WO2021011504A1 - Nanoparticle systems for targeted delivery of crispr/cas13 and methods of using same - Google Patents

Nanoparticle systems for targeted delivery of crispr/cas13 and methods of using same Download PDF

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WO2021011504A1
WO2021011504A1 PCT/US2020/041857 US2020041857W WO2021011504A1 WO 2021011504 A1 WO2021011504 A1 WO 2021011504A1 US 2020041857 W US2020041857 W US 2020041857W WO 2021011504 A1 WO2021011504 A1 WO 2021011504A1
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nucleic acid
grna
sequences
mrna
seq
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PCT/US2020/041857
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French (fr)
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Qianben WANG
Zhifen CUI
Yizhou Dong
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Duke University
Ohio State Innovation Foundation
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Priority to EP20840456.6A priority Critical patent/EP3999117A4/en
Priority to US17/626,482 priority patent/US20220347115A1/en
Publication of WO2021011504A1 publication Critical patent/WO2021011504A1/en

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    • A—HUMAN NECESSITIES
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    • A61K9/50—Microcapsules having a gas, liquid or semi-solid filling; Solid microparticles or pellets surrounded by a distinct coating layer, e.g. coated microspheres, coated drug crystals
    • A61K9/51—Nanocapsules; Nanoparticles
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    • A61K9/5146—Organic macromolecular compounds; Dendrimers obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyethylene glycol, polyamines, polyanhydrides
    • A61K9/5153—Polyesters, e.g. poly(lactide-co-glycolide)
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    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
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    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
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    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
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    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases RNAses, DNAses
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y5/00—Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2330/00—Production
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    • C12N2800/00—Nucleic acids vectors
    • C12N2800/10—Plasmid DNA

Definitions

  • the present application relates to nanoparticles for the targeted delivery of
  • Androgen deprivation therapy is an effective strategy to control androgen-dependent prostate cancer (ADPC) progression.
  • ADPC androgen-dependent prostate cancer
  • AR Next generation androgen receptor-targeted drugs, including abiraterone acetate (Attard et al. J. Clin. Oncol.27: 3742-3748 (2009); Bono et al. N. Engl. J. Med.364: 1995-2005 (2011); Ryan N. Engl. J. Med.
  • SARS-CoV-2 SARS-coronavirus 2
  • SARS-CoV-2 relies on certain host proteases, including TMPRSS2 and Cathepsin L, for S protein priming.
  • TMPRSS2 host proteases
  • Cathepsin L Cathepsin L
  • lung cell entry of SARS-CoV-2 but not SARS- CoV is pre-activated by the proprotein convertase FURIN.
  • Shang et al. PNAS 117: 11727- 11734 (2020); Hoffmann et al. Mol. Cell 78: 779-784 (2020) disruption of the relevant host proteases represents a novel therapeutic pathway toward the treatment of COVID- 19.
  • Gene therapy is a critical alternative strategy for targeting not only AR, but also other undruggable oncogenic transcription factors such as HoxB13, FoxA1, FoxA2, and AR-V7 in CRPC, as well as other diseases like COVID-19.
  • CRISPR/Cas9 has been a powerful toolbox for targeted gene editing in various cell types and organisms (Barrangou et al., Nat. Biotechnol., 34: 933–941 (2016)), unwanted DNA changes caused by CRISPR/Cas9 gene editing is a major concern.
  • RNA-editing CRISPR/Cas13d system can knock down RNA with high specificity without altering the genome and without the widespread off-target effects associated with RNA interference (RNAi) strategies due to their key roles in endogenous processes (Konermann et al., Cell, 173: 665-676 (2016); Sigoillo et al., Nat. Methods, 9: 363- 366 (2012)). While the small size of the Cas13d gene makes it easy to package into a low- capacity adeno-associated virus (AAV) vector, clinical application of AAV vectors is limited by mutagenesis, carcinogenesis, and other undesired consequences. (Colella et al. Mol. Ther.
  • the present invention provides a nanoparticle (NP) for targeted delivery of a CRISPR/Cas13 system comprising a nanoparticle carrier, a first nucleic acid sequence encoding a Cas13, and one or more additional nucleic acid sequences encoding direct repeat RNA sequences and one or more guide RNA or pre-guide RNA sequences.
  • the Cas13 is Cas13d.
  • the NP further comprises a cell penetrating peptide.
  • the NP further comprises a nucleic acid aptamer immobilized on the surface of the NP.
  • the aptamer targets certain prostate cancer cells.
  • the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences encode gRNAs or pre-gRNAs to a prostate cancer associated transcription factor.
  • the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences encode gRNAs or pre-gRNAs to a COVID-19 associated protein.
  • the NPs of the invention are formulated with SORT technology to be lung-, liver-, or spleen-selective.
  • the present invention provides a composition comprising the NPs of the invention and a pharmaceutically acceptable carrier or excipient.
  • the present invention provides a method of treating a subject with prostate cancer comprising administering to the subject a therapeutically effective amount of the NPs of the invention.
  • the present invention provides a method of treating a subject with COVID-19 comprising administering to the subject a therapeutically effective amount of the NPs of the invention.
  • FIGS.1A-1B illustrate the evaluation of the CRISPR/Cas13d-mediated gene knockdown system.
  • FIG.1A shows a graph illustrating mRNA knockdown through CasRx targeting of four endogenous transcripts. Each transcript is targeted with two guides and a non- targeting (NT) guide in 293FT cells (transcript levels are relative to NT guide control).
  • FIG.1B shows a graph representing mRNA knockdown through CasRx targeting of two additional genes, NF2 and HRAS, in 22RV1 (castration resistant prostate cancer (CRPC)) cells. Transcript levels are relative to NT guide control.
  • CRPC ration resistant prostate cancer
  • FIGS.2A-2B shows graphs representing mRNA knockdown through CasRx targeting of HoxB13 using four guide RNAs and pre-guide RNAs in 293FT cells. Transcript levels are relative to NT guide control.
  • FIG.2B shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 using a single gRNA in 22RV1 cells.
  • FIGS.3A-3B illustrates the construction and use of an all-in-one plasmid comprising CasRx and pre-gRNAs.
  • FIG.3A shows a diagram of an all-in-one hU6-pregRNAs-EF1a- CasRx-2AEGFP that can express CasRx and pre-gRNAs.
  • FIG.3B shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 in 22RV1 cells using arrays of three pre-gRNAs. Transcript levels are relative to NT guide control.
  • FIG.4 shows a graph of HoxB13 mRNA expression measured after transfection of CasRx mRNA and pre-gRNA oligo targeting the HoxB13 gene at various weight ratios in 22Rv1 cells. Transcript levels are relative to NT guide control.
  • FIG.5 is a schematic representation of a synthesis of nanoparticles (NPs) and plasmid encapsulation strategy.
  • Positively charged TAT and CasRx plasmid and gRNA/pre- gRNA targeting a transcription factor (“TF”) plasmid self-assemble with PLGA in DMF.
  • Polymer cores are then coated with lipid-PEG-COOH.
  • NPs can optionally be conjugated to Alexa Fluor 647-amine-functionalized aptamers by carbodiimide coupling chemistry.
  • an Alexa Fluor labeled aptamer that specifically binds PSMA is used.
  • FIGS.6A-6B show the characterization of nanoparticle size distribution with TAT (FIG.6A) or without TAT (FIG.6B).
