# Patent

## Title
Methods and compositions for treating cancer

## Abstract

Treatment of cancer by regional and prolonged release of one or more nucleotide-based agents is provided.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This is a Continuation of International Patent Application No. PCT/IL2013/050944, filed Nov. 14, 2013, which claims the benefit of U.S. Provisional Patent Application No. 61/726,029, filed Nov. 14, 2012. The contents of these patent applications are incorporated by reference herein in their entirety.


FIELD
Treatment of cancer by regional and prolonged release of one or more nucleotide-based agents is provided.
BACKGROUND
RNA Interference
Non-coding RNAi molecules regulate genes post-transcriptionally and can lead to gene silencing. Endogenous dsRNA initiates RNAi by activating the ribonuclease protein Dicer, which binds and cleaves double-stranded RNAs (dsRNAs) to produce double-stranded fragments of 20-25 base pairs with a 2-nucleotide overhang at the 3′ end, known as siRNAs. These interfering RNAs (siRNAs) are integrated into an active RNA-induced silencing complex (RISC), while being separated into single “sense” and “antisense” strands. Within the RISC, the antisense strand then base-pairs to its target mRNA and induces cleavage of the mRNA, thereby preventing it from being used as a translation template. Synthetic RNAi molecules can vary significantly in their design, including the specific sequence along the mRNA, accessibility to Dicer and RISC, the length of each strand, optional symmetrical, asymmetrical, blunt, and loop structures, and chemical modifications of many types.
The delivery of RNAi to target tissue is a major challenge. Systemic injection of siRNA into the vascular system needs to overcome renal filtration and phagocytosis and degradation in the bloodstream, and needs to achieve targeting to the diseased site, transport across the vascular endothelial barrier, diffusion through the extracellular matrix, uptake into the cell, escape from the endosome, and unpackaging and releasing the siRNA to the cell RNAi machinery. Systemic delivery today is limited to a small number of target tissues, in particular to the liver.
Even direct injection of naked siRNA to topical targets (for example the eye, skin, mucus membranes, and localized tumors) and intranasal/intratracheal instillation of aerosolized siRNA into the lung is subject to rapid dose decline by diffusion and degradation and increased pressure (in some cases of injection). Repeated injections at a frequency of about one per week are often required.
Alshamsan et al. (STAT3 Silencing in Dendritic Cells by siRNA Polyplexes Encapsulated in PLGA Nanoparticles for the Modulation of Anticancer Immune Response, Molecular Pharmaceutics 7(5): 1643-1654, 2010) reported nanoparticles containing siRNA complexed with polyethylenimine (PEI). However, these devices exhibit fast drug release, typically on the order of one week, and are ineffective to carry high drug loads to a wide tissue area, for a sufficient treatment period.
US Patent Publication No. US2008/0124370 (Marx) describes reagents, methods and systems to treat inflammation and pain in a subject using small interfering RNA (siRNA) molecules targeted to either TNF-alpha, IL1, IL6 and other pro-inflammatory cytokines.
US Patent Publication No. US 2011/0195123 (Shemi) describes an implantable medical device eluting drug locally and for a prolonged period, treatment methods, and implantation methods. The device comprises a polymeric substrate and a drug, for example gene silencing drugs based on RNA interference (RNAi), including siRNA, against targets such as K-ras. The human ras family consists of three closely related proto-oncogenes: c-Harvey (H)-ras, c-Kirsten (K)-ras, and N-ras, which share 90% of their peptide sequence. Ras proteins are localized in the inner cell membrane, bind GDP and GTP, and possess an intrinsic GTPase activity, implicated in the regulation of their activity. Ras proteins influence proliferation, differentiation, transformation, and apoptosis by relaying mitogenic and growth signals into the cytoplasm and the nucleolus. In a normal cell, most of the ras molecules are present in an inactive GDP-bound conformation.
A continuing need exists for improved RNAi-containing compositions to effectively treat solid tumors, including the identification of targets that work particularly well with this technology.
SUMMARY
Provided herein are systems and methods for treatment of solid tumors and the identification of targets that work particularly well with this technology. The described systems and methods may include manufacturing and implanting polymeric implant(s) loaded with a nucleotide-based agent. Additionally included, in some embodiments, are particular release parameters enabling treatment periods of various lengths, exploiting the RNAi machinery for specific silencing and RNAi for non-specific immune triggering, the shielding of the agent against degradation until it is released from the implant, the selected targets, and the release of naked, modified, complexed or conjugated types of siRNA. Such modifications can enable improved treatment efficiency by enhancing cellular uptake and/or spatial distribution, and can reduce toxicity levels.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows exemplary time-release curves of siRNA, as measured in PBS, pH ̃7.
FIGS. 2A and 2B show working examples of siRNA release in PBS and its dependence on coating, additives, percent of additives, and conjugation. FIG. 2A: short release periods ( ̃1.5 month). NC=uncoated drug delivery device (DDD); C=coated DDD; Additive I=Mannitol (“Add1”, 5% and 10%); Additive II=Trehalose (“Add2”, 1%, 5% and 10%); “Conjugated”=cholesterol-conjugated (with Mannitol 10%). All samples were non-coated, except for the one indicated as coated. FIG. 2B: longer release periods  ̃(3-6 months).
FIG. 3 shows the effect of down-regulation of Androgen Receptor (AR), by two different siRNA sequences, on cell viability of PC3 prostate cancer cells. Also shown are the calibration and selection of siRNA doses. AR1 & AR2 refer to siAR-1 and siAR-2, respectively. Mock=mock-transfected; u/t=untransfected; SC=scrambled (non-targeting) siRNA. Testing was done at 0.5×104 (left panels) and 0.75×104 (right panels) cells/well. Vertical axis: upper panel—OD; lower panel—percentage of viable cells (calculated relative to mock transfected cells). Horizontal axis: siRNA concentration. All changes were significant, with a p value of less than 0.001.
FIGS. 4A-4D show the effect of treatment by various siRNA on viability of PC3 cells, ordered by efficacy (FIG. 4A), and on mRNA levels (FIGS. 4B, 4C, and 4D). PC3 were seeded in E-well plates one day before transfection. Transfection was performed using Lipofectamine 2000 transfection reagent. The indicated siRNas were used at a 150 nM concentration, which is 6-μg/well. Scrambled (non-targeting) siRNA was used as a transfection control. For the viability test, cells were grown for 72 hrs, fixed in 4% PFA and stained as by Methylene blue (MB). Percentage viability was normalized to the viability of the scrambled-transfected cells. In each case, the difference between the siRNA-treated cells the scrambled-transfected cells was significant when compared to the difference between the quadruplicate samples. For RNA quantization, 24-hrs post-transfection, total RNA was purified using Trizol® reagent (InvitrogenTM). cDNA was prepared using gScriptTM cDNA Synthesis kit (Quanta Biosciences). Relative mRNA level was assessed compared to HPRT endogenous control using the Image Gauge computer program.
FIG. 5 shows release profiles of DDDs that “hibernate” (i.e. do not release a significant amount of drug) during an initial period. In the depicted examples, the cumulative drug released during the first three months is less than  ̃10% (in vitro at 37° C. in PBS; data set A) and/or the release during the first month is less than  ̃5% (in vivo, inside a mouse; data set B). The DDDs contain trehalose.
FIG. 6 shows a picture of the distal end of an 18-gauge biopsy needle and DDDs of dimensions 0.8 mm×1.7 mm.
FIG. 7A shows the Argonaut (Ago) cleavage site on an siRNA with overhangs and exemplary sites for modifications. FIG. 7B. shows the Ago cleavage site on a blunt-ended siRNA, and exemplary sites for modifications.
FIG. 8: Effect of DDDs containing anti BMI-1 (si-BMI1) and anti-hTERT siRNA on cell viability in several cancer cell lines, namely prostate, pancreas, colon (two lines), lung (two lines), neuroblastoma, embryonic kidney, and hepato-cellular carcinoma.
FIGS. 9A-9D: Expression of BMI-1 (FIG. 9A), hTERT (FIG. 9B), gp130 (FIG. 9C) and K-Ras (including mutated forms of K-Ras) (FIG. 9D), showing the high expression of these targets in cancers other than prostate cancer, including pancreatic, cervical cancer, breast, colon, thyroid and lung cancers.
FIG. 10: In-vivo study of down-regulation of K-Ras G12V: Nude mice were injected with Capan-1-LV-Luc (dominant mutation: K-Ras G12V mutation) cell into the pancreas. One month later, DDDs were implanted. Depicted is survival curve of Nude mice treated as follows: (1. DDD without drug (“empty”); 2. DDDs with siRNA against G12V-mutated K-Ras (“siG12V DDD”); 3 non-targeting siRNA (siGFP DDD); 4. mock-treatment (“PBS”); 5. direct intraperitoneal (I.P.) injection of siRNA without DDD (“IP siG12V”); and 6. I.P. injection of non-targeting siRNA (“IP siGFP”). 72 days after implantation, all surviving mice were sacrificed. 80% of the siG12V DDD-treated mice survived, vs. 10-40% of the other groups.



BRIEF DESCRIPTION OF THE DESCRIBED SEQUENCES
The nucleic and/or amino acid sequences provided herewith are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. The Sequence Listing is submitted as an ASCII text file named 2142_7_3_seq.txt, created May 14, 2015, about 400 KB, which is incorporated by reference herein.
DETAILED DESCRIPTION
Described herein is a DDD, comprising: (a) biocompatible polymeric composition; and (b) a nucleotide-based agent that targets a gene, where the nucleotide-based agent is within the composition, and where the gene is selected from the targets described herein, for treating a cancer other than prostate carcinoma. Typically, the polymeric composition is a biodegradable polymeric matrix, comprising a biodegradable polymer. In some embodiments, the RNAi agent is incorporated within the biodegradable matrix. In other embodiments, the RNAi agent is dispersed within the biodegradable matrix. Alternatively or in addition, the nucleotide-based agent is an RNAi agent.
In some embodiments, the target gene is selected from the group consisting of BMI1 polycomb ring finger oncogene (BMI-1), TERT telomerase reverse transcriptase (hTERT), IL6ST interleukin 6 signal transducer/gp130, and CD44.
In more particular embodiments, the gene is BMI-1. Recently, Song et al (Cancer Sci 2010; 101:1754-1760) found that BMI-1 plays an important role in the late progression of pancreatic cancer and may represent a novel therapeutic target for the treatment of pancreatic cancer.
In other embodiments, the gene is hTERT (human telomerase reverse transcriptase). hTERT is a ribonucleoprotein polymerase that maintains telomere ends by addition of the telomere repeat TTAGGG. The enzyme consists of a protein component with reverse transcriptase activity, encoded by hTERT, and an RNA component which serves as a template for the telomere repeat. hTERT expression plays a role in cellular senescence, as it is normally repressed in postnatal somatic cells, resulting in progressive shortening of telomeres. Deregulation of hTERT expression in somatic cells may be involved in oncogenesis. Studies in mouse models suggest that TERT also participates in chromosomal repair, since de novo synthesis of telomere repeats may occur at double-stranded breaks. Alternatively spliced variants encoding different isoforms of hTERT have been identified.
In other embodiments, the gene is gp130. The protein encoded by this gene is a signal transducer shared by many cytokines, including interleukin 6 (IL6), ciliary neurotrophic factor (CNTF), leukemia inhibitory factor (LIF), and oncostatin M (OSM). This protein functions as a part of the cytokine receptor complex. The activation of this protein is dependent upon the binding of cytokines to their receptors. vIL6, a protein related to IL6 and encoded by the Kaposi sarcoma-associated herpesvirus, can bypass the interleukin 6 receptor (IL6R) and directly activate this protein. Alternatively spliced transcript variants encoding distinct isoforms have been described.
In other embodiments, the gene is CD44. CD44 is a multifunctional protein involved in cell adhesion and signaling. Studies have shown both tumor-promoting and tumor-inhibiting effects of CD44 in cancer development and progression (Patrawala et al).
In yet other embodiments, a DDD described herein comprises nucleotide-based agents, in some embodiments RNAi agents, in more specific embodiments siRNA agents, targeting at least 2 genes selected from the group consisting of: BMI-1, hTERT, gp130, and CD44.
In other embodiments, the target is selected from PAPPA pregnancy-associated plasma protein A (Pappalysin), Neurophilin and tolloid-like 2 (NETO2), Protein tyrosine phosphatase receptor a (PTPRA), BRD4 bromodomain containing 4 (BRD4), ErbB3/HER3, PSCA prostate stem cell antigen (PSCA), Enhancer of zeste homolog 2 (EZH2), TMPRSS2/ERG, CA12 Carbonic anhydrase XII (CA12), MEK4/MAP2K4, p63/KET, Transmembrane and coiled-coil protein 1 (TMCC1), TMCC2, TMCC3, Neurotrimin, CD70, Tmem50b, Claudin-11, and Neuroplastin NPTN. Each target represents a separate embodiment.
In certain, more specific embodiments, the target is associated with cancer stem cells. Non-limiting examples of cancer stem cell targets are CA12, p63, Pappalysin, NETO2, Protein tyrosine phosphatase receptor a, TMCC1, TMCC2, TMCC3, Neurotrimin, CD70, Tmem50b, Claudin-11, and Neuroplastin NPTN. In other embodiments, the target is another cancer stem cell-specific target.







TABLE 1







Exemplary RNAi Targets:











Synonyms/GenBank Gene
Exemplary




ID No./representative
GenBank


Name
SEQ ID No(s):
Accession #'s
Remarks





Androgen
KD; AIS; TFM; DHTR;
NM_000044.3



Receptor
SBMA; HYSP1; NR3C4;
NM_001011645.2



SMAX1; HUMARA
NM_000044.2



Gene ID #: 367.
M20132.1



SEQ ID No: 37
FJ235918




NM_001011645.1


Pappalysin
PAPPA pregnancy-
NM_002581.3



associated plasma protein A



Gene ID #: 5069.



