CN117120611A

CN117120611A - Antisense oligonucleotides for increasing FOXG1 expression

Info

Publication number: CN117120611A
Application number: CN202280027385.3A
Authority: CN
Inventors: S·赖希; H-P·冯洛歇; A·盖克; B·贝滕科特
Original assignee: Illigan State LLC
Current assignee: Illigan State LLC
Priority date: 2021-02-10
Filing date: 2022-02-09
Publication date: 2023-11-24

Abstract

Provided herein are compositions and methods for treating and/or ameliorating FOXG1 syndrome or symptoms associated therewith. The compositions and methods disclosed herein utilize antisense oligonucleotides targeted to long non-coding RNAs (incrnas) to increase FOXG1 expression in cells, thereby restoring FOXG1 function.

Description

Antisense oligonucleotides for increasing FOXG1 expression

Cross reference

The present application claims the benefit of U.S. provisional patent application No. 63/148,030, filed on day 2021, month 2, and day 10, and the present application claims the benefit of U.S. provisional patent application No. 63/224,314, filed on day 2021, month 7, and day 21, which are incorporated herein by reference in their entirety.

Background

FOXG1 syndrome is a rare neurological disorder associated with heterozygous variants in the fork-box G1 (FOXG 1) gene and is characterized by impaired neurological development and/or altered brain physiology. The observed FOXG1 syndrome phenotype mainly includes a specific pattern of structural changes in the brain caused by inherited headmutations in the FOXG1 gene. Such structural changes include a reduction in the formation of the sulcus and gyrus on the brain surface and/or a reduction in white matter content, by a thin or underdeveloped corpus callosum connecting the right and left hemispheres of the brain. FOXG1 syndrome affects most aspects of childhood development, and the major clinical features observed in connection with FOXG1 variants include postnatal growth disorders, primary (congenital) or secondary (postnatal) small head malformations, severe intellectual disability with loss of language development, epilepsy, notch behaviors and dyskinesias, sleep pattern abnormalities, crying of unknown origin, gastroesophageal reflux and repeated aspiration.

Disclosure of Invention

Provided herein are compositions and methods for treating and/or ameliorating FOXG1 syndrome or symptoms associated therewith. The compositions and methods described herein utilize antisense oligonucleotides targeted to long non-coding RNAs (lncrnas) to increase FOXG1 expression. In certain instances, the targeted long non-coding RNA (lncRNA) down-regulates FOXG1 expression (e.g., mRNA or protein), wherein the antisense oligonucleotide (ASO) thereby prevents or inhibits or reduces lncRNA-mediated FOXG1 expression down-regulation. The ability to restore or increase expression of functional FOXG1 in cells provides a basis for treating FOXG1 syndrome or alleviating symptoms associated therewith. The compositions and methods described herein are based in part on the following findings: FOXG1 expression can be increased by targeting long non-coding RNAs (lncrnas) with antisense oligonucleotides. Thus, the present disclosure provides (i) that FOXG1 expression can be increased by targeting long non-coding RNAs (lncrnas) with antisense oligonucleotides, and (ii) assays and methods for identifying antisense oligonucleotides that increase FOXG1 expression by targeting long non-coding RNAs (lncrnas).

Provided herein are antisense oligonucleotides (ASOs) comprising sequences that hybridize to a target nucleic acid sequence of long non-coding RNAs (lncrnas). In some embodiments, the lncRNA modulates expression of FOXG 1. In some embodiments, the lncRNA reduces expression of FOXG1 messenger RNA. In some embodiments, the lncRNA reduces transcription of FOXG1 messenger RNA molecules. In some embodiments, the lncRNA reduces expression of FOXG1 protein. In some embodiments, the lncRNA reduces translation of FOXG1 protein molecules.

In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises a modification. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the modification comprises a modified internucleoside linker, a modified nucleoside, or a combination thereof. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises modified internucleoside linkages. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises phosphodiester internucleoside linkages. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises a modified nucleoside. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the modified nucleoside comprises a modified sugar. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the modified sugar is a bicyclic sugar. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the modified sugar comprises a 2' -O-methoxyethyl group.

In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the sequence is complementary to a target nucleic acid sequence of a long non-coding RNA (lncRNA). In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the long non-coding RNA (lncRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1. In some embodiments, an antisense oligonucleotide of any one of the preceding embodiments is provided, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1 (https:// www.ncbi.nlm.nih.gov/gene/103695363), long non-protein coding RNA 1551 (LINC 01151); see https:// www.ncbi.nlm.nih.gov/gene/387978), long intergenic non-protein coding RNA 2282 (LINC 02282); see https:// www.ncbi.nlm.nih.gov/gene/105370424) or combinations thereof.

In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the sequence comprises a nucleobase sequence as set forth in any one of table 3. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 4. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 3. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein any one or more of the positions provided in table 3 are adjacent to a base position contained within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 4, in some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein adjacent to any one or more of the positions provided in table 4 comprises a base position within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'.

In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein hybridization of the sequence of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein hybridization of the sequence of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein expression of FOXG1 is mRNA expression. In some embodiments, an antisense oligonucleotide of any one of the preceding embodiments is provided, wherein expression of FOXG1 is protein expression. A composition comprising one or more of the antisense oligonucleotides of any of the foregoing embodiments. A pharmaceutical composition comprising an antisense oligonucleotide of any of the preceding embodiments and a pharmaceutically acceptable carrier or diluent.

Further provided are methods of modulating expression of FOXG1 in a cell comprising contacting the cell with a composition comprising an antisense oligonucleotide that hybridizes to a target nucleic acid sequence of a long non-coding RNA (lncRNA). Also provided are methods of treating or ameliorating a FOXG1 disease or disorder in an individual having or at risk of having a FOXG1 disease or disorder, comprising administering to the individual an antisense oligonucleotide, wherein the antisense oligonucleotide comprises a sequence that hybridizes to a target nucleic acid sequence of long non-coding RNA (lncRNA).

In some embodiments, there is provided a method of any one of the preceding embodiments, wherein the cell is located in the brain of the individual. In some embodiments, there is provided a method of any one of the preceding embodiments, wherein the individual is a human. In some embodiments, a method of any one of the preceding embodiments is provided, wherein the individual comprises reduced FOXG1 expression or FOXG1 deficiency. In some embodiments, there is provided a method of any one of the preceding embodiments, wherein the individual has a FOXG1 disease or disorder. In some embodiments, there is provided a method of any one of the preceding embodiments, wherein the FOXG1 disease or disorder is FOXG1 syndrome.

In some embodiments, a method of any one of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises a sequence complementary to a target nucleic acid sequence of a long non-coding RNA (lncRNA).

In some embodiments, a method of any one of the preceding embodiments is provided, wherein the long non-coding RNA (lncRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1. In some embodiments, a method of any one of the preceding embodiments is provided, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1, long non-protein coding RNA 1551 (LINC 01151), long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof.

In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 3. In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 4. In some embodiments, methods of any of the preceding embodiments are provided wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 3. In some embodiments, methods of any of the preceding embodiments are provided wherein the base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3' are contained adjacent to any one or more of the positions provided in table 3. In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 4, in some embodiments, methods of any of the preceding embodiments are provided, wherein any one or more adjacent to any one or more of the positions provided in table 4 comprises a base position within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'.

In some embodiments, methods of any of the preceding embodiments are provided, wherein hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA. In some embodiments, methods of any of the preceding embodiments are provided, wherein hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1. In some embodiments, a method of any one of the preceding embodiments is provided, wherein the expression of FOXG1 is mRNA expression. In some embodiments, methods of any of the preceding embodiments are provided, wherein the expression of FOXG1 is protein expression.

In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide is configured as a gapmer. In some embodiments, a method of any one of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage. In some embodiments, there is provided a method of any one of the preceding embodiments, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage. In some embodiments, a method of any one of the preceding embodiments is provided, wherein the antisense oligonucleotide comprises at least one phosphodiester internucleoside linkage. In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide comprises a modified nucleoside. In some embodiments, methods of any of the preceding embodiments are provided, the modified nucleoside comprising a modified sugar. In some embodiments, methods of any of the preceding embodiments are provided, wherein the modified sugar is a bicyclic sugar. In some embodiments, methods of any of the preceding embodiments are provided wherein the modified sugar comprises a 2' -O-methoxyethyl group.