  • FIG.7 shows a graph of HoxB13 mRNA expression measured after incubation of CasRx mRNA-HoxB13 pre-gRNA-LNPs with 22RV1 cells at a weight ratio of 1:1.5
  • FIG.8 shows an immunohistochemical (IHC) analysis of HoxB13 in normal prostate, ADPC and CRPC patient tissues.
  • FIG.9 shows a box plot that compares H-scores of HoxB13 nuclear staining in 234 tissue samples as shown in FIG.8 showing increased abundance of HoxB13 during prostate cancer progression from ADPC to CRPC.
  • FIGS.10A-10B illustrate Assays for Transposase Accessible Chromatin by sequencing (ATAC-seq) results in two CRPC patient tissues and correlated chromatin accessibility with HoxB13 genomic binding in the same tissue from the same patients.
  • FIG. 10A shows UCSC Genome Browser views of representative HoxB13 binding sites and ATAC- seq peaks, showing strong correlation between the two.
  • FIG.10B shows a correlation plot between HoxB13 binding signals and ATAC-seq signal.
  • FIGS.11A-11F illustrate Cas13d-mediated mRNA knockdown of human and mouse transcripts for mediating SARS-CoV-2 cell entry.
  • FIG.11A shows graphs representing mRNA knockdown of human TMPRSS2 mRNA with four different pre-gRNAs, with preg2 showing the most effective knockdown.
  • FIG.11B shows graphs representing mRNA knockdown of murine Tmprss2 with four different pre-gRNAs, with preg4 showing the most effective knockdown.
  • FIG.11C shows graphs representing mRNA knockdown of human mRNA with four different pre-gRNAs, with preg4 showing the most effective knockdown CTSL.
  • FIG.11D shows graphs representing mRNA knockdown of murine Ctsl mRNA with four different pre-gRNAs, with preg3 showing the most effective knockdown.
  • FIG.11E shows graphs representing mRNA knockdown of human FURIN mRNA with four different pre-gRNAs, with preg3 showing the most effective knockdown.
  • FIG.11F shows graphs representing mRNA knockdown of murine Furin mRNA with four different pre-gRNAs, with preg4 showing the most effective knockdown.
  • Transcript levels for both figures, are relative to NT guide control.
  • Articles“a” and“an” are used herein to refer to one or to more than one (i.e. at least one) of the grammatical object of the article.
  • “an element” means at least one element and can include more than one element.
  • “About” is used to provide flexibility to a numerical range endpoint by providing that a given value may be“slightly above” or“slightly below” the endpoint without affecting the desired result.
  • any feature or combination of features set forth herein can be excluded or omitted.
  • any feature or combination of features set forth herein can be excluded or omitted.
  • treatment refers to the clinical intervention made in response to a disease, disorder or physiological condition manifested by a patient or to which a patient may be susceptible.
  • the aim of treatment includes the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and/or the remission of the disease, disorder or condition.
  • the term "effective amount” or“therapeutically effective amount” refers to an amount sufficient to effect beneficial or desirable biological and/or clinical results.
  • the term “subject” and “patient” are used interchangeably herein and refer to both human and nonhuman animals.
  • nonhuman animals of the disclosure includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dog, cat, horse, cow, chickens, amphibians, reptiles, and the like.
  • the present invention advantageously provides nanoparticles that allow for the targeted delivery of a CRISPR/Cas13 system for gene therapy, which overcomes shortcomings of prior gene therapy methods such as unwanted DNA changes and difficulties in delivery associated with the use of CRISPR/Cas9 DNA systems, off target effects of interfering RNAs, and clinical shortcomings (e.g., mutagenesis, carcinogenesis) associated with the delivery of gene therapy tools using AAV vectors.
  • Cas13a there are multiple subtypes within the Cas13 family, including at least Cas13a, Cas13b, Cas13c, and Cas13d. Of the subtypes, only Cas13d is small enough for in vivo delivery via an AAV vector.
  • the NPs of the invention are not limited in the same manner, and accordingly the present invention may advantageously be used with any subtype of Cas13, i.e. at least any of Cas13a, Cas13b, Cas13c, and Cas13d.
  • any reference to Cas13d within the disclosure is equally applicable to any other Cas13 subtype. It is to be understood then that, unless otherwise apparent from the context, the present disclosure and all inventive aspects disclosed herein are intended to, and do, encompass embodiments in which references to Cas13d are replaced with another Cas13 subtype as though so specifically stated.
  • the present invention provides a nanoparticle (NP) comprising a nanoparticle carrier, a first nucleic acid sequence encoding a Cas13d, and one or more additional nucleic acid sequences encoding direct repeat (DR) RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences.
  • NP nanoparticle
  • DR direct repeat
  • gRNA guide RNA
  • pre-gRNA pre-guide RNA
  • a nanoparticle carrier is any composition comprising one or more materials that can be formulated into nanoparticles that are capable of encapsulating or otherwise retaining (e.g. by adsorption or otherwise) the first and the one or more additional nucleic acid sequences.
  • the NP carrier may be formulated out of any suitable material, including, but not limited to a polymer-lipid, a lipid (to form a lipid nanoparticle (LNP)), or gold.
  • the NP carrier is a lipid.
  • the NPs may comprise a cationic cell penetrating peptide (cpp), examples of which include the transactivator of transcription peptide (TAT) and nuclear localization sequences (NLS).
  • cpp cationic cell penetrating peptide
  • TAT transactivator of transcription peptide
  • NLS nuclear localization sequences
  • the NPs of the invention may further comprise a nucleic acid aptamer (Apt) immobilized on the surface of the NP.
  • the aptamer serves to achieve cell-specific targeting, including, but not limited to, targeting cancer cells, by recognizing certain cell membrane markers on the desired cells.
  • a prostate-specific membrane antigen (PSMA) aptamer may be utilized to recognize and target PSMA positive castration resistant prostate cancer (CRPC) cells.
  • the NPs may be prepared with an Apt to recognize and target neuroendocrine prostate cancer (NEPC) cells.
  • PSMA prostate-specific membrane antigen
  • NEPC neuroendocrine prostate cancer
  • Suitable aptamers for NEPC cell recognition include, but are not limited to, an NCAM1 aptamer, a CHGA aptamer, a SYP aptamer, a SNAP25 aptamer, or a CEACAM5 aptamer.
  • the NPs of the invention have bi-specific targeting capabilities, i.e. they both target cells of interest by way of an Apt immobilized on the NP surface, and target particular transcription factors or other genes whose knock-down or downregulation is desired by way of the CRISPR/Cas13d system, i.e. the gRNA or pre-gRNA sequences.
  • the first nucleic acid sequence encoding a Cas13d may be a plasmid, or it may be an mRNA sequence.
  • the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more gRNA or pre-gRNA sequences may be a plasmid, or may be an mRNA sequence.
  • both the first nucleic acid sequence and the one or more additional nucleic acid sequences are a plasmid.
  • the first nucleic acid sequence and the one or more additional nucleic acid sequences may comprise separate plasmids, or they may comprise the same plasmid.
  • both the first nucleic acid sequence and the one or more additional nucleic acid sequences are an mRNA sequence.
  • the first nucleic acid sequence is in the form of a plasmid and the one or more additional nucleic acid sequences are an mRNA sequence.
