequence complementary to the mRNA being targeted. Such oligonucleotides are referred to herein as “antisense oligonucleotides” (AONs).
This disclosure provides antisense technology to modulate splicing of mRNA encoding an FcεRIβ protein, thereby causing a decrease in the amount or “level” of FcεRI protein expressed on the surface of a cell. Accordingly, a method of this disclosure can generally be accomplished by contacting a cell expressing an MS4A2 transcript, with an antisense oligomer targeted to a region of the MS4A2 pre-mRNA. Such contact results in uptake of the antisense oligomer by the cell, hybridization of the oligomer to the MS4A2 mRNA, and subsequent modulation of splicing of the MS4A2 pre-mRNA. In preferred methods, such modulation of splicing of the MS4A2 mRNA decreases cell-surface expression of FcεRI.
This invention is not limited to the particular embodiments described herein, as such may vary. Additionally, the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting on the finally claimed invention, since the scope of the invention will be limited only by the claims.
As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. For example, a nucleic acid molecule refers to one or more nucleic acid molecules. As such, the terms “a”, “an”, “one or more” and “at least one” can be used interchangeably. Similarly, the terms “comprising”, “including” and “having” can be used interchangeably. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like, in connection with the recitation of claim elements, or use of a “negative” limitation.
As used herein, an MS4A2 gene, MS4A2, and the like, refer to a gene encoding an FcεRIβ protein from a mammal. Examples of MS4A2 genes include, but are not limited to, accession numbers NM 000139.4 (human) and NM 013516.2 (mouse). Similarly, an MS4A2 coding sequence refers to a nucleic acid sequence encoding at least a portion of an FcεRIβ protein. Such a portion can be a fragment of the protein (e.g., a 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 contiguous amino acid segment from any part of the whole protein), an exon, or a domain (e.g., a transmembrane domain), or it can refer to the entire protein, including any splicing variants. MS4A2 genes or coding sequences of this disclosure can be from any mammal having such gene or coding sequence. The MS4A2 gene or coding sequence may be from a human, mouse, canine, feline or equine.
As used herein, an MS4A2 transcript is an RNA molecule transcribed from an MS4A2 gene. Preferably, MS4A2 transcripts targeted by oligomers of this disclosure are primary transcripts or pre-mRNA molecules. As used herein, primary mRNA or pre-mRNA is an mRNA transcript that has not yet undergone splicing. Accordingly, a mature mRNA molecule is an mRNA molecule that has undergone splicing.
As used herein, the term antisense oligomer refers to a polymeric molecule comprising nucleobases, which is capable of hybridizing to a sequence in a nucleic acid molecule, such as an mRNA molecule. The term nucleobase, as used herein, refers to the heterocyclic base portion of a nucleoside. In general, a nucleobase is any group that contains one or more atoms, or groups of atoms, capable of hydrogen bonding to a base of another nucleoside. In addition to “unmodified” or “natural” nucleobases such as the purine nucleobases adenine (A) and guanine (G), and the pyrimidine nucleobases thymine (T), cytosine (C) and uracil (U), modified nucleobases or nucleobase mimetics known to those skilled in the art are also amenable to this disclosure. The term “modified nucleobase” refers to a nucleobase that is similar in structure to the parent nucleobase, such as for example, a 7-deaza purine, a 5-methyl cytosine, a G-clamp, or a tricyclic phenoxazine nucleobase mimetic. Methods for preparation of these modified nucleobases are known to those skilled in the art.
As is known in the art, a nucleoside is a base-sugar combination. The base portion of the nucleoside is normally a heterocyclic base (e.g., a nucleobase or simply a “base”). The two most common classes of such heterocyclic bases are purines and the pyrimidines. Nucleotides are nucleosides that further include a phosphate group covalently linked to the sugar portion of the nucleoside. For those nucleosides that include a pentofuranosyl sugar, the phosphate group can be linked to the 2′, 3′ or 5′ hydroxyl moiety of the sugar. In forming oligonucleotides, the phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound. Within oligonucleotides, the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide. The normal linkage or backbone of RNA and DNA is a 3′ to 5′ phosphodiester linkage.
It is understood in the art that RNA molecules often have a short half-life, making their use as therapeutic agents problematic. Thus, it is often preferable to include chemical modifications in oligonucleotides to alter their activity. Chemical modifications can alter oligomer activity by, for example, increasing affinity of an antisense oligomer for its target RNA, increasing nuclease resistance (e.g., resistance to ribonucleases such as RNaseH), and/or altering the pharmacokinetics (e.g. half-life) of the oligomer. For example, it is possible to replace sugars, nucleobases and/or internucleoside linkages with a group that maintains the ability of the oligomer to hybridize to its target sequence, but which imparts a desirable characteristic to the oligomer (e.g., resistance to degradation, increased half-life, etc.). Such groups can be referred to as analogs (e.g., sugar analog, nucleobase analog, etc.). Generally, an analog is used in place of the sugar or sugar-internucleoside linkage combination, and the nucleobase is maintained for hybridization to a selected target. Representative examples of a sugar mimetic include, but are not limited to, cyclohexenyl or morpholino. Representative examples of a mimetic for a sugar-internucleoside linkage combination include, but are not limited to, peptide nucleic acids (PNA) and morpholino groups linked by uncharged, achiral linkages. In some instances, an analog is used in place of the nucleobase. Representative nucleobase mimetics are well known in the art and include, but are not limited to, tricyclic phenoxazine analogs and universal bases (Berger et al., Nuc. Acid Res. 2000, 28:2911-14, incorporated herein by reference). Examples of such sugar, nucleoside and nucleobase mimetics are disclosed in U.S. Pat. Nos. 8,765,703 and 8,946,183, which are incorporated herein by reference). Methods of synthesis of sugar, nucleoside and nucleobase mimetics, and the use of such mimetics to produce oligonucleotides are well known to those skilled in the art.
The term oligomer includes oligonucleotides, oligonucleosides, oligonucleotide analogs, oligonucleotide mimetics and chimeric combinations thereof. Such molecules are generally known to those skilled in the art. Oligomers of this disclosure include, but are not limited to, primers, probes, antisense compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, and siRNAs. As such, these compounds can be introduced in the form of single-stranded, double-stranded, circular, branched or hairpins and can contain structural elements such as internal or terminal bulges or loops.
Oligomers of this disclosure can be any length suitable for administering to a cell or individual in order to modulate splicing of an mRNA molecule. For example, antisense oligomers of this disclosure can comprise from about 10 to about 50 nucleobases (i.e. from about 10 to about 50 linked nucleosides). One having ordinary skill in the art will appreciate that this embodies antisense oligomers of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleobases. In one embodiment, antisense oligomers of this disclosure can comprise, or consist of, 10 to 30 nucleobases, or 10 to 25 nucleobases. Methods of determining the appropriate length for antisense oligomers of this disclosure are known to those skilled in the art.
As used herein, the terms “targeted to,” “targeting,” and the like, refer to a process of designing an antisense oligomer so that it specifically hybridizes with a desired nucleic acid molecule, such as a desired mRNA molecule. The terms “hybridizes,” “hybridization,” “hybridize to,” and the like, are terms of art, and refer to the pairing of nucleobases in complementary strands of oligonucleotides (e.g., an antisense oligomer and a target sequence in a mRNA molecule). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleobases). For example, the natural base adenine is complementary to the natural nucleobases thymidine and uracil, which pair through the formation of hydrogen bonds. Similarly, the natural base guanine is complementary to the natural bases cytosine and 5-methyl cytosine.
In the context of this disclosure, the phrase “specifically hybridizes” refers to the capacity of an antisense oligomer of this disclosure to preferentially bind an mRNA (e.g., pre-mRNA) encoding a FcεRIβ protein rather than binding an mRNA encoding a protein unrelated in structure to a FcεRIβ protein. Further, an antisense oligomer that preferentially binds a target sequence is one that hybridizes with an mRNA encoding a FcεRIβ protein (a FcεRIβ pre-mRNA), but which does not exhibit significant hybridization with mRNA molecules encoding proteins unrelated in structure to a FcεRIβ protein. In the context used herein, significant hybridization is, for example, binding of an oligomer of this disclosure to an mRNA encoding a protein unrelated in structure to a FcεRIβ protein, with an affinity or avidity sufficiently high enough to interfere with the ability of the antisense oligomer to achieve the desired effect. Examples of such desired effects include, but are not limited to, modulation of splicing of a MS4A2 pre-mRNA, reduction in the level of surface expression of FcεRI protein, and a reduction or inhibition in allergic symptoms in an individual. Thus, it will be understood by those skilled in the art that an antisense oligomer is considered specific for a target sequence (is specifically hybridizable, specifically hybridizes, etc.) when there is a sufficient degree of complementarity between the linear sequence of nucleobases in the antisense oligomer and a linear sequence of nucleobases in the target sequence, to avoid significant binding of the antisense oligomer to non-target nucleic acid sequences under conditions in which specific binding is desired (i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays are performed in the case of in vitro assays).