In some embodiments, there is provided a method of any one of the preceding embodiments, wherein modulating expression comprises increasing expression of FOXG1 protein in the cell.

In some embodiments, a method of any one of the preceding embodiments is provided, wherein modulating expression comprises increasing translation of FOXG1 protein in the cell.

In some embodiments, there is provided a method of any of the preceding embodiments, wherein the antisense oligonucleotide is administered to the individual by intrathecal injection, intraventricular injection, inhalation, parenteral injection or infusion, or orally.

Also provided herein are gapmer antisense oligonucleotides comprising sequences that hybridize to a target nucleic acid sequence of a long non-coding RNA (lncRNA), wherein the lncRNA reduces expression of FOXG 1. In some embodiments, FOXG1 expression is measured by FOXG1 mRNA expression. In some embodiments, FOXG1 expression is measured by FOXG1 protein expression.

In some embodiments, the antisense oligonucleotide comprises a modification. In some embodiments, the modification comprises a modified internucleoside linker, a modified nucleoside, or a combination thereof. In some embodiments, the antisense oligonucleotide comprises modified internucleoside linkages. In some embodiments, the sequence comprises a nucleobase sequence as set forth in any one of table 3. In some embodiments, the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 4. In some embodiments, the target nucleic acid sequence comprises one or more nucleobases complementary to a sequence selected from table 3. In some embodiments, the target nucleic acid sequence comprises one or more nucleobases within or adjacent to any one of the reference positions selected from table 3. In some embodiments, the target nucleic acid sequence comprises one or more nucleobases complementary to a sequence selected from table 4. In some embodiments, the target nucleic acid sequence comprises one or more nucleobases within or adjacent to any one of the reference positions selected from table 4.

In some embodiments, hybridization of the antisense oligonucleotide increases expression of FOXG1 in the cell. In some embodiments, the FOXG1 expression is FOXG1 mRNA expression. In some embodiments, the FOXG1 mRNA expression is measured by a probe-based quantitative assay. In some embodiments, the long non-coding RNA (lncRNA) is FOXG1-AS1, long intergenic non-protein coding RNA 1551, long intergenic non-protein coding RNA2282 (LINC 02282), or a combination thereof.

Incorporated by reference

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

Drawings

The novel features believed characteristic of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings, of which:

FIG. 1 shows a schematic of FOXG1 transcripts.

FIGS. 2A, 2B and 2C show gapmer antisense oligonucleotides (ASOs) targeting long non-coding RNAs and increasing FOXG1 expression.

Detailed Description

Deletion or mutation in a single allele of the fork box G1 (FOXG 1) gene can cause FOXG1 syndrome. FOXG1 syndrome is a rare disease characterized by developmental delay, severe intellectual disability, epilepsy, language deficiency, and movement disorders. Markers of brain physiological changes associated with FOXG1 syndrome include cortical atrophy and callus hypoplasia. FOXG1 gene/protein is a member of the fork transcription factor family and is specifically expressed in the neural progenitor cells of the forebrain. The FOXG1 gene consists of one coding exon, and it is notable that the location or type of FOXG1 mutation can be correlated with or indicative of clinical severity.

FOXG1 protein plays an important role in brain development, particularly in the area of the embryonic brain known as the telencephalon. The brain eventually develops into several key structures, including the largest part of the brain (i.e., the brain), which controls most voluntary activities, language, sensory perception, learning, and memory. As observed in individuals with mutations or deletions in a single FOXG1 allele (i.e., heterozygous individuals), the absence of a functional FOXG1 protein disrupts normal brain patterning and development.

Expression of the target can be regulated at multiple levels by long non-coding ribonucleic acids (lncRNA). For example, lncRNA can regulate transcription of adjacent and distant genes by interacting with DNA, RNA, and proteins, and affect RNA splicing, stability, and translation.

Thus, described herein are compositions and methods for modulating the status, activity or expression of long inserted (which includes intronic and intergenic) non-coding RNAs (lncRNA) in a cell, tissue or organism. Also provided are compositions and methods for treating pathological conditions and diseases in mammals caused by or modulated by the regulatory, structural, catalytic or signaling properties of lncRNA. Thus, disclosed herein are compositions and methods useful for increasing the amount of functional FOXG1, such as FOXG1 protein or FOXG1 messenger ribonucleic acid (mRNA), in cells with a deficiency of functional FOXG 1. Such compositions and methods are useful in their application for treating individuals suffering from FOXG 1-related diseases or disorders, wherein the absence or lack of a functional FOXG1 protein can be remedied. To achieve an increase in FOXG1 expression in a cell or individual, antisense oligonucleotides targeting lncRNA are used.

Antisense oligonucleotides

Antisense oligonucleotides (ASOs) are small (about 18-30 nucleotides), synthetic, single stranded nucleic acid polymers that can be used to regulate gene expression by a variety of mechanisms. Antisense oligonucleotides (ASOs) can be subdivided into two broad classes: RNASEH dependent (combentit) and sterically hindered. For RNASEH-dependent antisense oligonucleotides, the endogenous RNASEH enzyme recognizes an RNA-DNA heteroduplex substrate formed when the antisense oligonucleotide binds to its cognate mRNA transcript to catalyze degradation of the RNA. Sterically hindered oligonucleotides are antisense oligonucleotides (ASOs) designed to bind to a target transcript with high affinity but not induce degradation of the target transcript.

To achieve efficient targeting of lncRNA, the antisense oligonucleotides (ASOs) described herein hybridize to target nucleic acid sequences of long non-coding RNAs (lncRNA). In some cases, lncRNA may generally be defined as an RNA molecule having greater than about 200 nucleotides, wherein the RNA molecule does not encode a protein sequence or a translated protein sequence or a translatable protein sequence. In certain instances, the lncRNA is transcribed from an intergenic region or an intronic region. In some embodiments, the lncRNA comprises greater than about 200 kilobases (kb), 400kb, 500kb, 1000kb, 2000kb.

lncRNA can modulate FOXG1 by one or more different or differential mechanisms. In some embodiments, the lncRNA reduces expression of FOXG1 messenger RNA. In some embodiments, the lncRNA reduces transcription of FOXG1 messenger RNA molecules. In some embodiments, wherein the lncRNA reduces expression of FOXG1 protein. In some embodiments, the lncRNA reduces translation of FOXG1 protein molecules.

In some embodiments, a targeted (e.g., hybridized) lncRNA disclosed herein is an antisense nucleotide (ASO) comprising a specific sequence that is complementary or substantially complementary (e.g., has at least 70%, 80%, 90%, 95% or 100% sequence identity) to a target nucleic acid sequence of a long non-coding RNA (lncRNA). In some embodiments, the sequence is complementary to a target nucleic acid sequence of a long non-coding RNA (lncRNA). In some embodiments, the long non-coding RNA (lncRNA) is FOXG1-AS1, long non-protein coding RNA 1551 (LINC 01151), long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof. In some embodiments, the sequence comprises the nucleobase sequence shown in any one of SEQ ID NOS.1-288.

In some embodiments, the sequence is complementary to a target nucleic acid sequence at or near (e.g., surrounding) position 200-350 or 375-525 of long non-coding RNA (lncRNA) FOXG1-AS1 (e.g., reference sequence NR_ 125758.1). In some embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence at or near (e.g., surrounding) positions 200-350 or 375-525 of long non-coding RNA (lncRNA) FOXG1-AS 1. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence at or near (e.g., surrounding) the position provided in table 3 or 4 for long non-coding RNA (lncRNA) FOXG1-AS 1. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence near (e.g., around) a position provided in table 3 for long non-coding RNA (lncRNA) FOXG1-AS1, wherein the near or around comprises base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence near (e.g., around) a position provided in table 4 for long non-coding RNA (lncRNA) FOXG1-AS1, wherein the near or around comprises base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 20 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 40 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 50 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 75 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 100 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 150 base positions of 5 'and/or 3'.