  • the first nucleic acid sequence is an mRNA sequence and the one or more additional nucleic acid sequences are a plasmid. Based on studies with Cas9, there may be certain advantages (faster gene editing kinetics and fewer off-target effects) to the co-delivery of the first nucleic acid sequence and the one or more additional nucleic acid sequences by mRNA rather than plasmids.
  • the NPs comprise a core encapsulating a plasmid encoding a Cas 13d and the one or more additional plasmids encoding DR RNA sequences and gRNA or pre-gRNA for the desired target, and a shell surrounding the core.
  • the core may encapsulate a plasmid that encodes both the first nucleic acid sequence and the one or more additional nucleic acid sequences.
  • a cpp may be used to encapsulate the plasmids within the core. The cpp to nucleic acid weight ratio may be readily adjusted by one of skill in the art to a suitable level to keep the plasmids from leaching out of the encapsulated core.
  • the core may comprise poly lactic-co-glycolic acid (PLGA), and the shell may comprise a polyethylene glycol (PEG).
  • PEG polyethylene glycol
  • the PEG is carboxy-modified PEG, e.g. lipid-PEG-COOH.
  • the lipid-PEG-COOH may be, for example, m-PEG-DSPE.
  • PLGA and PEG have certain benefits for use with the invention in that they are FDA approved for therapeutic use.
  • the first nucleic acid sequence encoding a Cas13d may encode CasRx, a
  • the one or more additional nucleic acid sequences encoding DR RNA sequences and gRNA or pre-gRNA for the desired target may comprise any suitable gRNA or pre-gRNA for that target, including traditionally“undruggable” oncogenic transcription factors.
  • Specific sequences for use with the invention can be derived by one of skill in the art, and may include certain modifications to improve functionality, e.g. modifications to avoid degradation in vivo.
  • Target regions having low secondary structure are ideal targets for gRNA or pre-gRNA.
  • the gRNA or pre-gRNA targets prostate cancer associated transcription factors.
  • exemplary transcription factors include, but are not limited to, AR, AR-V7, HoxB13, FoxA1, FoxA2, and GATA2.
  • the gRNA or pre-gRNA sequences of this embodiment may, for example, comprise any one of SEQ ID NOs: 1-4, 55-58, and 62 (HOXB13).
  • SARS-CoV-2 uses the host receptor ACE2 for cell entry and the serine protease TMPRSS2 and/or the cysteine protease Cathepsin L (CTSL) for S protein priming. Hoffmann et al. Cell 181: 271-280 (2020); Zhou et al. Nature 579: 270-273 (2020). Additionally, recent studies found that lung cell entry of SARS-CoV-2 but not SARS- CoV is pre-activated by the proprotein convertase FURIN. Shang et al. PNAS 117: 11727- 11734 (2020); Hoffmann et al. Mol. Cell 78: 779-784 (2020)).
  • the gRNA or pre-gRNA targets COVID-19 associated proteins including, but not limited to, TMPRSS2, Cathepsin L (CTSL), and Furin.
  • the gRNA or pre- gRNA (preg) sequences of this embodiment may, for example, comprise the various pre-guide 1, pre-guide 2, pre-guide 3, and pre-guide 4 sequences as disclosed herein, infra, or any one of SEQ ID NOs: 5-8, 13-16, 63, and 65 (TMPRSS2), SEQ ID NOs: 9-12, 17-20, 64, and 66 (CTSL), and SEQ ID NOs: 21-24, 25-28, 68, and 69 (Furin).
  • the NPs of the invention may have a size of 10 nm to 900 nm, or any individual value or range of values within, inclusive of the upper and lower values, whether specifically recited or not.
  • the NPs may, for example, have a size of 50-500 nm, of 100-200 nm, or 150-200 nm.
  • the average size may be, for example, about 100 nm, about 125 nm, about 150 nm, about 175 nm, or about 200 nm.
  • the NPs of the invention may have a zeta potential of about 2.25 mV.
  • the weight ratio of the first nucleic acid sequence to the additional nucleic acid sequences within the NPs may be between 1:1 and 1:2, inclusive, including about 1:1.5.
  • the NPs of the invention may have a cpp to plasmid or RNA weight ratio of about 0.1 to about 20, or any individual value or range of values within, inclusive of the upper and lower values, whether specifically recited or not.
  • the NPs may, for example, have a cpp to plasmid or RNA weight ratio of about 1 to about 18, of about 3 to about 16, or of about 5 to about 15.6.
  • the NPs of the invention may be prepared by any suitable mechanism which can be readily ascertained by one of skill in the art.
  • the NPs may be prepared by self- assembled nano-precipitation. Apt may be immobilized on the NP surface by way of, e.g., carbodiimide coupling chemistry between the–COOH group of carboxy modified PEG and the amino group at the end of the PSMA Apt.
  • one of skill in the art can optimize the nano-precipitation time and weight ratio of cpp to plasmid/nucleic acid to help minimize any batch-to-batch variability.
  • the NPs may be formulated with selective organ targeting (SORT) technology, as disclosed in Cheng et al. Nat. Nanotechnol.15: 313-320 (2020), the contents of which are incorporated herein by reference.
  • SORT enables the selective delivery of NPs comprising CRISPR/Cas9 to lungs, spleens and livers.
  • lipid NPs typically comprise ionizable cationic lipids, amphipathic phospholipids, cholesterol and PEG lipids, the addition of charge-modifying agents results in targeted delivery of the LNPs to particular organs.
  • NPs of the invention for the treatment of COVID-19 may be delivered to the lungs, whereas NPs of the invention for the treatment of prostate cancer patients having metastases to the lungs and/or liver may be delivered to the lungs and/or liver.
  • the NP carrier is a LNP that comprises a charge-modifying agent in accordance with Cheng et al.
  • the particular LNP formulation for use with the invention may be as disclosed in Cheng et al., or it may be a modification thereof within the purview of one of skill in the art.
  • the NP carrier is formulated with SORT technology to be lung-selective, i.e. for the NPs to be delivered to the lungs.
  • the NP carrier may comprise 1,2-dioleoyl- 3-trimethylammonium-propane (DOTAP), dimethyldioctadecylammonium (DDAB), or 1,2- dimyristoyl-sn-glycero-3-ethylphosphocholine (EPC).
  • DOTAP 1,2-dioleoyl- 3-trimethylammonium-propane
  • DDAB dimethyldioctadecylammonium
  • EPC 1,2- dimyristoyl-sn-glycero-3-ethylphosphocholine
  • the NP carrier may be formulated with SORT technology to be liver-selective.
  • the NP carrier may comprise 1,2-dioleoyl-3-dimethylammonium-propane (DODAP) or 5A2-SC8.
  • DODAP 1,2-dioleoyl-3-dimethylammonium-propane
  • 5A2-SC8 1,2-diole
  • the NP carrier may comprise 1,2-dioleoyl-sn-glycero-3- phosphate (18PA), 1,2-dimyristoyl-snglycero-3-phosphate (14PA), or sn-(3-oleoyl-2-hydroxy)- glycerol-1-phospho-sn-3'-(1',2'-dioleoyl)-glycerol (18BMP).
  • PA 1,2-dioleoyl-sn-glycero-3- phosphate
  • 14PA 1,2-dimyristoyl-snglycero-3-phosphate
  • BMP sn-(3-oleoyl-2-hydroxy)- glycerol-1-phospho-sn-3'-(1',2'-dioleoyl)-glycerol
  • the LNPs may comprise, in a non-limiting example, DLin- MC3-DMA, DSPC, cholesterol, DMG-PEG2000 and DOTAP in a 25/5/19.3/0.5/50 ratio.
