# US 9,518,261 B2 · Modulation of enhancer RNA mediated gene expression

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 9,518,261 B2
- Document ID: US9518261B2
- Status: Granted
- Kind: B2
- Application number: 14/403,103
- Filed: 2013-05-22
- Published: 2015-06-25
- Granted: 2016-12-13
- Earliest claimed: 2012-05-22
- Assignees: Ionis Pharmaceuticals, Inc.; The Regents of the University of California
- Applicants: Ionis Pharmaceuticals, Inc.; Christopher K. Glass; Michael G. Rosenfeld; Wenbo Li; Michael T. Lam
- Inventors: Susan M. Freier; Christopher K. Glass; Michael G. Rosenfeld; Wenbo Li; Michael T. Lam
- Web page: https://patentgrep.com/patent/US9518261B2

## CPC

- C12N 15/113: Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)}
- C12N 15/85: for animal cells
- C12N 2310/11: Antisense
- C12N 2310/113: targeting other non-coding nucleic acids, e.g. antagomirs
- C12N 2310/315: Phosphorothioates
- C12N 2310/321: 2'-O-R Modification
- C12N 2310/3231: having an additional ring, e.g. LNA, ENA
- C12N 2310/33: of the base
- C12N 2310/3341: 5-Methylcytosine
- C12N 2310/341: Gapmers, i.e. of the type ===---===
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

Disclosed herein are methods and compounds for inhibiting gene expression by inhibiting enhancer RNAs (eRNAs). Such methods and compounds are useful for reducing expression of certain genes, many of which are associated with a variety of diseases and disorders.

## Claims

### Claim 1

A method of inhibiting MMP9 gene expression in a mammalian cell comprising contacting the mammalian cell with a single-stranded antisense compound consisting of the sequence of SEQ ID NO: 3, wherein the antisense compound comprises:
a gap segment consisting of linked deoxynucleosides;
a 5′ wing segment consisting of linked nucleosides; and
a 3′ wing segment consisting of linked nucleosides;
wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment, wherein each nucleoside of each wing segment comprises a modified sugar, wherein the antisense compound targets an enhancer RNA (eRNA) transcribed from a genomic enhancer sequence or region, wherein the eRNA is an MMP9 eRNA sequence comprising the nucleic acid sequence of SEQ ID NO: 1, thereby inhibiting expression of the MMP9 gene in the mammalian cell.

### Claim 2 (depends on 1)

The method of claim 1, wherein the eRNA transcription is initiated from a RNA polymerase II (PolII) binding site and is capable of elongating bidirectionally.

### Claim 3 (depends on 2)

The method of claim 2, wherein the eRNA is capable of enhancing transcription of the MMP9 gene.

### Claim 4 (depends on 3)

The method of claim 3, wherein the genomic enhancer sequence or region has a higher level of monomethylated lysine 4 of histone 3 (H3K4me1) than trimethylated lysine 4 of histone 3 (H3K4me3).

### Claim 5 (depends on 3)

The method of claim 3, wherein the genomic enhancer sequence or region is enriched for bound RNA polymerase II (PolII).

### Claim 6 (depends on 3)

The method of claim 3, wherein the genomic enhancer sequence or region is enriched for bound Rev-Erbα or Rev-Erbβ.

### Claim 7 (depends on 1)

The method of claim 1, wherein the transcriptional start site of the MMP9 gene is located on a chromosome at least about 1 kilobase (kb) from the genomic enhancer sequence or region.

### Claim 8 (depends on 1)

The method of claim 1, wherein the mammalian cell is a hematopoietic cell, a monocyte, a macrophage, a neuron, a breast cell, or a cancer cell.

### Claim 9 (depends on 8)

The method of claim 8, wherein the mammalian cell contacted with the antisense compound is in a subject.

### Claim 10

A compound comprising a single-stranded antisense compound consisting of the sequence of SEQ ID NO: 3, wherein the antisense compound comprises:
a gap segment consisting of linked deoxynucleosides;
a 5′ wing segment consisting of linked nucleosides; and
a 3′ wing segment consisting of linked nucleosides;
wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment, wherein each nucleoside of each wing segment comprises a modified sugar, targeting an enhancer RNA (eRNA) transcribed from a genomic enhancer sequence or region, wherein the eRNA is an MMP9 eRNA sequence comprising the nucleic acid sequence of SEQ ID NO:1.