A used herein, the terms “complement,” “complementary,” “complementarity,” and the like, refer to the capacity for precise pairing between nucleobases in an oligomer and nucleobases in a target sequence. Thus, if a nucleobase (e.g., adenine) at a certain position of an oligomer is capable of hydrogen bonding with a nucleobase (e.g., uracil) at a certain position in a target sequence in a target nucleic acid, then the position of hydrogen bonding between the oligomer and the target nucleic acid is considered to be a complementary position. Usually, the terms complement, complementary, complementarity, and the like, are viewed in the context of a comparison between a defined number of contiguous nucleotides in a first nucleic acid molecule (e.g., an oligomer) and a similar number of contiguous nucleotides in a second nucleic acid molecule (e.g., a mRNA molecule), rather than in a single base to base manner. For example, if an antisense oligomer is 25 nucleotides in length, its complementarity with a target sequence is usually determined by comparing the sequence of the entire oligomer, or a defined portion thereof, with a number of contiguous nucleotides in a mRNA molecule. An oligomer and a target sequence are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleobases which can hydrogen bond with each other. Positions are corresponding when the bases occupying the positions are spatially arranged such that, if complementary, the bases form hydrogen bonds. As an example, when comparing the sequence of an oligomer to a similarly sized sequence in a target sequence, the first nucleotide in the oligomer is compared with a chosen nucleotide at the start of the target sequence. The second nucleotide in the oligomer (3′ to the first nucleotide) is then compared with the nucleotide directly 3′ to the chosen start nucleotide. This process is then continued with each nucleotide along the length of the oligomer. Thus, the terms “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of precise pairing or complementarity over a sufficient number of contiguous nucleobases such that stable and specific binding occurs between the antisense compound and a target nucleic acid.
Hybridization conditions under which a first nucleic acid molecule will specifically hybridize with a second nucleic acid molecule are commonly referred to in the art as stringent hybridization conditions. It is understood by those skilled in the art that stringent hybridization conditions are sequence-dependent and can be different in different circumstances. Thus, stringent conditions under which an oligomer of this disclosure specifically hybridizes to a target sequence are determined by the complementarity of the oligomer sequence and the target sequence and the nature of the assays in which they are being investigated. Persons skilled in the relevant art are capable of designing complementary sequences that specifically hybridize to a particular target sequence for a given assay or a given use.
The process of designing an antisense oligomer that is targeted to a nucleic acid molecule usually begins with identification of a target nucleic acid, the expression of which is to be modulated, and determining the sequence of the target nucleic acid molecule. As used herein, the terms “target nucleic acid,” “nucleic acid encoding a FcεRIβ protein,” and the like, encompass, for example, DNA encoding a FcεRIβ protein, RNA (including pre-mRNA and mRNA) transcribed from such DNA, and cDNA derived from such RNA. For example, the target nucleic acid can be a cellular gene (or pre-mRNA or mRNA transcribed therefrom), the expression of which is associated with a particular disorder or disease state. Thus, in one embodiment a useful target nucleic acid encodes an FcεRIβ protein. In one embodiment, the target nucleic acid is an MS4A2 transcript. In one embodiment, the target nucleic acid is a MS4A2 pre-mRNA.
Once a target nucleic acid has been identified, the targeting process includes determining at least one target region in which the antisense interaction will occur, thereby modulating splicing of the target nucleic acid. As used herein, a target region is defined as a portion of the target nucleic acid having at least one identifiable structure, function, or characteristic. Preferred target regions are those comprising sequences involved in splicing of pre-mRNA molecules. Examples of such identifiable structures, functions, or characteristics include, but are not limited to, at least a portion of an intron or exon, an intron/exon junction, a splice donor site, a splice acceptor site, a splice branch point or a splice enhancer site. Thus, in one embodiment, the target region comprises at least part of an intron or exon, a splice donor site, a splice acceptor site, a splice branch point, and/or a splice enhancer site. In one embodiment, the target region comprises at an intron or exon, a splice donor site, a splice acceptor site, a splice branch point, and/or a splice enhancer site.
Following identification of a target region, a target sequence within the target region can then be identified. As used herein, a target sequence is a nucleic acid sequence in a target region, to which an antisense oligomer of this disclosure specifically hybridizes. Preferred target sequences are those involved in splicing of pre-mRNA. Once a target sequence has been identified, the antisense oligomer is designed to include a nucleobase sequence sufficiently complementary to the target sequence so that the antisense oligomer specifically hybridizes to the target nucleic acid. More specifically, the nucleotide sequence of the antisense oligomer is designed so that it contains a region of contiguous nucleotides sufficiently complementary to the target sequence so that the antisense oligomer specifically hybridizes to the target nucleic acid. Such a region of contiguous, complementary nucleotides in the oligomer can be referred to as an “antisense sequence” or a “targeting sequence.”
It is well known in the art that the greater the degree of complementarity between two nucleic acid sequences, the stronger and more specific is the hybridization interaction. It is also well understood that the strongest and most specific hybridization occurs between two nucleic acid molecules that are fully complementary. As used herein, the term fully complementary refers to a situation when each nucleobase in a nucleic acid sequence is capable of hydrogen binding with the nucleobase in the corresponding position in a second nucleic acid molecule. In one embodiment, the targeting sequence is fully complementary to the target sequence. In one embodiment, the targeting sequence comprises an at least 6 contiguous nucleobase region that is fully complementary to an at least 6 contiguous nucleobase region in the target sequence. In one embodiment, the targeting sequence comprises an at least 8 contiguous nucleobase sequence that is fully complementary to an at least 8 contiguous nucleobase sequence in the target sequence. In one embodiment, the targeting sequence comprises an at least 10 contiguous nucleobase sequence that is fully complementary to an at least 10 contiguous nucleobase sequence in the target sequence. In one embodiment, the targeting sequence comprises an at least 12 contiguous nucleobase sequence that is fully complementary to an at least 12 contiguous nucleobase sequence in the target sequence. In one embodiment, the targeting sequence comprises an at least 14 contiguous nucleobase sequence that is fully complementary to an at least 14 contiguous nucleobase sequence in the target sequence. In one embodiment, the targeting sequence comprises an at least 16 contiguous nucleobase sequence that is fully complementary to an at least 16 contiguous nucleobase sequence in the target sequence. In one embodiment, the targeting sequence comprises an at least 18 contiguous nucleobase sequence that is fully complementary to an at least 18 contiguous nucleobase sequence in the target sequence. In one embodiment, the targeting sequence comprises an at least 20 contiguous nucleobase sequence that is fully complementary to an at least 20 contiguous nucleobase sequence in the target sequence.
It will be understood by those skilled in the art that the targeting sequence may make up the entirety of an antisense oligomer of this disclosure, or it may make up just a portion of an antisense oligomer of this disclosure. For example, in an oligomer consisting of 30 nucleotides, all 30 nucleotides can be complementary to a 30 contiguous nucleotide target sequence. Alternatively, for example, only 20 contiguous nucleotides in the oligomer may be complementary to a 20-contiguous nucleotide target sequence, with the remaining 10 nucleotides in the oligomer being mismatched to nucleotides outside of the target sequence. In preferred embodiment, oligomers of this disclosure have a targeting sequence of at least 10 nucleobases, at least 11 nucleobases, at least 12 nucleobases, at least 13 nucleobases, at least 14 nucleobases, at least 15 nucleobases, at least 16 nucleobases, at least 17 nucleobases, at least 18 nucleobases, at least 19 nucleobases, at least 20 nucleobases, at least 21 nucleobases, at least 22 nucleobases, at least 23 nucleobases, at least 24 nucleobases, at least 25 nucleobases, at least 26 nucleobases, at least 27 nucleobases, at least 28 nucleobases, at least 29 nucleobases, or at least 30 nucleobases in length.
It will be understood by those skilled in the art that the inclusion of mismatches between a targeting sequence and a target sequence is possible without eliminating the activity of the oligomer (e.g., modulation of splicing). Moreover, such mismatches can occur anywhere within the antisense interaction between the targeting sequence and the target sequence, so long as the antisense oligomer is capable of specifically hybridizing to the targeted nucleic acid molecule. Thus, antisense oligomers of this disclosure may comprise up to about 20% nucleotides that are mismatched, thereby disrupting base pairing of the antisense oligomer to a target sequence, as long as the antisense oligomer specifically hybridizes to the target sequence. In preferred embodiments, antisense oligomers comprise no more than 20%, no more than about 15%, no more than about 10%, no more than about 5% or not more than about 3% of mismatches, or less. In a preferred embodiment, there are no mismatches between nucleotides in the antisense oligomer involved in pairing and a complementary target sequence. Preferably, mismatches do not occur at contiguous positions. For example, in an antisense oligomer containing 3 mismatch positions, it is preferred if the mismatched positions are separated by runs (e.g., 3, 4, 5, etc.) of contiguous nucleotides that are complementary with nucleotides in the target sequence
The use of percent identity is a common way of defining the number of mismatches between two nucleic acid sequences. For example, two sequences having the same nucleobase pairing capacity would be considered 100% identical. Moreover, it should be understood that both uracil and thymidine will bind with adenine. Consequently, two molecules that are otherwise identical in sequence would be considered identical, even if one had uracil at position x and the other had a thymidine at corresponding position x. Percent identity may be calculated over the entire length of the oligomeric compound, or over just a portion of an oligomer. For example, the percent identity of a targeting sequence to a target sequence can be calculated to determine the capacity of an oligomer comprising the targeting sequence to bind to a nucleic acid molecule comprising the target sequence. In one embodiment, the targeting sequence is at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, at least 98% identical or at least 99% identical over its entire length to a target sequence in a target nucleic acid molecule. In one embodiment, the targeting sequence is identical over its entire length to a target sequence in a target nucleic acid molecule.