  • the NPs of the invention may be administered by any suitable technique, including, but not limited to oral, aerosol, intranasal, injection, systemic, parenteral, subcutaneous, intravenous, intramuscular, intrathecal, intraperitoneal and rectal.
  • the NPs are administered by intravenous injection, intratumoral injection, or by oral administration.
  • the NPs may be administered at a frequency established based on NP half-life, which can readily be assessed by one of skill in the art.
  • NPs provided herein can be administered to a subject, either alone or in combination with a pharmaceutically acceptable excipient and/or carrier, in an amount sufficient to induce an appropriate biological response (e.g., knock down of the desired target).
  • an effective amount of the NPs described herein may be given in one dose, but is not restricted to one dose.
  • the administration can be two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or more, administrations of the NPs.
  • the administrations can be spaced by time intervals of one minute, two minutes, three, four, five, six, seven, eight, nine, ten, or more minutes, by intervals of about one hour, two hours, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 hours, and so on.
  • the term "about” means plus or minus any time interval within 30 minutes.
  • the administrations can also be spaced by time intervals of one day, two days, three days, four days, five days, six days, seven days, eight days, nine days, ten days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, and combinations thereof.
  • the present disclosure is not limited to dosing intervals that are spaced equally in time, but encompass doses at non-equal intervals, such as a priming schedule consisting of administration at 1 day, 4 days, 7 days, and 25 days, just to provide a non-limiting example.
  • NPs disclosed herein may be administered with a pharmaceutically or diagnostically acceptable excipient.
  • diagnostic excipient includes but is not limited to, sterile distilled water, saline, phosphate buffered solutions, amino acid-based buffers, or bicarbonate buffered solutions.
  • An excipient selected and the amount of excipient used will depend upon the mode of administration. Administration may in certain instances comprise an injection, infusion, or a combination thereof.
  • An effective amount for a particular subject/patient may vary depending on factors such as the condition being treated, the overall health of the patient, the route and dose of administration and the severity of side effects. Guidance for methods of treatment and diagnosis is available (see, e.g., Maynard, et al. (1996) A Handbook of SOPs for Good
  • a dosing schedule of, for example, once/week, twice/week, three times/week, four times/week, five times/week, six times/week, seven times/week, once every two weeks, once every three weeks, once every four weeks, once every five weeks, and the like, is available for the present disclosure.
  • the dosing schedules encompass dosing for a total period of time of, for example, one week, two weeks, three weeks, four weeks, five weeks, six weeks, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, eleven months, and twelve months.
  • the cycle can be repeated about, e.g., every seven days; every 14 days; every 21 days; every 28 days; every 35 days; 42 days; every 49 days; every 56 days; every 63 days; every 70 days; and the like.
  • An interval of non-dosing can occur between a cycle, where the interval can be about, e.g., seven days; 14 days; 21 days; 28 days; 35 days; 42 days; 49 days; 56 days; 63 days; 70 days; and the like.
  • the term "about” means plus or minus one day, plus or minus two days, plus or minus three days, plus or minus four days, plus or minus five days, plus or minus six days, or plus or minus seven days.
  • the NPs according to the present disclosure may also be administered with one or more additional therapeutic agents (e.g., small molecule therapeutics, anti-cancer agents, etc.).
  • the NPs may be functionalized with the one or more additional therapeutic agents, or the one or more additional therapeutic agents may be co-administered with the NPs.
  • Methods for co- administration with an additional therapeutic agent are well known in the art (Hardman, et al.
  • Co-administration need not refer to administration at the same time in an individual, but rather may include administrations that are spaced by hours or even days, weeks, or longer, as long as the administration of multiple therapeutic agents is the result of a single treatment plan.
  • the co-administration may comprise administering the NPs according to the present disclosure before, after, or at the same time as the one or more additional therapeutic agents.
  • the NPs of the present disclosure may be given as an initial dose in a multi-day protocol, with one or more additional therapeutic agent given on later administration days; or the one or more additional therapeutic agents given as an initial dose in a multi-day protocol, with the NPs of the present disclosure given on later administration days.
  • one or more additional therapeutic agents and the NPs of the present disclosure may be administered on alternate days in a multi-day protocol.
  • a mixture of one or more additional therapeutic agents and the NPs of the present disclosure may be concurrently. This is not meant to be a limiting list of possible administration protocols.
  • An effective amount of a therapeutic agent is one that will knock down the target by at least 10%, more normally by at least 20%, most normally by at least 30%, typically by at least 40%, more typically by at least 50%, most typically by at least 60%, often by at least 70%, more often by at least 80%, and most often by at least 90%, conventionally by at least 95%, more conventionally by at least 99%, and most conventionally by at least 99.9% as compared to no treatment.
  • Specific dosing regimens are within the purview of one of ordinary skill in the art.
  • Formulations of therapeutic agents may be prepared for storage by mixing with physiologically acceptable carriers, excipients, or stabilizers in the form of, e.g., lyophilized powders, slurries, aqueous solutions or suspensions (see, e.g., Hardman, et al. (2001) Goodman and Gilman's The Pharmacological Basis of Therapeutics, McGrawHill, New York, N.Y.; Gennaro (2000) Remington: The Science and Practice of Pharmacy, Lippincott, Williams, and Wilkins, New York, N.Y.; Avis, et al. (eds.) (1993) Pharmaceutical Dosage Forms: Parenteral Medications, Marcel Dekker, NY; Lieberman, et al.
  • the NPs of the invention may be used therapeutically for the treatment of a wide range of diseases and disorders. Of particular interest are those diseases or disorders that are considered“undruggable,” i.e. those that have not responded or have not responded well to traditional small molecule therapeutics.
  • the diseases or disorders that may be treated with the NPs of the invention include, but are not limited to, cancer.
  • Exemplary cancers include prostate cancer, such as androgen dependent prostate cancer (ADPC), castration resistant prostate cancer (CRPC), and neuroendocrine prostate cancer (NEPC), the most aggressive form of prostate cancer.
  • the present invention provides a method of treating a subject with prostate cancer comprising administering to the subject a therapeutically effective amount of the NPs of the invention.
  • the prostate cancer may be ADPC, CRPC, NEPC, or AR-7 variant prostate cancer.
  • the present invention provides a method of treating a subject with prostate cancer that has metastasized to the lungs and/or the liver comprising administering to the subject a therapeutically effective amount an NP of the invention that has been formulated with SORT technology to target the lungs and/or the liver.
  • the invention provides a method of treating a subject with COVID-19 comprising administering to the subject a therapeutically effective amount of an NP of the invention that has been formulated with SORT technology to target the lungs.
  • One functional aspect of a bi-targeting Cas13d delivery system is the ability to successfully knock down mRNA levels for gene products implicated in a disease state of interest.
  • quantitative reverse transcriptase PCR was utilized to quantify the ability of CasRx (SEQ ID NO: 76), a Cas13d isolated from Ruminococcus flavefaciens by Konermann et al., to knock down mRNA transcript levels.
  • CasRx SEQ ID NO: 76
  • the effect of CasRx mRNA targeting on end protein levels were assessed via western blots.
