COMPOSITIONS AND METHODS FOR TREATING CANCER
1. A method of treating cancer, comprising:
- administering an agent that blocks the expression or activity of ARlnc1 to a subject diagnosed with cancer under conditions such that a sign or symptom of said cancer is reduced.
Provided herein are compositions and methods for treating cancer. In particular, provided herein are compositions, methods, and uses of inhibitors of ARlnc1 for treating cancer.
- 1. A method of treating cancer, comprising:
administering an agent that blocks the expression or activity of ARlnc1 to a subject diagnosed with cancer under conditions such that a sign or symptom of said cancer is reduced.
- View Dependent Claims (2, 3, 4, 5, 6, 7)
- 8. A method, comprising:
a) assaying a sample from a subject diagnosed with cancer, wherein said sample comprises cancer tissue or cells for the level of expression of ARlnc1; and b) administering an agent that blocks the expression or activity of ARlnc1 when expression of ARlnc1 is present in said sample.
- View Dependent Claims (9, 10, 11)
- 12. A composition, comprising:
a) an agent that inhibits expression of ARlnc1; and b) a pharmaceutically acceptable carrier.
This application claims priority to U.S. provisional patent application Ser. No. 62/655,308, filed Apr. 10, 2018, which is incorporated herein by reference in its entirety.
This invention was made with government support under grants CA186786 and CA214170 awarded by the National Institutes of Health and under W81XWH-13-1-0284 and W81XWH-16-1-0314 awarded by the U.S. Army, Medical Research and Materiel Command. The government has certain rights in the invention.
Provided herein are compositions and methods for treating cancer. In particular, provided herein are compositions, methods, and uses of inhibitors of ARlnc1 for treating cancer.
27,000 Americans will die from prostate cancer (PCa) in 2017. PCa is the most common cancer in men and the number two killer overall. For patients with metastatic PCa that fail hormone therapy, the last line of defense are the taxane-derived chemotherapeutic agents docetaxel (Taxotere) or cabazitaxel (Jevtana). Response to taxane therapy is not durable. Progression-free survival on docetaxel treatment approaches 0% by 3 years (see, e.g., Petrylak D P, et al., New Engl J Med. 2004; 351(15):1513-20).
There is a need for additional diagnostic and treatment options, particularly treatments customized to a patient'"'"'s tumor.
Provided herein are compositions and methods for treating cancer. In particular, provided herein are compositions, methods, and uses of inhibitors of ARlnc1 for treating cancer.
For example, in some embodiments, provided herein is a method of treating cancer, comprising: administering an agent that blocks the expression or activity of ARlnc1 to a subject diagnosed with cancer under conditions such that a sign or symptom of the cancer is reduced. The present disclosure is not limited to particular agents. Examples include, but are not limited to, a nucleic acid (e.g., antisense, siRNA, miRNA, shRNA, etc.) that inhibits expression of ARlnc1. The present disclosure is not limited to a particular cancer. In some embodiments, the cancer is prostate cancer. In some embodiments, the cancer expresses ARlnc1. For example, in some embodiments, ARlnc1 is overexpressed in the cancer relative to the level of expression in non-cancerous cells. In some embodiments, the method further comprises the step of assaying a sample of the cancer for the level of expression of ARlnc1.
Further embodiments provide a method, comprising: a) assaying a sample from a subject diagnosed with cancer, wherein the sample comprises cancer tissue or cells, for the level of expression of ARlnc1; and b) administering an agent that blocks the expression or activity of ARlnc1 when expression or overexpression of ARlnc1 is present in the sample.
Additional embodiments provide the use of an agent that inhibits expression of ARlnc1 to treat cancer in a subject.
Certain embodiments provide a composition comprising an agent that inhibits expression of ARlnc1 for use in the treatment of cancer in a subject.
Also provided herein is a composition, comprising: a) an agent that inhibits expression of ARlnc1; and b) a pharmaceutically acceptable carrier.
Additional embodiments are described herein.
To facilitate an understanding of the present disclosure, a number of terms and phrases are defined below:
As used herein, the term “subject” refers to any animal (e.g., a mammal), including, but not limited to, humans, non-human primates, rodents, and the like, which is to be the recipient of a particular treatment. Typically, the terms “subject” and “patient” are used interchangeably herein in reference to a human subject.
As used herein, the term “subject suspected of having cancer” refers to a subject that presents one or more symptoms indicative of cancer. A subject suspected of having cancer may also have one or more risk factors. A subject suspected of having cancer has generally not been tested for cancer. However, a “subject suspected of having cancer” encompasses an individual who has received a preliminary diagnosis but for whom a confirmatory test has not been done or for whom the level or severity of cancer is not known.
As used herein, the term “subject diagnosed with cancer” refers to a subject who has been tested and found to have cancer. As used herein, the term “initial diagnosis” refers to a test result of initial disease that reveals the presence or absence of disease.
As used herein, the term “non-human animals” refers to all non-human animals including, but not limited to, vertebrates such as rodents, non-human primates, ovines, bovines, ruminants, lagomorphs, porcines, caprines, equines, canines, felines, ayes, etc.
As used herein, the term “cell culture” refers to any in vitro culture of cells. Included within this term are continuous cell lines (e.g., with an immortal phenotype), primary cell cultures, transformed cell lines, finite cell lines (e.g., non-transformed cells), and any other cell population maintained in vitro.
As used herein, the term “eukaryote” refers to organisms distinguishable from “prokaryotes.” It is intended that the term encompass all organisms with cells that exhibit the usual characteristics of eukaryotes, such as the presence of a true nucleus bounded by a nuclear membrane, within which lie the chromosomes, the presence of membrane-bound organelles, and other characteristics commonly observed in eukaryotic organisms. Thus, the term includes, but is not limited to such organisms as fungi, protozoa, and animals (e.g., humans).
As used herein, the term “in vitro” refers to an artificial environment and to processes or reactions that occur within an artificial environment. In vitro environments can consist of, but are not limited to, test tubes and cell culture. The term “in vivo” refers to the natural environment (e.g., an animal or a cell) and to processes or reaction that occur within a natural environment.
The terms “test compound” and “candidate compound” refer to any chemical entity, pharmaceutical, drug, and the like that is a candidate for use to treat or prevent a disease, illness, sickness, or disorder of bodily function (e.g., cancer). Test compounds comprise both known and potential therapeutic compounds. A test compound can be determined to be therapeutic by screening using the screening methods of the present disclosure.
As used herein, the term “sample” is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum and the like. Environmental samples include environmental material such as surface matter, soil, water, and industrial samples. Such examples are not however to be construed as limiting the sample types applicable to the present disclosure.
As used herein, the term “effective amount” refers to the amount of a compound (e.g., a compound described herein) sufficient to effect beneficial or desired results. An effective amount can be administered in one or more administrations, applications or dosages and is not limited to or intended to be limited to a particular formulation or administration route.
As used herein, the term “co-administration” refers to the administration of at least two agent(s) (e.g., ARlnc1 inhibitor described herein) or therapies to a subject. In some embodiments, the co-administration of two or more agents/therapies is concurrent. In other embodiments, a first agent/therapy is administered prior to a second agent/therapy. Those of skill in the art understand that the formulations and/or routes of administration of the various agents/therapies used may vary. The appropriate dosage for co-administration can be readily determined by one skilled in the art. In some embodiments, when agents/therapies are co-administered, the respective agents/therapies are administered at lower dosages than appropriate for their administration alone. Thus, co-administration is especially desirable in embodiments where the co-administration of the agents/therapies lowers the requisite dosage of a known potentially harmful (e.g., toxic) agent(s).
As used herein, the term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo, or ex vivo.
As used herein, the term “toxic” refers to any detrimental or harmful effects on a cell or tissue as compared to the same cell or tissue prior to the administration of the toxicant.
“Amelioration” or “ameliorate” or “ameliorating” refers to a lessening of at least one indicator, sign, or symptom of an associated disease, disorder, or condition. The severity of indicators may be determined by subjective or objective measures, which are known to those skilled in the art.
“Antisense activity” means any detectable or measurable activity attributable to the hybridization of an antisense compound to its target nucleic acid. In certain embodiments, antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid.
“Antisense compound” means an oligomeric compound that is capable of undergoing hybridization to a target nucleic acid through hydrogen bonding. Examples of antisense compounds include, but are not limited to, single-stranded and double-stranded compounds, such as, antisense oligonucleotides, siRNAs and shRNAs.
“Antisense inhibition” means reduction of target nucleic acid levels or target protein levels in the presence of an antisense compound complementary to a target nucleic acid compared to target nucleic acid levels or target protein levels in the absence of the antisense compound.
“Antisense oligonucleotide” means a single-stranded oligonucleotide having a nucleobase sequence that permits hybridization to a corresponding region or segment of a target nucleic acid.