In some embodiments, the sequence is complementary to a target nucleic acid sequence at or near (e.g., surrounding) position 950-1150 or 1450-1650 or 2150-2350 or 3450-3730 of long non-coding RNA (lncRNA) LINC01551 (e.g., exons of reference sequences NR_026732.1 and NR_ 026731.1-merge). In some embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence at or near (e.g., surrounding) position 950-1150 or 1450-1650 or 2150-2350 or 3450-3730 of long non-coding RNA (lncRNA) LINC 01551. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence at or near (e.g., around) the position provided for long non-coding RNA (lncRNA) LINC01551 in table 3 or 4. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence near (e.g., around) a position provided in table 3 for long non-coding RNA (lncRNA) LINC01551, wherein the near or around comprises base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence near (e.g., around) a position provided in table 4 for long non-coding RNA (lncRNA) LINC01551, wherein the near or around comprises base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 20 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 40 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 50 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 75 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 100 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 150 base positions of 5 'and/or 3'.

In some embodiments, the sequence is complementary to a target nucleic acid sequence at or near (e.g., surrounding) the position 100-300 or 360-560 or 730-970 or 780-1083 or 1228-1349 of long non-coding RNA (lncRNA) LINC02282 (e.g., the exons of the reference sequences NR 026732.1 and NR 026731.1-merge). In some embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence at or near (e.g., around) position 100-300 or 360-560 or 730-970 or 780-1083 or 1228 to 1349 of long non-coding RNA (lncRNA) LINC 01551. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence at or near (e.g., around) the position provided for long non-coding RNA (lncRNA) LINC02282 in table 3 or 4. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence near (e.g., around) a position provided in table 3 for long non-coding RNA (lncRNA) LINC02282, wherein the near or around comprises base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In certain embodiments, the antisense oligonucleotide hybridizes to a target nucleic acid sequence that is near (e.g., around) a position provided in table 4 for long non-coding RNA (lncRNA) LINC02282, wherein near or around comprises base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 20 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 40 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 50 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 75 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 100 base positions of 5 'and/or 3'. In certain embodiments, the position near or around the base position is within 150 base positions of 5 'and/or 3'.

In certain instances, targeting (e.g., hybridizing) the lncRNA increases FOXG1 expression. In certain instances, targeting (e.g., hybridizing) the lncRNA prevents lncRNA-mediated FOXG1 down-regulation by promoting degradation of the lncRNA. In certain instances, targeting (e.g., hybridizing) the lncRNA prevents lncRNA-mediated FOXG1 down-regulation by promoting degradation of the lncRNA. Thus, in some embodiments, hybridization of the sequence of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA. In some embodiments, hybridization of the sequence of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1. In certain embodiments, the expression of FOXG1 is mRNA expression. In certain embodiments, the expression of FOXG1 is protein expression. Such ASOs are suitable for use in the methods described herein. FIG. 1 shows a schematic of FOXG1 mRNA transcripts. Table 1 discloses sequences and antisense oligonucleotide (ASO) sequences for targeting lncRNA.

Compositions comprising one or more ASOs described herein are useful. In certain embodiments, a combination of two or more ASOs having different sequences is used to increase FOXG1 expression in a cell. In certain embodiments, the composition is a pharmaceutical composition.

To improve the pharmacodynamic, pharmacokinetic and biodistribution properties of antisense oligonucleotides (ASOs), antisense oligonucleotides can be designed and engineered to comprise one or more chemical modifications (e.g., modified internucleoside linkers, modified nucleosides, or combinations thereof). Thus, in some embodiments, the antisense oligonucleotide is a modified oligonucleotide. In some embodiments, the antisense oligonucleotide comprises one or more modifications. In certain embodiments, the modification comprises a modified internucleoside linker, a modified nucleoside, or a combination thereof.

Modified internucleoside linker

Modifications of the internucleoside linker (i.e., backbone) can be used to increase pharmacodynamic, pharmacokinetic and biodistribution properties. For example, internucleoside linker modifications prevent or reduce degradation of cellular nucleases, thereby increasing the pharmacokinetics and bioavailability of antisense oligonucleotides. Typically, modified internucleoside linkers include any linker that covalently couples two nucleosides together, except for Phosphodiester (PO) linkers. In some embodiments, the modified internucleoside linker increases nuclease resistance of the antisense oligonucleotide as compared to the phosphodiester linker. For naturally occurring antisense oligonucleotides, the internucleoside linker comprises a phosphate group that creates a phosphodiester linkage between adjacent nucleosides. The modified internucleoside linker is particularly useful in stabilizing antisense oligonucleotides for in vivo use and may function to protect against nuclease cleavage.

In some embodiments, the antisense oligonucleotides comprise one or more internucleoside linkers modified from a native phosphodiester to, for example, a linker that is more resistant to nuclease attack. In some embodiments, a region (e.g., the 5 'and/or 3' region) or regions (e.g., the 5 'and 3' regions) or contiguous nucleotides of an antisense oligonucleotide comprise a modified internucleoside linker. In certain embodiments, the 5 'and 3' regions of the ASO comprise modified linkers. In certain embodiments, the 5 'and 3' regions of the ASO comprise modified linkers, wherein the ASO comprises an unmodified region or segment between the 5 'and 3' modified regions of the ASO. In some embodiments, all internucleoside linkers of the antisense oligonucleotides or contiguous nucleotide sequences thereof are modified. In some embodiments, all of the internucleoside linkers of the antisense oligonucleotides or contiguous nucleotide sequences thereof are nuclease resistant internucleoside linkers. In some embodiments, the internucleoside linkage comprises sulfur (S), such as a phosphorothioate internucleoside linkage.

In some cases phosphorothioate internucleoside linkers are particularly useful due to nuclease resistance and improved pharmacokinetics. In some embodiments, one or more internucleoside linkers of the antisense oligonucleotide or contiguous nucleotide sequences thereof comprise phosphorothioate internucleoside linkers. In some embodiments, all of the internucleoside linkers of the antisense oligonucleotides or contiguous nucleotide sequences thereof comprise phosphorothioate internucleoside linkers.

Modified nucleosides

Modifications to ribose or nucleobases can also be used to increase pharmacodynamic, pharmacokinetic and biodistribution properties. Similar to modifications of internucleoside linkers, nucleoside modifications prevent or reduce degradation by cellular nucleases, thereby increasing the pharmacokinetics and bioavailability of antisense oligonucleotides. Typically, the modified nucleoside includes the introduction of one or more modifications of the sugar moiety or nucleobase moiety.

As described, the antisense oligonucleotides can comprise one or more nucleosides that contain a modified sugar moiety, wherein the modified sugar moiety is a modification of the sugar moiety when compared to ribose sugar moieties found in deoxyribonucleic acid (DNA) and RNA. Many modified nucleosides having a ribose moiety can be utilized, primarily for the purpose of improving certain properties of the oligonucleotide, such as affinity and/or nuclease resistance. Such modifications include those in which the ribose ring structure is modified. These modifications include substitution with a hexose ring (HNA), a bicyclic ring with a double-base bridge between the C2 and C4 carbons on the ribose ring (e.g., locked Nucleic Acid (LNA)), or an unconnected ribose ring (e.g., UNA) that typically lacks a bond between the C2 and C3 carbons. Other sugar modified nucleosides include, for example, dicyclohexyl nucleic acids or tricyclic nucleic acids. Modified nucleosides also include nucleosides in which the sugar moiety is replaced by a non-sugar moiety, for example in the case of Peptide Nucleic Acids (PNAs) or morpholino nucleic acids.

Sugar modifications also include modifications made by changing substituents on the ribose ring to groups other than hydrogen or 2' -OH groups naturally found in DNA and RNA nucleosides. Substituents may be introduced, for example, at the 2', 3', 4 'or 5' positions. Nucleosides having modified sugar moieties also include 2 'modified nucleosides, such as 2' substituted nucleosides. Indeed, much attention has been focused on developing 2 'substituted nucleosides, and many 2' substituted nucleosides have been found to have beneficial properties when incorporated into oligonucleotides, such as enhanced nucleoside resistance and enhanced affinity. The 2' sugar modified nucleoside is a nucleoside having a substituent other than H or-OH at the 2' position (2 ' substituted nucleoside) or comprises a 2' linked diradical, and includes 2' substituted nucleosides and LNA (2 ' -4' diradical bridged) nucleosides. Examples of 2 '-substituted modified nucleosides are 2' -O-alkyl-RNA, 2 '-O-methyl-RNA, 2' -alkoxy-RNA, 2 '-O-methoxyethyl-oligomer (MOE), 2' -amino-DNA, 2 '-fluoro-RNA and 2' -F-ANA nucleosides. In some embodiments, the antisense oligonucleotide comprises one or more modified sugars. In some embodiments, the antisense oligonucleotide comprises only modified sugars. In certain embodiments, the antisense oligomer comprises greater than 10%, 25%, 50%, 75% or 90% modified sugar. In some embodiments, the modified sugar is a bicyclic sugar. In some embodiments, the modified sugar comprises a 2' -O-Methoxyethyl (MOE) group.