  • HEK 293FT and human prostatic carcinoma 22RV1 cells were transfected (Lipofectamine) with the CasRx plasmid (SEQ ID NO: 78) and with non-targeting gRNA/pre-gRNA (Konermann et al. Cell, 173: 665-676 (2016)) or with targeting gRNA (using CasRx gRNA cloning backbone (SEQ ID NO: 76)) or pre-gRNA (using CasRx pre-gRNA cloning backbone (SEQ ID NO: 77)) of interest and cultured for 48 hours, then total RNA was isolated with the RNeasy Mini kit (Qiagen, 74104).
  • qRT-PCR was conducted using the MultiScribe Reverse Transcriptase and Power SYBR Green PCR Master Mix reagents (Applied Biosystems) or Taqman Fast Advanced Master Mix (Applied Biosystem), according to the manufacturer’s instructions. Each assay was repeated three to four times, and transcript levels were quantified.
  • Primer sequences were as follows: HOXB13 forward PCR primer, 5'- ACAGAACCCACCAGGTCCCTTT -3' (SEQ ID NO: 29); HOXB13 reverse PCR primer, 5'- TACGGAATGCGTTTCTTGCGGC -3' (SEQ ID NO: 30); Human b-actin forward PCR primer, 5'- AGGCACCAGGGCGTGAT -3' (SEQ ID NO: 45); Human b-actin reverse PCR primer, 5'- GCCCACATAG GAATCCTTCTGAC -3' (SEQ ID NO: 46); NF2 forward PCR primer 5'- TTGCGAGATGAAGTGGAAAGG -3' (SEQ ID NO: 47); NF2 reverse PCR primer, 5'- CAAGAAGTGAAAGGTGACTGGTT-3' (SEQ ID NO: 48); NFKB1 forward PCR primer, 5'- AACAGAGAGGATTTCGTTTCCG-3' (SEQ ID NO: 49); NFKB1 reverse PCR primer
  • Guide RNAs comprise the spacer (or recognition, or targeting) sequence of a specific sequence identifier number (SEQ ID NO) and a single direct repeat sequence at the 5’ end of the spacer sequence (SEQ ID NO: 60).
  • Pre-guide RNAs comprise the 30 nucleotide spacer sequence of a specific sequence identifier number (SEQ ID NO) and 36 nucleotide direct repeats flanking each end of the spacer sequence of SEQ ID NO: 61).
  • FIG.1A shows a graph illustrating mRNA knockdown through CasRx targeting of four endogenous transcripts, NF2, NFKB1, PPARG, and NRAS. Each transcript is targeted with two guide RNAs and a non-targeting (NT) guide in 293FT cells. Transcript levels are relative to NT guide control. All transcripts were significantly knocked down, with an average knockdown of approximately 60%.
  • FIG.1B shows a graph illustrating CasRx-mediated mRNA knockdown of NF2 and HRAS in 22RV1 cells, with abundance relative to NT guide control. Again, significant knockdown of mRNA was achieved in this human prostatic carcinoma cell line.
  • FIG.2A shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 using four guide RNAs (or gRNA), with guide 1 having the spacer sequence of (SEQ ID NO: 55), guide 2 having the spacer sequence of (SEQ ID NO: 56), guide 3 having the spacer sequence of (SEQ ID NO: 57), and guide 4 having the spacer sequence of (SEQ ID NO: 58), and four pre-guide RNAs (or pre-gRNA), with pre-guide 1 having the spacer sequence of (SEQ ID NO: 1), pre-guide 2 having the spacer sequence of (SEQ ID NO: 2), pre-guide 3 having the spacer sequence of (SEQ ID NO: 3), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 4), all
  • FIG.2B shows a graph representing a similar set of experiments of mRNA knockdown through CasRx targeting of HoxB13 in 22RV1 cells.
  • the most effective gRNA (SEQ ID NO: 58) and pre-gRNA (SEQ ID NO: 4) from Fig.2A were used.
  • Significant knockdown of HOXB13 transcripts were observed with both gRNA 4 and pre-gRNA 4.
  • the membrane was blocked with 5% milk powder (Bio-Rad) then incubated with specific antibodies (PSMA #ab19071 from Abcam, HOXB13 #SC-66923 from Santa Cruz Biotechnology, b-actin # from ab8227 from Abcam) at 4 ⁇ C overnight. Following incubation with secondary antibodies, immunoblots were visualized using the C-DiGit Chemiluminescent western Blot Scanner (Li-Cor). The results correlated well with the mRNA knockdown experiments, with all four gRNAs and all four pre-gRNAs substantially suppressing final protein levels relative to NT guide controls.
  • a plasmid was constructed that comprised both CasRx and three pre-gRNAs, starting with the plasmid AddGene #109049 (SEQ ID NO: 78).
  • Pre-gRNA sequences 2, 3, and 4 ((SEQ ID NO: 2 through SEQ ID NO: 4, respectively), separated by direct repeats (SEQ ID NO: 61), were inserted into the MLUI restriction site.
  • FIG.3A shows a schematic diagram of the hU6- pre-gRNA-EF1 ⁇ -CasRx-2A-EGFP“all-in-one” plasmid. 22RV1 cells were then transfected with the plasmid (Lipofectamine), and mRNA and protein levels were assessed.
  • FIG.3B shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 in 22RV1 cells using arrays of three pre-gRNAs. mRNA knockdown of approximately 80% was observed. Transcript levels are relative to NT guide control. As described previously, western blots were also performed that showed a near elimination of HoxB13 protein product compared to controls. CasRx mRNA delivery
  • Plasmid-based gene therapy faces several obstacles to its clinical application, such as the substantial time requirement for gene editing and the potential to generate small insertions at the target site or large insertions at off-target sites.
  • Co-delivery of Cas9 mRNA with gRNAs into cells has been shown to provide faster gene editing kinetics and fewer off-target effects compared with plasmid-based delivery.
  • 22RV1 Cells were transfected (Lipofectamine) with CasRx mRNA and HoxB13 pre-gRNA-4 oligonucleotide at various weight ratios (1:1, 1:1.2, 1:1.5 and 1:2 CasRx mRNA to pre-gRNA oligos). Results show greater than 80% knockdown for all four weight ratios, with a trend of increased knockdown with increased weight ratio (FIG. 4).
  • HEK cell line 293FT Human embryonic kidney (HEK) cell line 293FT (Thermo Fisher) was maintained in DMEM (4.5 g/L glucose), supplemented with 10% FBS (GE Life Sciences) and 10 mM HEPES at 37°C with 5% CO2. Upon reaching 80–90% confluency, cells were dissociated using TrypLE Express (Life Technologies) and passaged at a ratio of 1:2. This cell line was purchased directly from the manufacturer and was not otherwise authenticated. Cell culture of human prostatic carcinoma cell line 22RV1.
  • Human prostatic carcinoma cell line 22Rv1 (ATCC, Cat. # CRL-2505) were purchased from American Type Culture Collection (ATCC) and were authenticated by short tandem repeat (STR) profiling and karyotyping. Cells were grown in a humidified incubator with 5% CO2 at 37°C. Cells were routinely tested for mycoplasma contamination using MycoAlertTM PLUS Mycoplasma Detection Kit (Lonza, Cat. # LT07). Cell lines were cultured in RPMI 1640 medium (Corning, Cat. # 10-040-CV) supplemented with 10% fetal bovine serum (Corning, Cat. # 35010CV), penicillin-streptomycin (Corning, Cat.