It is understood by those skilled in the art that an antisense oligomer need not be identical to the oligomer sequences disclosed herein to function similarly to the antisense oligomers described herein. Shortened versions of antisense oligomers taught herein, or non-identical versions of the antisense oligomers taught herein, fall within the scope of this disclosure. Non-identical versions are those wherein each base does not have 100% identity with the antisense oligomers disclosed herein. Alternatively, a non-identical version can include at least one base replaced with a different base with different pairing activity (e.g., G can be replaced by C, A, or T). Percent identity is calculated according to the number of bases that have identical base pairing corresponding to the oligomer to which it is being compared. The non-identical bases may be adjacent to each other, dispersed throughout the oligomer, or both. For example, a 16-mer having the same sequence as nucleobases 2-17 of a 20-mer is 80% identical to the 20-mer. Alternatively, a 20-mer containing four nucleobases not identical to the 20-mer is also 80% identical to the 20-mer. A 14-mer having the same sequence as nucleobases 1-14 of an 18-mer is 78% identical to the 18-mer. Such calculations are well within the ability of those skilled in the art. Thus, antisense oligomers of this disclosure comprise oligonucleotide sequences at least 80% identical, at least 85% identical, at least 90% identical, at least 92% identical, at least 94% identical at least 96% identical or at least 98% identical to sequences disclosed herein, as long as the antisense oligomers are able to modulate splicing of a desired mRNA molecule.
Antisense oligomers of this disclosure are capable of modulating splicing of mRNA molecules. As used herein, “modulation” of splicing refers to the ability of an antisense oligomer to affect the processing of a pre-mRNA transcript such that the resulting spliced mRNA molecule contains a desired combination of exons as a result of exon skipping (or exon inclusion), a deletion in one or more exons, or additional sequence not normally found in the spliced mRNA (e.g., intronic sequences). For example, modulation of splicing can refer to affecting the splicing of a MS4A2 pre-mRNA such that the spliced mRNA (mature mRNA) is missing at least a portion, or the entirety, of one exon. In one embodiment, the spliced mRNA lacks at least a portion of exon 3.
It has previously been discussed that a truncated isoform of the FcεRIβ protein (t-FcεRIβ) is present in cells, and that such truncation is due to a truncation in exon 3 of the mRNA encoding the FcεRIβ protein. The inventors have also shown that the number or “level” of such truncated mRNA molecules is far less than the level of MS4A2 mRNA molecules including full-length exon 3. Thus, for the purposes of describing this disclosure, splicing of an MS4A2 pre-mRNA, due to the influence of an antisense oligomer, to produce a truncated mRNA encoding a truncated FcεRIβ protein, can be referred to as alternative splicing. Further, an MS4A2 mRNA transcript lacking at least a portion, or the entirety, of exon 3, due to the influence of an antisense oligomer, is a product of alternative splicing. Thus, in the context of this disclosure, modulation of splicing can refer to inducing alternative splicing of an MS4A2 pre-mRNA molecule, thereby reducing the level of mRNA molecules containing the entirely of exon 3, and increasing the level of mRNA molecules lacking at least a portion of exon 3.
One embodiment of this disclosure is an antisense oligomer comprising 10 to 50 linked nucleosides, wherein the oligomer is targeted to a region of an RNA molecule encoding an FcεRIβ protein. In a preferred embodiment, hybridization of the oligomer to the RNA molecule modulates splicing of the RNA molecule.
One embodiment of this disclosure is an antisense oligomer comprising a nucleic acid sequence sufficiently complementary to a target sequence in a target region of an MS4A2 mRNA molecule, such that the antisense oligomer specifically hybridizes to the target sequence, thereby modulating splicing of an MS4A2 mRNA transcript.
These antisense oligomers may consist of 10 to 50 linked nucleosides. These antisense oligomers may comprise 15 to 35 linked nucleotides. These antisense oligomers may consist of 15 to 35 linked nucleotides. These antisense oligomers may comprise or consist of 10 linked nucleosides, 11 linked nucleosides, 12 linked nucleosides, 13 linked nucleosides, 14 linked nucleosides, 15 linked nucleosides, 16 linked nucleosides, 17 linked nucleosides, 18 linked nucleosides, 19 linked nucleosides, 20 linked nucleosides, 21 linked nucleosides, 22 linked nucleosides, 23 linked nucleosides, 24 linked nucleosides, 25 linked nucleosides, 26 linked nucleosides, 27 linked nucleosides, 28 linked nucleosides, 29 linked nucleosides, 30 linked nucleosides, 31 linked nucleosides, 32 linked nucleosides, 33 linked nucleosides, 34 linked nucleosides, 34 linked nucleosides, 36 linked nucleosides, 37 linked nucleosides, 38 linked nucleosides, 39 linked nucleosides, 40 linked nucleosides, 41 linked nucleosides, 42 linked nucleosides, 43 linked nucleosides, 44 linked nucleosides, 45 linked nucleosides, 46 linked nucleosides, 47 linked nucleosides, 48 linked nucleosides, 49 linked nucleosides, or 50 linked nucleosides.
The mRNA molecule may encode an FcεRIβ protein from any mammal that produces an FcεRIβ protein. Examples of such mammals include, but are not limited to, a human, a mouse, a dog, a cat, and a horse. In one embodiment, the mRNA comprises a nucleotide sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to SEQ ID NO:1 or SEQ ID NO:3. In one embodiment, the mRNA encodes a protein comprising an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99% identical to SEQ ID NO:2 or SEQ ID NO:4. In one embodiment, the mRNA encodes a protein comprising SEQ ID NO:2 or SEQ ID NO:4.
The RNA molecule may be an MS4A2 transcript. In one embodiment, the RNA molecule is an MS4A2 mRNA molecule. In preferred embodiments, the RNA molecule is an MS4A2 pre-mRNA.
The target region targeted by the antisense oligomer can be any region of the RNA molecule that is functionally involved in splicing of the RNA molecule. By “functionally involved in splicing” is meant the sequences in the target region are utilized by the cellular splicing apparatus (e.g., the spliceosome or components thereof) to effect splicing of the mRNA molecule. Examples of such regions include, but are not limited to, regions comprising intron sequences, regions comprising exon sequences, regions comprising intron/exon junctions, regions comprising splice donor site sequences, regions comprising splice acceptor site sequences, regions comprising splice enhancer site sequences, regions comprising branch point sequences, and regions comprising polypyrimidine tracts. Such sequences are known to those skilled in the art. Such sequences are also disclosed herein.
Thus in one embodiment, the target region comprises at least a portion of a sequence selected from the group consisting of an exon sequence, an intron sequence, a sequence comprising an exon/intron junction, a splice donor site sequence, a splice acceptor site sequence, a splice enhancer site sequence, a branch point sequence, and a polypyrimidine tract. In the context of this disclosure, “at least a portion” refers to at least 5 nucleosides, at least 6 nucleosides, at least 7 nucleosides, at least 8 nucleosides, at least 9 nucleosides, at least 10 nucleosides, at least 11 nucleotides, at least 12 nucleosides, at least 13 nucleotides, at least 14 nucleosides, at least 15 nucleosides, at least 16 nucleosides, at least 17 nucleosides, at least 18 nucleosides, at least 19 nucleosides, or at least 20 nucleosides in length. In one embodiment, the at least a portion comprises at least 10%, at least 25%, at least 50%, at least 75%, at least 90%, at least 90%, at least 95% or at least 97% of a known splice donor site sequence, splice acceptor site sequence, splice enhancer site sequence, branch point sequence or polypyrimidine sequence. The splice donor site sequence, splice acceptor site sequence, splice enhancer site sequence, branch point sequence or polypyrimidine sequence may be from an MS4A2 pre-MRNA.
In one embodiment, the target region comprises at least a portion of an MS4A2 sequence of this disclosure, which may be any one of SEQ ID Nos: 1-1015, including SEQ ID NOs:22-1006. In one embodiment, the at least a portion comprises at least 10%, at least 25%, at least 50%, at least 75%, at least 80%, at least 90% at least 95% or at least 97% of an MS4A2 sequence of this disclosure. In one embodiment, the at least a portion comprises a polynucleotide sequence at least 80%, at least 90% at least 95% or at least 97% identical to a portion of an MS4A2 sequence of this disclosure.
In one embodiment, the target region comprises a nucleotide sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to at least a portion of a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. In one embodiment, the target region comprises at least a portion of a sequence selected from the group consisting of SEQ ID NOs:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. In one embodiment, the target region comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015.
In one embodiment, the antisense oligomer is targeted to a region or sequence involved in splicing of an MS4A2 pre-mRNA. In one embodiment, the antisense oligomer is target to an MS4A2 intron sequence, an MS4A2 exon sequence, an MS4A2 splice donor site sequence, an MS4A2 splice acceptor site sequence, an MS4A2 splice enhancer site sequence, an MS4A2 branch point sequence, or an MS4A2 polypyrimidine tract. In one embodiment, the antisense oligomer is targeted to exon 3 of an MS4A2 pre-mRNA. In one embodiment, the antisense oligomer is targeted to an MS4A2 exon 3 splice donor sequence, an exon 3 splice acceptor sequence, or an exon 3 spice enhancer sequence.
In one embodiment, the antisense oligomer is targeted to a target molecule comprising a sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. In one embodiment, the antisense oligomer is targeted to a target molecule comprising a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015.
In one embodiment, the antisense oligomer is targeted to a sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence selected from the group consisting of SEQ ID NOs:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. In one embodiment, the antisense oligomer is targeted to a sequence selected from the group consisting of SEQ ID NOs:5-17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015.