In some embodiments, the antisense oligonucleotide comprises an internucleoside modification and a nucleoside modification. In some embodiments, a region (e.g., the 5 'and/or 3' region) or regions (e.g., the 5 'and 3' regions) of an ASO comprises a linker modification and a nucleoside modification. In certain embodiments, the 5 'and 3' regions of the ASO comprise modified linkers and nucleoside modifications. In certain embodiments, the 5 'and 3' regions of the ASO comprise modified linkers and nucleoside modifications, wherein the ASO comprises an unmodified region or segment between the 5 'and 3' modified regions of the ASO.

Gapmer

Further provided herein are modified ASOs that promote degradation of target lncRNA, wherein such ASOs may be referred to as gapmer ASOs. In some cases, gapmer or gapped ASO represents an oligomeric compound having two modified outer regions and one unmodified inner or central region or segment. For example, gapmer generally represents and encompasses antisense oligonucleotides comprising a region (gap) of RNASE H recruitment oligonucleotide flanked at 5 'and 3' by regions (flanks or wings) comprising one or more affinity enhancing modified nucleosides. The Gapmer oligonucleotides are typically used to inhibit target RNAs in cells via an antisense mechanism, such as inhibitory lncRNA (and thus may also be referred to as antisense Gapmer oligonucleotides). Gapmer oligonucleotides generally comprise a region of at least about 5 contiguous nucleotides, which is capable of recruiting RNASEH (gap region), such as a region of DNA nucleotides, e.g., 6-14 DNA nucleotides, flanked at 5' and 3' by regions comprising affinity-enhancing modified nucleosides, such as LNA or 2' substituted nucleotides. In some embodiments, the flanking regions may be 1-8 nucleotides in length.

High affinity modified nucleosides generally include and refer to modified nucleotides that, when incorporated into an oligonucleotide, enhance the affinity of the oligonucleotide for its complementary target, e.g., as exemplified by a melting temperature (T ^m ) Measured. The high affinity modified nucleosides of the invention preferably result in each modifiedThe melting temperature of the nucleoside +0.5 to +12 ℃, more preferably +1.5 to +10 ℃, and most preferably +3 to +8 ℃. Affinity modified nucleosides generally include, for example, a number of 2' -substituted nucleosides and Locked Nucleic Acids (LNAs).

In some embodiments, the parent and offspring oligonucleotides are gapmer oligonucleotides comprising a central region of at least 5 or more consecutive nucleosides (such as at least 5 consecutive DNA nucleosides) and a 5 'flanking region comprising 1-6 high affinity nucleoside analogs (such as LNA nucleosides) and a 3' flanking region comprising 1-6 high affinity nucleoside analogs (such as LNA 1-6 nucleosides). LNA gapmer oligonucleotides are oligonucleotides comprising at least one LNA nucleoside in the wing region, and may for example comprise at least one LNA in the 5 'and 3' wing regions.

For example, in some embodiments, the three regions are contiguous sequences, wherein the sugar moiety of the outer region is different from the sugar moiety of the inner region, and wherein the sugar moiety of a particular region is substantially the same. In certain embodiments, each specific region has the same sugar moiety. In some cases, the sugar moieties of the outer region are identical and the gapmer is considered a symmetrical gapmer. In another case, the saccharide moiety used in the 5 '-external region is different from the saccharide moiety used in the 3' -external region, and the gapmer is an asymmetric gapmer. In certain embodiments, the outer regions are each independently 1, 2, 3, 4, or about 5 nucleotide subunits and comprise a non-naturally occurring sugar moiety. In other embodiments, the interior region comprises β -D-2' -deoxyribonucleosides. In certain embodiments, the outer regions each independently comprise 1 to about 5 nucleotides having a non-naturally occurring sugar moiety, and the inner region comprises 6 to 18 unmodified nucleosides. In other embodiments, the interior region or gap generally comprises β -D-2' -deoxyribonucleosides, but may comprise non-naturally occurring sugar moieties.

In some embodiments, the gapped oligomeric compound comprises an interior region of a β -D-2' -deoxyribonucleoside and one of two exterior regions comprising a tricyclic nucleoside as disclosed herein. In certain embodiments, the gapped oligomeric compounds comprise an inner region of β -D-2' -deoxyribonucleosides and two outer regions comprising tricyclic nucleosides as provided herein. In certain embodiments, provided herein are gapped oligomeric compounds, wherein all nucleotides comprise a non-naturally occurring sugar moiety, as described herein.

Also provided in Table 1 are Gapmer nucleobase sequences which encompass SEQ ID NOS.1-274. In some embodiments, the ASOs or gapmers described herein promote degradation of lncRNA molecules. In certain embodiments, the degradation is RNASE-dependent (e.g., RNASE H) degradation.

In some embodiments, hybridization of the antisense oligonucleotide increases FOXG1 expression in the cell. In some embodiments, the FOXG1 expression is FOXG1 mRNA expression. In some embodiments, the FOXG1 mRNA expression is measured by a probe-based quantitative assay. In some embodiments, the long non-coding RNA (lncRNA) is FOXG1-AS1, long intergenic non-protein coding RNA 1551, long intergenic non-protein coding RNA2282 (LINC 02282), or a combination thereof.

Pharmaceutical composition

Further provided herein are pharmaceutical compositions comprising any of the disclosed antisense oligonucleotides and a pharmaceutically acceptable diluent, carrier, salt and/or adjuvant. Pharmaceutically acceptable diluents include Phosphate Buffered Saline (PBS), and pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts. In some embodiments, the pharmaceutically acceptable diluent is sterile phosphate buffered saline. In some embodiments, the oligonucleotide is used in a pharmaceutically acceptable diluent at a concentration of 50-300 μm solution. In some embodiments, the oligonucleotide as described is administered at a dose of 10-1000 μg.

The antisense oligonucleotides or oligonucleotide conjugates of the present disclosure can be mixed with pharmaceutically acceptable active or inert substances to prepare pharmaceutical compositions or formulations. The compositions and methods for formulating pharmaceutical compositions depend on a number of criteria, including but not limited to the route of administration, the extent of the disease or the dosage to be administered.

Application method

Antisense oligonucleotides (ASOs) provided herein can be used to target lncRNA, wherein the antisense oligonucleotides increase FOXG1 expression (e.g., expression of functional FOXG1 mRNA and/or protein) in a cell. Antisense oligonucleotides targeting lncRNA as described herein are further useful in methods of increasing expression and/or amount of functional FOXG1 (e.g., amount of functional FOXG1 mRNA or protein) in a cell. Accordingly, provided herein are methods of modulating expression of FOXG1 in a cell comprising contacting the cell with a composition comprising an antisense oligonucleotide that hybridizes to a target nucleic acid sequence of long non-coding RNA (lcRNA).

Further provided are methods of treating or ameliorating a FOXG1 disease or disorder in an individual having or at risk of having a FOXG1 disease or disorder, comprising administering to the individual an antisense oligonucleotide, wherein the antisense oligonucleotide comprises a sequence that hybridizes to a target nucleic acid sequence of long non-coding RNA (lcRNA).

Typically, the cells of interest include neuronal cells and/or cells associated with brain or brain development. In some embodiments, the cell is located in the brain of the individual. In some embodiments, the cell is a neural cell. In certain embodiments, the cell is a neuron, an astrocyte, or a fibroblast. In some embodiments, the individual is a human. In certain embodiments, the human is an unborn human. In some embodiments, the cell and/or individual comprises a mutated FOXG1 gene, reduced FOXG1 expression, or FOXG1 deficiency. In some embodiments, the individual has been diagnosed with or is at risk of a FOCG1 disease or disorder. In some embodiments, the FOXG1 disease or disorder is FOXG1 syndrome.