  • FIG.5 A schematic representation of the strategy for nanoparticle (NP) synthesis and plasmid encapsulation is shown in FIG.5.
  • a nucleic acid of interest in this case two plasmids, one encoding CasRx and another cloned guide RNA and/or pre-guide RNA to the target of interest, were encapsulated into a poly(lactic-co-glycolic acid) (PLGA) core.
  • PLGA poly(lactic-co-glycolic acid)
  • CasRx mRNA with pre-gRNA oligonucleotides were also encapsulated in a similar manner.
  • a shell was formed over the core by lipid-PEG with Alexa Fluor 647 dye labeling.
  • PEG can optionally be functionalized to help target the NP to a desired tissue.
  • the shell was formed by prostate specific membrane antigen-specific (PSMA) aptamer-modified lipid-PEG with Alexa Fluor 647 dye labeling.
  • PSMA prostate specific membrane antigen-specific
  • lipid-PEG with Alexa Fluor 647 dye labeling.
  • This cell-specific binding helps a NP dock and deliver its nucleic acid payload to the appropriate cell type.
  • Additional types of nanoparticle delivery systems can be used, such as DNA nanoclew vectors, nanogold and cationic lipid-assisted NPs.
  • TAT peptide was used for plasmid complexation at varying weight ratios of TAT to CasRx and gRNA (0.1:1, 0.5:1, 1:1, 5:1, 10:1, and 20:1). Agarose gel electrophoresis showed that TAT effectively condensed the two plasmids at a weight ratio of 5 or above with no visible evidence of constituent parts of the NP leaking from the NP as compared to NPs without TAT. This indicated that most plasmids were successfully encapsulated. In addition, the organic solvent DMF had no influence on plasmid properties. Previous evidence has shown that polyethylene glycol (PEG)-functionalized NPs are more protected against systemic clearance than similar NPs without PEG.
  • PEG polyethylene glycol
  • lipid-PEG m-PEG-DSPE, or 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N- [methoxy(polyethylene glycol) to form a shell
  • NPs 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N- [methoxy(polyethylene glycol)
  • Zeta potential was nearly neutral (2.25 mv). Nanoparticle delivery of nucleic acid payload.
  • CasRx mRNA and HoxB13 pre-gRNA oligonucleotides were incorporated into lipid- NPs (LNPs) as described above. HoxB13 mRNA expression was measured after incubation of CasRx mRNA- HoxB13 pre-gRNA-LNPs with 22Rv1 cells at a weight ratio of 1:1.5
  • poly(lactic-co-glycolic acid) (PLGA) and TAT peptide (SEQ ID NO: 59) were dissolved separately in DMF at concentrations of 5 mg ml -1 and 2.5 mg ml -1 , respectively. Then, 250 mg PLGA and 250 mg TAT were mixed in a small glass vial. Plasmid (16 mg at 1 mg ml -1 concentration) in aqueous solution was mixed into the PLGA-TAT organic solution (weight ratio of Plasmid: PLGA: TAT was 1:15:15) to form cationic lipid-Plasmid nanocomplexes.
  • the NPs were used fresh or kept at -80 ⁇ to use later for various in vitro and in vivo studies.
  • the plasmid NPs Sizes and Zeta potential were measured by Zetasizer (Malvern), the morphology was visualized by transmission electron microscopy (TEM) at Duke Pathology Research Electron Microscopy Service. Plasmid encapsulation evaluation and complexation ability of TAT.
  • HoxB13 as an Exemplary Target for Nanoparticles.
  • HoxB13 in promoting or inhibiting full-length androgen receptor (AR) function in androgen dependent prostate cancer (ADPC).
  • ADPC androgen dependent prostate cancer
  • HOXB13 acts as a pioneer transcription factor for AR- V7 (an AR splicing variant) and governs AR-V7-positive CRPC growth.
  • IHC immunohistochemical
  • Assays for Transposase Accessible Chromatin by sequencing were performed in two CRPC patient tissues and correlated chromatin accessibility with HoxB13 genomic binding in the same tissue from the same patients. Strong HoxB13 binding was observed, correlated with high chromatin accessibility.
  • UCSC Genome Browser views of representative HOXB13 binding sites and ATAC-seq peaks show strong correlation (FIG.10A and FIG.10B), suggesting that HoxB13 may function as a general pioneer factor in opening chromatin.
  • FIG.8 and FIG.9 HoxB13 appears to function as a general, oncogenic pioneer transcription factor to drive CRPC growth and is thus an attractive target for NP as described herein.
  • Nanoparticles of the disclosure comprising nucleic acids (plasmids and mRNAs shown herein) have been shown to deliver their nucleic acid payload to cells in their vicinity.
  • prostate cancer cell types like 22RV1 and LNCaP95, have not only been shown to transcribe a specific, disease-associated mRNA (HoxB13 in this case), but they have also been shown to express one or more specific moieties on their cell surfaces that are not ubiquitously found in the body.
  • an example is PSMA.
  • PSMA is common to most CRPC cell lines.
  • targeting a cell surface antigen on the cell type of interest increases the probability that a nucleic acid payload in a NP will be delivered where it can confer a benefit.
  • Other disease states share similar opportunities for specific targeting, and NP formulations can also be tuned to facilitate tissue-specific targeting.
  • the membrane was blocked with 5% milk powder (Bio-Rad) then incubated with specific antibodies (PSMA #ab19071 from Abcam, HOXB13 #SC-66923 from Santa Cruz Biotechnology, b-actin #ab8227 from from Abcam) at 4 oC overnight. Following incubation with secondary antibodies, immunoblots were visualized using the C-DiGit Chemiluminescent western Blot Scanner (Li- Cor). The results show that HOXB13 was expressed approximately as abundantly as the b-actin control and PSMA expressed more strongly that b-actin in 22RV1 cells. LNCaP95 cells expressed HoxB13 modestly more than the b-actin control and PSMA approximately 50% as much as the control. Immunohistochemistry (IHC) analysis.
  • IHC Immunohistochemistry
  • Tumor microarrays containing normal prostate (141 samples), androgen dependent prostate cancer (74 samples), or castration-resistant prostate cancer (19 samples) were constructed. Immunohistochemical staining of these samples was performed with a HoxB13 antibody (ab53931, Abcam). Briefly, following deparaffinization, antigen retrieval was performed for 40 min using Reveal Decloaker solution (Biocare Medical), followed by 20 minutes cooling. This was followed by application of Protein Block (Biocare Medical) for 15 minutes and Endogenous Peroxidase Quench (Biocare Medical) for 6 minutes. Primary antibody was applied for 60 min at a dilution of 1:250, while secondary antibody detection was performed as part of the MACH 4TM detection system (Biocare Medical).
  • H-scores ranged from 0 to 300 and were calculated as the product of the Intensity Score for the epithelial region of maximum HOXB13 staining intensity in each sample (assigned on a scale from 0 to 3) multiplied by the percentage of epithelial cells in that sample showing maximum staining intensity (0-100%).
  • Nuclei were counted after addition of trypan blue, which stains all nuclei due to membrane permeabilization from freezing.50,000 counted nuclei were then transferred to a tube containing 1 ml of ATAC-seq RSB with 0.1% Tween-20. Nuclei were pelleted by centrifugation at 500 r.c.f. for 10 min in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed using the two pipetting steps described above.