In one embodiment, the antisense oligonucleotide is targeted to a sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence selected from the group consisting of SEQ ID NOs:11-17. In one embodiment, the antisense oligonucleotide is targeted to a sequence selected from the group consisting of SEQ ID NOs:11-17.
In one embodiment, the antisense oligomer comprises a targeting sequence at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to a sequence fully complementary to at least a portion of a splice donor site sequence, a splice acceptor site sequence, a splice enhancer site sequence, a branch point sequence or a polypyrimidine sequence from an MS4A2 mRNA. In one embodiment, the antisense oligomer comprises a targeting sequence fully complementary to at least a portion of a splice donor site sequence, a splice acceptor site sequence, a splice enhancer site sequence, a branch point sequence, or a polypyrimidine sequence from an MS4A2 mRNA. In one embodiment, the antisense oligomer comprises a targeting sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence fully complementary to at least a portion of a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. In one embodiment, the antisense oligomer comprises a targeting sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence fully complementary to at least a portion of a sequence selected from the group consisting of SEQ ID NOs:11-17. The portion is preferably least 10 nucleotides in length. The antisense oligomer may modulate splicing of an MS4A2 pre-mRNA molecule.
In one embodiment, the targeting sequence comprises a sequence at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, the targeting sequence consists of a sequence at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, the targeting sequence comprises a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, the targeting sequence consists of a sequence selected from the group consisting of SEQ ID NOs:22-SEQ ID NO:1006. The portion is preferably at least 10 nucleotides in length. The antisense oligomer may modulate splicing of an MS4A2 pre-mRNA molecule.
In one embodiment, the target region comprises at least a portion of a sequence selected from an MS4A2 splice donor site sequence, an MS4A2 splice acceptor site sequence, an MS4A2 splice enhancer site sequence, an MS4A2 branch point sequence and an MS4A2 polypyrimidine sequence. In one embodiment, the at least a portion comprises at least 10%, at least 25%, at least 50%, at least 75%, at least 90% or at least 90% of an MS4A2 splice donor site sequence, an MS4A2 splice acceptor site sequence, an MS4A2 splice enhancer site sequence, an MS4A2 branch point sequence or an MS4A2 polypyrimidine sequence. The MS4A2 splice donor site sequence, the MS4A2 splice acceptor site sequence, the MS4A2 splice enhancer site sequence, the MS4A2 branch point sequence, or the MS4A2 polypyrimidine sequence, may be from exon 3 of an MS4A2 pre-mRNA. The portion may be at least 10 nucleotides in length. The antisense oligomer may modulate splicing of an MS4A2 pre-mRNA molecule.
In one embodiment, the complementary nucleic acid sequence comprised by the antisense oligomer (i.e., the “targeting sequence”) is at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to a sequence fully complementary to at least a portion of a splice donor site sequence, splice acceptor site sequence, splice enhancer site sequence, branch point sequence or polypyrimidine sequence from an MS4A2 mRNA. In one embodiment, the complementary nucleic acid sequence comprised by the antisense oligomer comprises a sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence fully complementary to a portion of a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, and an MSR4A2 sequence comprising any one of SEQ ID NOs:1007-1015. In one embodiment, the complementary nucleic acid sequence comprised by the antisense oligomer comprises a sequence at least 80%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to a sequence fully complementary to a portion of a sequence selected from the group consisting of SEQ ID NOs:11-17. The portion may be at least 10 nucleotides in length. The antisense oligomer may modulate splicing of an MS4A2 pre-mRNA molecule.
In one embodiment, the complementary nucleic acid sequence of the antisense oligomer comprises a sequence at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, the complementary nucleic acid sequence comprised by the antisense oligomer consists of a sequence at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, the complementary nucleic acid sequence comprised by the antisense oligomer comprises a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, the complementary nucleic acid sequence comprised by the antisense oligomer consists of a sequence selected from the group consisting of SEQ ID NOs:22-1006.
In one embodiment, an antisense oligomer comprises a sequence at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs:22-1006. In one embodiment, an antisense oligomer comprises a sequence selected from the group consisting of SEQ ID NO:22-1006.
One embodiment of this disclosure is an expression vector that expresses an antisense oligomer of this disclosure. As used herein, an “expression vector” is a nucleic acid molecule comprising a polynucleotide sequence functionally linked to a promoter, such that transcription of the polynucleotide sequence by a polymerase results in production of an antisense oligomer of this disclosure. Exemplary expression vectors include polynucleotide molecules, preferably DNA molecules, that are derived, for example, from a plasmid, bacteriophage, yeast or virus (e.g., adenovirus, adeno-associated virus, lentivirus, retrovirus, etc.), into which a polynucleotide can be inserted or cloned. Suitable expression vectors are known to those skilled in the art.
One embodiment of this disclosure is a pharmaceutical composition comprising an antisense oligomer or expression vector of this disclosure. Such compositions are suitable for the therapeutic delivery of antisense oligomers, or expression vectors, described herein. Hence, this disclosure provides pharmaceutical compositions that comprise a therapeutically-effective amount of one or more of the antisense oligomers or expression vectors described herein, formulated together with one or more pharmaceutically-acceptable carriers (additives) and/or diluents. While it is possible for an antisense oligomer or expression vector of this disclosure to be administered alone, it is preferable to administer the compound as a pharmaceutical composition.
Pharmaceutical compositions of this disclosure may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; (8) inhaled into the lungs, for example, by nebulizer or aerosol inhaler; or (9) nasally. Examples of suitable carriers, additives and diluents are described in U.S. Patent Publication No. 2015/0361428, which is incorporated herein by reference in its entirety.
As has been described above, antisense oligomers of this disclosure are capable of reducing cell-surface expression of FcRI. Such reduction is achieved by modulating splicing of an mRNA molecule encoding a FcεRIβ protein. More specifically, antisense oligomers of this disclosure decrease the production of FcεRIβ-encoding mRNA molecules comprising exon 3, and increase the production of FcεRIβ-encoding mRNA molecules lacking exon 3. Because these latter FcεRIβ-encoding mRNA molecules lack exon 3, the encoded FcεRIβ proteins lack the first transmembrane domain, which is required for trafficking of the FcεRI complex to the cell membrane.
Thus, one embodiment of this disclosure is a method of modulating splicing of an FcεRIβ mRNA in a cell, the method comprising contacting the cell with an antisense oligomer of this disclosure. The cell may be any cell expressing an FcεRIβ mRNA molecule. Accordingly, the cell can be a cell in culture, or a cell in the body of an individual. In one embodiment, the cell is an epidermal Langerhans cell, an eosinophil, a mast cell, or a basophil. In a specific embodiment, the cell is a mast cell.
The mRNA may comprise a nucleotide sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% identical to SEQ ID NO:1 or SEQ ID NO:3. In one embodiment, the mRNA encodes a protein comprising an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to SEQ ID NO:2 or SEQ ID NO:4. In one embodiment, the mRNA encodes a protein comprising SEQ ID NO:2 or SEQ ID NO:4.
In one embodiment, the antisense oligomer hybridizes to a target region that is involved in splicing of MS4A2 pre-mRNA. In one embodiment, the antisense oligomer hybridizes to a target region in the mRNA comprising at least a portion of a sequence selected from the group consisting of an MS4A2 splice donor site sequence, an MS4A2 splice acceptor site sequence, an MS4A2 splice enhancer site sequence, an MS4A2 branch point sequence and an MS4A2 polypyrimidine sequence. The MS4A2 splice donor site sequence, the MS4A2 splice acceptor site sequence, the MS4A2 splice enhancer site sequence, the MS4A2 branch point sequence, or the MS4A2 polypyrimidine sequence may be from exon 3 of an MS4A2 pre-mRNA.
Modulation of splicing of FcεRIβ pre-mRNA by antisense oligomers of this disclosure can result in production of a truncated mRNA (t-FcεRIβ mRNA), which produces a truncated form of the FcεRIβ protein. t-FcεRIβ mRNA differs from full-length FcεRIβ mRNA (FL-FcεRIβ mRNA) in that it is truncated in exon 3, thereby producing an FcεRIβ protein lacking the first and second membrane-spanning regions. Normally, the amount of FL-FcεRIβ mRNA in mast cells is greater than the amount of t-FcεRβ mRNA. Thus, one embodiment of this disclosure is a method of altering the ratio of FL-FcεRIβ mRNA to t-FcεRIβ mRNA in a mast cell, the method comprising contacting the mast cell with an antisense oligomer of this disclosure. Contact of a mast cell with an antisense oligomer of this disclosure may cause a decrease in the amount of FL-FcεRβ mRNA and an increase in the amount of t-FcεRβ mRNA. Contact of a mast cell with an antisense oligomer of this disclosure may result in a decreased FL-FcεRβ mRNA/t-FcεRβ mRNA ratio. In one embodiment, the amount of FL-FcεRβ produced by the cell is decreased by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, least 97%, or at least 99%.
One embodiment of this disclosure is a method of reducing cell surface expression of FcεRI protein in a cell, the method comprising contacting the cell with an antisense oligomer of this disclosure. In embodiments of this disclosure, the cell can be any cell expressing an FcεRI protein on its surface. Accordingly, the cell can be a cell in culture (e.g., tissue culture) or a cell in the body of an individual. In one embodiment, the cell is an epidermal Langerhans cell, an eosinophil, a mast cell or a basophil. In a specific embodiment, the cell is a mast cell.