“Base complementarity” refers to the capacity for the precise base pairing of nucleobases of an antisense oligonucleotide with corresponding nucleobases in a target nucleic acid (i.e., hybridization), and is mediated by Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen binding between corresponding nucleobases. “Bicyclic sugar moiety” means a modified sugar moiety comprising a 4 to 7 membered ring (including but not limited to a furanosyl) comprising a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure. In certain embodiments, the 4 to 7 membered ring is a sugar ring. In certain embodiments the 4 to 7 membered ring is a furanosyl. In certain such embodiments, the bridge connects the 2′-carbon and the 4′-carbon of the furanosyl.
“Oligonucleotide” means a polymer of linked nucleosides each of which can be modified or unmodified, independent one from another.
Long non-coding RNAs (lncRNAs) are a class of transcripts with diverse and largely uncharacterized biological functions1-3. Through cross-talk with chromatin, DNA, RNA species, and proteins, lncRNAs function via chromatin remodeling, transcriptional and post-transcriptional regulation4-9. High-throughput RNA sequencing (RNA-Seq) has enabled the identification of lncRNAs with oncogenic and tumor suppressive roles, including involvement in the pathogenesis of prostate cancer (PCa)7,10-12. Primary PCa is often hormone-dependent and relies on signaling through the androgen receptor (AR); therefore, the majority of patients are responsive to front-line treatment with androgen deprivation therapy (ADT)13-15. However, approximately 20% of cases progress to an incurable stage of the disease known as castration-resistant prostate cancer (CRPC), which still critically relies on AR signaling16,17, as evidenced by the clinical benefit afforded through the use of enzalutamide18-21 or abiraterone22-24. While substantial efforts have been undertaken to identify mechanisms of sustained AR signaling in CRPC (e.g., AR mutations, AR splice variants, and alternative activation pathways)25-31, few studies have investigated the role of AR-regulated lncRNAs. Therefore, described herein is a comprehensive RNA-Seq profiling investigation of AR-regulated, cancer-associated lncRNAs from prostate cancer cell lines and patient tissue samples. During such experiments, ARlnc1 was identified as a target in prostate cancer.
Accordingly, provided herein are compositions and methods for treating cancer by inhibiting the expression and/or function of ARlnc1.
In some embodiments, the ARlnc1 inhibitor is selected from, for example, a nucleic acid (e.g., siRNA, shRNA, miRNA or an antisense nucleic acid), a small molecule, a peptide, or an antibody.
In some embodiments, the ARlnc1 inhibitor is a nucleic acid. Exemplary nucleic acids suitable for inhibiting ARlnc1 (e.g., by preventing expression of ARlnc1) include, but are not limited to, antisense nucleic acids and RNAi. In some embodiments, nucleic acid therapies are complementary to and hybridize to at least a portion (e.g., at least 5, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides) of ARlnc1.
In some embodiments, compositions comprising oligomeric antisense compounds, particularly oligonucleotides are used to modulate the function of nucleic acid molecules encoding ARlnc1, ultimately modulating the amount of ARlnc1 expressed. This is accomplished by providing antisense compounds that specifically hybridize with one or more nucleic acids encoding ARlnc1. The specific hybridization of an oligomeric compound with its target nucleic acid interferes with the normal function of the nucleic acid. This modulation of function of a target nucleic acid by compounds that specifically hybridize to it is generally referred to as “antisense.” The functions of DNA to be interfered with include replication and transcription. The functions of RNA to be interfered with include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity that may be engaged in or facilitated by the RNA. The overall effect of such interference with target nucleic acid function is decreasing the amount of ARlnc1 proteins in the cell.
In certain embodiments, antisense compounds have chemically modified subunits arranged in patterns, or motifs, to confer to the antisense compounds properties such as enhanced inhibitory activity, increased binding affinity for a target nucleic acid, or resistance to degradation by in vivo nucleases. Chimeric antisense compounds typically contain at least one region modified so as to confer increased resistance to nuclease degradation, increased cellular uptake, increased binding affinity for the target nucleic acid, and/or increased inhibitory activity. A second region of a chimeric antisense compound may confer another desired property e.g., serve as a substrate for the cellular endonuclease RNase H, which cleaves the RNA strand of an RNA:DNA duplex.
Antisense activity may result from any mechanism involving the hybridization of the antisense compound (e.g., oligonucleotide) with a target nucleic acid, wherein the hybridization ultimately results in a biological effect. In certain embodiments, the amount and/or activity of the target nucleic acid is modulated. In certain embodiments, the amount and/or activity of the target nucleic acid is reduced. In certain embodiments, hybridization of the antisense compound to the target nucleic acid ultimately results in target nucleic acid degradation. In certain embodiments, hybridization of the antisense compound to the target nucleic acid does not result in target nucleic acid degradation. In certain such embodiments, the presence of the antisense compound hybridized with the target nucleic acid (occupancy) results in a modulation of antisense activity. In certain embodiments, antisense compounds having a particular chemical motif or pattern of chemical modifications are particularly suited to exploit one or more mechanisms. In certain embodiments, antisense compounds function through more than one mechanism and/or through mechanisms that have not been elucidated. Accordingly, the antisense compounds described herein are not limited by particular mechanism.
Antisense mechanisms include, without limitation, RNase H mediated antisense; RNAi mechanisms, which utilize the R.sub.1SC pathway and include, without limitation, siRNA, ssRNA and microRNA mechanisms; and occupancy based mechanisms. Certain antisense compounds may act through more than one such mechanism and/or through additional mechanisms.
In certain embodiments, antisense activity results at least in part from degradation of target RNA by RNase H. RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex. It is known in the art that single-stranded antisense compounds which are “DNA-like” elicit RNase H activity in mammalian cells. Accordingly, antisense compounds comprising at least a portion of DNA or DNA-like nucleosides may activate RNase H, resulting in cleavage of the target nucleic acid. In certain embodiments, antisense compounds that utilize RNase H comprise one or more modified nucleosides. In certain embodiments, such antisense compounds comprise at least one block of 1-8 modified nucleosides. In certain such embodiments, the modified nucleosides do not support RNase H activity. In certain embodiments, such antisense compounds are gapmers, as described herein. In certain such embodiments, the gap of the gapmer comprises DNA nucleosides. In certain such embodiments, the gap of the gapmer comprises DNA-like nucleosides. In certain such embodiments, the gap of the gapmer comprises DNA nucleosides and DNA-like nucleosides.
Certain antisense compounds having a gapmer motif are considered chimeric antisense compounds. In a gapmer an internal region having a plurality of nucleotides that supports RNaseH cleavage is positioned between external regions having a plurality of nucleotides that are chemically distinct from the nucleosides of the internal region. In the case of an antisense oligonucleotide having a gapmer motif, the gap segment generally serves as the substrate for endonuclease cleavage, while the wing segments comprise modified nucleosides. In certain embodiments, the regions of a gapmer are differentiated by the types of sugar moieties comprising each distinct region. The types of sugar moieties that are used to differentiate the regions of a gapmer may in some embodiments include .beta.-D-ribonucleosides, .beta.-D-deoxyribonucleosides, 2′-modified nucleosides (such 2′-modified nucleosides may include 2′-MOE and 2′-O—CH.sub.3, among others), and bicyclic sugar modified nucleosides (such bicyclic sugar modified nucleosides may include those having a constrained ethyl). In certain embodiments, nucleosides in the wings may include several modified sugar moieties, including, for example 2′-MOE and bicyclic sugar moieties such as constrained ethyl or LNA. In certain embodiments, wings may include several modified and unmodified sugar moieties. In certain embodiments, wings may include various combinations of 2′-MOE nucleosides, bicyclic sugar moieties such as constrained ethyl nucleosides or LNA nucleosides, and 2′-deoxynucleosides.
Each distinct region may comprise uniform sugar moieties, variant, or alternating sugar moieties. The wing-gap-wing motif is frequently described as “X—Y-Z”, where “X” represents the length of the 5′-wing, “Y” represents the length of the gap, and “Z” represents the length of the 3′-wing. “X” and “Z” may comprise uniform, variant, or alternating sugar moieties. In certain embodiments, “X” and “Y” may include one or more 2′-deoxynucleosides. “Y” may comprise 2′-deoxynucleosides. As used herein, a gapmer described as “X—Y-Z” has a configuration such that the gap is positioned immediately adjacent to each of the 5′-wing and the 3′ wing. Thus, no intervening nucleotides exist between the 5′-wing and gap, or the gap and the 3′-wing. Any of the antisense compounds described herein can have a gapmer motif. In certain embodiments, “X” and “Z” are the same; in other embodiments they are different. In certain embodiments, “Y” is between 8 and 15 nucleosides. X, Y, or Z can be any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30 or more nucleosides.
In certain embodiments, the antisense compound has a gapmer motif in which the gap consists of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 linked nucleosides.