SEQ ID No: 38


NETO2
Neurophilin (NRP) and
NM_001081324.1
Transcript



tolloid (TLL)-like 2;
NM_001201477.1
variants 1 and/or



BTCL2; NEOT2.
(variant 2)
2 can be targeted



Gene ID #: 81831.
NM_018092.4



SEQ ID No: 39
(variant 1)


Protein tyrosine
LRP; HLPR; PTPA; HEPTP;
NM_080840.2


phosphatase
HPTPA; RPTPA; PTPRL2;
NM_001163688.1


receptor α
HPTPalpha; R-PTP-alpha.


(PTPRA)
Gene ID #: 5786.



SEQ ID No: 40


BMI-1
BMI1 polycomb ring finger
NM_005180



oncogene,



Gene ID # 648.



SEQ ID No: 41


gp130
IL6ST interleukin 6 signal
NM_001190981.1



transducer; CD130;
NM_175767.2



CDW130; IL-6RB.
NM_002184.3



Gene ID # 3572.



SEQ ID No: 42-44


hTERT
TERT telomerase reverse
NM_001193376



transcriptase
NM_198253.2



Gene ID #7015.



SEQ ID No: 45-46


BRD4
BRD4 bromodomain
NM_014299.2



containing 4; CAP; MCAP;
NM_058243.2



HUNK1; HUNKI.



Gene ID # 23476.



SEQ ID No: 47


ErbB3
HER3; LCCS2; ErbB-3; c-
NM_001005915.1



erbB3; erbB3-S; MDA-BF-1
NM_001982.3



Gene ID # 2065.
NP_001973



SEQ ID No: 48


PSCA
PSCA prostate stem cell
NM_005672.4



antigen; PRO232
NP_005663



Gene ID # 8000.



SEQ ID No: 49


EZH2
Enhancer of zeste homolog
NM_004456.4



2; ENX1; EZH1; KMT6;
NM_152998.2



WVS2; ENX-1; KMT6A.
NM_001203247.1



Gene ID # 2146.
NM_001203248.1



SEQ ID No: 50
NM_001203249.1


CD44
Gene ID# 960.
NM_001202557.1



SEQ ID No: 51-58
NM_001202556.1




NM_001202555.1




NM_001001392.1




NM_001001391.1




NM_001001390.1




NM_001001389.1




NM_000610.3









TMPRSS2/ERG fusion gene is a fusion of ERG (v-ets erythroblastosis virus E26 oncogene homolog; also known as erg-3; Gene ID#: 2078) to TMPRSS2 transmembrane protease, serine 2 (also known as PP9284 or PRSS10; Gene ID#: 7113). It is expressed in 15-80% of prostate cancer lesions. Representative GenBank sequences: NM_001136154.1 (ERG) and NM_001135099.1 (TMPRSS2).
CA12 Carbonic anhydrase XII (also known as CAXII or HsT18816; Gene ID #: 771) is a transmembrane and extracellular enzyme involved in the regulation of microenvironment acidity and tumor malignancy. CA XII has a central role in hypoxia and tumor acidosis, invasion and metastasis. Representative GenBank sequence: NM_001218.3.
MEK4 (also known as MAP2K4; JNKK; MEK4; MKK4; SEK1; JNKK1; SERK1; MAPKK4; PRKMK4; SAPKK1; and SAPKK-1; Gene ID #: 6416) regulates prostate cancer cell invasion/metastasis. See US 2009/0124569. Representative GenBank sequence: NM_003010.2.
p63 (also known as KET, p51A/B, CUSP, p40, and p73L; Gene ID #: 8626) is a transcription factor and homologue of p53. Representative GenBank sequences: NM_001114978.1, NM_001114979.1, NM_001114980.1, NM_001114981.1, NM_001114982.1, and NM_003722.4.
Transmembrane and coiled-coil proteins (TMCCs) are a group of putative proteins that contain a coiled-coil domain and two transmembrane domains. Both transmembrane domains are located in the C-terminal region (571-653a.a.). There are three family members in humans, which share high sequence homology, namely TMCC1, TMCC2, and TMCC3 (GenBank Gene ID #'s 23023, 9911, and 57458, respectively). Representative GenBank sequence: NM_001017395.3, NM_001242925.1, and NM_020698.2, respectively.
Neurotrimin is a glycosylphosphatidylinositol (GPI)-anchored cell adhesion molecule expressed on neuronal populations (GenBank Gene ID #50863). Representative GenBank sequences: NM_001048209.1, NM_001144058.1, NM_001144059.1, and NM_016522.2.
CD70, a member of the tumour necrosis factor (TNF) superfamily, is a type II integral membrane protein and the ligand for CD27 (GenBank Gene ID #970). Representative GenBank sequence: NM_001252.3.
Tmem50B (GenBank Gene ID #757) is one of two genes in the transmembrane 50 group. Representative GenBank sequence: NM_006134.6.
Claudin-11, also known as oligodendrocyte-specific protein, was first identified to be specifically expressed in the tight junction (TJ) strands of oligodendrocytes in brain and in sertoli cells of rats and mice (GenBank Gene ID #5010). Representative GenBank sequences: NM_001185056.1 and NM_005602.5.
Neuroplastin NPTN (previously known as stromal cell derived factor receptor I) is a cell adhesion molecule of the immunoglobulin (Ig) superfamily (GenBank Gene ID #27020). Representative GenBank sequences: NM_001161363.1, NM_001161364.1, NM_012428.3, and NM_017455.3.
PSCA: Marra et al (BMC Cancer. 2010 Apr. 7; 10:129) showed that PSCA is a glycosylphosphatidylinositol (GPI)-anchored protein expressed not only in prostate, but also in pancreas and bladder cancer. Delay of growth of human bladder cancer cells by PSCA downregulation was associated with activation of immune signaling pathways.
Androgen Receptor (AR): Wu et al (Urology, volume 75, Issue 4, Pages 820-827, April 2010) found that Androgen Receptor (AR) is a potential therapeutic target for bladder cancer. AR expression knockdown produced increased apoptosis, decreased proliferation, and migration of bladder cancer cells.
All isoforms of the proteins mentioned herein may be included. The mention of particular representative sequences is not intended to exclude isoforms not exemplified herein.
In other embodiments, a DDD of methods and compositions described herein comprises two or more separate nucleotide-based agents, in some embodiments RNAi agents, in more specific embodiments siRNA agents. In other embodiments, 2 of the above-listed genes are targeted.
In still other embodiments, a DDD described herein further comprises a nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, targeting Kirsten rat sarcoma 2 viral oncogene homolog (K-ras). K-ras mutations appear inter alia in lung cancer, CRC, and pancreatic cancer. Representative GenBank sequences: BC013572, BC010502, BC029545.1, BT007153, JX512447, and EU332849 (SEQ ID Nos 59-64).
In certain embodiments, the DDD comprises at least one nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, that targets a gene selected from BMI-1, hTERT, gp130, and CD44, and another nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, that targets K-ras.
In certain embodiments, the DDD comprises at least one nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, that targets a gene selected from Pappalysin, NETO2, PTPRA, BRD4, ErbB3/HER3, PSCA, EZH2, TMPRSS2/ERG, CA12, MEK4/MAP2K4, p63/KET, TMCC1, TMCC2, TMCC3, Neurotrimin, CD70, Tmem50b, Claudin-11, and Neuroplastin NPTN; and another agent that targets K-ras.
In certain embodiments, the target K-ras is a G12D-mutated K-ras. In some embodiments, the nucleotide sequence of the duplex region of the sense strand of the nucleotide-based agent consists of:

    
    
        a sequence selected from SEQ ID No: 1-7, namely GUUGGAGCUGAUGGCG (SEQ ID No: 1), GUUGGAGCUGUUGGCG (SEQ ID No: 2), GUUGGAGCUGCUGGCG (SEQ ID No: 3), GUUGGAGCUAGUGGCG (SEQ ID No: 4), GUUGGAGCUUGUGGCG (SEQ ID No: 5), GUUGGAGCUGGUGACG (SEQ ID No: 6), and GUUGGAGCUGGUUGCG (SEQ ID No: 7), either alone or followed by:
        a sequence selected from: (i) UAGGCAAGAGUGCC (SEQ ID No: 8) and (b) a 5′-fragment of 1-13 nucleotides inclusive of SEQ ID No: 8. “Followed by” in this regard means that the 3′-terminus of the sequence selected from SEQ ID No: 1-7 is connected to the 5′-terminus of SEQ ID No: 8 or a fragment thereof.

For purposes of illustration, the following sense strands contain SEQ ID No: 1 and all or a portion of SEQ ID No: 8: GUUGGAGCUGAUGGCGU (SEQ ID No: 16), GUUGGAGCUGAUGGCGUA (SEQ ID No: 17), GUUGGAGCUGAUGGCGUAG (SEQ ID No: 18), GUUGGAGCUGAUGGCGUAGG (SEQ ID No: 19), GUUGGAGCUGAUGGCGUAGGC (SEQ ID No: 20), GUUGGAGCUGAUGGCGUAGGCA (SEQ ID No: 21), GUUGGAGCUGAUGGCGUAGGCAA (SEQ ID No: 22), GUUGGAGCUGAUGGCGUAGGCAAG (SEQ ID No: 23), GUUGGAGCUGAUGGCGUAGGCAAGA (SEQ ID No: 24), GUUGGAGCUGAUGGCGUAGGCAAGAG (SEQ ID No: 25), GUUGGAGCUGAUGGCGUAGGCAAGAGU (SEQ ID No: 26), GUUGGAGCUGAUGGCGUAGGCAAGAGUG (SEQ ID No: 27), GUUGGAGCUGAUGGCGUAGGCAAGAGUGC (SEQ ID No: 28), and GUUGGAGCUGAUGGCGUAGGCAAGAGUGCC (SEQ ID No: 29) Similar sense strains may be readily derived from each of SEQ ID No: 2-7 together with all or a portion of SEQ ID No: 8.

    
    


In certain embodiments, the aforementioned 5′ fragment of SEQ ID No: 8 is at least 3 nucleotides in length; thus, the duplex region of the antisense nucleotide is at least 19 nucleotides in length.
In other embodiments, the duplex region is 19 nucleotides in length (thus comprising both one of SEQ ID No: 1-7 with a 3-nucleotide fragment of SEQ ID No: 8). More specific embodiments of such sequences are those selected from GUUGGAGCUGAUGGCGUAG (SEQ ID No: 9), GUUGGAGCUGUUGGCGUAG (SEQ ID No: 10), GUUGGAGCUGCUGGCGUAG (SEQ ID No: 11), GUUGGAGCUAGUGGCGUAG (SEQ ID No: 12), GUUGGAGCUUGUGGCGUAG (SEQ ID No: 13), and GUUGGAGCUGGUGACGUAG (SEQ ID No: 14), and GUUGGAGCUGGUUGCGUAG (SEQ ID No: 15).
In other embodiments, the duplex region is 16 nucleotides in length (thus consisting of one of SEQ ID No: 1-7 alone). In other embodiments, the duplex region is 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 nucleotides in length (thus comprising one of SEQ ID No: 1-7, together with a fragment of SEQ ID No: 8 that is 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 nucleotides, respectively). In other embodiments, the duplex region is 30 nucleotides in length (thus comprising one of SEQ ID No: 1-7, together with SEQ ID No: 8 in its entirety).
Reference herein to the “duplex region of the sense strand” indicates the portion of the sense strand that exists in a duplex structure after hybridization to the antisense strand. Similarly, reference to the “duplex region of the antisense strand” indicates the portion of the antisense strand that exists in a duplex structure after hybridization to the sense strand. In various embodiments, the duplex region of the sense strand may be either the entire sense strand or a fragment thereof. Similarly, the duplex region of the antisense strand may be either the entire antisense strand or a fragment thereof.
In certain preferred embodiments, the duplex region is perfectly complementary. Thus, the duplex region of the antisense strand is complementary to the duplex region of the sense strand. For purposes of illustration, the following antisense strands have a sequence perfectly complementary to SEQ ID No: 1-7, respectively: CGCCAUCAGCUCCAAC (SEQ ID No: 30), CGCCAACAGCUCCAAC (SEQ ID No: 31), CGCCAGCAGCUCCAAC (SEQ ID No: 32), CGCCACUAGCUCCAAC (SEQ ID No: 33), CGCCACAAGCUCCAAC (SEQ ID No: 34), CGUCACCAGCUCCAAC (SEQ ID No: 35), and CGCAACCAGCUCCAAC (SEQ ID No: 36).
In other embodiments, the nucleotide sequence of the sense strand of the anti-mutated K-ras agent is GUUGGAGCUGAUGGCGUAGdTdT (SEQ ID No: 65), and the sequence of the antisense strand is CUACGCCAUCAGCUCCAACdTdT (SEQ ID No: 66).
In other embodiments, the mutated K-ras is a G12V-mutated K-ras. siRNA's that specifically recognize G12V-mutated K-ras, for example the siRNA having sense and antisense sequences such as GUUGGAGCUGUUGGCGUAG (SEQ ID No: 10), and CUACGCCAACAGCUCCAAC (SEQ ID No: 67), respectively, can in another embodiment be utilized. siRNA G12V is relevant to treatment of a number of malignancies, among them lung cancer and colon cancer.
In other embodiments, the DDD further comprises a nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, that targets a gene involved in vasculogenesis, angiogenesis and endothelial growth, and/or epidermal growth. In a more specific embodiment, the target is selected from VEGF (Vascular endothelial growth factor), Aurora B kinase (AURKB), and EGFR (epidermal growth factor receptor).
VEGF is also known as vascular endothelial growth factor A. Its NCBI Gene ID No. is 7422. Representative nucleotides sequences are NM_001025366, NM_001025367, NM_001025368, NM_001025369, NM_001025370, NM_001033756, NM_001171622, NM_001171623, NM_001171624, NM_001171625, NM_001171626, NM_001171627, NM_001171628, NM_001171629, NM_001171630, NM_001204384, NM_001204385, and NM_003376 (SEQ ID Nos: 185-202).
AURKB's NCBI Gene ID No. is 9212. Representative nucleotides sequences are NM_001256834, NM_001284526, and NM_004217.3 (SEQ ID Nos: 203-205).
EGFR NCBI Gene ID No. is 1956. Representative nucleotides sequences are NM_005228, NM_201282, NM_201283, and NM_201284 (SEQ ID Nos: 206-209).
In other embodiments, the angiogenesis target is targeted together with gene from Table 1. For example, a DDD may comprise (a) a first agent that targets a gene selected from BMI-1, hTERT, gp130, and CD44; and (b) a second agent that targets a gene selected from VEGF, AURKB, and EGFR. In other embodiments, the first agent targets a gene selected from Pappalysin, NETO2, PTPRA, BMI1, IL6ST/gp130, hTERT, BRD4, ErbB3/HER3, PSCA, EZH2, TMPRSS2/ERG, CA12, MEK4/MAP2K4, p63/KET, TMCC1, TMCC2, TMCC3, Neurotrimin, CD70, Tmem50b, Claudin-11, Neuroplastin NPTN, and CD44; and the second agent targets a gene selected from VEGF, AURKB, and EGFR. In other embodiments, the DDD comprises a first agent that targets a gene selected from Pappalysin, NETO2, PTPRA, BMI-1, IL6ST/gp130, hTERT, BRD4, ErbB3/HER3, PSCA, and EZH2; and a second agent that targets a gene selected from VEGF, AURKB, and EGFR. In still other embodiments, the DDD comprises a first agent that targets a gene selected from Pappalysin, NETO2, PTPRA, BMI-1, IL6ST/gp130, BRD4, and EZH2; and a second agent that targets a gene selected from VEGF, AURKB, and EGFR.
In other embodiments, the angiogenesis target is targeted together with a cancer stem cell target. In other embodiments, the DDD comprises a first nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, that targets a gene selected from CA12, p63, Pappalysin, NETO2, Protein tyrosine phosphatase receptor a, TMCC1, TMCC2, TMCC3, Neurotrimin, CD70, Tmem50b, Claudin-11, and Neuroplastin NPTN; and a second nucleotide-based agent, in some embodiments an RNAi agent, in more specific embodiments an siRNA agent, that targets a gene selected from VEGF, AURKB, and EGFR.
In other embodiments, the angiogenesis gene is targeted together with two targets listed in Table 1.
In other embodiments, the target of an siRNA present in a DDD of the methods and compositions described herein is one of the target sequences set forth in Table 2.
In other embodiments, the sense sequence of an siRNA present in a DDD of the described methods and compositions is one of the sense siRNA sequences set forth in Table 2. In other embodiments, the antisense sequence of an siRNA present in a DDD of the described methods and compositions is one of the antisense siRNA sequences set forth in Table 2:







TABLE 2







Exemplary target sequences and siRNA sequences.









Sequence
Target sequence/siRNA sense



name/
sequence/siRNA antisense
Position and


siRNA
sequence, 5′-3′ SEQ ID No
GenBank Accession 


number*
follows sequences in parenthesis
No. of targets





siAR-1
UGCCAGGGACCAUGUUUUG (68)
NM_000044.3;


201
UGCCAGGGACCAUGUUUUGdTdT (69)
NM_001011645.2



CAAAACAUGGUCCCUGGCAdTdT (70)



 


siAR-2
CGGAAAUGUUAUGAAGCAG (71)
NM_000044.3


202
CGGAAAUGUUAUGAAGCAGdTdT (72)
NM_001011645.2



CUGCUUCAUAACAUUUCCGdTdT (73)



 


siAR-3
GCUGAAGAAACUUGGUAAU (74)
NM_000044.3


203
GCUGAAGAAACUUGGUAAUdTdT (75)
NM_001011645.2



AUUACCAAGUUUCUUCAGCdTdT (76)



 


siAR-4
UGAUUUAUACUUCUCUGUU (77)
NM_000044.3


204
UGAUUUAUACUUCUCUGUUdTdT (78)
NM_001011645.2



AACAGAGAAGUAUAAAUCAdTdT (79)



 


siBMI1-1
UGAUUUAUACUUCUCUGUU (80)
NM_005180


205
UGAUUUAUACUUCUCUGUUdTdT (81)




AACAGAGAAGUAUAAAUCAdTdT (82)



 


siBMI1-2
AUGAAUGGAACCAGCAACA (83)
See above


206
AUGAAUGGAACCAGCAACAdTdT (84)




UGUUGCUGGUUCCAUUCAUdTdT (85)



 


siCDC44-1
CUGAGCAUCGGAUUUGAGACUG (86)
NM_001202557.1;


207
CUGAGCAUCGGAUUUGAGAdTdT (87)
NM_001202556.1;



UCUCAAAUCCGAUGCUCAGdTdT (88)
NM_001202555.1;




NM_001001392.1;




NM_001001391.1;




NM_001001390.1;




NM_001001389.1;




NM_000610.3


 


siCDC44-2
GGCGCAGAUCGAUUUGAAU (89)
See above


208
GGCGCAGAUCGAUUUGAAUdTdT (90)




UGAGACGCUCGGCCCUCUUdTdT (91)



 


si-
AAGAGGGCCGAGCGUCUCA (92)
NM_198253.2


hTERT-1
AAGAGGGCCGAGCGUCUCAdTdT (93)
NM_001193376.1


209
AUUCAAAUCGAUCUGCGCCdTdT (94)



 


si-
GAACGUUCCGCAGAGAAAA (95)
See above


hTERT-2
GAACGUUCCGCAGAGAAAAdTdT (96)



210
UUUUCUCUGCGGAACGUUCdTdT (97)



 


si-
GCACUUCCUCUACUCCUCA (98)
See above


hTERT-3
GCACUUCCUCUACUCCUCAdTdT (99)



211
UGAGGAGUAGAGGAAGUGCdTdT (100)



 


si-
CACCAAGAAGUUCAUCUCC (101)
See above


hTERT-4
CACCAAGAAGUUCAUCUCCdTdT (102)



212
GGAGAUGAACUUCUUGGUGdTdT (103)



 


si-
CAUCGCCAGCAUCAUCAAA (104)
See above


hTERT-5
CAUCGCCAGCAUCAUCAAAdTdT (105)



213
UUUGAUGAUGCUGGCGAUGdTdT (106)



 


siNETO2-1
GACUCAUAUCCACCAAACA (107)
NM_001201477.1


214
GACUCAUAUCCACCAAACAdTdT (108)
NM_018092.4



UGUUUGGUGGAUAUGAGUCdTdT (109)



 


siNETO2-2
CAGGGAGAUUCAUGUGGAU (110)
See above


215
CAGGGAGAUUCAUGUGGAUdTdT (111)




AUCCACAUGAAUCUCCCUGdTdT (112)



 


siNETO2-3
GUCUUGGUCCUUCUCAUUA (113)
See above


216
GUCUUGGUCCUUCUCAUUAdTdT (114)




UAAUGAGAAGGACCAAGACdTdT (115)



 


siAR-3-
GCUGAAGAAACUUGGUAAU (116)
See above 


O-Me
GCoUGAAGAAACUoUGGoUAAU (117)
(siAR-1)


217
AUoUACoCAAGUUUCUUoCAGC (118)



 


siNETO2-1-
GACUCAUAUCCACCAAACA (119)
See above 


O-Me
GACUoCAoUAUCoCACoCAAAoCA (120)
(siNETO2-1)


218
oUGUUoUGGoUGGAUAoUGAGUC (121)



 


gp130
GGCAUACCUUAAACAAGCU (122)
NM_001190981.1


219
GGCAUACCUUAAACAAGCUdTdT (123)
NM_175767.2



AGCUUGUUUAAGGUAUGCCdTdT (124)
NM_002184.3


 


PTPRA-1
GACGACAAUAAGCUCUUCA (125)
NM_080840.2


220
GACGACAAUAAGCUCUUCAdTdT (126)




UGAAGAGCUUAUUGUCGUCdTdT (127)



 


PTPRA-2
CCUUAUGACCACUCUAGAG (128)
See above


221
CCUUAUGACCACUCUAGAGdTdT (129)




CUCUAGAGUGGUCAUAAGGdTdT (130)



 


PTPRA-3
GAUGAGACACCAAUUAUUG (131)
See above


222
GAUGAGACACCAAUUAUUGdTdT (132)




CAAUAAUUGGUGUCUCAUCdTdT (133)



 


PTPRA-4
GCCAAAACUUCAAAUCCAA (134)
See above


223
GCCAAAACUUCAAAUCCAAdTdT (135)




UUGGAUUUGAAGUUUUGGCdTdT (136)



 


PTPRA-5
CCACAAGAACAGCAAGCAC (137)
See above


224
CCACAAGAACAGCAAGCACdTdT (138)




GUGCUUGCUGUUCUUGTGGdTdT (139)



 


PAPPA-1
CGACGACAUGAAUAAGAUC (140)
NM_002581.3


225
CGACGACAUGAAUAAGAUCdTdT (141)




GAUCUUAUUCAUGUCGUCGdTdT (142)



 


PAPPA-2
CCAUCAGCUACCCAUAUUC (143)
See above


226
CCAUCAGCUACCCAUAUUCdTdT (144)




GAAUAUGGGUAGCUGAUGGdTdT (145)



 


PAPPA-3
GGAAGGCAACCAGCUGUUA (146)
See above


227
GGAAGGCAACCAGCUGUUAdTdT (147)




UAACAGCUGGUUGCCUUCCdTdT (148)



 


siErbB3-1
GCUGAGAACCAAUACCAGA (149)
NM_001982.3


228
GCUGAGAACCAAUACCAGAdTdT (150)
NM_001005915.1



UCUGGUAUUGGUUCUCAGCdTdT (151)



 


siErbB3-2
CAACUCUCAGGCAGUGUGU (152)
See above


229
CAACUCUCAGGCAGUGUGUdTdT (153)




ACACACUGCCUGAGAGUUGdTdT (154)



 


siPSCA-1
CACGAAGGCUGUGCUGCUU (155)
NM_005672.4


230
CACGAAGGCUGUGCUGCUUdTdT (156)




AAGCAGCACAGCCUUCGUGdTdT (157)



 


siPSCA-2
CGUGCUGUGACACCGACUU (158)
See above


231
CGUGCUGUGACACCGACUUdTdT (159)




AAGUCGGUGUCACAGCACGdTdT (160)



 


siBrd4-1
CCAACGCAGCCAGCACCAA (161)
NM_014299.2


232
CCAACGCAGCCAGCACCAAdTdT (162)
NM_058243.2



UUGGUGCUGGCUGCGUUGGdTdT (163)



 


siBrd4-2
CUGGAAUGCUCAGGAAUGU (164)
See above


233
CUGGAAUGCUCAGGAAUGUdTdT (165)




ACAUUCCUGAGCAUUCCAGdTdT (166)



 


siEZH2-1
CCUGACCUCUGUCUUACUU (167)
NM_004456.4,


234
CCUGACCUCUGUCUUACUUdTdT (168)
NM_152998.2,



AAGUAAGACAGAGGUCAGGdTdT (169)
NM_001203247.1,




NM_001203248.1,




NM_001203249.1


 


siEZH2-2
CUGGGAAGAAAUCUGAGAA (170)
See above


235
CUGGGAAGAAAUCUGAGAAdTdT (171)




UUCUCAGAUUUCUUCCCAGdTdT (172)





*“siRNA number” refers to the internal reference number used in FIG. 4A.






RNAi Agents

The term “nucleotide-based agent”, as used herein, refers to a single-stranded or double-stranded nucleotide molecule containing DNA, RNA, or a mixture thereof, including modified bases. In certain embodiments, when modified bases are used, only modified bases that retain the qualities of the unmodified bases (such as, for example, hybridization to a complementary sequence or ability to program a ribosome) are utilized.
The term “RNAi agent”, as used herein, refers to a nucleotide molecule that decreases or “downregulates” the level of an RNA target in a cell in a sequence-specific manner. In other embodiments, the RNA target is a messenger RNA.
In particular embodiments, RNAi nucleotides are short (or small) interfering RNA (siRNA), short hairpin RNA (shRNA), and microRNA. Other embodiments include longer polynucleotide molecules that are processed intracellularly to yield siRNA. Such molecules include DsiRNA, which are cleaved by the RNase III class endoribonuclease dicer into 21-23 base duplexes having a 2-base 3′-overhang; UsiRNAs, which are duplex siRNAs that are modified with non-nucleotide acyclic monomers, termed unlocked nucleobase analogs (UNA), in which the bond between two adjacent carbon atoms of ribose is removed—these may be designed to enter the RNAi (RNA inhibitory) pathway via Dicer enzyme or directly into RISC; self-delivering RNA (sdRNA) such as rxRNA® of RXi Therapeutics, which has a single-stranded phosphorothioate region, a short duplex region, and contains a variety of nuclease-stabilizing and lipophilic chemical modifications; aptamers, triple-helix antisense nucleotides, DNAzymes; and agents inhibiting the pre-mRNA maturation step of polyA tail addition such as the U1 adaptor (Integrated DNA Technologies (IDT) Inc). The U1 adaptor consists of two parts, a target-gene binding domain and a U′1 domain that attracts and inhibits the cellular splicing apparatus. By combining both capabilities in the same molecule, the U1 adaptor can inhibit the pre-mRNA maturation step of polyA tail addition.
Modifications of Specific Sequences
The above sequences are, in some embodiments, one or both strands of an siRNA described herein is modified by 2′-OMe, 2′-F, or other modifications. In some embodiments, the positions identified below with an “o” may be modified with 2′-OMe:









AR siRNA (internal ref. no. 217):



Sense:



(SEQ ID No: 117)



5′ GCoUGAAGAAACUoUGGoUAAU



 



Anti sense:



(SEQ ID No: 118)



3′ AUoUACoCAAGUUUCUUoCAGC



 



siNETO2 (internal ref. no. 218):



Sense:



(SEQ ID No: 120)



5′ GACUoCAoUAUCoCACoCAAAoCA



 



Antisense:



(SEQ ID No: 121)



5′ oUGUUoUGGoUGGAUAoUGAGUC.