In one embodiment, the amount of FcεRI expressed on the surface of the cell is decreased by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or at least 99%.
Mast cells are tissue-bound cells of the innate immune system which are well known for immunoglobulin (Ig)E-triggered degranulation in allergic reactions. Consequently, mast cells express large quantities of FcεRI receptor on their surface. As the binding of IgE to FcεRI is essentially irreversible, mast cells are largely covered with IgE. The main function of mast cells is considered to be degranulation, with immunoglobulin (Ig)E as the main trigger. Once an IgE molecule encounters a specific antigen or allergen, IgE:FcεRI-crosslinking and calcium influx leads to degranulation of the mast cells. As a result, histamine is released and causes the well-known symptoms such as bronchoconstriction or pruritus. Thus, one embodiment of this disclosure is a method of modulating FcεRI-dependent mast-cell degranulation, the method comprising contacting a mast cell with an antisense oligomer of this disclosure. In accordance with this disclosure, the cell can be a cell in culture (e.g., tissue culture) or a cell in the body of an individual.
Upon activation, mast cells rapidly release pre-formed mediators from cytoplasmic granules, such as vasoactive amines (e.g., histamine and serotonin), proteoglycans (e.g., heparin), proteases (e.g., tryptases and chymases), and some pre-stored cytokines (e.g., TNFα). They also release a plethora of mediators, including growth factors, cytokines, and chemokines, such as IL-1, IL-6, IL-8, IL-10, TNFα, VEGF, TGFβ, CCL2-4, as well as pro-inflammatory lipid mediators, such as prostaglandins and leukotrienes. Thus, one embodiment of this disclosure is a method of modulating the release of one or more mediators from a mast cell, the method comprising contacting a mast cell with an antisense oligomer of this disclosure, where the one or more mediators is selected from the group consisting of a mast cell-produced vasoactive amine, a mast cell-produced proteoglycan, a mast cell-produced protease, a cytokine, a growth factor, a chemokine, and a pro-inflammatory lipid mediator. The one or more mediator may be any one of histamine, serotonin, heparin, tryptase, chymase, TNFα, IL-1, IL-6, IL-8, IL-10, TNFα, VEGF, TGFβ, CCL2-4, a prostaglandin, and a leukotriene. In specific embodiments, the mast cell can be a cell in culture, or a cell in the body of an individual.
As players in innate immunity, mast cells have the capacity to initiate and amplify immune responses (see, Bulfone-Paus and Rahri, Front. Immunol. 2015; 6:394). Several lines of evidence have demonstrated that mast cells participate in the sensitization phase of acquired immune responses via the secretion of mediators, which sustain dendritic cell (DC) maturation, function, and recruitment to the tissue or their migration to local draining lymph nodes. However, mast cells also exert important effector functions, since mast cells and T cells of different origin and subsets establish tight cell-cell interactions and modulate their respective effector functions in a bidirectional manner; this has been shown in a variety of models. Thus, one embodiment of this disclosure is a method of reducing an immune response in an individual, the method comprising administering an antisense oligomer of this disclosure to the individual. Such immune response can, but need not be, IgE-mediated immune responses.
An antisense oligomer of this disclosure may be administered to any individual expressing an FcεRIβ protein. As used herein, the terms individual, subject, patient, and the like, are meant to encompass any mammal that expresses an FcεRIβ protein, with a preferred mammal being a human. The terms individual, subject, and patient by themselves do not denote a particular age, sex, race, and the like. Thus, individuals of any age, whether male or female, are intended to be covered by this disclosure. Likewise, the methods of this disclosure can be applied to any race of human, including, for example, Caucasian (white), African-American (black), Native American, Native Hawaiian, Hispanic, Latino, Asian, and European. In some embodiments of this disclosure, such characteristics may be significant. In such cases, the significant characteristic(s) (e.g., age, sex, race, etc.) will be indicated. Additionally, the term “individual” encompasses both human and non-human animals. Suitable non-human animals to which antisense oligomers of this disclosure may be administered include, but are not limited to companion animals (i.e. pets), food animals, work animals, or zoo animals. Preferred animals include, but are not limited to, cats, dogs, horses, ferrets and other Mustelids, cattle, sheep, swine, and rodents.
Antisense oligomers of this disclosure can be administered to an individual by any suitable route of administration. Examples of such routes include, but are not limited to, oral and parenteral routes, (e.g., intravenous (IV), subcutaneous, intraperitoneal (IP), and intramuscular), inhalation (e.g., nebulization and inhalation) and transdermal delivery (e.g., topical). Any methods effective to deliver an antisense oligomer of this disclosure into the bloodstream of an individual are also contemplated in these methods. For example, transdermal delivery of antisense oligomers may be accomplished by use of a pharmaceutically acceptable carrier adapted for topical administration. Antisense oligomers can be administered in the absence of other molecules, such as proteins or lipids, or they be administered in a complex with other molecules, such as proteins or lipids. For example, the use of cationic lipids to encapsulate antisense oligomers is disclosed in U.S. Pat. Nos. 8,569,256, and 6,806,084, which are incorporated herein by reference in their entirety. Similarly, the use of peptide-linked morpholino antisense oligonucleotides is disclosed in U.S. Patent Publication No. 2015/0238627, which is incorporated herein by reference. IgE and IgE-mediated immune responses are known to be involved in numerous allergic conditions. Because antisense oligomers of this disclosure can reduce FcεRI-mediated responses, such antisense oligomers can be used to treat allergic conditions. Thus, one embodiment of this disclosure is a method of treating an allergic condition in an individual, by administering to an individual in need of such treatment an antisense oligomer of this disclosure. Allergic conditions being treated can be any condition mediated by a pathway comprising FcεRI. Such conditions include, but are not limited to, asthma, food allergies allergic conjunctivitis, and atopic dermatitis.
In an allergic person, whose tissue mast cells and other cell types already have antigen-specific IgE bound to FcεRI, re-exposure to the original or a cross-reactive bivalent or multivalent antigen results in the cross-linking of adjacent FcεRI-bound IgE and the consequent aggregation of surface FcεRI. When the FcεRI aggregation is of sufficient strength and duration, it triggers mast cells and basophils to initiate complex signaling events that ultimately result in the secretion of a diverse group of biologically active products. In aggregate, mediators released shortly after antigen- and IgE-induced mast cell degranulation induce a response termed an immediate hypersensitivity (or early phase) reaction within minutes of their release. If localized to the airways, this response is characterized by increased vascular permeability, contraction of the airway smooth muscle and enhanced secretion of mucus, resulting in acutely reduced airflow and wheezing. If the response is systemic, it can result in anaphylaxis, a catastrophic immune response that can rapidly result in death if not properly treated (for a review, see Galli and Tsai, Nature Medicine. 2012 May 4; 18(5):693-704). Thus, one embodiment of this disclosure is a method for preventing or treating an anaphylactic reaction in an individual, the method comprising administering to an individual in need of such treatment an antisense oligomer of this disclosure. The antisense oligomer of this disclosure may be administered in advance of an anaphylactic reaction or anticipated anaphylactic reaction in the individual. The antisense oligomer of this disclosure is preferably administered at regular intervals to prevent or reduce the incidence and/or severity of any anaphylactic reaction in an individual at risk of having an anaphylactic reaction or developing anaphylactic shock. The individual being treated may or may not be at immediate risk for having an anaphylactic reaction. One embodiment of this disclosure is a method of modulating an anaphylactic reaction in an individual, the method comprising administering to an individual in need of such treatment an antisense oligomer of this disclosure.
Mastocytosis is a rare mast cell activation disorder caused by an individual having too many mast cells and mast cell precursors. Because mast cells are involved in atopic responses, individuals suffering from mastocytosis are susceptible to hives, itching and anaphylactic shock. Thus, one method of this disclosure is a method of treating an individual suffering from mastocytosis, the method comprising administering to an individual in need of such treatment an antisense oligomer of this disclosure. The individual may or may not already be exhibiting symptoms of mastocytosis, such as itching, hives and anaphylaxis. In one embodiment, an antisense oligomer is administered to an individual at risk for developing symptoms of mastocytosis.
Mast cells are produced in the bone marrow and are found throughout the connective tissue of the body. In some individuals, mast cells accumulate the skin, forming clusters that appear as a bump. Such clusters of mast cells are referred to as mastocytomas. A common symptom resulting from a mastocytoma is itching, although afflicted individuals can also experience urticarial, pigmentosa, flushing, nausea, vomiting, diarrhea and abdominal pain. One method of this disclosure is a method of treating an individual diagnosed with a mastocytoma or suspected of having a mastocytoma, by administering to the individual an antisense oligomer of this disclosure. In one embodiment, administration of an antisense oligomer eliminates one or more symptom(s) resulting from a mastocytoma.
This disclosure also provides kits for modulating splicing of an FcεRIβ mRNA, reducing cell surface expression of an FcεRI protein, modulating an anaphylactic reaction in an individual, and/or treating an individual for an allergic condition, the kit comprising at least one antisense oligomer of this disclosure. The kit may also comprise instructions for using the kit, and various reagents, such as buffers, necessary to practice the methods of this disclosure. These reagents or buffers may be useful for administering an antisense oligomer of this disclosure to a cell or an individual. The kit may also comprise any material necessary to practice the methods of this disclosure, such as syringes, tubes, swabs, and the like.