In certain embodiments, antisense compounds including those particularly suited for use as single-stranded RNAi compounds (ssRNA) comprise a modified 5′-terminal end. In certain such embodiments, the 5′-terminal end comprises a modified phosphate moiety. In certain embodiments, such modified phosphate is stabilized (e.g., resistant to degradation/cleavage compared to unmodified 5′-phosphate). In certain embodiments, such 5′-terminal nucleosides stabilize the 5′-phosphorous moiety. Certain modified 5′-terminal nucleosides may be found in the art, for example in WO/2011/139702.
In certain embodiments, antisense compounds, including those particularly suitable for ssRNA comprise one or more type of modified sugar moieties and/or naturally occurring sugar moieties arranged along an oligonucleotide or region thereof in a defined pattern or sugar modification motif. Such motifs may include any of the sugar modifications discussed herein and/or other known sugar modifications.
In certain embodiments, the oligonucleotides comprise or consist of a region having uniform sugar modifications. In certain such embodiments, each nucleoside of the region comprises the same RNA-like sugar modification. In certain embodiments, each nucleoside of the region is a 2′-F nucleoside. In certain embodiments, each nucleoside of the region is a 2′-OMe nucleoside. In certain embodiments, each nucleoside of the region is a 2′-MOE nucleoside. In certain embodiments, each nucleoside of the region is a cEt nucleoside. In certain embodiments, each nucleoside of the region is an LNA nucleoside. In certain embodiments, the uniform region constitutes all or essentially all of the oligonucleotide. In certain embodiments, the region constitutes the entire oligonucleotide except for 1-4 terminal nucleosides.
In certain embodiments, oligonucleotides comprise one or more regions of alternating sugar modifications, wherein the nucleosides alternate between nucleotides having a sugar modification of a first type and nucleotides having a sugar modification of a second type. In certain embodiments, nucleosides of both types are RNA-like nucleosides. In certain embodiments the alternating nucleosides are selected from: 2′-OMe, 2′-F, 2′-MOE, LNA, and cEt. In certain embodiments, the alternating modifications are 2′-F and 2′-OMe. Such regions may be contiguous or may be interrupted by differently modified nucleosides or conjugated nucleosides.
In certain embodiments, the alternating region of alternating modifications each consist of a single nucleoside (i.e., the pattern is (AB).sub.xA.sub.y wherein A is a nucleoside having a sugar modification of a first type and B is a nucleoside having a sugar modification of a second type; x is 1-20 and y is 0 or 1). In certain embodiments, one or more alternating regions in an alternating motif includes more than a single nucleoside of a type.
In certain embodiments, oligonucleotides having such an alternating motif also comprise a modified 5′ terminal nucleoside, such as those of formula IIc or IIe.
In certain embodiments, antisense compounds, including those particularly suited for use as ssRNA comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif. In certain embodiments, oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
In certain embodiments, the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide.
Additional modifications are described, for example, in U.S. Pat. No. 9,796,976, herein incorporated by reference in its entirety.
In some embodiments, nucleic acids are RNAi nucleic acids. “RNA interference (RNAi)” is the process of sequence-specific, post-transcriptional gene silencing initiated by a small interfering RNA (siRNA), shRNA, or microRNA (miRNA). During RNAi, the RNA induces degradation of target mRNA with consequent sequence-specific inhibition of gene expression.
In “RNA interference,” or “RNAi,” a “small interfering RNA” or “short interfering RNA” or “siRNA” or “short hairpin RNA” or “shRNA” molecule, or “miRNA” an RNAi (e.g., single strand, duplex, or hairpin) of nucleotides is targeted to a nucleic acid sequence of interest, for example, ARlnc1.
An “RNA duplex” refers to the structure formed by the complementary pairing between two regions of a RNA molecule. The RNA using in RNAi is “targeted” to a gene in that the nucleotide sequence of the duplex portion of the RNAi is complementary to a nucleotide sequence of the targeted gene. In certain embodiments, the RNAi is are targeted to the sequence encoding ARlnc1. In some embodiments, the length of the RNAi is less than 30 base pairs. In some embodiments, the RNA can be 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11 or 10 base pairs in length. In some embodiments, the length of the RNAi is 19 to 32 base pairs in length. In certain embodiment, the length of the RNAi is 19 or 21 base pairs in length.
In some embodiments, RNAi comprises a hairpin structure (e.g., shRNA). In addition to the duplex portion, the hairpin structure may contain a loop portion positioned between the two sequences that form the duplex. The loop can vary in length. In some embodiments the loop is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 nucleotides in length. In certain embodiments, the loop is 18 nucleotides in length. The hairpin structure can also contain 3′ and/or 5′ overhang portions. In some embodiments, the overhang is a 3′ and/or a 5′ overhang 0, 1, 2, 3, 4 or 5 nucleotides in length.
“miRNA” or “miR” means a non-coding RNA between 18 and 25 nucleobases in length which hybridizes to and regulates the expression of a coding RNA. In certain embodiments, a miRNA is the product of cleavage of a pre-miRNA by the enzyme Dicer. Examples of miRNAs are found in the miRNA database known as miRBase.
As used herein, Dicer-substrate RNAs (DsiRNAs) are chemically synthesized asymmetric 25-mer/27-mer duplex RNAs that have increased potency in RNA interference compared to traditional RNAi. Traditional 21-mer RNAi molecules are designed to mimic Dicer products and therefore bypass interaction with the enzyme Dicer. Dicer has been recently shown to be a component of RISC and involved with entry of the RNAi into RISC. Dicer-substrate RNAi molecules are designed to be optimally processed by Dicer and show increased potency by engaging this natural processing pathway. Using this approach, sustained knockdown has been regularly achieved using sub-nanomolar concentrations. (U.S. Pat. No. 8,084,599; Kim et al., Nature Biotechnology 23:222 2005; Rose et al., Nucleic Acids Res., 33:4140 2005).
The transcriptional unit of a “shRNA” is comprised of sense and antisense sequences connected by a loop of unpaired nucleotides. shRNAs are exported from the nucleus by Exportin-5, and once in the cytoplasm, are processed by Dicer to generate functional RNAi molecules. “miRNAs” stem-loops are comprised of sense and antisense sequences connected by a loop of unpaired nucleotides typically expressed as part of larger primary transcripts (pri-miRNAs), which are excised by the Drosha-DGCR8 complex generating intermediates known as pre-miRNAs, which are subsequently exported from the nucleus by Exportin-5, and once in the cytoplasm, are processed by Dicer to generate functional miRNAs or siRNAs.
“Artificial miRNA” or an “artificial miRNA shuttle vector”, as used herein interchangeably, refers to a primary miRNA transcript that has had a region of the duplex stem loop (at least about 9-20 nucleotides) which is excised via Drosha and Dicer processing replaced with the siRNA sequences for the target gene while retaining the structural elements within the stem loop necessary for effective Drosha processing. The term “artificial” arises from the fact the flanking sequences (e.g., about 35 nucleotides upstream and about 40 nucleotides downstream) arise from restriction enzyme sites within the multiple cloning site of the RNAi. As used herein the term “miRNA” encompasses both the naturally occurring miRNA sequences as well as artificially generated miRNA shuttle vectors.
The RNAi can be encoded by a nucleic acid sequence, and the nucleic acid sequence can also include a promoter. The nucleic acid sequence can also include a polyadenylation signal. In some embodiments, the polyadenylation signal is a synthetic minimal polyad n certain embodiments, provided herein are compounds comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising a portion of at least 8, at least 10, at least 12, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 contiguous nucleobases complementary to an equal length portion of ARlnc1.
In some embodiments, hybridization occurs between an antisense compound disclosed herein and an ARlnc1 nucleic acid. The most common mechanism of hybridization involves hydrogen bonding (e.g., Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding) between complementary nucleobases of the nucleic acid molecules.
Hybridization can occur under varying conditions. Stringent conditions are sequence-dependent and are determined by the nature and composition of the nucleic acid molecules to be hybridized.
An antisense compound and a target nucleic acid are complementary to each other when a sufficient number of nucleobases of the antisense compound can hydrogen bond with the corresponding nucleobases of the target nucleic acid, such that a desired effect will occur (e.g., antisense inhibition of a target nucleic acid, such as an ARlnc1 nucleic acid).
Non-complementary nucleobases between an antisense compound and an ARlnc1 nucleic acid may be tolerated provided that the antisense compound remains able to specifically hybridize to a target nucleic acid. Moreover, an antisense compound may hybridize over one or more segments of an ARLNC1 nucleic acid such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure, mismatch or hairpin structure).
In certain embodiments, the antisense compounds provided herein, or a specified portion thereof, are, or are at least, 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% complementary to an ARlnc1 nucleic acid, a target region, target segment, or specified portion thereof. Percent complementarity of an antisense compound with a target nucleic acid can be determined using routine methods.