2′-OMe-modified oligonucleotides may be used with or, in other embodiments without, overhangs at the 3′ end of each of the strands. In certain embodiments, the overhangs each consist of two unpaired nucleotides. In more specific embodiments, as exemplified herein, the overhangs are each dTdT (2 deoxythymidine residues). Specific, non-limiting examples of siRNA molecules with 2′-OMe-modifications and dTdT tails are shown further below.
In other embodiments, the following 4 sequence criteria are used to design additional siRNA molecules:
(1) AU richness in the 5′-terminal, 7-bp-long region of the antisense strand;
(2) G/C at the 5′ end of the sense strand; and
(3) the absence of any long GC stretch of >9 bp in length.
(4) a G/C content ranging from 36% to 52%.
In certain embodiments, an RNAi agent that is used is between 25-30 nt, inclusive, in length. More specifically, the length may be 25-27 nt. In other embodiments, the length is 19-25-nt. In other embodiments, the length is 19 nt. In other embodiments, the sense strand and/or the antisense strand further comprises a 1-6-nt 3′-overhang. In other embodiments, a two-base 3′ overhang is present. In more specific embodiments, the sense strand and the antisense strand each further comprises a 2-nt 3′-overhang.
siRNA structure determinants: In one embodiment, the A-form helix of the guide strand-mRNA duplex is preferred. A 25-30-nt asymmetric dsRNAs with a 5′ blunt end and a 2-nt 3′ overhang on the other end is also preferred. In certain embodiments, a blunt structure at the 3′ end is present, followed by a 5′ overhang.
Loops, if present, may be preferably on the 3′ end of the sense strand, or also may be on the 5′ end of the sense strand. The loop may contain nucleotides optionally in combination with non-nucleotide residues.
In other embodiments, an siRNA used in the described methods and compositions has a 19+2 overhang design, namely sense and anti-sense of 19 base-paired nucleotides and two unpaired nucleotides at the 3′ end of each of the strands. In certain embodiments, as exemplified herein, the overhangs are each dTdT (2 deoxythymidine residues). Non-limiting examples of siRNA molecules with dTdT tails are shown in Table 2. Additional examples are GUUGGAGCUGUUGGCGUAGdTdT (SEQ ID No: 173), CUACGCCAACAGCUCCAACdTdT (SEQ ID No: 174), and the AR and siNETO sequences below.









AR siRNA + tail:



Sense:



(SEQ ID No: 175)



5' GCoUGAAGAAACUoUGGoUAAUdTdT



 



Antisense:



(SEQ ID No: 176)



3' AUoUACoCAAGUUUCUUoCAGCdTdT 



 



siNETO2 + tail:



Sense:



(SEQ ID No: 177)



5' GACUoCAoUAUCoCACoCAAAoCAdTdT 



 



Antisense:



(SEQ ID No: 178)



5' oUGUUoUGGoUGGAUAoUGAGUCdTdT.






Chemical Modifications

In other embodiments, an RNAi agent, for example an siRNA agent, used in the described methods and compositions may be chemically modified. In another embodiment, the modification is a backbone or linkage modification. In another embodiment, the modification is a nucleoside base modification. In another embodiment, the modification is a sugar modification. In more specific embodiments, the modification is selected from the modifications appearing in Table 2 hereinbelow. In more specific embodiments, the modification is selected from a 2′-O-methyl (2′-OMe), 2′-O-(2-methoxyethyl) (MOE) and 2′-fluorine modification. In still more specific embodiments, the modification is a 2′-O-methyl (2′-OMe) modification. In other embodiments, the modification is selected from a locked nucleic acid (LNA) and/or peptide nucleic acid (PNA) backbone.
In some embodiments, siRNA modifications are designed based on the following guidelines:

    
    
        1. Cluster modifications around endonuclease cleavage sites: 5′-UA, 5′-CA, 5′-UG
        2. When choosing modification sites use the following guiding rules:
        
            a. Fewer modifications on the antisense strand compared to the sense strand.
            b. Avoid modifications on the Argonaut (Ago) cleavage site (the 10nth nucleotide on antisense strand; FIGS. 7A-B).
            c. As modification increases duplex stability, therefore make fewer modifications on the 3′ end of the sense strand or the 5′ end of antisense strand.
        
        
        3. Order modifications in diagonal 5′ to 5′.
        4. Use of blunt ends instead of overhangs lower exonuclease activity.
    
    









TABLE 3







Selected chemical modifications.








Modification
Position of the substitution










Sugar modifications








dNTPs-dTdT
3′-overhangs of sense and anti-sense strands


dNTPs-dNPs
Any number of residues in the sense strand; 0-4



residues at the 5′ end of the antisense strand


2′-O-methyl (2′OMe)
Any number of residues in the sense and


rNPs
antisense strands


2′-fluoro (2′-F)
Any number of pyrimidine residues in the sense


rNPs
and antisense strands


combined use of 2′OMe
Any number of pyrimidine residues in the sense


and 2′-F
and antisense strands to 2′-F; and any number



of purine residues in the sense and antisense



strands to 2′-OMe.


2′-O-(2-methoxyethyl)
Any number of pyrimidine residues in the sense


(MOE) rNPs
and antisense strands


2′-fluoro-β-D (FANA)
Any number of pyrimidine residues in the sense


rNPs
strand


Locked nucleic acids
from none till 4 last ribonucleotides at the 3′


(LNA)
end of the sense strand; and 3′ overhangs of the



antisense strand


combined use of DNA
substitution of any number of pyrimidine (T


and 2′-F
and C) ribonucleotides to 2′-F ribonu-



cleotides and any number of purines (A



and G) to deoxyribonucleotides in sense and



antisense strands







phosphate linkage modifications - phosphorotioate (PS)








phosphodiester
substitution of any number of ribonucleotides



in sense and antisense strands


phosphothioate (PS)
substitution of any number of ribonucleotides



in sense and antisense strands


boranophosphate DNA
substitution of any number of ribonucleotides


or RNA
in sense and antisense strands


amide-linked
substitution of any number of ribonucleotides



in sense and antisense strands


phosphoramidate
substitution of any number of ribonucleotides



in sense and antisense strands


methylphosphonate
substitution of any number of ribonucleotides



in sense and antisense strands


2′,5′-linked DNA or
substitution of any number of ribonucleotides


RNA
in sense strand







Base modifications








5-bromouracil (5-Br-
substitution of any number of ribouraciles in


Ura)
sense and antisense strands


5-iodouracil (5-I-Ura)
substitution of any number of ribouraciles in



sense and antisense strands


dihydrouracil
substitution of any number of ribouraciles in



sense and antisense strands


2-thiouracil
substitution of any number of ribouraciles in



sense and antisense strands


4-thiouracil
substitution of any number of ribouraciles in



sense and antisense strands


pseudouracil
substitution of any number of ribouraciles in



sense and antisense strands


diaminopurine
substitution of any number of adenines in both



sense and antisense


difluorotoruene
substitution of any number of adenines in both



sense and antisense


peptide nucleic acids
substitution of any number of ribonucleotides


(PNAs)
in sense and antisense strands


(2-aminoethylglycine)







modifications to the overhangs and termini








2-nt-3′-DNA overhang
3′ end of sense and antisense strands


2-nt-3′-RNA overhang
3′ end of sense and antisense strands


blunt-ended duplexes
3′ end of sense and antisense strands







chemical conjugation








cholesterol
covalently attached to sense strand


vitamin-E (α-tocopherol)
covalently attached to sense strand









In other embodiments, the chemical modification is a modification described in paragraphs 0040-0050 of US Patent Application Pub. No. 2011/0195123, the contents of which are incorporated herein by reference.
In other embodiments, the chemical modification is a modification to the overhang(s) and/or termini, or to the duplex architecture, as described in paragraphs 0061 and 0062, respectively, of US Patent Application Pub. No. 2011/0195123.
In other embodiments, an RNAi agent, for example an siRNA agent, used in the described methods and compositions may be conjugated to a molecule. In more specific embodiments, a non-nucleotide molecule is used. In more specific embodiments, the molecule may be cholesterol, a cell penetrating peptide, or alpha-tocopherol-vitamin E. In certain embodiments, the cholesterol may be conjugated to the 3′ end of the sense strand. In other embodiments, the cholesterol may be conjugated to the 5′ end of the sense strand. In certain embodiments, in the case of a hairpin-shaped molecule, the cholesterol may be conjugated to the loop. In other embodiments, the non-nucleotide molecule is a molecule described in paragraphs 0051-0060 of US Patent Application Pub. No. 2011/0195123.
In certain embodiments, the RNAi agent, for example an siRNA agent, is associated, either via covalent attachment or via non-covalent complexation, with a cell-penetrating peptide (CPP), also referred to as protein transduction domains (PTDs). A CPP is a peptide that has the ability to traverse the plasma membrane and facilitate the delivery of a molecular cargo to the cytoplasm. CPP's include HIV-1 Tat (NCBI Gene ID: 155871) or a fragment thereof comprising the sequence YGRKKRRQRRR (SEQ ID No: 179); pAntp (penetratin) and pIsl, which originate from the third helix of homeodomain proteins (Antennapedia (NCBI Gene ID: 40835; Terrone et al) and Is1-1 (NCBI Gene ID: 3670 and Magzoub et al), respectively); Transportan, a synthetic chimera of galanin and mastoparan (GWTLNSAGYLLGKINLKALAALAKKIL-amide; Pooga et al; SEQ ID No: 180), MPG (GALFLGFLGAAGSTMGA; SEQ ID No: 181); Pep-1 (KETWWETWWTEW; SEQ ID No: 182); and secondary amphipathic peptides based on aromatic tryptophan and arginine residues linked with lysine as spacer (“CADY”; SEQ ID No: 183), which contain a short peptide sequence of 20 amino acids, with the sequence “Ac-GLWRALWRLLRSLWRLLWRA-cysteamide” (SEC) ID No: 184). CPP's are known to those skilled in the art and are described inter alia in Deshayes et al.
In other embodiments, an RNAi agent used in the described methods and compositions is a hairpin-shaped siRNA molecule. In another embodiment, an RNAi agent used in the described methods and compositions is a double-stranded molecule containing 2 separate strands. In another embodiment, the RNAi agent is selected from the group consisting of a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a Dicer-substrate siRNAs (DsiRNAs), a microRNA, and a non-coding RNA.
Millimeter-Scale Implant/Drug Delivery Technology
The drug delivery device of the described methods and compositions may be a cylinder, a sphere, or any other shape suitable for an implant (i.e. that can be implanted in a subject). In certain embodiments, the device is a cylinder.
“Millimeter-scale”, as used herein, refers to a device whose smallest diameter is a least 0.3 mm. In certain embodiments, each of the dimensions (diameter, in the case of a sphere or cylinder; and height and/or width or length, in the case of a cylinder, box-like structure, cube, or other shape with flat walls) is between 0.3-20 mm, inclusive. In other embodiments, each dimension is between 0.5-15 mm, inclusive. In still other embodiments, each dimension is between 0.6-5.2 mm, inclusive, between 0.7-4 mm, inclusive, or between 0.78-3 mm, inclusive.
Table 3 presents the range of needle gauge and internal diameters that may be used in some embodiments. In some embodiments, the internal diameter of the needle dictates the diameter of the DDD, that is typically designed to be reduced by 1%-15% percent.







TABLE 3







(Source: Hamilton Company, Reno USA)