EXAMPLES

Example 1. Design of Antisense Oligonucleotides (AONs)

Antisense technology was utilized to demonstrate that manipulation of MS4A2 mRNA splicing to favor t-FcεRIβ formation would disrupt FcεRI expression and signaling, thereby rendering cells unresponsive to IgE-mediated antigen challenge. To achieve this, AONs were designed to target exon 3 of MS4A2 mRNA for the human (NM 000139.4) or mouse (NM 013516.2) genes. Specifically, AONs were designed to hybridize to the MS4A2 exon 3 splice donor site, the MS4A2 splice acceptor site and a potential MS4A2 splice enhancer site. AON constructs were then purchased from Gene-Tools (Philomath, Oreg.), and contained proprietary morpholino chemistry. For the mouse AON, a region within the splicing acceptor region was targeted with the sequence
(SEQ ID NO: 22)

5′-GTGTTGCCTGTGGAAAACATGAATT-3′

For the human AON, an open sequence within exon was targeted with the AON sequence:
(SEQ ID NO: 14)

5′-AGTACAGAGCAGACAACTGTTCA-3′

The standard control AON, provided by Gene-Tools, had sequence:
(SEQ ID NO: 23)

5′-CCTCTTACCTCAGTTACAATTTATA-3′

For in vivo studies, Vivo-Morpholino Chemistry (Gene-Tools) was used.

Example 2. Transfection Efficiency and Cytotoxicity of AONs

The inventors examined the ability of AONs of this disclosure to efficiently transfect mast cells using a FITC-conjugated morpholino AON in primary mouse bone marrow-derived mast cells (BMMC), and in the transformed human mast cell lines HMC-1.1, HMC-1.2, and LAD-2 cells. Human mast cell lines were cultured in StemPro-34 medium containing StemPro-34 Nutrient Supplement, L-glutamine (2 mM), Penicillin (100 U/ml)/Streptomycin (100 μg/ml) (GIBCO) with 100 ng/ml recombinant human SCF added (Peprotech). Half of the medium supplemented with SCF was changed every 7 days. 2×10⁶mast cells were used for each transfection. To determine transfection efficiency, 10 μM of FITC-conjugated standard control 25mer AON was used (purchased from Gene-Tools). All other AONs were not conjugated. Transfection was achieved using the Nucleofector II and Cell Line Kit V (Lonza). Program U-025 (aortic smooth muscle program) was used for LAD-2 human mast cells and program X-001 was used for mouse BMMCs.
Greater than 80% transfection efficiency was achieved in all cells tested, as determined using FITC-conjugated AON (FIG. 1A). Greater than 95% efficiency was observed in mouse BMMC and human LAD-2 cells at 24 h (FIGS. 1A and 1B) and 48 h. There was no further increase in transfection efficiency at 48 h when compared to 24 h. Cell viability was determined by propridium iodide staining. No evidence of cytotoxicity with AON transfection in either human LAD-2 cells or mouse BMMCs was observed.

Example 3. Induction of Exon-Skipping in Mast Cells

AONs targeted to either mouse MS4A2 or human MS4A2 exon 3 were measured for their ability to induce exon-skipping in human and mouse mast cells. Murine mast cells were transfected with either 10 μM of standard control AON (non-matching 25-mer morpholino AON; SEQ ID NO:15) or 10 μM of 25-mer morpholino AON targeted against a region within the splicing acceptor site at the intron-exon boundary (SEQ ID NO:13). Human mast cells were transfected with either 10 μM of standard control AON (non-matching 25-mer morpholino AON) or 10 μM of 25-mer morpholino AON targeted against an exposed exonic splicing enhancer site within MS4A2 exon 3 (SEQ ID NO:14). AONs were transfected as described in Example 2 and the resulting effect on splicing determined by PCR. Briefly, 24 h after transfection, mast cells were washed twice in ice cold PBS and total RNA was isolated using the RNAeasy plus mini-kit (QIAGEN™) according to the manufacturer's instructions with inclusion of the QIAShredder step. RT-PCR was carried out using the QIAGEN™ One-Step RT-PCR kit with 2 μg of total RNA and 1 μM of each primer. Reverse transcription and PCR was carried out in the same tube in one step with 1 cycle at 50° C. for 30 min, 1 cycle at 95° C. for 15 min, 35 cycles of 94° C. for 45 sec-55° C. for 45 sec-72° C. for 1 min, followed by a final 1 cycle at 72° C. for 10 min. The primers used were designed to amplify the open reading frames. For mouse FcεRIβ mRNA the following primers were used:
Forward-

(SEQ ID NO: 18)

5′-ATGGACACAGAAAATAGGAGCA-3′

Reverse-

(SEQ ID NO: 19)

5′-TGAATCAACTGGAGAAGATGTTT-3′

For human FcεRIβ mRNA the following primers were used:
Forward-

(SEQ ID NO: 20)

5′-ATGGACACAGAAAGTAATAGGAG-3′

Reverse-

(SEQ ID NO: 21)

5′-TTATAAATCAATGGGAGGAGAC-3′.

The results of this analysis, which are shown in FIGS. 2A and 2D, demonstrate that both the mouse and human FcεRIβ AONs induced exon-skipping of FcεRIβ mRNA in mouse and human mast cells, respectively, when compared to cells transfected with an equivalent amount of 25-mer standard control AON.

Example 4. Effect of AONs on FcεRI Surface Expression in Mast Cells

The first transmembrane domain of FcεRIβ is required for trafficking of the receptor complex, whilst the C-terminal immunoreceptor tyrosine-based activation motif (ITAM) amplifies signaling. A truncation of MS4A2 exon 3 (t-FcεRIβ) leads to loss of the first two transmembrane domains of FcεRIβ resulting in the expression of t-FcεRIβ that does not traffic to the plasma membrane nor associate with FcεRI. Therefore, AON-induced skipping of exon 3 should result in preferential production of t-FcεRIβ instead of FL FcεRIβ with subsequent loss of expression of surface FcεRI, which is dependent on FL FcεRIβ. Thus, surface expression of FcεRI in the mast cells of Example 3 were measured by flow cytometry. The results of this analysis, which are shown in FIGS. 2A, 2B and 2C, demonstrate that surface FcεRI expression in mouse BMMCs was reduced by 95.6±0.4% (n=5, p<0.001) (FIG. 2B), thus virtually eliminating FcεRI expression (FIG. 2A). In human LAD-2 mast cells, surface FcεRIα expression was reduced by 48.7±2.8% (n=5, p<0.001) (FIG. 2C). Thus, both the mouse and human AONs reduced surface FcεRI expression and induced exon-skipping (FIG. 2D) in a dose-dependent manner. Loss of surface FcεRI expression was evident as soon as 4 h and maximal by 24 h with no evidence of loss of efficacy over the 5-day time-course tested in both human and mouse cells.