For example, an antisense compound in which 18 of 20 nucleobases of the antisense compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. In this example, the remaining noncomplementary nucleobases may be clustered or interspersed with complementary nucleobases and need not be contiguous to each other or to complementary nucleobases. As such, an antisense compound which is 18 nucleobases in length having 4 (four) noncomplementary nucleobases which are flanked by two regions of complete complementarity with the target nucleic acid would have 77.8% overall complementarity with the target nucleic acid and would thus fall within the scope of the present invention. Percent complementarity of an antisense compound with a region of a target nucleic acid can be determined routinely using BLAST programs (basic local alignment search tools) and PowerBLAST programs known in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403 410; Zhang and Madden, Genome Res., 1997, 7, 649 656). Percent homology, sequence identity or complementarity, can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482 489).
In certain embodiments, the antisense compounds provided herein, or specified portions thereof, are fully complementary (i.e., 100% complementary) to a target nucleic acid, or specified portion thereof. For example, an antisense compound may be fully complementary to an Alnc1 nucleic acid, or a target region, or a target segment or target sequence thereof. As used herein, “fully complementary” means each nucleobase of an antisense compound is capable of precise base pairing with the corresponding nucleobases of a target nucleic acid. For example, a 20 nucleobase antisense compound is fully complementary to a target sequence that is 400 nucleobases long, so long as there is a corresponding 20 nucleobase portion of the target nucleic acid that is fully complementary to the antisense compound. Fully complementary can also be used in reference to a specified portion of the first and/or the second nucleic acid. For example, a 20 nucleobase portion of a 30 nucleobase antisense compound can be “fully complementary” to a target sequence that is 400 nucleobases long. The 20 nucleobase portion of the 30 nucleobase oligonucleotide is fully complementary to the target sequence if the target sequence has a corresponding 20 nucleobase portion wherein each nucleobase is complementary to the 20 nucleobase portion of the antisense compound. At the same time, the entire 30 nucleobase antisense compound may or may not be fully complementary to the target sequence, depending on whether the remaining 10 nucleobases of the antisense compound are also complementary to the target sequence.
The location of a non-complementary nucleobase may be at the 5′ end or 3′ end of the antisense compound. Alternatively, the non-complementary nucleobase or nucleobases may be at an internal position of the antisense compound. When two or more non-complementary nucleobases are present, they may be contiguous (i.e., linked) or non-contiguous. In one embodiment, a non-complementary nucleobase is located in the wing segment of a gapmer antisense oligonucleotide.
In certain embodiments, antisense compounds that are, or are up to 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleobases in length comprise no more than 4, no more than 3, no more than 2, or no more than 1 non-complementary nucleobase(s) relative to a target nucleic acid, such as an ARlnc1 nucleic acid, or specified portion thereof.
In certain embodiments, antisense compounds that are, or are up to 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleobases in length comprise no more than 6, no more than 5, no more than 4, no more than 3, no more than 2, or no more than 1 non-complementary nucleobase(s) relative to a target nucleic acid, such as an Alnc1 nucleic acid, or specified portion thereof.
The antisense compounds provided herein also include those which are complementary to a portion of a target nucleic acid. As used herein, “portion” refers to a defined number of contiguous (i.e. linked) nucleobases within a region or segment of a target nucleic acid. A “portion” can also refer to a defined number of contiguous nucleobases of an antisense compound. In certain embodiments, the antisense compounds, are complementary to at least an 8 nucleobase portion of a target segment. In certain embodiments, the antisense compounds are complementary to at least a 12 nucleobase portion of a target segment. In certain embodiments, the antisense compounds are complementary to at least a 15 nucleobase portion of a target segment. In certain embodiments, the antisense compounds are complementary to at least an 18 nucleobase portion of a target segment. Also contemplated are antisense compounds that are complementary to at least a 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more nucleobase portion of a target segment, or a range defined by any two of these values.
The present disclosure contemplates the use of any genetic manipulation for use in modulating the expression of ARlnc1. Examples of genetic manipulation include, but are not limited to, gene knockout (e.g., removing the ARlnc1 gene from the chromosome using, for example, recombination), expression of antisense constructs with or without inducible promoters, and the like. Delivery of nucleic acid construct to cells in vitro or in vivo may be conducted using any suitable method. A suitable method is one that introduces the nucleic acid construct into the cell such that the desired event occurs (e.g., expression of an antisense construct).
Introduction of molecules carrying genetic information into cells is achieved by any of various methods including, but not limited to, directed injection of naked DNA constructs, bombardment with gold particles loaded with said constructs, and macromolecule mediated gene transfer using, for example, liposomes, biopolymers, and the like. Exemplary methods use gene delivery vehicles derived from viruses, including, but not limited to, adenoviruses, retroviruses, vaccinia viruses, and adeno-associated viruses. Because of the higher efficiency as compared to retroviruses, vectors derived from adenoviruses are the preferred gene delivery vehicles for transferring nucleic acid molecules into host cells in vivo. Adenoviral vectors have been shown to provide very efficient in vivo gene transfer into a variety of solid tumors in animal models and into human solid tumor xenografts in immune-deficient mice.
Examples of adenoviral vectors and methods for gene transfer are described in PCT publications WO 00/12738 and WO 00/09675 and U.S. Pat. Nos. 6,033,908, 6,019,978, 6,001,557, 5,994,132, 5,994,128, 5,994,106, 5,981,225, 5,885,808, 5,872,154, 5,830,730, and 5,824,544, each of which is herein incorporated by reference in its entirety. Vectors may be administered to subject in a variety of ways. For example, in some embodiments of the present disclosure, vectors are administered into tumors or tissue associated with tumors using direct injection. In other embodiments, administration is via the blood or lymphatic circulation (See e.g., PCT publication 1999/02685 herein incorporated by reference in its entirety). Exemplary dose levels of adenoviral vector are preferably 108 to 1011 vector particles added to the perfusate.
In some embodiments, CRISPR/Cas9 systems are used to delete or knock out genes. Clustered regularly interspaced short palindromic repeats (CRISPR) are segments of prokaryotic DNA containing short, repetitive base sequences. These play a key role in a bacterial defence system, and form the basis of a genome editing technology known as CRISPR/Cas9 that allows permanent modification of genes within organisms.
In some embodiments, the present disclosure provides antibodies that inhibit ARlnc1. Any suitable antibody (e.g., monoclonal, polyclonal, or synthetic) may be utilized in the therapeutic methods disclosed herein. In some embodiments, the antibodies are humanized antibodies. Methods for humanizing antibodies are well known in the art (See e.g., U.S. Pat. Nos. 6,180,370, 5,585,089, 6,054,297, and 5,565,332; each of which is herein incorporated by reference).
In some embodiments, candidate ARlnc1 inhibitors are screened for activity (e.g., using the methods described herein or another suitable assay).
The present disclosure further provides pharmaceutical compositions (e.g., comprising the compounds described above). The pharmaceutical compositions of the present disclosure may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
Compositions and formulations for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets or tablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders may be desirable.
Compositions and formulations for parenteral, intrathecal or intraventricular administration may include sterile aqueous solutions that may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.
Pharmaceutical compositions of the present disclosure include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions may be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids.
The pharmaceutical formulations of the present disclosure, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.
The compositions of the present disclosure may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present disclosure may also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further contain substances that increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.
Agents that enhance uptake of oligonucleotides at the cellular level may also be added to the pharmaceutical and other compositions of the present disclosure. For example, cationic lipids, such as lipofectin (U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (WO 97/30731), also enhance the cellular uptake of oligonucleotides.
The compositions of the present disclosure may additionally contain other adjunct components conventionally found in pharmaceutical compositions. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions of the present disclosure, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present disclosure. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.
Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. The administering physician can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC50s found to be effective in in vitro and in vivo animal models or based on the examples described herein. In general, dosage is from 0.01 μg to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly. The treating physician can estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues. Following successful treatment, it may be desirable to have the subject undergo maintenance therapy to prevent the recurrence of the disease state, wherein the oligonucleotide is administered in maintenance doses, ranging from 0.01 μg to 100 g per kg of body weight, once or more daily, to once every 20 years.
Provided herein are methods of treating cancer (e.g., prostate cancer). In some embodiments, a sample of tumor or cancerous tissue from the subject is first tested for expression of ARlnc1. In some embodiments, treatment is administered to individuals with expression of ARlnc1 and/or individuals with levels of expression of ARlnc1 greater than the levels in non-cancerous tissue. In some embodiments, samples of tumor or cancer tissue are tested during treatment in order to determine whether or not to continue treatment.
In some embodiments, the compounds and pharmaceutical compositions described herein are administered in combination with one or more additional agents, treatment, or interventions (e.g., agents, treatments, or interventions useful in the treatment of cancer).
In some embodiments, ARlnc1 inhibitors are co-administered with an anti-cancer agent (e.g., chemotherapeutic). The present disclosure is not limited by type of anti-cancer agent co-administered.
The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present disclosure and are not to be construed as limiting the scope thereof.