In some embodiments, the antisense oligonucleotide comprises a sequence complementary to a target nucleic acid sequence of long non-coding RNA (lcRNA). In some embodiments, the long non-coding RNA (lcRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1. In some embodiments, the long non-coding RNA (lcRNA) is FOXG1-AS1, long non-protein coding RNA 1551 (LINC 01151), long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof. In some embodiments, the antisense oligonucleotide comprises the nucleobase sequence shown in any one of SEQ ID NOS: 1-274. In some embodiments, hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA. In some embodiments, hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1. In certain embodiments, the expression of FOXG1 is mRNA expression. In certain embodiments, the expression of FOXG1 is protein expression.

Formulations of therapeutic and diagnostic agents may be prepared by mixing with physiologically acceptable carriers, excipients or stabilizers, for example, in the form of lyophilized powders, slurries, aqueous solutions, lotions or suspensions. (see, e.g., hardman et al, goodman andGilman's ThePharmacologicalBasis of Therapeutics, mcGraw-Hill, new York, N.Y.,2001;Gennaro,Remington:The Science and Practice ofPharmacy,Lippincott,Williams, and Wilkins, new York, N.Y.,2000; avis, et al (eds.), pharmaceutical Dosage Forms: parenteral Medications, marcel Dekker, NY,1993; lieberman, et al (eds.), pharmaceutical Dosage Forms:Tablets, marcel Dekker, NY,1990; lieberman, et al (eds.) Pharmaceutical Dosage Forms:Disperse Systems, inc., new York, N.Y., 2000).

Compositions comprising antisense oligonucleotides (ASOs) as disclosed herein may be provided by dosages at intervals of, for example, one day, one week, or 1-7 times per week. A particular dosage regimen is one that involves a maximum dose or dose frequency that avoids significant undesirable side effects.

The disclosed antisense oligonucleotides or pharmaceutical compositions thereof can be administered topically (such as to the skin, inhalation, eye or ear) or enterally (such as orally or through the gastrointestinal tract) or parenterally (such as intravenously, subcutaneously, intramuscularly, intracerebrally, intraventricularly or intrathecally). In some embodiments, the antisense oligonucleotide or pharmaceutical composition thereof is administered by a parenteral route, including intravenous, intra-arterial, subcutaneous, intraperitoneal, or intramuscular injection or infusion, intrathecal or intracranial, e.g., intra-cerebral or intra-ventricular administration. In some embodiments, the active oligonucleotide or oligonucleotide conjugate is administered intravenously.

Definition of the definition

Unless defined otherwise, all technical terms, notations and other technical and scientific terms or nomenclature used herein are intended to have the same meaning as commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein is not necessarily to be construed as indicating a substantial difference over the commonly understood meaning in the art.

The term "FOXG1" as used herein generally refers to genes and gene products encoding a member of the fork-head transcription factor family. The encoded protein functioning as a transcriptional repressor is highly expressed in neural tissue during brain development. Mutations at this locus have been associated with rayleigh syndrome and a variety of neurological disorders defined as part of FOXG1 syndrome. Depending on the context in which it is used, "FOXG1" may represent a FOXG1 gene, FOXG1 deoxyribonucleic acid molecule (DNA), FOXG1 ribonucleic acid molecule (RNA), or FOXG1 protein. The mRNA sequence of FOXG1 is described in "NM-005249.5 →NP-005240.3 fork box protein G1" or "accession No. NM-005249.5" or mRNA encoded by "NCBI gene ID: 2290". Functional FOXG1 proteins describe wild-type or unmutated FOXG1 genes, mRNA and/or proteins. Generally, "FOXG1" means a functional "FOXG1" gene or gene product that has normal function/activity in a cell. A deletion or mutation or variant of FOXG1 indicates a non-functional FOXG1 variant with reduced, suppressed or eliminated FOXG1 function. As disclosed herein, the compositions and methods disclosed herein are directed generally to modulating or increasing or restoring the amount of FOXG1 (i.e., functional FOXG 1) in a cell and/or individual.

The term "oligonucleotide" as used herein generally refers to a molecule comprising two or more covalently linked nucleosides. Such covalently bound nucleosides may also be referred to as nucleic acid molecules or oligomers. Oligonucleotides are typically prepared in the laboratory by solid phase chemical synthesis and then purified. When referring to the sequence of an oligonucleotide, it refers to the sequence or order of covalently linked nucleotides or nucleobase portions of nucleosides or modifications thereof. The oligonucleotides of the present disclosure are artificial and chemically synthesized, and are typically purified or isolated. The disclosed oligonucleotides may comprise one or more modified nucleosides or nucleotides.

The term "antisense oligonucleotide" as used herein means an oligonucleotide capable of modulating expression of a target gene by hybridization to the target nucleic acid, particularly to a contiguous sequence on the target nucleic acid. Preferably, the antisense oligonucleotides of the present disclosure are single stranded. In some embodiments, the antisense oligonucleotide is single stranded.

The term modified oligonucleotide refers to an oligonucleotide comprising one or more sugar modified nucleosides, modified nucleobases and/or modified internucleoside linkers.

The term "modified nucleoside" or "nucleoside modification" as used herein refers to a nucleoside modified by the introduction of one or more modifications of a sugar moiety or (nucleobase) moiety, as compared to an equivalent DNA or RNA nucleoside. In some embodiments, the modified nucleoside comprises a modified sugar moiety. The term modified nucleoside is also used interchangeably herein with the term "nucleoside analog" or modified "unit" or modified "monomer".

The term "modified internucleoside linkage" refers to a linker other than a Phosphodiester (PO) linker that covalently couples two nucleosides together. Nucleotides having modified internucleoside linkages are also referred to as "modified nucleotides". In some embodiments, the modified internucleoside linkage increases nuclease resistance of the oligonucleotide as compared to a phosphodiester linkage. For naturally occurring oligonucleotides, the internucleoside linkages include phosphate groups that create phosphodiester linkages between adjacent nucleosides. The modified internucleoside linker is particularly useful in stabilizing oligonucleotides for in vivo use and may be used to protect against nuclease cleavage at the DNA or RNA nucleoside region.

The term "nucleobase" includes purine (e.g., adenine and guanine) and pyrimidine (e.g., uracil, thymine, and cytosine) moieties present in nucleosides and nucleotides that form hydrogen bonds in nucleic acid hybridization. The term nucleobase also encompasses modified nucleobases, which may be different from naturally occurring nucleobases, but which are functional during nucleic acid hybridization. In this context, "nucleobase" means naturally occurring nucleobases such as adenine, guanine, cytosine, thymidine, uracil, xanthine and hypoxanthine, as well as non-naturally occurring variants.

The nucleobase moiety may be modified by changing a purine or pyrimidine to a modified purine or pyrimidine, such as a substituted purine or substituted pyrimidine, such as a nucleobase selected from the group consisting of isocytosine, pseudoisocytosine, 5-methylcytosine, 5-thiazolo-cytosine, 5-propynyl-uracil, 5-bromouracil 5-thiazolo-uracil, 2-thio-uracil, 2' thio-thymine, inosine, diaminopurine, 6-aminopurine, 2, 6-diaminopurine and 2-chloro-6-aminopurine.

The nucleobase moiety may be indicated by a letter code, such as A, T, G, C or U, for each respective nucleobase, wherein each letter may optionally comprise a modified nucleobase having an equivalent function. For example, in an exemplary oligonucleotide, the nucleobase moiety is selected from A, T, G, C and 5-methylcytosine. In some embodiments, the cytosine nucleobase in the 5'cg3' motif is a 5-methylcytosine.

The terms "hybridize to" … … "or" hybridize "or" target "or" bind "describe that two nucleic acid strands (e.g., an oligonucleotide and a target nucleic acid) form hydrogen bonds between base pairs on opposite strands, thereby forming a duplex. The binding affinity between two nucleic acid strands is the intensity of hybridization. It is often described in terms of a melting temperature (Tm), which is defined as the temperature at which half of an oligonucleotide forms a duplex with a target nucleic acid.

The oligonucleotides comprise contiguous nucleotide regions that are complementary to or hybridize to a subsequence or region of a target nucleic acid molecule. The term "target sequence" as used herein refers to a nucleotide sequence present in a target nucleic acid that comprises a nucleobase sequence that is complementary to a contiguous nucleotide region or sequence of an oligonucleotide of the disclosure. In some embodiments, the target sequence consists of a region on the target nucleic acid that is complementary to a contiguous nucleotide region or sequence of an oligonucleotide of the disclosure. In some embodiments, the target sequence is longer than the complementary sequence of a single oligonucleotide, and may, for example, represent a preferred region of a target nucleic acid that may be targeted by several oligonucleotides of the present disclosure.