  • the transposition mix (25 ml 2 ⁇ TD buffer, 2.5 ml transposase (100 nM final), 16.5 ml PBS, 0.5 ml 1% digitonin, 0.5 ml 10% Tween-20, 5 ml water) was added directly to the nuclear pellet and mixed by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns.
  • Paired ⁇ end sequencing was performed using an Illumina HiSeq 4000 instrument. Nextera-based sequencing primers and reagents were used. Paired-end 50-cycle reads generally provide accurate alignments with reasonable costs. For inferring differences in open chromatin within human samples >50M mapped reads are generally used. Sequence reads were obtained and mapped to the human (hg19) genomes using Bowtie2 with standard parameters and a maximum fragment length of 2,000. Picard was then used to remove duplicate reads. ChIP-exo and Data Analysis.
  • CRPC samples were trimmed and chopped into small pieces on ice and fixed immediately with 1% formaldehyde for 20 min at room temperature. Chromatin was sonicated and incubated overnight with 4 ⁇ g antibodies against HOXB13 (H-80, Santa Cruz
  • T4 DNA polymerase, T4 PNK and Klenow DNA Polymerase were used together for end polishing.
  • the ligation step was performed with 1mM dithiothreitol.
  • Protein A Dynal magnetic beads were washed using modified RIPA buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25% sodium deoxycholate, 1% NP-40, 0.5 M LiCl) followed by Tris pH 8.0 twice during each step.
  • the library was amplified with only 10-12 cycles and prepared without gel- based size selection. Paired-end sequencing (50 bp) was performed using Illumina HiSeq2500 at the OSUCCC sequencing core.
  • Raw reads were aligned to the human reference genome (hg19) using Bowtie with default parameter settings.
  • the binding locations for AR-V7, AR-FL and HoxB13 were identified by BELT and Genomics Suite (v6.6, Partek) from ChIP-exo Reads 2.
  • ChIP-exo borders were called by the MALD model from ChIP-exo Reads 1, and DNA motifs were precisely defined by the BPMotif approach. Briefly, the enriched DNA motifs were defined by a multi-phase cross-validation procedure.
  • Genomics Suite (v6.6) and MEME Suite v4.9 were used to find the candidate motifs.
  • Initial motif candidates were generated using default program settings (one instance per sequence, less than 40 bp of border extension).
  • Motifs were then clustered with the Pearson correlation coefficient. Exo signal was measured to define border patterns and classify motifs. A set of overrepresented motifs was then used to correct border extension according to the enriched motif position. Motif discovery was repeated twice. Motifs with E ⁇ 1e-10 or that were found in 10% of sequences were retained as reliable predictions for the next round of analysis. Finally, motifs satisfying the following extensible criteria were identified: 1) Motif similarity compared to ARE or Homeobox motifs in the transcription factor binding databases or between core motifs defined in HoxB13 ChIP-exo data; 2) At least one common protected border exists upstream and downstream of the strand-specific motif; and 3) Same distance from borders to the most conserved nucleotides in variable motifs. For those core motifs that did not meet criteria (1), motif comparison and clustering based on criteria 2) and 3) using the exo-defined matrix were also performed. Immunostaining assays.
  • SARS-CoV-2 uses the host receptor ACE2 for cell entry and the serine protease TMPRSS2 and/or the cysteine protease Cathepsin L (CatL/CTSL) for S protein priming.
  • ACE2 serine protease
  • CatL/CTSL cysteine protease Cathepsin L
  • RNA editing NP system of the disclosure can be used to target the TMPRSS2 and CatL/CTSL genes in lung with minimized off-target effects.
  • lung cell entry of SARS-CoV-2, but not SARS-CoV is pre-activated by the proprotein convertase, furin. Effective pre-gRNAs for guiding CasRx to target furin have been determined and used to target human FURIN and murine Furin mRNA.
  • TMPRSS2 knockout mice exhibit no detectable histological or functional abnormalities in organs such as the lungs, liver, or prostate, suggesting that the role of TMPRSS2 in normal physiology may be dispensable (Kim et al. Mol. Cell. Biol. 26: 965-75 (2006)), TMPRSS2 does affirmatively contribute to SARS-CoV spread and immunopathology in the airway of mouse models. (Iwata-Yoshikawa et al. J. Virol. 93 (2019), doi:10.1128/JVI.01815-18).
  • FIG.11A shows a graph representing mRNA knockdown of human TMPRSS2 through CasRx targeting using four pre-guide RNAs (or pre- gRNA), with pre-guide 1 having the spacer sequence of (SEQ ID NO: 5), pre-guide 2 having the spacer sequence of (SEQ ID NO: 6), pre-guide 3 having the spacer sequence of (SEQ ID NO: 7), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 8), all in 293FT cells. Knockdown range varied from about 30% for pre-gRNA 1 to about 80%, with pre-gRNA 2 being the most effective.
  • FIG.11B shows a graph representing mRNA knockdown of murine Tmprss2 through CasRx targeting using four pre-guide RNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 13), pre-guide 2 having the spacer sequence of (SEQ ID NO: 14), pre-guide 3 having the spacer sequence of (SEQ ID NO: 15), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 16), all in 293FT cells. Knockdown range varied from about 25% for pre-gRNA 2 to about 75%, with pre-gRNA 4 being the most effective.
  • FIG.11C shows a graph representing mRNA knockdown of human CTSL through CasRx targeting using four pre- gRNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 9), pre-guide 2 having the spacer sequence of (SEQ ID NO: 10), pre-guide 3 having the spacer sequence of (SEQ ID NO: 11), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 12), all in 293FT cells.
  • FIG.11D shows a graph representing mRNA knockdown of murine Ctsl through CasRx targeting using four pre-guide RNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 17), pre-guide 2 having the spacer sequence of (SEQ ID NO: 18), pre-guide 3 having the spacer sequence of (SEQ ID NO: 19), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 20), all in 293FT cells. Knockdown range varied from about 30% for pre-gRNA 2 to about 70%, with pre-gRNA 3 being the most effective.
  • FIG.11E shows a graph representing mRNA knockdown of human FURIN through CasRx targeting using four pre- gRNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 21), pre-guide 2 having the spacer sequence of (SEQ ID NO: 22), pre-guide 3 having the spacer sequence of (SEQ ID NO: 23), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 24), all in 293FT cells. Knockdown range varied from about 70% to about 90%, with pre-gRNA 3 being the most effective.
  • FIG.11F shows a graph representing mRNA knockdown of murine Furin through CasRx targeting using four pre-guide RNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 25), pre-guide 2 having the spacer sequence of (SEQ ID NO: 26), pre-guide 3 having the spacer sequence of (SEQ ID NO: 27), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 28), all in 293FT cells. Knockdown range varied from about 50% for pre-gRNA 3 to about 85%, with pre-gRNA 4 being the most effective. All transcript levels are relative to Vector controls.
  • 293FT is a TMPRSS2-negative cell line
  • a TMPRSS2-encoding vector was co-transfected with the CasRx and pre-gRNA plasmids.
  • 293FT were co-transfected with murine the Tmprss2, Ctsl or Furin encoding vector along with the CasRx and pre-gRNA plasmids.