Cell lines were purchased from the American Type Culture Collection (ATCC) and maintained using standard media and conditions. VCaP cells were maintained in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS). LNCaP cells were maintained in RPMI 1640 (Invitrogen) supplemented with 10% FBS. MDA-PCa-2b cells were maintained in ATCC-formulated F-12K medium, supplemented with 20% FBS, 25 ng/ml cholera toxin, 10 ng/ml mouse epidermal growth factor, 100 μg/ml hydrocortisone, 0.005 mM phosphoethanolamine, 45 nM selenous acid, and 0.005 mg/ml bovine insulin. All cell lines were grown at 37° C. in 5% CO2 cell culture incubators, genotyped by DNA fingerprinting analysis, and tested for mycoplasma infection every two weeks. All cell lines used in this study were mycoplasma-negative.
DHT treatment was performed to identify AR-regulated genes. DHT was purchased from Sigma-Aldrich and used at a final concentration of 10 nM. VCaP and LNCaP cells were grown in charcoal-stripped serum containing media for 48 hours and then stimulated with 10 nM DHT for six or 24 hours.
Total RNA was extracted from LNCaP and VCaP cells following DHT treatment using the miRNeasy kit (QIAGEN). RNA quality was assessed using the Agilent Bioanalyzer. Each sample was sequenced using the Illumina HiSeq 2000 (with a 100-nt read length) according to published protocols52.
RNA-Seq Data Analysis to Identify AR-Regulated Genes.
RNA-Seq data were analyzed as previously described53. Briefly, the strand-specific paired-end reads were inspected for sequencing and data quality (e.g. insert size, sequencing adapter contamination, rRNA content, sequencing error rate). Libraries passing QC were trimmed of sequencing adapters and aligned to the human reference genome, GRCh38. Expression was quantified at the gene level using the “intersection non-empty” mode54 as implemented in featureCounts55 using the Gencode v2256 and/or MiTranscriptome assemblies10. All pairwise differential expression analyses were carried out using the voom-limma approach57,58 with all default parameters. Relative expression levels (FPKMs, fragments per kilobase of transcript per million mapped reads) were normalized for differences in sequencing depth using scaling factors obtained from the calcNormFactors (default parameters) function from edgeR59.
AR-regulated genes (ARGs) were identified from expression data of VCaP and
LNCaP cells treated with DHT after six and 24 hours using three linear models: separate models for each of the cell lines treating the two time-points as biological replicates, and a merged model with all treated samples as replicates. ARGs were defined as genes that were significant (P value<0.1 and absolute log fold-change>2) in both separate models and/or the merged model.
Identification of Prostate Cancer Associated Protein-Coding Genes and lncRNAs.
Raw RNA-Seq data for primary and metastatic patients were obtained from the TCGA/PRAD and PCF/SU2C projects, respectively. External transcriptome samples were re-analyzed using in-house pipelines (see above) to facilitate direct comparisons of expression levels and identification of DEGs. Pan-cancer analyses based on the MiTranscriptome assembly10 were leveraged as FPKMs and enrichment scores (SSEA) computed as part of that project. To visualize data, fold changes were computed relative to median expression levels estimated across the combined (normal, primary, metastatic) cohorts and subjected to unsupervised hierarchical clustering separately within each cohort. Tissue lineage (prostate) and prostate cancer-specific genes were identified using the sample set enrichment analysis (SSEA) method as previously described10. Briefly, the SSEA test was used to determine whether each gene was significantly associated with a set of samples (e.g. prostate cancer), or cancer progression in a given lineage (e.g. prostate normal to prostate cancer). The genes were ranked according to their strength of association.
Oncomine Concept Analysis of the ARlnc1 Signature.
Genes with expression levels significantly correlated with ARlnc1 were separated into positively and negatively correlated gene lists. These two lists were then imported into Oncomine as custom concepts and queried for association (similarity) with other prostate cancer concepts housed in Oncomine. All the prostate cancer concepts with odds ratio>2.0 and p-value<1×10−4 were selected. For simplicity, top concepts (based on odds ratios) were selected for representation. We exported these results as the nodes and edges of a concept association network and visualized the network using Cytoscape version 3.3.0. Node positions were computed using the Edge-weighted force directed layout in Cytoscape using the odds ratio as the edge weight. Node positions were subtly altered manually to enable better visualization of Mode labels60.
Chromatin Immunoprecipitation (ChIP)-Seq Data Analysis.
ChIP-Seq data from published external and in-house data sets, GSE56288 and GSE55064, were reanalyzed using a standard pipeline. Briefly, groomed reads (vendor QC, adapter removal) were aligned to the GRCh38 reference genome using STAR settings that disable spliced alignment: outFilterMismatchNoverLmax: 0.05, outFilterMatchNmin: 16, outFilterScoreMinOverLread: 0, outFilterMatchNminOverLread: 0, alignIntronMax: 1. Improperly paired alignments and non-primary alignments were discarded. Peaks were called using MACS2 (callpeak—broad—qvalue 0.05—broad-cutoff 0.05 and callpeak—call-summits—qvalue 0.05)62 and Q (−n 100000)57. ChIP enrichment plots were computed from alignment coverage files (BigWig63) as trimmed (trim=0.05) smooth splines (spar=0.05). The baseline (non-specific) ChIP signal was estimated from genomic windows furthest from the center of the queried region (peak summit, transcription start site) and subtracted from each signal before plotting.
AR Binding Motif Search.
Unsupervised motif search was carried out using MEME59. For each AR ChIP-Seq dataset, the 10,000 most significant AR-binding sites were identified, pruned of likely artifacts, and reduced64 to a set of most significant, recurrent “uni” AR peaks. DNA sequences (GRch38) from the uni-peak regions overlapping promoters (5 kb upstream, 1 kb downstream of the assembled or known TSS) of ARGs were used as input to MEME (default parameters).
AR ChIP was performed following a previous protocol32. Antibodies: AR, Millipore Cat#06-680; FOXA1, Thermo Fisher Cat# PAS-27157; NKX3-1, CST Cat#83700S.) Quantitative PCR (qPCR) analysis was performed using primers listed in Table 1. Primers targeting CYP2B7 promoter were purchased from CST, Cat #84846.
RNA In Situ Hybridization (RNA ISH) on Tissue Microarray.
In situ hybridization assays were performed on tissue microarray sections from Advanced Cell Diagnostics, Inc. as described previously7. In total, 133 tissue samples were included, including 11 from benign prostate, 85 from localized prostate cancer, and 37 from metastatic prostate cancer. ARlnc1 ISH signals were examined in morphologically-intact cells and scored manually by a study, using a previously described expression value scoring system65. For each tissue sample, the ARLNC1 product score was averaged across evaluable TMA tissue cores. Mean ARLNC1 product scores were plotted in
5′ and 3′ RACE were performed to determine the transcriptional start and termination sites of ARlnc1, using the GeneRacer RLM-RACE kit (Invitrogen), according to the manufacturer'"'"'s instructions.
Northern Blot Analysis.
To validate the presence of ARlnc1 in MDA-PCa-2b cells, Northern blotting was performed using the NorthernMax Kit (Ambion) following the manufacturer'"'"'s protocol. Briefly, 20 μg of total RNA was extracted from MDA-PCa-2b or DU145 cells, denatured with formaldehyde loading dye solution for 10 minutes at 70° C., and separated on a 1% agarose formaldehyde gel. The RNA was then transferred to nylon membrane (Roche), cross-linked to the membrane (UV Stratalinker 1800; Stratagene), and the membrane was pre-hybridized in ultrahybridization solution at 68° C. for 1 hour. Hybridization followed at 68° C. overnight with the ARlnc1-specific biotinylated riboprobe added to the ultrahybridization solution. The membrane was washed, and the bound biotinylated probe was detected with the CDP-Star Chemiluminescent Substrate (Sigma-Aldrich). For the synthesis of ARlnc1-specific biotinylated riboprobe, biotin was randomly incorporated into the ARlnc1 antisense RNA upon transcription using ARlnc1 full-length PCR product as template (Roche). The primer sequences used for generating the probes are given in Table 1.
RNA Isolation and cDNA Synthesis.
Total RNA from cell lines was isolated using QIAzol Lysis reagent (QIAGEN) and miRNeasy kit (QIAGEN) with DNase I digestion according to manufacturer'"'"'s instructions. cDNA was synthesized using Superscript III (Invitrogen) and random primers (Invitrogen).
Relative RNA levels determined by qRT-PCR were measured on an Applied Biosystems 7900HT Real-Time PCR System, using Power SYBR Green MasterMix (Applied Biosystems). All of the primers were obtained from Integrated DNA Technologies (IDT), and gene-specific sequences are listed in Table 1. GAPDH, HMBS, or ACTB were used as internal controls for quantification of gene targets. The relative expression of RNAs was calculated using ΔΔCt method.