Needle gauge
Internal Diameter (ID) in millimeters














25
0.26



24
0.311



23s
0.116



23
0.337



22s
0.168



22
0.413



21
0.514



20
0.603



19
0.686



18
0.838



17
1.067










In yet other embodiments, the device is a cylinder, having a diameter in the range of 0.4-0.84 mm. In other preferred embodiments, the cylinder has a length of 5 mm. In other embodiments, the cylinder has a diameter of 0.8 mm and a length of 5 mm. In other embodiments, a DDD of the described methods and compositions has the diameter of an 18-gauge needle.
In yet other embodiments, the device is cylindrical, with an 0.83-mm diameter ( ̃0.033′′) and a length of 5 mm.
In other embodiments, the volume of the device is between 0.1 mm3 and 1000 mm3, between 0.2 mm3 and 500 mm3, between 0.5 mm3 and 300 mm3, between 0.8 mm3 and 250 mm3, between 1 mm3 and 200 mm3, between 2 mm3 and 150 mm3, between 3 mm3 and 100 mm3, or between 5 mm3 and 50 mm3.
An exemplary embodiment of a DDD has a diameter of 0.8 mm and a length of 5 mm, containing 25% w/w siRNA, namely about 650 μg of siRNA. In other embodiments, the DDD's contain siRNA; PLGA 85:15; D-Mannitol, and sodium bicarbonate. In other experiments, the DDD's contain siRNA, PLGA, trehalose, and sodium bicarbonate. In more particular embodiments, the molecular weight of the PLGA is between 5-15 kDa, inclusive.
In other embodiments, the w/w agent:polymer load ratio is above 1:100. In more preferred embodiments, the load is above 1:20. In more preferred embodiments, the load is above 1:9. In more preferred embodiments, the load is above 1:3
In other embodiments, the device is DDD that is described in US Patent Application Pub. No. 2011/0195123.
The DDD is designed in some embodiments to preferably employ degradable polymers, wherein the release mechanism includes both bulk erosion and diffusion; or in some embodiments, non degradable, or slowly degraded polymers are used, wherein the main release mechanism is diffusion rather than bulk erosion, so that the outer part functions as membrane, and its internal part functions as a drug reservoir, which practically is not affected by the surroundings for an extended period (for example from about a week to about a few months). Combinations of different polymers with different release mechanisms may also optionally be used. The concentration gradient at the surface is preferably maintained effectively constant during a significant period of the total drug releasing period, and therefore the diffusion rate is effectively constant (termed “zero mode” diffusion). The term “constant” refers to a diffusion rate that is preferably maintained above the lower threshold of therapeutic effectiveness, but which may still optionally feature an initial burst and/or fluctuate, for example increasing and decreasing to a certain degree. In other embodiments, there is an initial burst of less than 10% of the total amount of drug, which may be considered negligible. In other embodiments, there is an initial burst of about 20% of the total amount of drug. In other embodiments, the design enables initial a strong burst of 30% or more of the total amount of drug. The diffusion rate is preferably so maintained for a prolonged period, and it can be considered constant to a certain level to optimize the therapeutically effective period, for example the effective silencing period. These embodiments are described in US Patent Application Pub. No. 2011/0195123.
In other embodiments, the described DDD comprises small particles incorporated into a polymeric matrix, wherein the small particles themselves contain, in some embodiments, a polymeric material, and the compositions can contain the drug within the matrix in addition to the drug encapsulated in the particles. In certain embodiments, the diameter (or longest dimension, in the case of a non-spherical device) of the DDD is at least 100-fold greater than the mean particle diameter by a factor of 100, and the volume of the DDD is at least 1,000,000-fold greater than the mean particle volume.
In certain embodiments, the small particles also comprise a polymeric material. In these embodiments, the polymeric material in the particles is referred to below as the “first polymeric material”, while the polymeric material in the matrix is referred to as the “second polymeric material”. In various embodiments, the polymeric material in the particles may be entirely different from, similar to, or identical to that in the matrix. “Entirely different from” refers to a polymer made from different building blocks from that in the matrix, for example PCL (poly-caprolactone) as opposed to poly(lactic-co-glycolic acid) (PLGA). “Similar to” refers to a polymer sharing at least one building block with the polymer in the matrix, for example poly(lactic acid) (PLA) as opposed to PLGA. Another example of similar polymers are polymers containing a particular enantiomer as opposed to a racemic mixture of a given building block (L-PLA vs. DL-PLA), polymers containing the same building blocks in a different ratio (having either the same or different molecular weight (MW), or containing the same building blocks but having a different MW (having either the same or different ratio. “Identical to” refers to polymers with the same building blocks, in the same ratio, and with the same MW. “Identical to” in this context does not preclude polymers that contain different materials other than the polymer building blocks). In certain embodiments, the polymer in the particles is non-identical to the polymer in the matrix.
In certain embodiments, all the RNAi agent in the composition is contained within the small particles. In other embodiments, there is also RNAi agent present within the matrix.
In other embodiments, the presence of drug both within and outside the particles enables biphasic drug release. The presence of drug outside the particles can achieve a higher drug load, for example as high as  ̃30% of the mass of the device. On the other hand, the presence of drugs within the particles enables a larger effective volume of drug penetration (FIG. 1). The combination of these two phases thus simultaneously optimizes drug load and effective radius for certain applications.
In other embodiments, less than 50% by weight of the RNAi agent in the composition, for example less than 45%, 40%, 35%, 30%, or 25% of the RNAi agent is contained within the small particles. In still other embodiments, less than 20% by weight of the RNAi agent in the composition is contained within the small particles. In yet other embodiments, less than 18%, 16%, 14%, 12%, 10%, 8%, 7%, 6%, 5%, or 4% by weight of the RNAi agent in the composition is contained within the small particles.
In other embodiments the volume ratio [total volume of particles/volume of DDD] is less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, or less than 20%, and the extra-particle volume contains additional drug.
DDD's containing nanoparticles are described inter alia in US Patn. Appl. Publ. No. 2013/0122096 to Shemi Amotz et al, the contents of which are incorporated herein by reference.
Suitable Release Profiles
In preferred embodiments, a device of the described methods and compositions is designed to release the nucleotide-based agent, in some embodiments the RNAi agent, in more specific embodiments the siRNA agent, in a controlled fashion. It will be apparent to those of skill in the art, in light of the knowledge in the art taken together with the information provided herein, that the PLA:PGA ratio, composition and additives, and/or the molecular weight (MW) of the polymer, and controlling the surface-to-volume ratio of the implant may be adjusted to achieve a particular release profile. For example, deviating the PLA:PGA ratio from 50:50, or increasing the MW, or reducing surface-to-volume ratio can increase the release time.
In other embodiments, the DDD of the described methods and compositions is designed with a particular release profile. One relevant parameter is the time point at which 95% of the active agent has been released. In some embodiments, the DDD releases 95% of the active agent in vivo, for example in a human pancreas, at a time point between 3-24 months inclusive, for example, in various embodiments, 3, 4, 5, 6, 8, 10, 12, 14, 16, 18, 20, 22, or 24 months. In other embodiments, the time point of release of 95% of the active agent is between 3-12 months inclusive, between 2-24 months inclusive, between 2-15 months inclusive, between 3-15 months inclusive, between 3-12 months inclusive, between 3-10 months inclusive, between 4-24 months inclusive. Another relevant parameter is the time point at which 90% of the active agent has been released; this may be any of the aforementioned time frames.
Another relevant parameter is the percent of active agent released at a given time point. For example, in some embodiments, 80-99% inclusive of the active agent is released at the 3-month timepoint. In other embodiments, 80-99% inclusive of the active agent is released at the 2-month timepoint or the 4-month, 6-month, 9-month, 12-month, or 24-month timepoint, each of which is considered a separate embodiment.
Alternatively or in addition, in some embodiments no more than 30-50% of the active agent of a DDD of the described methods and compositions is released during the first 3 weeks.
In other embodiments, a delayed-release DDD is utilized. “Delayed-release”, as used herein, refers to DDD's that do not release more than 10% of their drug load within the first 2 months (discounting an initial burst of up to 20%, which sometimes occurs). In other embodiments, the DDD does not release more than 10% of its drug load within the first 3 months. The inventors have discovered that, in some embodiments, DDD's containing 1% trehalose exhibit delayed release. Trehalose has the additional advantage that, in some embodiments, it is effective at a concentration of only 1% (as opposed to 5-10% for mannitol, for example), thus allowing an increased drug load.
In other embodiments, the DDD is coated (by dipping, spraying, or any other method known to those skilled in the art) with a slowly-degraded polymer that contains no drug. Various embodiments of slowly-degraded polymers are described herein, each of which can be utilized to create a delayed-release DDD. In some embodiments, the coating comprises a linear-chain monosaccharide; a disaccharide; a cyclic monosaccharide, a cyclic disaccharide. In other embodiments, the coating comprising an additive selected from lactose, sucrose, dextran, and hydroxyethyl starch. In yet other embodiments, the coating comprises mannitol. Alternatively, the coating may comprise trehalose. In still other embodiments, the coating does not comprise a sugar.
In certain embodiments, less than 5% of the RNAi agent is released from the DDD during the first 1 month starting from implantation. In other embodiments, less than 10% of the RNAi agent is released from the DDD during the first 1 month starting from implantation. In other embodiments, less than 10% of the RNAi agent is released during the first three months starting from implantation.
In other embodiments, a delayed-release DDD is provided, comprising an siRNA against a target that is not a prostate-cancer-related target gene. In some embodiments, the target is an oncogene that is not overexpressed in prostate cancer.
In other embodiments, a therapeutic package is provided, comprising both (a) one or more delayed-release DDD and (b) one or more DDD that is not delayed-release. In some embodiments, the DDD comprise an siRNA against a prostate-cancer-related target gene. In other embodiments, siRNA is against a target that is not a prostate-cancer-related target gene, which in some embodiments is an oncogene.
In other embodiments, a DDD described herein is a delayed-release DDD. In other embodiments, a therapeutic package is provided, comprising both (a) one or more delayed-release DDD and (b) one or more DDD that is not delayed-release.
Other exemplary release profiles are depicted in FIG. 1.
In some embodiments the DDD is design as a polymeric uniform matrix. In some additional embodiments the DDD is designed as a reservoir. Drug is released approximately as per the following power lows t1/2 and t as follows:
Matrix

Q=(DpCp(2A−Cp))1⁄2×t1⁄2

Reservoir

Q=(DpCp)/h×t 

Where:

    
    
        Q: cumulative amount of drug released per unit area (mg/mm2),
        t: time (days),
        A: initial amount of drug loading per unit volume in a matrix system (mg/mm3),
        Dp: diffusion coefficient of the drug in the polymer (mm2/sec),
        Cp: solubility of the drug in the polymer (mg/mm3), and
        h: thickness of the sheet layer in the reservoir-type system (mm).

Suitable Biodegradable Matrices

    
    