In certain instances, the oligonucleotides comprise a contiguous nucleotide region of at least 10 nucleotides that is complementary to or hybridizes to a target sequence present in a target nucleic acid molecule. In certain instances, the contiguous nucleotide region (and thus the target sequence) comprises at least 10 contiguous nucleotides, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30 contiguous nucleotides, such as 15-30, such as 18-23 contiguous nucleotides.

The term "treatment" as used herein is used to refer to a drug or other intervention regimen for achieving a beneficial or desired result in a recipient. Beneficial or desired results include, but are not limited to, therapeutic benefits and/or prophylactic benefits. Therapeutic benefit may represent eradication or amelioration of symptoms or the underlying disorder being treated. Moreover, therapeutic benefit may be achieved by eradicating or ameliorating one or more of the physiological symptoms associated with the underlying disorder, such that an improvement is observed in the subject, although the subject may still be afflicted with the underlying disorder. Preventive effects include delaying, preventing or eliminating the appearance of a disease or disorder, delaying or eliminating the onset of symptoms of a disease or disorder, slowing, stopping or reversing the progression of a disease or disorder, or any combination thereof. For prophylactic benefit, a subject at risk of developing a particular disease or a subject reporting one or more physiological symptoms of a disease may receive treatment, even though a diagnosis of the disease may not have been made.

The term "therapeutically effective amount" of a compound of the application means an amount of a compound of the application that will elicit a biological or medical response in a subject (e.g., reduce or inhibit tumor cell proliferation, or ameliorate symptoms, alleviate a condition, slow or delay disease progression, or prevent disease, etc.). In one non-limiting embodiment, the term "therapeutically effective amount" means an amount of a compound of the application that, when administered to a subject, is effective to at least partially reduce, inhibit, prevent and/or ameliorate a condition or disorder or disease, or at least partially inhibit the activity of a targeted enzyme or receptor.

As used in this specification and the claims, the singular forms "a", "an", and "the" include plural referents unless the context clearly dictates otherwise. For example, the term "a sample" includes a plurality of samples, including mixtures thereof.

The terms "determine," "measure," "evaluate," "determine," and "analyze" are often used interchangeably herein to refer to the form of measurement. The term includes determining whether an element is present (e.g., detecting). These terms may include quantitative, qualitative, or both quantitative and qualitative determinations. The evaluation may be relative or absolute. "detecting … … for the presence" may include determining the amount of something present in addition to determining its presence or absence (depending on context).

The terms "subject," "individual," or "patient" are often used interchangeably herein. A "subject" may be a biological entity containing expressed genetic material. The biological entity may be a plant, animal or microorganism, including for example bacteria, viruses, fungi and protozoa. The subject may be a tissue, a cell, and its progeny of a biological entity obtained in vivo or cultured in vitro. The subject may be a mammal. The mammal may be a human. The subject may be diagnosed with the disease or suspected of being at high risk for the disease. In some cases, the subject is not necessarily diagnosed with the disease or is suspected of being at high risk for the disease.

The term "in vivo" is used to describe an event that occurs in a subject.

The term "ex vivo" is used to describe events that occur in vitro in a subject. No ex vivo assays were performed on subjects. Instead, it is performed on a sample separate from the subject. An example of an ex vivo assay performed on a sample is an "in vitro" assay.

The term "in vitro" is used to describe such events: it occurs in a container for holding laboratory reagents such that it is separated from the biological source from which the material was obtained. In vitro assays may encompass cell-based assays in which living or dead cells are employed. In vitro assays may also encompass cell-free assays in which intact cells are not employed.

The term "about" as used herein, a number means that the number is plus or minus 10% of the number. The term "about" a range means that the range minus 10% of its lowest value and plus 10% of its maximum value.

The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

Exemplary embodiments

Accordingly, provided herein are antisense oligonucleotides (ASOs) comprising sequences that hybridize to a target nucleic acid sequence of a long non-coding RNA (lncRNA). In some embodiments, the lncRNA modulates expression of FOXG 1. In some embodiments, the lncRNA reduces expression of FOXG1 messenger RNA. In some embodiments, the lncRNA reduces transcription of FOXG1 messenger RNA molecules. In some embodiments, the lncRNA reduces expression of FOXG1 protein. In some embodiments, the lncRNA reduces translation of FOXG1 protein molecules.

In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the sequence is complementary to a target nucleic acid sequence of a long non-coding RNA (lncRNA). In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the long non-coding RNA (lncRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1. In some embodiments, an antisense oligonucleotide of any of the preceding embodiments is provided, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1, long non-protein coding RNA1551 (LINC 01151), long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof.

Further provided are methods of modulating expression of FOXG1 in a cell comprising contacting the cell with a composition comprising an antisense oligonucleotide that hybridizes to a target nucleic acid sequence of a long non-coding RNA (lncRNA). Also provided are methods of treating or ameliorating a FOXG1 disease or disorder in an individual having or at risk of having a FOXG1 disease or disorder, comprising administering to the individual an antisense oligonucleotide, wherein the antisense oligonucleotide comprises a sequence that hybridizes to a target nucleic acid sequence of a long non-coding RNA (lncRNA).

In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 3.

In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 4. In some embodiments, methods of any of the preceding embodiments are provided wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 3. In some embodiments, methods of any of the preceding embodiments are provided wherein the base positions within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3' are contained adjacent to any one or more of the positions provided in table 3. In some embodiments, methods of any of the preceding embodiments are provided, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 4, in some embodiments, methods of any of the preceding embodiments are provided, wherein any one or more adjacent to any one or more of the positions provided in table 4 comprises a base position within 20, 40, 50, 75, 100, or 150 base positions of 5 'and/or 3'.

Examples

The following examples are included for illustrative purposes only and are not intended to limit the scope of the present disclosure.

Example 1 design and selection of ASO

Antisense oligonucleotides ("ASO" or "oligomers") directed against human FOXG1-AS1, LINC01151 and LINC02282 mRNA were selected AS follows. The icosamer ("20 mer") nucleotide subsequences reverse-complementary to the lncRNA targets FOXG1-AS1 (NR 125758.1), LINC01551 (exons of NR 026732.1 and NR 026731.1-merge), LINC02282 (NR 135255.1) were assembled. The oligomers were then initially subset using heat and sequence characteristics as follows:

Different features are used in the initial selection step (above). In the above, T _m =hybridization melting temperature; t (T) _{Hair clip} Hairpin formation temperature; t (T) _Homodimers Homodimer formation temperature, by biopthon software package (http:// biopyth)org) prediction. These selected 20-mers were then further selected for specificity via sequence alignment with the complete human RefSeq unspliced transcriptome (downloaded at 26 months 3 in 2020). The comparison was performed using the FASTA software suite (https:// FASTA. Bioch. Virginia. Edu/FASTA/fasta_list. Html).

TABLE 1 antisense oligonucleotides targeting lncRNA

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Example 2: identification of ASO that increases foxG1 expression in cells

MOEgapmer antisense oligonucleotides (ASOs) designed and selected in example 1 were tested for their ability to increase FOXG1 expression in cells. For the selection of gapmer antisense oligonucleotides (ASO), CCF-STTG1 cells (ATCC partner with LGC Standards of Wesel, germany, catalog number ATCC-CRL-1718) were obtained from ATCC, cultured in RPMI-1540 (# 30-2001, ATCC partner with LGC Standards of Wesel, germany) supplemented with 10% fetal bovine serum (1248D,Biochrom GmbH,Berlin,Germany) and 100U/ml penicillin/100. Mu.g/ml streptomycin (A2213, biochrom GmbH, berlin, germany). Cells were incubated at 37℃with 5% CO ₂ Growing in a humidity-preserving incubator under atmosphere. For ASO transfection, CCF-STTG1 cells were seeded into 96-well tissue culture plates (# 655180, GBO, germany) at a density of 15,000 cells/well.