Cytoplasmic and Nuclear RNA Purification
Cytoplasmic and nuclear fractionation was performed using the NE-PER nuclear extraction kit (Thermo Scientific) according to manufacturer'"'"'s instructions. RNA was extracted using the previously mentioned protocol.
siRNA oligonucleotides targeting ARLNC1, AR, FOXA1, BRD4, NKX3-1, LSD1, IRF1, POU1F1, or EZH2 and a non-targeting siRNA were purchased from Dharmacon. (si-AR-pool, Cat# L-003400-00-0005; si-FOXA1, Cat# LU-010319-00-0005; si-BRD4, Cat# LU-004937-00-0002; si-NKX3-1, Cat# LU-015422-00-0005; si-LSD1, Cat# LU-009223-00-0002; si-IRF1, Cat# LU-011704-00-0005; si-POU1F1, Cat# LU-012546-00-0005; si-EZH2, Cat# L-004218-00-0005; si-NT, Cat# D-001810-01-05.) siRNA sequences for ARLNC1 knockdown are listed in Table 1. For AR knockdown, two more siRNAs were purchased from Life Technologies (#HSS179972, #HSS179973). Transfections with siRNA (50 nM) were performed with Lipofectamine RNAiMAX according to the manufacturer'"'"'s instructions. RNA and protein were harvested for analysis 72 hours after transfection.
Antisense oligos targeting ARlnc1 were obtained from Ionis Pharmaceuticals. Transfections with ASOs (50 nM) were performed with Lipofectamine RNAiMAX according to the manufacturer'"'"'s instructions. RNA and protein were harvested for analysis 72 hours after transfection.
Gene Expression Profiling.
Total RNA was extracted following the aforementioned protocol. RNA integrity was assessed using the Agilent Bioanalyzer. Microarray analysis was carried out on the Agilent Whole Human Oligo Microarray platform, according to the manufacturer'"'"'s protocol. siRNA-mediated knockdown experiments were run in technical triplicates, comparing knockdown samples treated with two independent ARlnc1 siRNAs to samples treated with non-targeting control siRNA. ASO-mediated knockdown experiments were run in technical replicates, comparing knockdown samples treated with two ARlnc1 ASOs to samples treated with non-targeting control. An AR signature was generated using MDA-PCa-2b cells treated with 10 nM DHT, in technical triplicates.
Analysis of Agilent 44k microarrays was carried out using limma and included background subtraction (bc.method=“half”, offset=100) and within-array normalization (method=“loess”). Between array quantile normalization of average expression levels (but not log-fold changes) was performed using the function normalizeBetweenArrays (method=“Aquantile”). Control probes and probes with missing values were excluded from further analyses. Probes were annotated to Gencode v22 genes using the mapping downloaded from Ensembl (efg_agilent_wholegenome_4x44k_v2). Probes originally annotated as AK093002 were used to detect ARlnc1. Differentially-expressed genes following ARlnc1 knock-down in MDA-PCA-2b cells were identified from triplicate biological repeats using adj.P.Val<0.1 and absolute log fold-change>0.6 cut-offs. Consensus targets of ARlnc1 knockdown using siRNA and ASOs were identified using a merged linear model (all 10 samples treated replicates) and a P value<0.001 cut-off.
Gene Set Enrichment Analysis.
Enrichment analyses for custom and experimentally-derived signatures (i.e. AR targets, genes up- and down-regulated following DHT treatment) were carried out using the nonparametric GSEA software with all default settings. For Gene Ontology (GO) term enrichment, we applied the parametric randomSet66 enrichment statistic to voom-limma estimated fold-changes (see above).
Overexpression of ARlnc1.
Full-length ARlnc1 was amplified from MDA-PCa-2b cells and cloned into the pCDH clone and expression vector (System Biosciences). Insert sequences were validated by Sanger sequencing at the University of Michigan Sequencing Core. Full-length ARlnc1 sequence is listed in Table 2.
Single Molecule Fluorescent In Situ Hybridization (smFISH).
smFISH and image analysis was performed as described67,68. Probe sequences targeting AR, ARlnc1, PCAT1, DANCR, EZH2 and FOXA1 were designed using the probe design software in https://www.biosearchtech.com/stellaris-designer and are listed in Table 3. TERRA probes were designed as described69. Other probes were purchased directly from the LGC-Biosearch. U2-OS cells were seeded in 6-well dishes and transfected with ARlnc1 alone or in combination with AR expression vector using Fugene-HD (Promega) according to the manufacturer'"'"'s protocol. Cells were incubated for 24 hours, reseeded into 8-well chambered coverglasses, and formaldehyde-fixed for smFISH (as described above) after 24 hours. smFISH was carried out according to the above protocol. Number of molecules within large foci was calculated based on the scaled intensity of individual molecules of the appropriate RNA.
RNA In Vitro Transcription.
Linearized DNA templates for full-length ARlnc1, ARlnc1 fragments, ARlnc1 deletion, antisense ARlnc1, LacZ, SCHLAP1-AS, THOR, and AR-3′UTR-1-980 were synthesized using T7-containing primers. Sequences were confirmed by Sanger sequencing at the University of Michigan Sequencing Core. In vitro transcription assays were performed with T7 RNA polymerase (Promega) according to the manufacturer'"'"'s instructions. For BrU-labeled RNA synthesis, 5-Bromo-UTP was added to the incubation system. At the end of transcription, DNA templates were removed by Turbo DNase (ThermoFisher), and RNA was recovered using RNA Clean and Concentrator Kit (Promega). RNA size and quality was further confirmed by the Agilent Bioanalyzer.
RNA-RNA In Vitro Interaction Assay.
For each interaction assay, 25 μl of Protein A/G Magnetic Beads (Pierce) were washed twice with RIP Wash Buffer (Millipore, Cat# CS203177) before incubating with BrU antibody for one hour at room temperature. After antibody conjugation, beads were washed twice with RIP Wash Buffer and then resuspended in Incubation Buffer containing RIP Wash Buffer, 17.5 mM EDTA (Millipore, Cat# CS203175), and RNase Inhibitor (Millipore, Cat# CS203219). For validation of ARlnc1 and AR 3′UTR binding in vitro, equal amounts (5 pmol) of BrU-labeled RNAs (ARlnc1, ARlnc1-AS, LacZ, SCHLAP1-AS, THOR) were incubated with beads in Incubation Buffer for two hours at 4° C. Following incubation, 2.5 pmol of AR 3′UTR-1-980 RNA fragment was added into individual tubes and incubated overnight at 4° C. After incubation, beads were washed six times with RIP Wash Buffer. To recover RNA, beads were digested with proteinase K buffer containing RIP Wash Buffer, 1% SDS (Millipore, Cat# CS203174), and 1.2 μg/μL proteinase K (Millipore, Cat# CS203218) at 55° C. for 30 minutes with shaking. After digestion, RNA was extracted from supernatant using the miRNeasy kit (QIAGEN), and reverse transcription was performed using the Superscript III system (Invitrogen). The amount of AR 3′UTR-1-980 recovered in each interaction assay was quantified by qPCR analysis. Data were normalized to ARlnc1-AS control, using ΔCt method.
To identify the sites in ARlnc1 that mediate interaction with AR 3′UTR, an RNA-RNA interaction assay was performed following the aforementioned protocol, using BrU-labeled RNAs: ARlnc1, ARlnc1-AS, ARlnc1 fragments (ARlnc1-1-1300, ARlnc1-1301-2786, ARlnc1-1-700, ARlnc1-701-1300), and ARlnc1 deletion (ARlnc1-del-701-1300).
To further validate the interaction, antisense oligos blocking the interaction sites (blocking ASO, Ionis Pharmaceuticals) were used. In-vitro interaction assays between ARlnc1 and AR 3′UTR were performed following the aforementioned protocol, with the addition of control ASO or blocking ASO pool. Data were normalized to the control ASO, using the ΔCt method.
RNA Stability Assay.
LNCaP cells were treated with 5 μg/mL of actinomycin D for various times as indicated in the figure. RNA was extracted at different time points using QIAzol Lysis reagent (QIAGEN) and the miRNeasy kit (QIAGEN). Real-time RT-PCR was carried out as described above. RNA half-life (t1/2) was calculated by linear regression analysis (GraphPad Prism® software).
Cell Proliferation Assay.
To test the effects of knocking down ARlnc1 on cell proliferation, MDA-PCa-2b or LNCaP cells were seeded into 24-well plates in quadruplicate and allowed to attach. Cells were then transfected with siRNAs or ASOs using Lipofectamine RNAiMAX. Cell proliferation was determined by IncuCyte live-cell imaging system (Essen Biosciences).
MDA-PCa-2b, LNCa,P and PNT2 cells were grown in 6-well plates and transfected with nonspecific siRNA or siRNAs targeting ARlnc1. Apoptosis analysis was performed 48 hours after transfection, using Dead Cell Apoptosis Kit (Molecular Probes #V13241) according to manufacturer'"'"'s instructions.