In certain embodiments, the biodegradable matrix present in the drug delivery device comprises poly(lactic acid) (PLA). In other embodiments, the biodegradable matrix comprises poly(glycolic acid) (PGA). In other embodiments, the biodegradable matrix comprises both PLA and PGA (known as poly(lactic-co-glycolic acid) or PLGA).
Methods for making PLGA matrices that incorporate RNAi agents are well known in the art. Exemplary methods are described in described in US Patent Application Pub. No. 2011/0195123—for example in Examples 1.1 and 1.2 thereof.
In other embodiments, the PLA/PGA ratio of PLGA used in the methods and compositions is between 25:75 and 75:25. In other embodiments, the ratio is between 50:50 and 75:25, meaning that there is between 50-75% PLA and between 25-50% PGA in the biodegradable matrix (discounting substances other than polymer building blocks). In other embodiments, the PLA/PGA ratio is between 25:75 and 50:50, between 35:65 and 75:25, between 45:55 and 75:25, between 55:45 and 75:25, between 65:35 and 75:25, between 75:25 and 35:65, between 75:25 and 45:55, between 75:25 and 55:45, or between 75:25 and 65:25. In other embodiments, the PLA/PGA ratio is between 80:20 and 90:10, inclusive.
In other embodiments, the PLA/PGA ratio is larger than 75:25, between 75:25 and 85:15, or between 75:25 and 95:5. Alternatively, the ratio is smaller than 25:75, between 25:75 and 15:85, or between 25:75 and 5:95.
In other embodiments, the polymer comprises a polymer selected from the group consisting of poly(glycolide-co-lactide) (PLGA), polylactic acid (PLA) and polyglycolic acid (PGA) and polyethylene glycol (PEG). In other embodiments, the polymer comprises both PLA and PEG (poly(ethylene glycol)). In other embodiments, the polymer comprises PLA, PGA, PEG, PLGA, poly-caprolactone (PCL), dihydrolipoic acid (DHLA), and combinations thereof. In still other embodiments, the polymer is selected from PLA, PGA, PEG, PLGA, PCL, DHLA, and combinations thereof.
In other embodiments, tri-block PLA-PCL-PLA is used.
In other embodiments, Poly(D,L-lactide) (DL-PLA), poly(D,L-glycolide), or poly(D,L-lactide-co-glycolide) is used, each of which is considered a separate embodiment.
Design of biodegradable controlled drug-delivery carriers containing PLA, PGA, PEG, and/or PCL to have a specified release profile is well-within the ability of those skilled in the art, and is described inter alia in Makadia and Siegel, Poly Lactic-co-Glycolic Acid (PLGA) as Biodegradable Controlled Drug Delivery Carrier, Polymers 2011, 3:1377-1397.
In another embodiment, the polymer is a polymer described in paragraphs 0076-0078 of US Patent Application Pub. No. 2011/0195123.
In some embodiments, a polymer used in the methods and compositions described herein has a molecular weight (MW) of greater than 5 kilodaltons (kDa). In other embodiments, the MW is greater than 50 kDa. In other embodiments, the MW is greater than 7 kDa, greater than 10 kDa, greater than 15 kDa, greater than 20 kDa, greater than 30 Da, greater than 70 kDa, greater than 100 kDa, greater than 150 kDa, or greater than 200 kDa. In other embodiments, the MW is between 5-100 kDa, inclusive, between 7-80 kDa, inclusive, between 10-60 kDa, inclusive, between 20-50 kDa, inclusive, or between 25-50 kDa, inclusive. As provided herein (Example 2), very slow release (approximately 6 months) can be achieved, PLGA of high PLA:PGA ratio, such as 90:10, and MW (molecular weight) higher than 50 KDa. A similar effect can be achieved by use of PLA.
In some embodiments, the polymer is L-PLA that has a molecular weight of greater than 5 kilodaltons (kDa). In other embodiments, the MW of the L-PLA is greater than 50 kDa. In other embodiments, the MW is greater than 7 kDa, greater than 10 kDa, greater than 15 kDa, greater than 20 kDa, greater than 30 Da, greater than 70 kDa, greater than 100 kDa, greater than 150 kDa, or greater than 200 kDa. In other embodiments, the MW of the L-PLA is between 5-100 kDa, inclusive, between 7-80 kDa, inclusive, between 10-60 kDa, inclusive, between 20-50 kDa, inclusive, or between 25-50 kDa, inclusive.
In some embodiments, the polymer is PLGA that has a molecular weight of greater than 5 kilodaltons (kDa). In other embodiments, the MW of the PLGA is greater than 50 kDa. In other embodiments, the MW is greater than 7 kDa, greater than 10 kDa, greater than 15 kDa, greater than 20 kDa, greater than 30 Da, greater than 70 kDa, greater than 100 kDa, greater than 150 kDa, or greater than 200 kDa. In other embodiments, the MW of the PLGA is between 5-100 kDa, inclusive, between 7-80 kDa, inclusive, between 10-60 kDa, inclusive, between 20-50 kDa, inclusive, or between 25-50 kDa, inclusive.
In some embodiments, the polymer has a PLA:PGA ratio of between 80:20 and 90:10, inclusive, for example 80:20, 82:18, 84:16, 86:14, 88:12, or 90:10, and a MW of greater than 50 KDa, for example greater than 50 Da, greater than 70 kDa, greater than 100 kDa, greater than 150 kDa, or greater than 200 kDa. In other embodiments, the polymer has a PLA:PGA ratio larger than 75:25, for example 76:24, 78:22, 80:20, 82:18, 84:16, 86:14, 88:12, 90:10, 92:8, 94:6, 96:4, or 98:2, and a MW of greater than 50 KDa. In yet other embodiments, the polymer has a PLA:PGA ratio smaller than 25:75, inclusive, for example 24:76, 22:78, 20:80, 18:82, 16:84, or 14:86, 12:88, 10:90, 8:92, 6:94, 4:96, or 2:98, and a MW of greater than 50 KDa. Each of the aforementioned PLA:PGA ratio may be freely combined with each MW value.
Additives
In other embodiments, the biodegradable matrix further comprises an additive for modulating hydrophilic-hydrophobic interactions; in other embodiments for enabling dispersion of the drug and eliminating aggregation; in other embodiments for preserving the drug in hot-temperature or cold-temperature storage conditions, for example 55° C. and −20° C., respectively, or significantly colder, in the case of lyophilization with liquid nitrogen; in other embodiments for facilitating creation of cavities in the implant that affect to drug diffusion from the matrix. Hydrophilic-hydrophobic interactions may cause aggregation of the active substance in cases of hydrophilic active substances, such as siRNA, incorporated within a hydrophobic polymer, resulting in aggregation during production or subsequently when the device is implanted into the body of a subject and it is subjected for example to hydrolysis. Non-limiting examples of such additives are open monosaccharides, for example mannitol; disaccharides such as trehalose; sorbitol; and other cyclic monosaccharides such as glucose, fructose, galactose and disaccharides such as sucrose. The above additives, when chiral, may be in the form of the D-enantiomer, the L-enantiomer, or a racemic mixture. Additional, non-limiting examples of such additives are lactose, sucrose, dextran, and hydroxyethyl starch.
In other embodiments, more than one additive is present.
In other embodiments, the biodegradable matrix further comprises an additive for protecting the drug against low pH after implantation. The microenvironment in the implant interior tends to be acidic. Unlike chemotherapy, pH should preferably be maintained above a threshold. While doxorubicin is stable in an acidic environment, with minimal hydrolytic degradation within a pH range of 3 to 6.5, RNAi drugs might degrade at pH<3. In more specific embodiments, this additive may be selected from bicarbonates and carbonates, for example sodium bicarbonate, sodium carbonate, and magnesium hydroxide.
In other embodiments, the biodegradable matrix further comprises a small-molecule therapeutic agent against the cancer that is being treated.
In other embodiments, the DDD comprises an immunotherapy agent (Guo et al and references therein; Clinical Immunotherapy Trials Network www.CITNinfo.com). Non-limiting examples of immunotherapy agents are ipilimumab (Yervoy; Bristol-Myers Squibb), sipuleucel-T (Dendreon Corp, Seattle, Wash.), IL-7, CP-870,893 (Pfizer), Allovectin-7 (Vical), BiovaxID (Biovest International), IMA901 (Immatics Biotechnologies GmbH), MAGE-A3 (GlaxoSmithKline), Multikine (CEL-SCI Corporation), NeuVax (Galena Biopharma), PROSTVAC (Bavarian Nordic A/S), Rindopepimut (CDX-110) (Celldex Therapeutics), Stimuvax (Oncothyreon and Merck KGaA), Talimogene laherparepvec (Amgen), and TG4010 (Transgene and Novartis). In certain embodiments, the immunotherapy agent does not comprise live cells.
Numerous types of immunotherapeutic agents have been developed, and a number of intratumoral immunotherapies are currently being examined in clinical trials (Cancer Immunotherapy Trial Network www.CITNinfo.org). Agents include T-cell and NK-cell growth factors like IL-15, others that stimulate T cells or activate dendritic cells, so-called immune checkpoint inhibitors like ipilimumab, and others that inhibit or neutralize factors secreted by tumors that suppress the immune system. Recently, two agents have been selected to be tested in CITN-led trials, selected from the 20 identified in the CITN 2007 workshop, IL-15 and a dendritic cell-activating monoclonal antibody called CP-870,893.
Immunotherapy agent interleukin-15 (IL-15) is a recombinant agent that is chemically identical or similar to the endogenous cytokine interleukin-15 (IL-15) with immunomodulating activity. IL-15, secreted by mononuclear phagocytes (and some other cell types) following viral infection, regulates T and natural killer cell activation and proliferation. This cytokine induces activation of transcription activators STAT3, STATS, and STATE via JAK kinase signal transduction pathways in mast cells, T cells, and dendritic epidermal T cells.
CP-870,893 is a fully human monoclonal antibody (mAb) agonist of the cell surface receptor CD40 with potential immunostimulatory and antineoplastic activities. Similar to the CD40 ligand (CD40L or CD154), CD40 agonist monoclonal antibody CP-870,893 binds to CD40 on a variety of immune cell types, triggering the cellular proliferation and activation of antigen-presenting cells (APCs), activating B cells and T cells, and enhancing the immune response; in addition, this agent can activate CD40 present on the surfaces of some solid tumor cells, resulting in apoptosis and decreased tumor growth.
Dosage and Drug Percentage
A DDD of the described methods and compositions may, in certain embodiments, contain at least 10 μg siRNA. In other embodiments, the amount is between 10-2000 μg (inclusive) siRNA per device. In more specific embodiments, the amount is between 300-1700 (inclusive) μg siRNA per device. In still other embodiments, the amount is between 300-1100 (inclusive), in other embodiments, between 400-1000 (inclusive) μg siRNA per device.
In yet other embodiments, the amount of the nucleotide-based agent, in some embodiments the RNAi agent, in more specific embodiments the siRNA agent, in all the DDD's administered as a batch (a single dose) is at least 4 μg, for example, in various embodiments, at least 5 μg, at least 6 μg, at least 7 μg, at least 8 μg, at least 10 μg, at least 12 μg, or at least 15 μg. In still other embodiments, the amount of RNAi agent present per dose is between 2-10 μg, inclusive, for example 2, 3, 4, 5, 6, 7, 8, 9, or 10 μg.
In yet other embodiments, all the DDD's administered as a batch deliver a dose of 0.008-0.065 mg/kg/month, inclusive, for example 0.008 mg/kg/month, 0.01 mg/kg/month, 0.015 mg/kg/month, 0.02 mg/kg/month, 0.03 mg/kg/month, 0.05 mg/kg/month, or 0.065 mg/kg/month.
In certain embodiments, the drug percentage of a device of the described methods and compositions is at least 20%. In another embodiment, the drug percentage is at least 30%, for example 30%, 35%, 40%, 45%, 50%, 55%, or 60%. In another embodiment, the drug percentage is between 8-30%, inclusive, for example 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 22%, 24%, 26%, 28%, or 30%. Some exemplary formulations are as follows:
64-76% PLGA; 16-27% drug; 5-12% mannitol; an exemplary specific formulation is 70% PLGA; 20% drug; 10% mannitol.
In other embodiments, a trehalose-containing DDD is provided, comprising an siRNA against a target described herein. In still other embodiments, a DDD of the methods and compositions described herein comprises trehalose and does not comprise mannitol. In still other embodiments, the DDD comprises both trehalose and mannitol. In more specific embodiments, the DDD may contain 70-91.2% PLGA; 8-30% siRNA; 0.6-1.5% trehalose; and 0.1-0.4% sodium bicarbonate. In other embodiments, the DDD may contain 75-91.2% PLGA; 8-25% siRNA; 0.6-1.5% trehalose; and 0.1-0.4% sodium bicarbonate. In still other embodiments, the DDD may contain 80-91.2% PLGA; 8-20% siRNA; 0.6-1.5% trehalose; and 0.1-0.4% sodium bicarbonate. In yet other embodiments, the DDD may contain 85-91.2% PLGA; 8-15% siRNA; 0.6-1.5% trehalose; and 0.1-0.4% sodium bicarbonate. In additional embodiments, the DDD may contain 88-91.2% PLGA; 8-12% siRNA; 0.6-1.5% trehalose; and 0.1-0.4% sodium bicarbonate. In yet other embodiments, the DDD may contain 89-91% PLGA; 8-10% siRNA; 0.6-1.5% trehalose; and 0.1-0.4% sodium bicarbonate. In still other embodiments, the DDD may contain about 90% PLGA 85:15, about 9% siG12D, about 1% Trehalose, and about 0.2% NaHCO3.
In other embodiments, the DDD has less than 5% trehalose, for example in different embodiments 0.5%, 1%, 1.5%, 2%, 2.5%, 3%, 3.5%, 4%, or 4.5%. Those skilled in the art will appreciate that the release profiles and efficacies of DDD's having varying percentages of trehalose can readily be tested in light of the information provided herein.
Sodium bicarbonate is an excipient that in some embodiments facilitates cavity formation. In other embodiments, sodium bicarbonate facilitates modulation of or decrease in pH. An exemplary specific formulation is 70% PLGA; 28% drug; 1% trehalose; 1% sodium bicarbonate and/or >1% of an excipient that facilitates modulation of decrease in pH.
Additional Features
In other embodiments, a DDD of the described methods and compositions is coated. A coating can be designed for a number of characteristics, including modulating the release rate or preventing protein stickiness during long-term storage. The coating in some embodiments comprises the same material used to form the matrix, for example a PLGA matrix, only without the drug. In other embodiments, the coating comprises a material similar to that used to form the matrix (for example containing the same building blocks in a different ratio, or containing the same polymer but with a different MW), only without the drug. In other embodiments, the polymer of the coating comprises the same building blocks as the polymer used to form the matrix, together with at least one other building block such as PEG. In other embodiments, the coating is selected from polylactic acid (PLA) and PLA:PGA (polyglycolic acid) in a ratio of at least 80:20, inclusive for example 80:20, 82:18, 84:16, 85:15, 86:14, 88:12, 90:10, 92:8, 94:6, 96:4, 98:2, and 99:1, and a MW greater than 50 KDa, for example 60 KDa, 70 KDa, 80 KDa, 100 KDa, 120 KDa, 1500 KDa, or 200 KDa). In more particular embodiments, the coating comprises PLGA in a ratio of at least 80:20, inclusive, having a MW of 50,000-100,000, inclusive.
In certain embodiments, DDD's of dimensions larger than  ̃0.8 mm can be identified by standard ultrasound (US). In other embodiments, materials to visualization in a medical or surgical procedure, for example CT, MRI or US visualization are included. Non-limiting examples of contrast agents are barium, diatrizoate, ethiodized oil, gallium citrate, iocarmic acid, iocetamic acid, iodamide, iodipamide, iodoxamic acid, iogulamide, iohexyl, iopamidol, iopanoic acid, ioprocemic acid, iosefamic acid, ioseric acid, iosulamide meglumine, iosemetic acid, iotasul, iotetric acid, iothalamic acid, iotroxic acid, ioxaglic acid, ioxotrizoic acid, ipodate, meglumine, metrizamide, metrizoate, propyliodone, and thallous chloride.
Activating Device:
Some embodiments include activation via an external device, such as a radiation source or an ultrasound probe, to affect drug release, and/or penetration into cells. Activation can be performed along the time span of the DDD, at a single or several defined time points. The protocol defining such time points can be based on a pre-defined treatment plan and/or changes in patient read-outs.
Other embodiments provide methods of making DDDs described herein. Methods of making various DDD's similar to those presented herein are described in US Patent Application Pub. No. 2011/0195123.
Therapeutic Methods
Also provided is a method of treating a cancer other than prostate carcinoma, comprising the step of implanting the DDD described herein into the vicinity of said tumor. In certain embodiments, the cancer is a carcinoma. In other embodiments, the cancer is selected from the group consisting of cancer of the pancreas, colon, lung, neuroblastoma, glioblastoma, and kidney; hepato-cellular carcinoma, and ovarian cancer. In other embodiments, the cancer is selected from a pancreatic tumor, a colon tumor, a lung tumor, brain cancer, liver cancer, kidney cancer, melanoma, endometrial carcinoma, gastric carcinoma, renal carcinoma, biliary carcinoma, cervical carcinoma, thyroid cancer, cancer of the salivary glands, bladder carcinoma, and esophageal cancer. In more specific embodiments, the cancer is selected from pancreatic carcinoma, pancreatic ductal adenocarcinoma, small-cell lung carcinoma, and colorectal cancer.
In some preferred embodiments, a device is implanted intratumorally. In still other embodiments, the device is implanted into the vicinity of the tumor. In more specific embodiments, in the case of a well-defined solid tumor, several devices are spaced within the tumor volume. In yet other embodiments, several devices are implanted along a needle cavity within the tumor. In still other embodiments, the device or devices are implanted such that they are not in a direct contact with the perimeter of the tumor. Alternatively, in the case of a poorly defined solid tumor, the device is inserted into an area believed to contain tumor cells. In other embodiments, the DDD is implanted into the subject using a biopsy needle.
In other embodiments, the DDD is implanted into the subject using a delivery device as described in WO 2010/086849 to Silenseed Ltd.
Also provided herein is a device described herein, for treating a cancer other than prostate carcinoma. In certain embodiments the subject is a human patient. In other embodiments, the subject is a veterinary patient.
In certain, more specific embodiments, the DDD is designed for implantation into a subject using a biopsy needle via an ultrasound probe. In certain, still more specific embodiments, the needle is a needle in the range of 22-18 gauge, and the number of DDDs implanted is between 2-22, inclusive, for example 2, 4, 6, 8, 9, 10, 11, or 12, 14, 16, 18, 20, 22
In other embodiments, the DDD is designed for implantation into a subject using a delivery device as described in International Patent Publication No. WO 2010/086849 to Silenseed LTD, the contents of which are incorporated herein by reference.
In another embodiments the drug load in DDD is between 150-300 μg, in another embodiment about 200 μg, per mm length of the DDD.
In yet other embodiments, all the DDD's, administered as a batch, deliver a dose of 0.008-0.065 mg/kg/month, inclusive, for example 0.008 mg/kg/month, 0.01 mg/kg/month, 0.015 mg/kg/month, 0.02 mg/kg/month, 0.03 mg/kg/month, 0.05 mg/kg/month, or 0.065 mg/kg/month.
In still more specific embodiments, 8-32 DDD per patient are implanted, for example 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, or 32 DDD. In yet more specific embodiments, 12 DDD per patient are implanted.
In other embodiments, at least one DDD described herein that is a delayed-release DDD and at least one DDD described herein that is a non-delayed-release DDD are implanted together. “Together” in this embodiment, refers to implantation during the same procedure. Alternatively, the delayed-release DDD and non-delayed-release DDD are implanted on the same day. Provision of a combination of delayed-release and non-delayed-release DDD's in some embodiments enables a longer time course of significant siRNA release, without the need for repeated therapeutic intervention.
In other embodiments, a trehalose-containing DDD as described herein is administered to treat a solid tumor other than prostate cancer. In some embodiments, the cancer is selected from a pancreatic tumor, a colon tumor, a lung tumor, brain cancer, liver cancer, kidney cancer, melanoma, endometrial carcinoma, gastric carcinoma, renal carcinoma, biliary carcinoma, cervical carcinoma, and bladder carcinoma. In more specific embodiments, the cancer is selected from pancreatic carcinoma, pancreatic ductal adenocarcinoma, small-cell lung carcinoma, and colorectal cancer.
In still other embodiments, the described method further comprises the step of administering an anti-cancer agent to the patient. In more specific embodiments, the anti-cancer agent comprises a pyrimidine analogue, non-limiting examples of which are 5-azacytidine, 5-aza-2′-deoxycytidine, 5-fluoro-uracil, 5-fluoro-deoxyuridine (floxuridine), and 5-fluorodeoxyuridine monophosphate. In more specific embodiments, the anti-cancer agent is an inhibitor of ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1), non-limiting examples of which are motexafin gadolinium (CHEBI: 50161); hydroxyurea; gemcitabine (2′,2′-difluorodeoxycytidine); elacytarabine (CP-4055; an ara-C-5′elaidic-acid-ester) and CP-4126, (CO 1.01; a gemcitabine-5′elaidic-acid-ester; Adema A D et al, Metabolism and accumulation of the lipophilic deoxynucleoside analogs elacytarabine and CP-4126. Invest New Drugs. 2011 Oct. 15. [Epub ahead of print]), and those described in WO2011/062503, the contents of which are incorporated herein by reference. In even more specific embodiments, the anti-cancer agent comprises gemcitabine. In alternative embodiments, the anti-cancer agent is gemcitabine. In yet other embodiments, the anti-cancer agent is an EGFR tyrosine kinase inhibitor. In yet other embodiments, the anti-cancer agent comprises a thymidylate synthase inhibitor. In more specific embodiments, the anti-cancer agent comprises leucovorin (Folinic acid; 2-[[4-[(2-amino-5-formyl-4-oxo-1,6,7,8-tetrahydropteridin-6-yl)methylamino]benzoyl]amino]pentanedioic acid). In yet other embodiments, the anti-cancer agent comprises irinotecan. In yet other embodiments, the anti-cancer agent comprises oxaliplatin. In still other embodiments, the anti-cancer agent comprises FOLFIRIN (5-fluorouracil, leucovorin, and irinotecan in combination). In still other embodiments, the anti-cancer agent is FOLFIRINOX (5-fluorouracil, leucovorin, irinotecan, and oxaliplatin in combination), or any combination of a subset of the four agents in FOLFIRINOX. In yet other embodiments, the anti-cancer agent comprises an EGFR tyrosine kinase inhibitor. In more specific embodiments, the anti-cancer agent is Erlotinib.
In some embodiments, the anti-cancer agent is administered to the patient after administration of the DDD. In more specific embodiments, the anti-cancer agent may be administered to the patient up to 10 days after administration of the DDD. Alternatively, the anti-cancer agent is administered to the patient simultaneously with administration of the DDD. In still other embodiments, the anti-cancer agent is administered to the patient before administration of the DDD. In yet other embodiments, the DDD is administered during ongoing administration of the anti-cancer agent. In still other embodiments, the anti-cancer agent is administered to the patient intratumorally, by a method such as injection and controlled release, or including in other embodiments administration from the same DDD.
In still other embodiments, the described method further comprises the step of administering radiation therapy to the patient. In some embodiments, the radiation is administered to the patient after administration of the DDD. In more specific embodiments, the radiation may be administered to the patient up to 10 days after administration of the DDD. Alternatively, the radiation is administered to the patient simultaneously with administration of the DDD. In still other embodiments, the radiation is administered to the patient before administration of the DDD. In yet other embodiments, the DDD is administered during ongoing administration of the radiation.
Animal and Human Testing
In animal models, tumor progress may be monitored by any method known in the art. One method is by removing and weighing the tumor. This may be done, for example, by weighing slices after histology slice preparation.
The presence and amount of therapeutic siRNA in tissue samples may be determined by any method known in the art, for example by a method described herein. RNA quantity may be assessed, for example, by Nanodrop, and RNA quality by gel electrophoresis. RNA quantity may also be assessed by PCR, e.g. real-time PCR, Northern blot, HPLC, MSLC (Membrane surface liquid culture), or in situ hybridization.
Excised tumor tissue from human or animal studies may be preserved by any method known in the art, for example by freezing in liquid nitrogen (for subsequent studies requiring live cells), or may be fixed, for example in paraformaldehyde solution.
Characterization of tissue samples may include various methods known in the art, including but not limited to hematoxylin and eosin staining, immunohistochemistry staining, and measuring levels of gene products, such as the genes targeted by the therapeutic siRNA, in some cases in the presence of an internal control.
In other cases, the effects of devices described herein on the excised tissue sample may be studied, for example in an experimental animal or in culture.
EXPERIMENTAL DETAILS SECTION
Example 1: Production of DDD's Containing RNAi Molecules Against Various Targets
DDD's containing various RNAi molecules were produced in a biological-class hood in a clean room, as follows:
Step 1: Preparation of siRNA/D-Mannitol/Sodium Bicarbonate Mixture:
siRNA was added to the pre-weighed D-Mannitol and Sodium Bicarbonate, and they were dissolved in RNase-free sterile water.
Step 2: Freezing:
The liquid was placed into glass vials, frozen in dry ice, and lyophilized for 48 hours.
Step 3: PLGA Preparation:
PLGA was dissolved in Ethyl Acetate.
Step 4: Combining PLGA with D-Mannitol/Sodium Bicarbonate/siRNA:
The PLGA solution was poured into the glass vial containing the lyophilized D-Mannitol/Sodium Bicarbonate/siRNA in fractions and stirred until homogenization
Step 5: Solvent Evaporation.
The solution was poured into a Teflon-covered dedicated glass dish and left to evaporate inside a dedicated container for 3-5 days.
Step 6: Release of Film:
The film was released from the glass dish using tweezers and a scalpel.
Step 7: Excision of Individual DDDs:
Individual DDDs were excised using a dedicated puncher. Each DDD was of a cylindrical shape, with a length and diameter of  ̃1.3 mm and  ̃0.6 mm, respectively.
Example 2: In Vitro Testing of Release Characteristics of DDDs
FIG. 2 describes variations in release characteristics that were achieved by varying the composition of DDDs. The curve “1% add II” provides a working demonstration of very slow release that can last 6 months, for example using PLGA of high PLA:PGA ratio, such as 90:10, and MW (molecular weight) higher than 50 KDa.
The following protocol was used to make the DDD, covering all cases in FIG. 2:

    
    
        1. Mix siRNA 40 mg (naked, 5′-chol) RNAse free water solution with 1% NaHCO3 (Sigma) and with Mannitol (10% or 5%) or Trehalose (10%, 5% or 1%) and lyophilize overnight.
        2. Weight 450 mg PLGA 85:15 (Boehringer-Ingelheim), add to the lyophilized powder and mix. The viscosity of the PLGA was 0.63-0.67 dl/gr, and its estimated MW was 60,000-80,000.
        3. Add Ethyl acetate ( ̃1.5 ml) (Sigma) and mix to get clear white solution.
        4. Pour onto Teflon covered glass dish (D=2 cm).
        5. Dry (5-7 days) to get a film.
        6. Punch the film with 19 G puncher to get 19 G DDDs.

PLGA Coating:

        1. Dissolve PLGA 85:15 30% in Ethyl acetate and drip onto each DDD.
        2. Push the DDDs out of the drop after 2 sec.
        3. Dry.
    
    


Measurements of release were done by Nanodrop at a specific wavelength of 260 nm and/or 230 nm. Measurements were taken at time points of 0 h, 4 h, 12 h, 24 h, 3 d, 7 d, 2 w, 4 w, 6 w, and 8 w, and, in some experiments, at additional time points after and between these times. Each measurement utilized 1.5 microliters (μL) of siRNA solution (PBS or water) and results are given in nanogram/microliter. Prior to each measurement, a null measurement of solution only (PBS) was performed for subtraction. Each time point contained five parallel measurements (from five different DDDs). Presented in FIGS. 1-2 are the averages of such five points.
Example 3: Testing of Targets in Cell Culture
Methods
Viability Test
PC3 cells were seeded on 96-well plates one day before transfection. Transfection was performed using Lipofectamine 2000 transfection reagent, according to the manufacturer's protocol. siRNas were used at the indicated concentration. Scrambled non-targeting siRNA was used as transfection control. 72 hrs post transfection, viable cells were fixed and stained by Methylene Blue (MB). Relative cell amounts were assessed using a microplate absorbance reader. The results are presented relative to cells transfected with scrambled siRNA.
Methylene Blue (MB) Assay
The protocol was adapted from Oliver et al. Cells were seeded in a 96-well plate, then treated as follows:
1. Remove medium from plate.
2. Wash cells twice with PBS (250-400 ul)
3. Fix cells: Add 100-μl 4% formaldehyde. Keep at room temperature for 20 min or for up to several weeks at +4° C. (cold room, wrapped so the liquid will not evaporate).
4. Wash twice with PBS (250-400 μl).
3. Wash cells twice with 200 μl 0.2M borate buffer, pH 8.5.
4. Stain cells with 50 μl 1% Methylene blue in borate buffer. Incubate for 20 min at room temperature.
5. Wash with tap water until control well (without cells) is white.
6. Color elution: add 100 μl 0.1M HCl. Incubate at room temperature for at least 2 hrs, up to overnight (wrapped so the liquid will not evaporate)
7. Measure OD at 585 nM.
0.2M Borate Buffer pH 8.5:
Add 7.628 gr/100 ml of borate (sodium tetraborate) (Na2B4O7.10H2O; MW 381.3) and 1.2378 gr/100 ml boric acid (H3BO3; MW 61.83). Titrate with NaOH if needed.
0.1M HCl:
50 ml DDW+0.5 ml 37% HCl (=10.1 M)
PBS Solution:
0.26 g KH2PO4, 2.17 g Na2HPO4-7H2O, and 8.71 g NaCl in 800 mL dH2O. Adjust pH to 7.4 and bring volume to 1 L with dH2O.
Results
PC3 cells (ATCC #CRL-1435) were grown and tested for mycoplasma contamination, and were found to be mycoplasma free.
Viability testing was done by the MB assay. Based on growth calibration, two cell concentrations of 0.5 and 0.75×104 cells/well were tested with two AR siRNAs. For transfection calibration, cells were seeded at the indicated concentration and transfected at the indicated siRNA concentrations. The optimum concentration was found to be 125 nM, which corresponds to 0.375 μg siRNA/well (FIG. 3).
Next, viability testing was performed with siRNA molecules targeting various genes. As shown in Table 4 and FIG. 4, many of the constructs exhibited growth inhibition. Notably, the 2-O-Me-modified constructs retained a significant amount of activity. Their relative activity compared to non-modified constructs is expected to be greater in vivo, where their resistance to nucleases will confer an advantage of durability. Furthermore, the effects of anti-BMI-1-2, anti-NETO2-1, and anti-PTPRA-3 on the levels of their target genes were assessed. Each tested siRNA caused a significant decrease in the level of the target (FIGS. 4B-D).







TABLE 4







Viability testing of PC3 cells treated with indicated siRNA's.














Average






percentage of


target
no.
siRNA-name
viable cells
SEM %





Androgen
201
siAR-1
43%
2%


receptor
202
siAR-2
48%
4%



204
siAR-4
55%
2%



203
siAR-3
111% 
1%



217
siAR-1-O—Me
71%
2%


BMI1
205
siBMI1-1
94%
4%



206
siBMI1-2
 7%
1%


Brd4
233
siBrd4-2
22.2% 
1.7% 



232
siBrd4-1
37.6% 
1.5% 


CDC44
207
siCDC44-1
98%
8%



208
siCDC44-2
87%
1%


EtbB3
229
siErbB3-2
45.2% 
1.8% 



228
siErbB3-1
50.9% 
25.5%  


EZH2
235
siEZH2-2
34.0% 
2.0% 



234
siEZH2-1
64.8% 
2.1% 


gp130
219
gp130
38%
2%


hTERT
213
si-hTERT-5
50%
6%



211
si-hTERT-3
52%
1%



210
si-hTERT-2
53%
2%



209
si-hTERT-1
58%
2%



212
si-hTERT-4
81%
4%


NETO2
214
siNETO2-1
31%
3%



215
siNETO2-2
53%
3%



216
siNETO2-3
69%
3%



218
siNETO2-1-O—Me
84%
4%


PAPPA
227
PAPPA-3
21%
2%



225
PAPPA-1
34%
3%



226
PAPPA-2
54%
3%


PSCA
231
siPSCA-2
47.6% 
1.0% 



230
siPSCA-1
52.3% 
1.8% 


PTPRA
222
PTPRA-3
33%
1%



224
PTPRA-5
36%
1%



223
PTPRA-4
38%
3%



220
PTPRA-1
72%
1%



221
PTPRA-2
84%
4%









Example 4: Manufacturing and Testing of Trehalose-Containing DDD's
1% Trehalose-containing DDD's were produced as follows:

    1. Dissolve 40 mg siG12D (BioSpring GmbH) in 2 ml DNAse/RNAse free water.


The sequences of the sense and antisense strands of siG12D were GUUGGAGCUGAUGGCGUAGdTdT (SEQ ID No: 65) and CUACGCCAUCAGCUCCAACdTdT (SEQ ID No: 66), respectively.