Example 5. Effect of AONs on Mast Cell Ig-E Responsiveness

In view of the loss of surface FcεRI expression with FcεRIβ AON transfection, transfected mast cells were analyzed for a corresponding reduction in responses to antigen in BMMCs. To measure degranulation, mast cells transfected as described above were cultured for 32 h to allow for loss of surface FcεRI expression. The cells were then sensitized with 100 ng/ml of biotinylated IgE for human cells, or anti-DNP IgE (SPE7 clone) (Sigma) for mouse cells, and incubated overnight (16 h). Degranulation was assayed by β-hexosaminidase release as described by Kuehn et al. (Measuring Mast Cell Mediator Release. Current protocols in immunology/edited by John E. Coligan, et al. CHAPTER (2010): Unit7.38). Briefly, cells were washed twice in HEPES buffer (10 mM HEPES, 137 mM NaCl, 2.7 mM KCl, 0.4 mM Na2HPO₄.7H₂O, 5.6 mM glucose, 1.8 mM CaCl₂.2H₂O, and 1.3 mM MgSO₄.7H₂O with 0.04% BSA) and 1×10⁴(LAD-2 cells) or 2.5×10⁴(BMMCs) were plated into a 96 well plate in 100 μl HEPES buffer. Cells were stimulated with indicated stimuli and incubated for 30 min at 37° C. before centrifugation at 250×g for 5 min at 4° C. Supernatants were removed and the pellets were lysed with 0.1% triton-X 100 for calculation of released β-hexosaminidase.
The results of this analysis, which are shown in FIGS. 3A and 3B, show a dose-dependent decrease in degranulation in response to DNP with increasing concentrations of FcεRIβ AON (FIG. 3A). They also show that degranulation was eliminated with 10 μM FcεRIβ AON (FIG. 3A). However, 1 μM FcεRIβ AON resulted in 80% reduction in surface FcεRI expression (FIG. 2C) while the reduction in degranulation, though significant, was lower (˜25%) (FIG. 3A). A possible explanation for this disparity is that the number of FcεRI receptors and signaling capacity may far exceed the requirements for degranulation. It is estimated that RBL-2H3 mast cells have five-fold more receptors and capacity to generate inositol phosphate and calcium signals than is required for maximal secretory responses. FcεRI numbers vary during the cell cycle and among different mast cell types, with estimates ranging from 130,000 in human lung mast cells to 290,000/cell in RBL-2H3 cells and 120,000 to 380,000 in human cord blood-derived mast cell/basophil cultures. It is likely that mast cells in general harbor surplus FcεRI as significant degranulation is observed with aggregation of a few hundred receptors (Maeyama, K., et al, J. Biol. Chem. 261:2583-92 (1986)).
The specificity of FcεRIβ AON treatment was next determined by its effect on thapsigargin-induced degranulation. The results of these studies, which are shown in FIG. 3B, demonstrate that while FcεRI-dependent degranulation was eliminated in BMMCs (FIG. 3B, left panel), thapsigargin-induced degranulation was unaffected by FcεRIβ exon-skipping (FIG. 3B, right panel)).
In addition to measuring degranulation, changes in cytosolic Ca²⁺ levels were determined following loading of the cells with Fura-2 AM ester (Molecular Probes) as described by Tkaczyk, C., et al. (J. Biol. Chem., 278:48474-84). BMMCs were transfected as described above. Cells were cultured for 32 h and then sensitized with 100 ng/ml anti-DNP IgE (SPE7 clone) for 16 h. Fluorescence was measured at two excitation wavelengths (340 and 380 nm) and an emission wavelength of 510 nm. The ratio of the fluorescence readings was calculated following subtraction of the fluorescence of the cells that had not been loaded with Fura-2 AM. The results of this analysis, which are shown in FIG. 3C, demonstrate transfection with an AON causes a robust inhibition of the calcium signal in response to FcεRI aggregation (FIG. 3C, left panel). In contrast, the response to thapsigargin was unaffected (FIG. 3C, right panel). As with thapsigargin, IgE-mediated calcium influx is dependent upon store-operated calcium entry. Thus, FcεRIβ exon-skipping appears to selectively target IgE-dependent activation without disrupting cell responses to other stimuli. A similar trend was observed in human LAD-2 cells with a reduction in IgE-dependent degranulation (FIG. 4A) and no reduction in thapsigargin-induced degranulation (FIG. 4B), or compound 48:80-induced degranulation.

Example 6. Modulation of Cytokine Production by AONs

The effects of FcεRIβ exon-skipping on cell signaling events that regulate both degranulation and de novo cytokine synthesis were examined. Specifically, studies were conducted to determine whether residual weak signals that fail to stimulate degranulation were sufficient to induce synthesis of cytokines. Briefly, BMMCs were transfected as described above. Cells were cultured for 32 h and then BMMCs were sensitized with 100 ng/ml anti-DNP IgE (SPE7 clone) for 16 h (DNP stimulated cells only) and some cells were not sensitized with IgE (all other conditions). Cytokine release was assayed at a cell concentration of 1×10⁶BMMCs per ml. Mouse GM-CSF cytokines was measured using Duo-Set ELISAs (R & D Systems) according to the manufacturer's instructions.
No significant FcεRI-mediated phosphorylation of PLCγ1 was observed following FcεRIβ AON transfection. However, unlike FcεRI-mediated activation, thapsigargin did not induce phosphorylation since it acts independently of PLCγ (FIGS. 5A and 5B). While phosphorylation of AKT and ERK are more distal signals than PLCγ1 phosphorylation, the phosphorylation of both of AKT and ERK were also markedly reduced by FcεRIβ exon-skipping (FIGS. 5A, 5C and 5D). In contrast to PLCγ1, the AKT and ERK pathways are activated by thapsigargin, but neither AKT nor ERK phosphorylation was affected by FcεRIβ exon-skipping (FIGS. 5A, 5C and 5D). Low level activation of mast cells can result in the production of cytokines without evidence of acute signaling events. One such example is IgE alone, which did not elicit rapid phosphorylation of PLCγ1, AKT or ERK (FIG. 5A-5D), but did cause robust release of the cytokine GM-CSF after 6 h (FIG. 5E). Furthermore, this release, as well as that induced by IgE plus antigen to induce FcεRI aggregation, was blocked by FcεRIβ exon-skipping without affecting thapsigargin-induced GM-CSF release in BMMCs (FIG. 5E).

Example 7. Effect of AONs on Cell Migration

It has been reported that antigen induces IgE-dependent BMMC migration. Thus, the effects of exon-skipping on antigen-mediated BMMC migration were examined. Briefly, BMMCs were transfected as described above. Cells were cultured for 32 h and then some cells were sensitized with 100 ng/ml anti-DNP IgE (SPE7 clone) for 16 h (to measure migration towards DNP) while some cells were not sensitized with IgE (to measure migration towards SCF). Migration was assayed using transwell chambers as described by Cruse, G. et al. (I Allergy and Clin. Immun. 128:1303-09; and Thorax 61:880-85) with the exception that transwells with 5 μm pores were used for BMMCs instead of 8 μm pores for human cells. 2×10⁵BMMCs were loaded into the top chamber and the percentage of cells that migrated to the bottom chamber was calculated.
The results show that standard control AON treated BMMCs sensitized with IgE migrated towards antigen (DNP-BSA); however, FcεRIβ AON treated BMMCs did not (FIG. 5F). However, BMMC migration mediated through KIT, the receptor for stem cell factor (SCF) was not reduced and if anything, it was enhanced by FcεRIβ exon-skipping, although not to a statistically significant extent (FIG. 5F). Collectively, these data indicated that FcεRIβ exon-skipping selectively and completely abrogated FcεRI-dependent responses in BMMCs.