Cells were lysed in RIPA lysis and extraction buffer (Thermo Scientific #89900) supplemented with protease inhibitor cocktail (ROCHE #11836170001). Protein concentrations were quantified using the DC protein assay (BIO-RAD), and protein lysates were boiled in sample buffer. Protein extracts were then loaded and separated on SDS-PAGE gels. Blotting analysis was performed with standard protocols using polyvinylidene difluoride (PVDF) membrane (GE Healthcare). Membranes were blocked for 60 minutes in blocking buffer (5% milk in a solution of 0.1% Tween-20 in Tris-buffered saline (TBS-T)) and then incubated overnight at 4° C. with primary antibody. After three washes with TBS-T, membranes were incubated with HRP-conjugated secondary antibody. Signals were visualized with an enhanced chemiluminescence system as described by the manufacturer (Thermo Scientific Pierce ECL Western Blotting Substrate). Primary antibodies used in this study were: Androgen Receptor (1:1000 dilution, Millipore, #06-680, rabbit), GAPDH (1:5000 dilution, Cell Signaling, #3683, rabbit), PSA (1:5000 dilution, Dako, #A0562, rabbit), and cleaved PARP (1:1000 dilution, Cell Signaling, #9542, rabbit)
Androgen Receptor Reporter Gene Assay.
Dual luciferase reporter assays were performed using Cignal Androgen Receptor Reporter Kit (Qiagen) according to the manufacturer'"'"'s instructions. Briefly, MDA-PCa-2b cells and LNCaP cells were co-transfected with siRNAs (nonspecific, targeting AR or ARlnc1) and reporter vectors (negative control or AR reporter), using Lipofectamine 2000 transfection reagent (Thermo Fisher Scientific). 40 hours after transfection, DHT (or ethanol vehicle control) was added to induce AR signaling. The Dual Luciferase assay was conducted eight hours after DHT stimulation, using the Dual Luciferase Reporter Assay System from Promega (Cat #1910). Reporter activity was analyzed based on ratio of Firefly/Renilla to normalize for cell number and transfection efficiency.
In Vivo Experiments.
For tumor generation with shRNA-mediated knockdown, shRNA targeting ARLNC1 was cloned in pSIH1-H1-copGFP-T2A-Puro (System Biosciences). Lentiviral particles were generated at the University of Michigan Vector Core. LNCaP-AR cells were infected with lentivirus expressing ARLNC1 shRNA for 48 hours. Knockdown of ARLNC1 was confirmed by qPCR analysis. Male athymic nude mice were randomized into two groups at six to eight weeks of age. 5 million cells expressing sh-ARLNC1 or sh-vector were injected into bilateral flanks of mice. Caliper measurements were taken in two dimensions twice a week by an investigator blinded to the study objective and used to calculate tumor volume. The study was terminated when the tumor volume reached 1000 mm3. For ASO treatment in vivo, six to eight week old male athymic nude mice were inoculated subcutaneously with MDA-PCa-2b cells suspended in matrigel scaffold in the posterior dorsal flank region (5 million cells/site, two sites/animal). When the mean tumor volume reached approximately 150 mm3, mice were randomized into two groups, respectively treated with ARLNC1-specific or control ASO. ASOs, dosed 50 mg/kg, were subcutaneously injected between the scapulae once daily for three periods of five days on/two days off. Tumor size was measured twice per week using a digital caliper by a researcher blinded to the study design. Mouse body weights were monitored throughout the dosing period. When average tumor size in the control group reached 1500 mm3, mice were sacrificed and the primary tumors were excised for weight determination. One-third of the resected specimen was placed in 10% formalin buffer, and the remaining tissue was snap frozen.
BrU-Seq and BrUChase-Seq.
BrU-seq and BrUChase-seq assays were performed as previously described65,66 with MDA-PCa-2b cells treated with either siNT or siARlnc1 BrU-labeling was performed for 30 minutes, and chase experiments were performed for 6 h.
Statistical analysis was performed using Graphpad Prism 6 software. Data were presented as means±s.e.m. All experimental assays were performed in triplicate unless otherwise specified. Statistical analyses shown in figures represent two-tailed t-tests, one-way ANOVA, two-way ANOVA or Kruskal-Wallis rank sum test, as indicated. p<0.05 were considered significant. Details regarding the statistical methods employed during microarray, RNA-Seq and ChIP-Seq data analysis were included in aforementioned methods for bioinformatic analyses.
RNA-seq and Microarray data will be deposited into Gene Expression Omnibus upon manuscript acceptance.
To nominate AR-regulated genes (ARGs), RNA-Seq was performed on AR-dependent VCaP and LNCaP prostate cancer cell lines, stimulated with an AR ligand, dihydrotestosterone (DHT), for six and 24 hours (
To differentiate between direct and indirect ARGs, previously published AR chromatin immunoprecipitation (ChIP)-Seq data from LNCaP and VCaP cells were analyzed32. For direct AR targets, increased levels of AR binding at transcription start sites (TSS) in both LNCaP and VCaP cells was observed (
Finally, it was confirmed that the AR-regulated genes were also expressed in human prostate tissues. RNA-Seq data from normal prostate, clinically-localized PCa (The Cancer Genome Atlas, TCGA)35, and metastatic CRPC (Stand Up to Cancer-Prostate Cancer Foundation, SU2C-PCF)35 were interrogated (
ARLNC1 is a Prostate Lineage-Specific lncRNA with Elevated Expression in Cancer
It was hypothesized that lncRNAs associated with PCa progression and castration-resistance should either be upregulated if they enhance AR signaling or, conversely, downregulated if they attenuate AR signaling. Their expression is also expected to be AR-dependent and lineage-restricted if they are part of bona fide physiological feedback loops. Accordingly, a top-down strategy was developed in order to establish and prioritize clinically-relevant, prostate cancer and lineage-specific lncARGs. First, genes were identified that were both directly regulated by AR in VCaP/LNCaP cell lines and upregulated in primary (
Next, the prostate lineage and cancer specificity of prostate cancer-associated lncRNAs was identified by leveraging the MiTranscriptome assembly10, an online resource to interrogate lncRNA expression across a multitude of tissue and tumor types, and Sample Set Enrichment Analysis (SSEA), which indicates the strength of cancer and lineage association10. After applying an expression level filter (10 FPKM at the 95th percentile), 12 of the most prostate lineage and prostate cancer-specific lncRNAs were identified (
Expression of ARlnc1 was interrogated across cancer and normal tissue RNA-Seq samples from TCGA and the Genotype-Tissue Expression (GTEX) project37,38, respectively. In the TCGA cohort, ARlnc1 exhibited a highly prostate cancer-specific expression pattern, with little to no expression in other tumor types (
Since ARlnc1 was identified as an AR-regulated lncRNA, AR ChIP-Seq data from DHT-stimulated VCaP and LNCaP cells was interrogated for AR binding sites. An androgen-induced AR peak directly at the annotated promoter of ARlnc1 was identified in both VCaP and LNCaP cells (
To determine the function of ARlnc1 in prostate cancer, gene expression profiling of MDA-PCa-2b cells transfected with siRNAs targeting ARlnc1 was performed (
Non-coding RNAs have been shown to target mRNAs via direct or indirect RNA-RNA interaction9, 40, 42. To identify target mRNAs that could interact with ARlnc1, an unbiased prediction of RNA-RNA interactions was performed using IntraRNA43, 44. The 3′ UTR of the AR transcript was identified as a target of ARlnc1 (
Using in vitro RNA-RNA binding assay, nucleotides (nt) 700-1300 of ARlnc1 were identified as critical for binding to the AR 3′UTR (
The mechanism of ARlnc1-mediated AR regulation was investigated. The stability of these two transcripts was monitor and it was found that AR and ARlnc1 have similar half-lives of approximately 9 hours (
Having established a role for ARlnc1 in the regulation of AR signaling, the biological effects of ARlnc1 were further evaluated in prostate cancer cell lines. GO analysis of the knockdown microarray data showed that ARlnc1-regulated genes were involved in cell proliferation and apoptosis (
Since modulation of ARlnc1 levels resulted in a striking proliferation phenotype, it was contemplated that ARlnc1 inhibition finds use therapeutically for the treatment of prostate cancer. Antisense oligos (ASOs) have recently been shown to be effective in targeting RNA in vivo46-49, thus, ASOs targeting ARlnc1 (
As AR signaling remains a significant driver of CRPC pathogenesis, it is imperative to generate novel strategies for targeting of the pathway. Even with the addition of enzalutamide or abiraterone to CRPC treatment regimens, progression invariably occurs. Exploiting players other than AR itself that are pivotal to maintaining the magnitude of the androgen response is an alternative approach. This example describes a comprehensive profiling of AR-regulated, prostate cancer-associated lncRNAs and functionally characterized the top-ranking candidate, ARlnc1. A positive feedback loop between ARlnc1 and AR that maintains the androgen transcriptional program in AR-positive prostate cancer cells, specifically through regulating the cellular levels of AR, was identified (
- 1. Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long non-coding RNAs: insights into functions. Nat Rev Genet 10, 155-9 (2009).