ASO was transfected in CCF-STTG1 cells using Lipofectamine2000 (Invitrogen/Life technologies, karlsruhe, germany) and reverse transfected with 0.5. Mu. LLipofectamine 2000/well according to the manufacturer's instructions. A single dose screen was performed using quadruplicates of 50nM ASO, and AHSA 1-targeted ASO (MOE-gapmer) and mock transfected cells were used as controls. ASO targets one of three lncRNA expected to affect the expression level of FoxG1, thus reading FoxG1 mRNA expression. After 24 hours incubation with ASO (48 hours incubation time resulted in high toxicity (visible in the aggregation of cells) and low GapDH levels, and thus were ignored in the assay), the medium was removed and the cells were lysed in 150 μl of medium lysis mixture (1 volume of lysis mixture, 2 volumes of cell culture medium) and then incubated for 30 minutes at 53 ℃. Quantigene-single assays were performed for normalization using the probe set for human FoxG1 and GapDH according to the manufacturer's instructions (ThermoFisher, germany). After incubation at room temperature in the dark for 30 minutes, luminescence was read out using a 1420 luminescence counter (WALLAC VICTOR Light, perkin Elmer, rodgau-jugesheim, germany).

In subsequent experiments, 21 ASOs were selected from a single dose screen that either produced promising results in terms of FoxG1 upregulation or served as controls with FoxG1 downregulated in the initial screen. ASO was transfected at three concentrations, 50nM, 20nM and 2nM, while 50nM and 2nM Ahsa1 and mock transfected cells served as controls.

Ahsa1-ASO (a 2' -oMe and a MOE modification) was used as both a non-specific control for expression of the corresponding target mRNA and as a positive control to analyze transfection efficiency with respect to Ahsa1 mRNA levels. The mock transfected wells served as controls for the level of Ahsa1 mRNA by hybridization to the Ahsa1 probe set. The transfection efficiency of both doses in each 96-well plate and in the double dose screen was calculated by correlating the Ahsa 1-level using Ahsa1-ASO (normalized to GapDH) with the Ahsa1 level obtained with the simulated control.

For each well, target mRNA levels were normalized to corresponding GAPDH mRNA levels. The activity of a given ASO is expressed as the percentage of mRNA concentration of the corresponding target (normalized to GAPDH mRNA) in the treated cells, which is the target mRNA concentration (normalized to GAPDH mRNA) averaged over control wells (set to 100% target expression). mRNA expression was quantified using QuantiGene. Table 2 provides the human FoxG1 QG2.0 probe set (Access#NM-005249) and the human GapDHQG2.0 probe set (Access#NM-002046). The oligomer sequences "CE" and "LE" are described without a proprietary portion of their sequences. Cross-reactivity with the cyno sequence was obtained by adding additional probes.

Table 2 QuantiGene probe set.

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FIGS. 2A-C show that antisense gapmer oligonucleotides (ASOs) targeting long non-coding RNA (lncRNA) targets are capable of increasing FOXG1 expression in cells. FIGS. 2A-C provide the least squares mean percentage of FOXG1mRNA in CCF-STTG1 cells after treatment with 50nM antisense oligomer to knock down FOXG1-AS1 (FIG. 2A), LINC01551 (FIG. 2B) or LINC02282 (FIG. 2C) lncRNA targets. The oligomer is represented by the corresponding target mRNA position. FOXG1mRNA was measured 24 hours after transfection. Asterisks indicate statistical significance relative to the simulated and control (non-targeted) oligomers; * P <0.05; * P <0.01; * P <0.001. The arrows mark the down-and up-regulating oligomers selected for dose response analysis. Tables 3 and 4 show gapmer antisense oligonucleotides (ASOs) that increase FOXG1 expression, providing the least squares mean percentage, lncRNA, oligomer ID, sequence, position and statistical significance of FOXG1mRNA in CCF-STTG1 cells (P <0.05; P <0.01; P < 0.001). Table 5 shows dose response data for gapmer antisense oligonucleotides (ASO) at 2, 20 and 50nM dose concentrations, providing mean fold increase and standard error for target lncRNA, oligomer ID, response direction ("U", up; "D", down), FOXG1 expression.

TABLE 3 antisense oligonucleotides (ASO) that increase FOXG1 expression

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TABLE 4 antisense oligonucleotides (ASO) that increase FOXG1 expression

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Table 5: dose response data for antisense oligonucleotides (ASOs)

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Although preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. The following claims are intended to define the scope of the present disclosure and methods and structures within the scope of these claims and their equivalents are covered thereby.

Sequence(s)

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Claims

1. An antisense oligonucleotide comprising a sequence that hybridizes to a target nucleic acid sequence of a long non-coding RNA (lncRNA).

2. The antisense oligonucleotide of claim 1, wherein the lncRNA modulates expression of FOXG 1.

3. The antisense oligonucleotide of claim 2, wherein the lncRNA reduces expression of FOXG1 messenger RNA.

4. The antisense oligonucleotide of claim 2, wherein the lncRNA reduces transcription of FOXG1 messenger RNA molecules.

5. The antisense oligonucleotide of claim 2, wherein the lncRNA reduces expression of FOXG1 protein.

6. The antisense oligonucleotide of claim 2, wherein the lncRNA reduces translation of FOXG1 protein molecules.

7. The antisense oligonucleotide of any one of claims 1-6, wherein the antisense oligonucleotide comprises a modification.

8. The antisense oligonucleotide of claim 7, wherein the modification comprises a modified internucleoside linker, a modified nucleoside, or a combination thereof.

9. The antisense oligonucleotide of claim 8, wherein the antisense oligonucleotide comprises a modified internucleoside linkage.

10. The antisense oligonucleotide of claim 7, wherein the antisense oligonucleotide is configured as a gapmer antisense oligonucleotide.

11. The antisense oligonucleotide of any one of claims 7-10, wherein the antisense oligonucleotide comprises modified internucleoside linkages.

12. The antisense oligonucleotide of any one of claims 7-11, wherein the antisense oligonucleotide comprises a modified nucleoside.

13. The antisense oligonucleotide of claim 12, wherein the modified nucleoside comprises a modified sugar.

14. The antisense oligonucleotide of claim 13, wherein the modified sugar is a bicyclic sugar.

15. The antisense oligonucleotide of claim 13, wherein the modified sugar comprises a 2' -O-methoxyethyl group.

16. The antisense oligonucleotide of any one of claims 1-15, wherein the sequence is complementary to a target nucleic acid sequence of long non-coding RNA (lncRNA).

17. The antisense oligonucleotide of any one of claims 1-16, wherein the long non-coding RNA (lncRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1.

18. The antisense oligonucleotide of any one of claims 1-17, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1, long intergenic non-protein coding RNA 1551, long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof.

19. The antisense oligonucleotide of any one of claims 1-18, wherein the sequence comprises a nucleobase sequence as set forth in any one of table 3.

20. The antisense oligonucleotide of any one of claims 1-18, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 4.

21. The antisense oligonucleotide of any one of claims 1-18, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 3.

22. The antisense oligonucleotide of claim 21, wherein a base position within 20, 40, 50, 75, 100 or 150 base positions adjacent to any one or more of the positions provided in table 3 comprises 5 'and/or 3'.

23. The antisense oligonucleotide of any one of claims 1-22, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 4.

24. The antisense oligonucleotide of claim 23, wherein a base position within 20, 40, 50, 75, 100 or 150 base positions adjacent to any one or more of the positions provided in table 4 is comprised within 5 'and/or 3'.

25. The antisense oligonucleotide of any one of claims 1-24, wherein hybridization of the sequence of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA.

26. The antisense oligonucleotide of any one of claims 1-24, wherein hybridization of the sequence of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1.

27. The antisense oligonucleotide of claim 26, wherein expression of FOXG1 is mRNA expression.

28. The antisense oligonucleotide of claim 26, wherein expression of FOXG1 is protein expression.

29. A composition comprising one or more of the antisense oligonucleotides of any one of claims 1-28.

30. A pharmaceutical composition comprising the antisense oligonucleotide of any one of claims 1 to 29 and a pharmaceutically acceptable carrier or diluent.

31. A method of modulating expression of FOXG1 in a cell comprising contacting the cell with a composition comprising an antisense oligonucleotide that hybridizes to a target nucleic acid sequence of a long non-coding RNA (lncRNA).

32. The method of claim 31, wherein the cells are located in the brain of the individual.

33. The method of claim 32, wherein the individual is a human.

34. The method of claim 32, wherein the individual comprises reduced FOXG1 expression or FOXG1 deficiency.

35. The method of claim 32, wherein the individual has a FOXG1 disease or disorder.

36. The method of claim 35, wherein the FOXG1 disease or disorder is FOXG1 syndrome.

37. The method of any one of claims 31 to 36, wherein the antisense oligonucleotide comprises a sequence complementary to a target nucleic acid sequence of long non-coding RNA (lncRNA).