    2. Add siRNA solution to pre-weighed Trehalose (4 mg.) and NaHCO3 (1 mg) and vortex for several min.
    3. Freeze solution of siG12D, Trehalose and NaHCO3 in liquid nitrogen and lyophilize for 48 h.
    4. Combine 400 mg of lyophilized PLGA with the lyophilized siG12D, Trehalose and NaHCO3 powder and mixed.
    5. Dissolve the mixed powder in 1.5 ml Ethyl acetate to obtain a milky solution. Mix and pour into a Teflon-covered glass dish, diameter 2 cm.
    6. Dry for 3 days to obtain a film.
    7. Punch the film to obtain DDD's.


The final composition was 89.89% PLGA 85:15 (supplier: Boehringer Ingelheim Pharma GmbH), 9% siG12D, 1% Trehalose, and 0.22% NaHCO3. DDD dimensions were 2-3 mm×1 mm.
The release profiles of DDD's were measured in vitro at 37° C. in PBS and in vivo. For in vivo testing, C57b1/6 mice were anesthetized using ketamine and xylazine (for a 25-gram mouse, a 50 ill intra-peritoneal injection of 0.9 ml ketamine+0.1 ml xylazine). The DDD's were inserted subcutaneously into a minimal incision made in the skin.
Release in vitro was quantified using a Nanodrop® apparatus. For validation, release from in vivo trials was also quantified by electrophoresis in a 10% urea-acrylamide gel. Gels were visualized using Pharmacia Biotech ImageMasterTM VDS (cat #80-6246-82) and quantified using ImageGauge software.
In vitro, the trehalose-containing DDD's exhibited delayed release, with less than 10% of the siRNA released after 90 days, followed by a steady release of the next 55% of the siRNA over the next 70%. In vivo, these DDD's steadily released about 90% of the siRNA over the first 90 days, followed by a slower release of most of the remaining siRNA over the next 70 days (FIG. 5).
Example 5: Effect of Anti-BMI-1 and Anti-hTERT siRNA on Various Cancer Cell Lines
Anti BMI-1 (si-BMI1) and anti-hTERT-5 siRNAs were administered to several cancer cell lines, and the effect on cell viability was tested. The cell lines used included prostate, pancreas, colon (two lines), lung (two lines), neuroblastoma, embryonic kidney, and hepato-cellular carcinoma lines, as follows:
PC3 Human prostate adenocarcinoma.
Panel Human pancreatic ductal carcinoma.
HT29 Human colorectal adenocarcinoma.
H460 Human large cell lung carcinoma.
SHY86 Human neuroblastoma.
HEK293T Human embryonic kidney.
Huh7 Human hepatocellular carcinoma.
H1299 Human non-small cell lung carcinoma.
RKO Human colon carcinoma.
Experimental Description:
The indicated cell lines were seeded in a 96-well plate one day before transfection. Transfection was performed using Lipofectamine 2000 transfection reagent. The indicated siRNAs were used at a 125 nM concentration, which is 0.375-μg/well. Scrambled non-targeting siRNA was used as transfection control. 72 hrs post-transfection, the reaction was stopped, and viable cells were fixed and stained by Methylene blue. Relative cell amounts were assessed using a microplate absorbance reader) (Tecan Group Ltd, model Infinite F50), and data was processed using the MagellanTM program (Tecan). The siRNA's were each effective in a number of cancer cell lines (FIG. 8). The results are presented relative to scrambled siRNA-transfected cells.
Example 6: Expression of BMI-1 (A), hTERT (B), Gp130 (C) and K-RAS in Various Cell Lines
Methods
GeneNote, BioGPS Normal, and BioGPS Cancer Expression array images were utilized.
Tissue Types:
Duplicate measurements were obtained for 12 normal human tissues (out of 28 tissues shown) hybridized against Affymetrix GeneChips HG-U95A-E (GeneNote data) and for 22 normal human tissues hybridized against HG-U133A (BioGPS data). The intensity values (shown on the y-axis) were first averaged between duplicates, then probeset values were averaged per gene, global median-normalized and scaled to have the same median of about 70 (half-way between the GeneNote and BioGPS medians). HG-U133A expression data for 18 NCI60 cancer cell lines, available at BioGPS, was processed and added to the display (a single measurement was taken and normalized according to the BioGPS normal data).
Each gene was found to be highly expressed in a significant fraction of the cell lines, as shown for BMI-1 (FIG. 9A), hTERT (B), gp130 (C) and K-ras (D).
Example 7: Further In Vitro Testing of Targets
Following transfection with siRNA, siRNA functionality is measured by proliferation assay, colony-forming assay, and in other experiments by scratch assay, for example in one or more of the cells lines mentioned herein. In some experiments, kinetic studies are performed.
In other experiments, target mRNA inhibition is measured, for example using semi-quantitative PCR or quantitative PCR.
In other experiments, the effect on target protein level is measured, for example by Western blotting.
In other experiments, the stability of siRNAs in a RNase-rich environment is studied by incubation in a RNase-rich environment, followed by analysis of siRNA content, for example by gel electrophoresis.
In other experiments, siRNAs are modified to improve their stability and functionality, and their efficacy and stability are tested.
In other experiments, the release rate of siRNA is determined, for example using the methods described herein.
In other experiments, the effect of the siRNA's is tested in cancer stem cells, for example by colony-forming ability, proliferation assay, or apoptosis assay.
Example 8: In Vivo Testing of Anti-Cancer Activity of DDDs
FIG. 10 shows an in-vivo study of down-regulation of K-Ras G12V: Nude mice were injected with Capan-1-LV-Luc (dominant mutation: K-Ras G12V mutation) cells into the pancreas. One month later, DDDs were implanted. Depicted is survival curve of Nude mice treated as follows: (1. DDD without drug (“empty”); 2. DDDs with siRNA against G12V-mutated K-Ras (“siG12V DDD”); 3 non-targeting siRNA (siGFP DDD); 4. mock-treatment (“PBS”); 5. direct intraperitoneal (I.P.) injection of siRNA without DDD (“IP siG12V”); and 6. I.P. injection of non-targeting siRNA (“IP siGFP”). 72 days after implantation, all surviving mice were sacrificed. 80% of the siG12V DDD-treated mice survived, vs. 10-40% of the other groups. The sequences of the sense and antisense strands of siG12V were GUUGGAGCUGUUGGCGUAG (SEQ ID No: 10), and CUACGCCAACAGCUCCAAC (SEQ ID No: 67), respectively.
Example 9: In Vivo Testing of Additional DDDs
One or more DDDs are implanted in a mouse xenograft tumor model or other suitable cancer model, for example utilizing injection of Capan-1 cells into the pancreas. When tumors reach a suitable size, DDD's containing no-siRNA or anti-BMI1, anti-hTERT, anti-IL6ST/gp130, and/or anti-CD44 siRNA are implanted into the tumors. Tumor growth and/or the amount of therapeutic siRNA is assessed by imagining and/or by histopathology over the next several weeks. In some experiments, measurement of tumor volume is used to follow tumor growth. In other experiments, the survival of mice bearing the tumor is followed. Impaired tumor growth and/or tumor shrinkage is indicative of enhanced therapeutic efficacy.
In other experiments, an orthotopic model is utilized to follow tumor growth during and after treatment with siRNA's.
Example 10: Testing of Anti-Cancer Activity of DDDs in Humans
Humans with solid tumors are implanted with DDD's described herein and the anti-tumor activity is tested.
Example 11: Testing of Trehalose-Containing DDDs
Trehalose-containing DDD's are tested in an animal model, or in other experiments in human subjects, using an appropriate experimental setup, relative to mannitol-containing DDD's. Impaired tumor growth is indicative of enhanced therapeutic efficacy.
Example 12: Testing of Delayed-Release DDDs
Delayed-release DDDs (e.g. trehalose-containing DDD's) are tested in an animal model, or in other experiments in human subjects, using an appropriate experimental setup, relative to non-delayed-release DDDs. In some experiments, delayed-release DDDs are implanted together with non-delayed-release DDDs, and are compared to non-delayed-release DDDs alone. siRNA release and tumor progression are monitored. A longer time course of significant siRNA release and/or impaired tumor growth are indicative of enhanced therapeutic efficacy.
It will be apparent that the precise details of the methods and compositions described herein may be varied or modified without departing from the spirit of the described invention. We claim all such modifications and variations that fall within the scope and spirit of the claims below, including all equivalents thereof.
REFERENCES


    1. Patrawala et al, Highly purified CD44+ prostate cancer cells from xenograft human tumors are enriched in tumorigenic and metastatic progenitor cells. Oncogene (2006) 25:1696-1708).
    2. M. H. Oliver et al, “A rapid convenient assay for counting cells cultures in microwell plates: application for assessment of growth factors.” Journal of Cell Science 92, 513-519 (1989).
    3. Guo et al., In situ vaccination with CD204 gene-silenced dendritic cell, not unmodified dendritic cell, enhances radiation therapy of prostate cancer.” Molecular Cancer Therapeutics, Mol Cancer Ther. 2012 Nov. 6. [Epub ahead of print].
    4. Terrone et al, Penetratin and related cell-penetrating cationic peptides can translocate across lipid bilayers in the presence of a transbilayer potential. Biochemistry. 2003 Dec. 2; 42(47):13787-99.
    5. Magzoub et al, Interaction and structure induction of cell-penetrating peptides in the presence of phospholipid vesicles. Biochim Biophys Acta. 2001 May 2; 1512(1):77-89.
    6. Pooga et al, Cell penetration by transportan. FASEB J. 1998 January; 12(1):67-77.

## Claims

1. A method for treating a solid tumor other than prostate carcinoma, comprising:
administering to a subject having a non-prostate solid tumor selected from the group consisting of a pancreatic cancer, colon cancer, and lung cancer, a millimeter-scale drug delivery device (DDD) comprising
a biocompatible polymeric composition comprising a mixture of polylactic acid (PLA) and polyglycolic acid, wherein the PLA:PGA ratio is 50:50, or between 65:35 and 95:5, inclusive;
and at least one RNAi (RNA interference) agent incorporated within the biodegradable polymeric matrix, wherein the RNAi agent comprises a sense strand and an antisense strand, wherein the sequences of the sense strand and the antisense strand target BMI1 polycomb ring finger oncogene (BMI-1), and wherein the sequence of the sense strand consists essentially of the sequence set forth as SEQ ID NO: 83,


wherein the DDD is administered to the subject by implantation into at least one of within the solid tumor and into the vicinity of the solid tumor, thereby treating the solid tumor.

2. The method of claim 1, wherein the DDD comprises between 0.15-1.1, inclusive, milligrams of the RNAi agent per DDD.

3. The method of claim 1, wherein the polymeric composition has a molecular weight of greater than 50 KDa.

4. The method of claim 1, wherein the DDD further comprises at least one additive selected from the group consisting of a pH-modulating additive and trehalose.

5. The method of claim 1, wherein the DDD is coated with a coating comprising a biodegradable polymer.

6. The method of claim 5, wherein the DDD is a delayed-release DDD.

7. The method of claim 1, wherein at least two DDDs are implanted together, and wherein one of the implanted DDDs is a delayed release DDD, and one of the implanted DDDs is a non-delayed release DDD.

8. The method of claim 1, wherein 95% of said nucleotide-based agent is released from said DDD at a time point between 1-24 months, inclusive, after implantation.

9. The method of claim 1, wherein less than 5% of the RNAi agent is released from the DDD over a time period of one month starting from implantation.

10. The method of claim 1, wherein less than 10% of the RNAi agent is released from the DDD over a time period of three months starting from implantation.

11. The method of claim 1, wherein the number of DDDs per treatment is determined to achieve a dose of 0.008-0.065 mg/kg/month.

12. The method of claim 1, wherein the at least one RNAi agent includes an additional RNAi agent that targets a gene selected from the group consisting of Kirsten rat sarcoma 2 viral oncogene homolog (K-ras), EGFR, VEGF, and AURKB.

13. The method of claim 12, wherein said K-ras is a G12D-mutated K-ras.

14. The method of claim 1, wherein the at least one RNAi agent includes an additional RNAi agent that targets at least one gene selected from the group consisting of: hTERT, gp130, interleukin 6 signal transducer (IL6ST), and CD44.

15. The method of claim 1, wherein the at least one RNAi agent is chemically modified with a modification selected from the group consisting of 2′-O-methyl (2′-OMe), 2′-O-(2-methoxyethyl) (MOE), and 2′-fluorine.

16. The method of claim 1, wherein the at least one RNAi agent is conjugated to a moiety selected from the group consisting of a cholesterol moiety, spermine, hydrophobized hyaluronic acid-spermine conjugates (HHSCs), alpha-tocopherol-vitamin E; and a cell penetrating peptide; or is complexed with a cationic molecule.

17. The method of claim 1, wherein the sense and/or the antisense strand of the at least one RNAi agent each have a dTdT overhang at the 3′-end.

18. The method of claim 4, wherein the DDD comprises at least one pH-modulating additive selected from the group consisting of sodium bicarbonate, sodium carbonate, and magnesium hydroxide.