Oligonucleotides of human endogenous retrovirus 9 (ERV-9) long terminal repeat (LTR) and methods of use
Inventors
XU, LAI • Rosenberg, Amy S. • Elkahloun, Abdel • Candotti, Fabio
Assignees
US Department of Health and Human Services
Publication Number
US-8680065-B2
Publication Date
2014-03-25
Expiration Date
2029-09-11
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Abstract
Described herein are oligonucleotides that target the human endogenous retrovirus-9 (ERV-9) long terminal repeat (LTR). The ERV-9 LTR oligonucleotides specifically hybridize with either the coding strand or non-coding strand of ERV-9 LTR. It is disclosed herein that ERV-9 LTR oligonucleotides inhibit the proliferation of cancer cells, including breast cancer, liver cancer, prostate cancer, fibrosarcoma and myeloid cancer cells. Also described herein are methods of treating a subject diagnosed with cancer comprising administering to the subject an ERV-9 LTR oligonucleotide. In some examples, the methods further comprise administering a second therapeutic agent, such as an antisense compound or a chemotherapeutic agent.
Core Innovation
This disclosure concerns oligonucleotides that specifically target the human endogenous retrovirus-9 (ERV-9) long terminal repeat (LTR) and methods of their use for treating human diseases such as cancer. It is disclosed that oligonucleotides that hybridize specifically with either the coding or non-coding strand of ERV-9 LTR inhibit proliferation of a wide variety of cancer cell types. These oligonucleotides include sense and antisense oligonucleotides targeting sequences within the ERV-9 LTR, particularly the U3 and U5 regions, and small interfering RNAs (siRNAs) targeting the U3 region.
The background identifies the problem that human endogenous retrovirus sequences, especially the ERV-9 LTR, contain promoter and enhancer elements in the U3 region that can upregulate expression of proximate genes contributing to diseases such as cancer. Although ERV LTR sequences were once considered selfish DNA with no relevant function, evidence indicates that their enhancer activity can promote transcription of host genes associated with cancer progression. Therefore, there is a need to inhibit ERV enhancer activity to reduce aberrant gene expression linked to cancer.
The core innovation provides oligonucleotides specifically hybridizing to the ERV-9 LTR, which effectively inhibit proliferation of cancer cells, including breast, liver, prostate, fibrosarcoma, and myeloid cancers. Sense and antisense oligonucleotides, as well as siRNAs, directed to the U3 or U5 regions of ERV-9 LTR achieve this inhibition. Methods of treating subjects diagnosed with cancers associated with ERV-9 RNA expression involve administering therapeutically effective amounts of these oligonucleotides. Methods also include detecting ERV-9 RNA expression in samples from subjects, which can correlate to disease susceptibility and guide treatment with ERV-9 LTR-targeting oligonucleotides.
Claims Coverage
The claims define 18 inventive features focusing on the oligonucleotides targeting ERV-9 LTR sequences, their compositions, and methods of treating cancer and detecting ERV-9 RNA expression, encompassing specific sequences, modifications, and therapeutic combinations.
Isolated oligonucleotide analogs or modified oligonucleotides specific for ERV-9 LTR sequences
Oligonucleotide analogs, modified oligonucleotides, or labeled oligonucleotides having nucleotide sequences at least 90% identical to SEQ ID NO: 1 or SEQ ID NO: 2.
Compositions comprising ERV-9 LTR-targeting oligonucleotides and pharmaceutically acceptable carriers
Pharmaceutical compositions comprising oligonucleotide analogs, modified oligonucleotides, or labeled oligonucleotides as defined in the invention along with suitable carriers.
Oligonucleotides with modifications enhancing stability or detection
Oligonucleotides comprising one or more modified internucleoside linkages, modified sugar moieties, or modified bases. Labeled oligonucleotides include radioisotopes, fluorophores, or enzymes. Phosphorothioate internucleoside linkages at every position are specifically recited.
Isolated small interfering RNAs targeting the ERV-9 LTR U3 region
siRNAs comprising oligonucleotide analogs or modified oligonucleotides with at least 80-95% identity to SEQ ID NOs: 13 and 14, with defined compositions and pharmaceutical carriers.
Method of treating subjects with cancer associated with ERV-9 LTR RNA expression
Treatment methods involving selecting a subject in need thereof and administering therapeutically effective amounts of the defined ERV-9 LTR-targeting oligonucleotide analog, modified oligonucleotide, or labeled oligonucleotide to treat cancers.
Treatment of specified cancers with ERV-9 LTR oligonucleotides
The cancers include breast cancer, liver cancer, prostate cancer, fibrosarcoma, and myeloid cancer.
Combination therapy with ERV-9 LTR oligonucleotides and second therapeutic agents
Methods further comprising administration of a second therapeutic agent, which can be an antisense compound or a chemotherapeutic agent.
Use of antisense compounds specific for cancer-related genes in combination therapy
The antisense compound of the second therapeutic agent can target Bcl-2, telomerase, or MDM2.
Detection methods for ERV-9 RNA expression in cancer patient samples
Methods comprising isolation of RNA from tissue or bodily fluid samples, contacting the RNA with oligonucleotide analogs, modified oligonucleotides or labeled oligonucleotides, and detecting hybridization indicating expression of ERV-9 RNA.
Selecting subjects for treatment based on ERV-9 RNA expression levels
Methods include selecting treatment for subjects diagnosed with cancer by detecting expression of ERV-9 RNA and correlating increased expression to susceptibility to treatment with ERV-9 LTR oligonucleotides.
The claims protect isolated, modified, and labeled oligonucleotides specifically targeting the ERV-9 LTR sequences and their use in compositions, methods for treating cancers associated with ERV-9 RNA expression, combination therapies with other anticancer agents, and diagnostic methods detecting ERV-9 RNA expression in samples from cancer patients.
Stated Advantages
ERV-9 LTR oligonucleotides inhibit proliferation of a wide variety of cancer cell types.
The oligonucleotides can inhibit tumor growth in vivo more effectively than some known antisense oligonucleotides targeting cancer-related genes.
ERV-9 LTR oligonucleotides can be combined effectively with chemotherapeutic agents to enhance cancer cell proliferation inhibition.
These oligonucleotides do not significantly inhibit proliferation of normal human primary cells, indicating specificity for cancer cells.
ERV-9 LTR-targeting siRNAs offer increased potency at lower concentrations compared to DNA oligonucleotides.
Documented Applications
Treatment of various cancers including breast cancer, liver cancer, prostate cancer, fibrosarcoma, and myeloid cancers (such as myelogenous leukemia) using ERV-9 LTR oligonucleotides.
Combination cancer therapy using ERV-9 LTR oligonucleotides with chemotherapeutic agents like etoposide (VP16) or antisense compounds targeting Bcl-2, telomerase, or MDM2.
Detection of ERV-9 RNA expression in tissue or bodily fluid samples from subjects diagnosed with cancer to select patients for targeted treatment.
Use of ERV-9 LTR oligonucleotides for inhibiting proliferation of cancer cells in vitro and tumor growth in vivo models.
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