38. The method of any one of claims 31 to 37, wherein the long non-coding RNA (lncRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1.

39. The method of any one of claims 26 to 33, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1, long intergenic non-protein coding RNA 1551, long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof.

40. The method of any one of claims 31 to 39, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 3.

41. The method of any one of claims 31 to 40, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of Table 4.

42. The method of any one of claims 31 to 40, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 3.

43. The method of claim 42, wherein base positions within 20, 40, 50, 75, 100 or 150 base positions adjacent to any one or more of the positions provided in Table 3 are included in the 5 'and/or 3'.

44. The method of any one of claims 31 to 40, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 4.

45. The method of claim 44, wherein base positions within 20, 40, 50, 75, 100 or 150 base positions adjacent to any one or more of the positions provided in Table 4 are included in the 5 'and/or 3'.

46. The method of any one of claims 31 to 45, wherein hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA.

47. The method of any one of claims 31 to 46, wherein hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1.

48. The method of claim 47, wherein the expression of FOXG1 is mRNA expression.

49. The method of claim 47, wherein the expression of FOXG1 is protein expression.

50. The method of any one of claims 31 to 49, wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage.

51. The method of claim 50, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

52. The method of any one of claims 31 to 51, wherein the antisense oligonucleotide comprises at least one phosphodiester internucleoside linkage.

53. The method of any one of claims 31 to 52, wherein the antisense oligonucleotide comprises a modified nucleoside.

54. The method of claim 53, wherein the modified nucleoside comprises a modified sugar.

55. The method of claim 53, wherein the modified sugar is a bicyclic sugar.

56. The method of claim 54, wherein the modified sugar comprises a 2' -O-methoxyethyl group.

57. The method of any one of claims 31 to 56, wherein modulating expression comprises increasing expression of FOXG1 protein in the cell.

58. The method of any one of claims 31 to 57, wherein modulating expression comprises increasing translation of FOXG1 protein in the cell.

59. The method of any one of claims 31 to 58, wherein the antisense oligonucleotide is administered to the individual by intrathecal injection, intraventricular injection, inhalation, parenteral injection or infusion, or orally.

60. A method of treating or ameliorating a FOXG1 disease or disorder in an individual having or at risk of having a FOXG1 disease or disorder, the method comprising administering to the individual an antisense oligonucleotide, wherein the antisense oligonucleotide comprises a sequence that hybridizes to a target nucleic acid sequence of long non-coding RNA (lncRNA).

61. The method of claim 60, wherein the individual is a human.

62. The method of claim 61, wherein the human is an unborn human.

63. The method of any one of claims 60 to 62, wherein the individual comprises a mutated FOXG1 gene, reduced expression of FOXG1, a deficiency of FOXG1, or a combination thereof.

64. The method of any one of claims 60 to 63, wherein the FOXG1 disease or disorder is FOXG1 syndrome.

65. The method of any one of claims 60 to 64, wherein the antisense oligonucleotide comprises a sequence complementary to a target nucleic acid sequence of long non-coding RNA (lncRNA).

66. The method of any one of claims 60 to 65, wherein the long non-coding RNA (lncRNA) is located within 1 kilobase (kb), 2kb, 5kb, 8kb, or 10kb of the gene encoding FOXG 1.

67. The method of any one of claims 60 to 66, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1, long intergenic non-protein coding RNA 1551, long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof.

68. The method of any one of claims 60 to 67, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 3.

69. The method of any one of claims 60 to 68, wherein the antisense oligonucleotide comprises a nucleobase sequence as set forth in any one of table 4.

70. The method of any one of claims 60 to 68, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in table 3.

71. The method of claim 70, wherein base positions within 20, 40, 50, 75, 100 or 150 base positions adjacent to any one or more of the positions provided in table 3 are contained within 5 'and/or 3'.

72. The method of any one of claims 60 to 68, wherein the antisense oligonucleotide hybridizes to a target nucleic acid sequence comprising or adjacent to any one or more of the positions provided in Table 4,

73. the method of claim 72, wherein base positions within 20, 40, 50, 75, 100 or 150 base positions adjacent to any one or more of the positions provided in Table 4 are included in 5 'and/or 3'.

74. The method of any one of claims 60 to 73, wherein hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases degradation of the lncRNA.

75. The method of any one of claims 60 to 74, wherein hybridization of the antisense oligonucleotide to the target nucleic acid sequence increases expression of FOXG 1.

76. The method of claim 75, wherein the expression of FOXG1 is mRNA expression.

77. The method of claim 75, wherein the expression of FOXG1 is protein expression.

78. The method of any one of claims 60 to 77, wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage.

79. The method of claim 78, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

80. The method of any one of claims 60 to 79, wherein the antisense oligonucleotide comprises at least one phosphodiester internucleoside linkage.

81. The method of any one of claims 60 to 79, wherein the antisense oligonucleotide comprises a modified nucleoside.

82. The method of claim 81, wherein the modified nucleoside comprises a modified sugar.

83. The method of claim 82, wherein the modified sugar is a bicyclic sugar.

84. The method of claim 82, wherein the modified sugar comprises a 2' -O-methoxyethyl group.

85. The method of any one of claims 60 to 84, wherein modulating expression comprises increasing expression of FOXG1 protein in the cell.

86. The method of any one of claims 60 to 85, wherein modulating expression comprises increasing translation of FOXG1 protein in the cell.

87. The method of any one of claims 60 to 86, wherein the antisense oligonucleotide is administered to the individual by intrathecal injection, intraventricular injection, inhalation, parenteral injection or infusion, or orally.

88. A gapmer antisense oligonucleotide comprising a sequence that hybridizes to a target nucleic acid sequence of a long non-coding RNA (lncRNA), wherein said lncRNA reduces expression of FOXG 1.

89. The gapmer antisense oligonucleotide of claim 88 wherein expression of FOXG1 is measured by FOXG1 mRNA expression.

90. The antisense oligonucleotide of claim 88 wherein expression of FOXG1 is measured by FOXG1 protein expression.

91. The gapmer antisense oligonucleotide of any one of claims 88 to 90, wherein the antisense oligonucleotide comprises a modification.

92. The gapmer antisense oligonucleotide of claim 91, wherein the modification comprises a modified internucleoside linker, a modified nucleoside, or a combination thereof.

93. The gapmer antisense oligonucleotide of claim 92, wherein the antisense oligonucleotide comprises modified internucleoside linkages.

94. The gapmer antisense oligonucleotide of any one of claims 88 to 93, wherein the sequence comprises a nucleobase sequence shown in any one of table 3.

95. The gapmer antisense oligonucleotide of any one of claims 88 to 93, wherein the antisense oligonucleotide comprises a nucleobase sequence shown in any one of table 4.

96. The gapmer antisense oligonucleotide of any one of claims 88 to 93, wherein the target nucleic acid sequence comprises one or more nucleobases complementary to a sequence selected from table 3.

97. The gapmer antisense oligonucleotide of any one of claims 88 to 93, wherein the target nucleic acid sequence comprises one or more nucleobases within or adjacent to any one of the reference positions selected from table 3.

98. The gapmer antisense oligonucleotide of any one of claims 88 to 93, wherein the target nucleic acid sequence comprises one or more nucleobases complementary to a sequence selected from table 4.

99. The gapmer antisense oligonucleotide of any one of claims 88 to 93, wherein the target nucleic acid sequence comprises one or more nucleobases within or adjacent to any one of the reference positions selected from table 4.

100. The gapmer antisense oligonucleotide of any one of claims 88 to 99, wherein hybridization of the antisense oligonucleotide increases expression of FOXG1 in a cell.

101. The gapmer antisense oligonucleotide of claim 100, wherein the FOXG1 expression is FOXG1 mRNA expression.

102. The gapmer antisense oligonucleotide of claim 101, wherein the FOXG1 mRNA expression is measured by a probe-based quantitative assay.

103. The gapmer antisense oligonucleotide of any one of claims 88 to 102, wherein the long non-coding RNA (lncRNA) is FOXG1-AS1, long intergenic non-protein coding RNA 1551, long intergenic non-protein coding RNA 2282 (LINC 02282), or a combination thereof.