- 2. Wang, K. C. & Chang, H. Y. Molecular mechanisms of long noncoding RNAs. Mol Cell 43, 904-14 (2011).
- 3. Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annu Rev Biochem 81, 145-66 (2012).
- 4. Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-23 (2007).
- 5. Lee, N., Moss, W. N., Yario, T. A. & Steitz, J. A. EBV noncoding RNA binds nascent RNA to drive host PAXS to viral DNA. Cell 160, 607-18 (2015).
- 6. Wutz, A., Rasmussen, T. P. & Jaenisch, R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 30, 167-74 (2002).
- 7. Prensner, J. R. et al. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet 45, 1392-8 (2013).
- 8. Gupta, R. A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-6 (2010).
- 9. Faghihi, M. A. et al. Expression of a noncoding RNA is elevated in Alzheimer'"'"'s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14, 723-30 (2008).
- 10. Iyer, M. K. et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47, 199-208 (2015).
- 11. Malik, R. et al. The lncRNA PCAT29 inhibits oncogenic phenotypes in prostate cancer. Mol Cancer Res 12, 1081-7 (2014).
- 12. Shukla, S. et al. Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer. Neoplasia 18, 489-99 (2016).
- 13. Lu-Yao, G. L. et al. Fifteen-year survival outcomes following primary androgen-deprivation therapy for localized prostate cancer. JAMA Intern Med 174, 1460-7 (2014).
- 14. Huggins, C. & Hodges, C. V. Studies on prostatic cancer. I. The effect of castration, of estrogen and of androgen injection on serum phosphatases in metastatic carcinoma of the prostate. 1941. J Urol 167, 948-51; discussion 952 (2002).
- 15. Treatment and survival of patients with cancer of the prostate. The Veterans Administration Co-operative Urological Research Group. Surg Gynecol Obstet 124, 1011-7 (1967).
- 16. Chen, Y., Sawyers, C. L. & Scher, H. I. Targeting the androgen receptor pathway in prostate cancer. Curr Opin Pharmacol 8, 440-8 (2008).
- 17. Wong, Y. N., Ferraldeschi, R., Attard, G. & de Bono, J. Evolution of androgen receptor targeted therapy for advanced prostate cancer. Nat Rev Clin Oncol 11, 365-76 (2014).
- 18. Mukherji, D., Pezaro, C. J. & De-Bono, J. S. MDV3100 for the treatment of prostate cancer. Expert Opin Investig Drugs 21, 227-33 (2012).
- 19. Scher, H. I. et al. Increased survival with enzalutamide in prostate cancer after chemotherapy. N Engl J Med 367, 1187-97 (2012).
- 20. Tran, C. et al. Development of a second-generation antiandrogen for treatment of advanced prostate cancer. Science 324, 787-90 (2009).
- 21. Scher, H. I. et al. Antitumour activity of MDV3100 in castration-resistant prostate cancer: a phase 1-2 study. Lancet 375, 1437-46 (2010).
- 22. Stein, M. N., Goodin, S. & Dipaola, R. S. Abiraterone in prostate cancer: a new angle to an old problem. Clin Cancer Res 18, 1848-54 (2012).
- 23. Reid, A. H. et al. Significant and sustained antitumor activity in post-docetaxel, castration-resistant prostate cancer with the CYP17 inhibitor abiraterone acetate. J Clin Oncol 28, 1489-95 (2010).
- 24. de Bono, J. S. et al. Abiraterone and increased survival in metastatic prostate cancer. N Engl J Med 364, 1995-2005 (2011).
- 25. Watson, P. A., Arora, V. K. & Sawyers, C. L. Emerging mechanisms of resistance to androgen receptor inhibitors in prostate cancer. Nat Rev Cancer 15, 701-11 (2015).
- 26. Antonarakis, E. S. et al. AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer. N Engl J Med 371, 1028-38 (2014).
- 27. Attard, G., Richards, J. & de Bono, J. S. New strategies in metastatic prostate cancer: targeting the androgen receptor signaling pathway. Clin Cancer Res 17, 1649-57 (2011).
- 28. Hearn, J. W. et al. HSD3B1 and resistance to androgen-deprivation therapy in prostate cancer: a retrospective, multicohort study. Lancet Oncol 17, 1435-1444 (2016).
- 29. Chan, S. C., Li, Y. & Dehm, S. M. Androgen receptor splice variants activate androgen receptor target genes and support aberrant prostate cancer cell growth independent of canonical androgen receptor nuclear localization signal. J Biol Chem 287, 19736-49 (2012).
- 30. Robinson, D. et al. Integrative clinical genomics of advanced prostate cancer. Cell 161, 1215-28 (2015).
- 31. Visakorpi, T. et al. In vivo amplification of the androgen receptor gene and progression of human prostate cancer. Nat Genet 9, 401-6 (1995).
- 32. Asangani, I. A. et al. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature 510, 278-82 (2014).
- 33. Roche, P. J., Hoare, S. A. & Parker, M. G. A consensus DNA-binding site for the androgen receptor. Mol Endocrinol 6, 2229-35 (1992).
- 34. Pomerantz, M. M. et al. The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis. Nat Genet 47, 1346-51 (2015).
- 35. Cancer Genome Atlas Research, N. The Molecular Taxonomy of Primary Prostate Cancer. Cell 163, 1011-25 (2015).
- 36. Takayama, K. et al. Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. EMBO J 32, 1665-80 (2013).
- 37. Consortium, G. T. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648-60 (2015).
- 38. Mele, M. et al. Human genomics. The human transcriptome across tissues and individuals. Science 348, 660-5 (2015).
- 39. Rhodes, D. R. et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9, 166-80 (2007).
- 40. Engreitz, J. M. et al. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell 159, 188-99 (2014).
- 41. Kretz, M. et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493, 231-5 (2013).
- 42. Gong, C. & Maquat, L. E. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470, 284-8 (2011).
- 43. Wright, P. R. et al. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res 42, W119-23 (2014).
- 44. Mann, M., Wright, P. R. & Backofen, R. IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res 45, W435-W439 (2017).
- 45. Lennox, K. A. & Behlke, M. A. Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res 44, 863-77 (2016).
- 46. Meng, L. et al. Towards a therapy for Angelman syndrome by targeting a long non-coding RNA. Nature 518, 409-12 (2015).
- 47. Wheeler, T. M. et al. Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature 488, 111-5 (2012).
- 48. Hua, Y. et al. Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev 24, 1634-44 (2010).
- 49. Evers, M. M., Toonen, L. J. & van Roon-Mom, W. M. Antisense oligonucleotides in therapy for neurodegenerative disorders. Adv Drug Deliv Rev 87, 90-103 (2015).
- 50. Yeap, B. B. et al. Novel binding of HuR and poly(C)-binding protein to a conserved UC-rich motif within the 3′-untranslated region of the androgen receptor messenger RNA. J Biol Chem 277, 27183-92 (2002).
- 51. Lebedeva, S. et al. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol Cell 43, 340-52 (2011).
- 52. Prensner, J. R. et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29, 742-9 (2011).
- 53. Cieslik, M. et al. The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing. Genome Res 25, 1372-81 (2015).
- 54. Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-9 (2015).
- 55. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-30 (2014).
- 56. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22, 1760-74 (2012).
- 57. Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15, R29 (2014).
- 58. Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43, e47 (2015).
- 59. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-40 (2010).
- 60. Cline, M. S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2, 2366-82 (2007).
- 61. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137 (2008).
- 62. Hansen, P. et al. Saturation analysis of ChIP-seq data for reproducible identification of binding peaks. Genome Res 25, 1391-400 (2015).
- 63. Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S. & Karolchik, D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204-7 (2010).
- 64. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37, W202-8 (2009).
- 65. Mehra, R. et al. A novel RNA in situ hybridization assay for the long noncoding RNA SChLAP1 predicts poor clinical outcome after radical prostatectomy in clinically localized prostate cancer. Neoplasia 16, 1121-7 (2014).
- 66. Newton, M. A., Quintana, F. A., Den Boon, J. A., Sengupta, S. & Ahlquist, P. Random-Set Methods Identify Distinct Aspects of the Enrichment Signal in Gene-Set Analysis. Annals of Applied Statistics 1, 85-106 (2007).
- 67. Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5, 877-9 (2008).
- 68. Niknafs, Y. S. et al. The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression. Nat Commun 7, 12791 (2016).
- 69. Rossiello, F. et al. DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs. Nat Commun 8, 13980 (2017).
- 70. Paulsen, M. T. et al. Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc Natl Acad Sci USA 110, 2240-5 (2013).
- 71. Paulsen, M. T. et al. Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA. Methods 67, 45-54 (2014).
All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the disclosure will be apparent to those skilled in the art without departing from the scope and spirit of the disclosure. Although the disclosure has been described in connection with specific preferred embodiments, it should be understood that the disclosure as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the disclosure that are obvious to those skilled relevant fields are intended to be within the scope of the following claims.