Example 8. Survival

In addition to the classical view that IgE binding to FcεRI on mast cells primes mast cells for activation by bi/multi-valent antigens, it is now recognized that IgE binding to FcεRI can, by itself, lead to activation of mast cells to release pro-survival cytokines that maintain viability of the cells. In the absence of external supporting cytokines, mast cells rapidly undergo apoptosis, which is suppressed by the addition of IgE. Therefore, elevation of tissue IgE during allergic diseases, such as the lung in asthma, could contribute to increased mast cell numbers by promoting cytokine release and mast cell survival. Thus, studies were conducted to determine whether FcεRIβ exon-skipping would also eliminate the pro-survival effect of IgE on mast cells. BMMCs were deprived of the culture growth-promoting cytokine, IL-3, for 24 h after transfection with AONs. The results showed that over the course of 72 h, IgE almost completely protected mast cells from cell death and apoptosis after withdrawal of IL-3 in control AON-treated BMMCs (FIG. 6A and FIG. 6B, top panels). However, treatment of BMMCs with FcεRIβ AON, which resulted in loss of surface FcεRI expression (FIG. 6B, left panels) eliminated the protective effect of IgE after IL-3 withdrawal (FIG. 6B, bottom panels, FIGS. 6C and 6D). Therefore, FcεRIβ exon-skipping could suppress the pro-survival effect of elevated IgE in vivo and thus the increase in mast cell population, as well as reduce IgE-dependent degranulation in allergic disease.

Example 9. Proliferation

Studies were conducted to examine the effects of FcεRIβ exon-skipping (day 0) on mast cell proliferation while monitoring both surface FcεRI expression (FIG. 7A) and proliferation using a CellTrace Violet dilution assay (FIG. 7B). Briefly, BMMCs were washed once with PBS. 2×10⁶BMMCs were stained with CellTrace Violet (INVITROGEN™) according to the manufacturer's instructions. Cells were then stained for 15 min, followed by addition of 5× volume of complete RPMI 1640 medium with 10% FBS at 37° C. BMMCs were pelleted and transfected as described above. BMMCs were cultured in complete RPMI 1640 supplemented with 30 ng/ml recombinant mouse IL-3 at 37° C. for 5-7 days and stained with Aqua live/dead (INVITROGEN™) and FITC-FcεRIα (EBIOSCIENCE™). Flow cytometry was performed on an LSRII flow cytometer. Dead cells were gated out using the Aqua live/dead stain with an additional gate set for the single cell population
The results showed that the majority of the proliferation occurred between day 5 and day 7, with a population of cells appearing with diluted CellTrace dye at day 7 (FIG. 7B). There was no difference in proliferation with FcεRIβ exon-skipping at either 5 or 7 days. There was a population of BMMCs treated with FcεRIβ AON that began to express FcεRI on the surface at day 7, despite all of the cells at day 5 being negative for surface FcεRI (FIG. 7C) suggesting that these cells were regaining FcεRI expression. Gating the populations of cells based on surface FcεRI expression and plotting CellTrace Violet fluorescence demonstrated that the cells expressing surface FcεRI were the cells that had proliferated (FIG. 7B). These data indicate that while overall proliferation is not affected by FcεRIβ AON treatment, BMMCs that do proliferate dilute FcεRIβ AONs between daughter cells, reducing exon-skipping efficacy.

Example 10. Treatment of Cutaneous Anaphylaxis Using AONs

This example demonstrates the therapeutic utility of AONs of this disclosure for treating affected tissues in allergic diseases such as allergic rhinitis, asthma, or allergic dermatitis. The example utilizes the well-established model of passive cutaneous anaphylaxis (PCA) to test the efficacy of localized delivery of the AONs by means of the Vivo-Morpholino AONs. The experiments described below use morpholino AONs linked through the terminal 3′-N to an octaguanidinium dendrimer (Vivo-Morpholino), which were purchased from Gene-Tools. 20 μl of 0.5 mM standard control AON or FcεRIβ AON (approximately 100 μg of AON) was injected intradermally into one ear of each mouse at day 0.20 μl of PBS was injected into the other control ear. 24 h later, the AON or PBS injections were repeated. 24 h later, 75 ng of anti-DNP-HSA IgE (in 20 μl of PBS) was injected into the AON treated ears and 20 μl of PBS was injected into the control ears. 24 h later, 200 μg of DNP-HSA in 200 μl of PBS containing 0.5% Evan's blue dye was administered by intravenous injection to all mice. After 30 min, mice were euthanized with CO₂gas and AON treated and control ears were removed. Ears were minced and 700 μl of formamide was added to the tubes containing ear tissue and incubated for 2 h at 55° C. to extract the Evan's blue dye. Evan's blue dye extracted into the filtered formamide extract was measured by absorbance in a plate reader set at 620 nm and calculated as induction of inflammation in the AON treated ear compared to the internal control ear.
For a subset of mice, skin tissue was retrieved from the side of the head near the base of the ear after the ears had been removed. The skin tissue retrieved was within 10 mm of the AON injection site. Removed skin was immediately placed in RNA later and stored at 4° C. overnight. The following day, the tissue was removed from RNA later and submerged in lysis buffer from the RNAeasy plus mini kit (QIAGEN™). Skin tissue was then lysed and homogenized using a mechanical homogenizer. RNA was isolated from the homogenized lysate using the RNAeasy plus mini kit with added QIAShredder step according to the manufacturer's instructions. RT-PCR was carried out as described above.
The results of this study, shown in FIGS. 8A and 8B, revealed a substantial reduction in PCA reaction with administration of FcεRIβ AON when compared to control AON (FIG. 8A). Examination of total RNA isolated from skin adjacent to the injected ears by qualitative RT-PCR revealed that the administration of FcεRIβ AON had resulted in exon-skipping in vivo (FIG. 8B). However, the efficiency of exon-skipping in vivo was less than that observed in BMMC cultures, which is consistent with the partial reduction in the PCA reaction (FIG. 8A) as compared to near complete block of degranulation in BMMCs (FIG. 3B). In this PCA model, as in cell culture, FcεRI receptors are saturated with DNP-specific IgE whereas in an allergic disease, only a minor fraction of receptors may be occupied by an allergen-specific IgE and thus more susceptible to FcεRIβ exon-skipping therapy.
The foregoing examples of this disclosure have been presented for purposes of illustration and description. These examples are not intended to limit the disclosure to the form disclosed herein, as variations and modifications commensurate with the teachings of the description of the disclosure, and the skill or knowledge of the relevant art, are within the scope of this disclosure. It is intended that the appended claims be construed to include alternative embodiments to the extent permitted by the prior art.

Claims

1-34. (canceled)

35. A method of modulating splicing of FcεRIβ mRNA in cells or tissues, comprising contacting the cells or tissues with an antisense oligomer comprising 10 to 50 linked nucleosides, wherein the antisense oligomer is targeted to a region of a pre-mRNA encoding a FcεRIβ protein, and wherein the targeted region comprises sequences involved in splicing of the FcεRIβ-encoding pre-mRNA and/or an expression vector coding the same.

36. A method of reducing cell surface expression of FcεRI protein in a cell, comprising contacting the cell with.

37-38. (canceled)

39. A method of modulating cytokine release, comprising contacting a cytokine-producing cell with an antisense oligomer comprising 10 to 50 linked nucleosides, wherein the antisense oligomer is targeted to a region of a pre-mRNA encoding a FcεRIβ protein, and wherein the targeted region comprises sequences involved in splicing of the FcεRIβ-encoding pre-mRNA and/or an expression vector coding the same.

40. The method of claim 35, wherein the method is performed in an individual.

41-48. (canceled)

49. The method of claim 40, wherein the individual is a human, a mouse, a dog, a cat, or a horse.

50. The method of claim 35, wherein the antisense oligomer is a morpholino oligomer.

51. The method of claim 35, wherein the targeted region is selected from the group consisting of an exon 2 or 3 sequence, an exon 2 or 3 slice acceptor sequence, an exon 2 or 3 splice enhancer sequence, an exon 2 or 3 splice branch point sequence, and an exon 2 or 3 polypyrimidine tract of the pre-mRNA encoding the FcεRIβ protein.

52. The method of claim 51, wherein hybridization of the antisense oligomer to the pre-mRNA encoding the FcεRIβ protein results in production of a mature MS4A2 mRNA molecule that lacks at least a portion of exon 2 and/or exon 3.

53. The method of claim 35, wherein the antisense oligomer comprises a nucleotide sequence that is identical over its full length to a sequence selected from the group consisting of SEQ ID NOs: 243, 669, 670, 687, 943, and 968.

54. The method of claim 35, wherein the antisense oligomer is an antisense RNA molecule.

55. The method of claim 54, wherein the antisense RNA molecule comprises a modification selected from the group consisting of a nucleoside modification, an internucleoside modification, a sugar modification, a sugar-internucleoside linkage modification, and combinations thereof.

56. The method of claim 55, wherein the modification increases degradation of a target sequence by a ribonuclease when the antisense RNA molecule hybridizes to the target sequence in the presence of the ribonuclease.

57. The method of claim 39, wherein the antisense oligomer is a morpholino oligomer.

58. The method of claim 39, wherein the method is performed in an individual.

59. The method of claim 59, wherein the individual is a human, a mouse, a dog, a cat, or a horse.