  • 22RV1 cells were incubated with LNPs encapsulating GFP-mRNA (GFP mRNA- NP). Fluorescence microscopy revealed high efficiency delivery of GFP mRNA into the 22RV1 cells as evidenced by the presence of robust GFP under fluorescence and verified by bright-field contrast. Similar experiments were conducted in which the surfaces of empty LNPs were modified with the near-IR fluorescent cyanine dye DiR for tracking the location of LNPs. Incubation of the NPs with 22RV1 cells followed by visualization demonstrated co-location of the NPs with the cell surface.
  • NPs comprising the CasRx/gRNA system for specific knockdown of TMPRSS2 and CatL can be specifically targeted to the lungs using a recently developed selective organ targeting (SORT) technology (Lee, J. K. et al. Proc Natl Acad Sci USA 115, E4473-E4482, (2016)). Lung-targeting LNPs have been successfully generated, which LNPs have demonstrated high delivery efficiency in vitro (FIG.7). These NPs comprised DLin-MC3-DMA / DSPC / cholesterol / DMG-PEG2000 / DOTAP at a final molar ratio of 25/5/19.3/0.8/50. Organ-specific nanoparticle formation.
  • SORT selective organ targeting
  • lipids with specified molar ratios were dissolved in ethanol and RNA was dissolved in 10 mM citrate buffer (pH 4.0). The two solutions were rapidly mixed at an aqueous to ethanol ratio of 3/1 by volume (3/1, aq./ethanol, vol./vol.) to satisfy a final weight ratio of 40/1 (total lipids/mRNA), then incubated for 10 min at room temperature.
  • a lung-targeted LNPs (50% DOTAP) was prepared as follows.
  • a solution of lipids in ethanol was prepared consisting of DLin-MC3-DMA, DSPC, cholesterol, DMG-PEG2000 and DOTAP to make the final molar ratio of 25/5/19.3/0.8/50.
  • the systematic names for these reagents are as follows: DLin-MC3-DMA is (6Z,9Z,28Z,31Z)- Heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate; DSPC is 1,2-Distearoyl-sn- glycero-3-phosphocholine; DMG-PEG2000 is 1,2-dimyristoyl-rac-glycero-3- methoxypolyethylene glycol-2000; and, DOTAP is 1,2-dioleoyl-3-trimethylammonium-propane.
  • lipid solution was used per mg of RNA.
  • a mixture of 5.8 ml of lipid and 9.2 ml of ethanol were mixed (total 15 ml), and then a 45 ml nucleic acid solution was prepared consisting of 5 mg of nucleic acid RNA in citrate buffer (10 mM, pH 4.0). Then 45 ml of the nucleic acid solution was rapidly combined with 15 ml of the ethanol/lipid solution to form 50% DOTAP LNPs.
  • the formulations can be dialysed (Pur-A-Lyzer Midi Dialysis Kits, WMCO 3.5 kDa) against 1 ⁇ PBS for 2 hours and diluted with PBS to 15 ml g -1 for i.v. injections. Additional COVID-19 studies
  • organ-selective LNPs carrying CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, Furin or the three genes combined on normal mouse lung histology and function can be assessed.
  • the extent to which organ-selective LNPs carrying CasRx mRNA and pre- gRNA targeting Tmprss2, Ctsl, Furin, or the three genes combined can block SARS-CoV-2 entry can be evaluated in order to determine utility for antiviral intervention. Additional Methods
  • Human cells can be incubated with lung-selective LNPs encapsulating 1mg CasRx mRNA and 1.5 mg pre-gRNA oligo targeting TMPRSS2, CTSL and FURIN or combined 3 genes, respectively, at a weight ratio of 1:1.5 in 6-well plate, for different time points: 6, 12, 24, 48, 72 and 96 hours and subjected for analysis as described below.
  • RNA can be extracted from cells using RNeasy mini kit (Qiagen) and reverse transcribed by transcriptase (Thermo).
  • qRT-PCR primer can be ordered from Integrated DNA Technologies (IDT).
  • mRNA expression levels of TMPRSS2, CTSL and FURIN can be determined by SYBR Green gene expression assays (Thermo).
  • Real-time PCR reactions can be carried out in triplicate by using a qTOWER 3 system (Analytik Jena). The expression can be calculated with comparative Ct method and the raw data are normalized with the internal control b-actin.
  • cell lysates can be resolved on 4–15% SDS-PAGE, transferred to PVDF membranes and probed with corresponding antibodies.
  • Antibodies to TMPRSS2 (#ab92323), FURIN (#ab183495) and b-actin (#ab8227) are from Abcam (Boston, MA); to Cathepsin L (#MAB9521) from Novus Biological (Centennial, CO).
  • the protein expression can be quantified by densitometry and normalized to b-actin.
  • flow cytometric experiments will be performed by first washing cells with 1X PBS, treating with 1X Trypsin EDTA and fixing in 1.6% paraformaldehyde in PBS for 10 minutes. Cells will then be washed with FACS buffer (1X PBS, 0.3% BSA, 1mM EDTA). A BD Accuri C6 plus flow cytometer will used to collect raw data. Raw data can be processed with Cytobank (BD) software. Data can be presented as representative flow cytometry plots of forward versus side scatter (FSC versus SSC).
  • mice are preferably acclimated for one week before the study. All animal experiments are carried out according to a protocol approved by an Institutional Animal Care and Use Committee.
  • Lung-selective LNPs encapsulating CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, furin, or all three combined can be administered via the tail vein at a dose of 10 mg CasRx mRNA and 15 mg pre- gRNA oligos/10g body weight in a volume of 10 ml/10g body weight.
  • Mice can be sacrificed at the time points of 24, 72 and 120 hours after injection. Each time point should comprise at least 3 ⁇ 4 mice.
  • Lung tissues can be collected immediately, homogenized and subjected for qRT-PCR and WB analysis to determine its mRNA and protein levels of Tmprss2, Ctsl and Furin, as applicable.
  • FURIN(human)/Furin (mouse), or all three combined can block SARS-CoV-2 entry into human cells in vitro and into mouse lung in vivo, is important to evaluate their utility for antiviral intervention.
  • Calu-3 or Caco-2 cells can be: (1) pre-incubated with lung- selective LNPs encapsulating1mg CasRx mRNA and 1.5 mg pre-gRNA oligo targeting
  • TMPRSS2, CTSL and FURIN or all three combined, at a weight ratio of 1:1.5 in 6-well plates, for 24 hours prior to SAS-Cov2 challenge; (2) incubated with lung-selective LNPs encapsulating CasRx mRNA and pre-gRNA targeting TMPRSS2, CTSL, FURIN, or all three combined, for 24 or 48 hours after SAS-Cov2 challenge.
  • Cell supernatant can be collected for testing virus titer and levels of cytokines (IL-6, IL-8, IL-10, TNF-alpha, IFN-gamma) and chemokines (CCL2, CCL3, CCL4). Cells can also be collected for determination of viral copy number and expression levels of TMPRSS2, CTSL and FURIN.
  • K18-hACE2 mice (Jackson Laboratory) can be treated through tail vein with a single dose of lung-selective LNPs encapsulating CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, Furin, or all three combined, respectively, prophylactically at 18 hours prior to infection, therapeutically at 12 hours post infection, and infected with SARS-CoV-2 intranasally. Body weight can be monitored daily. On day 2 post infection, mice can be euthanized by isoflurane overdose and tissue samples can be harvested for analysis.
  • Lung virus titration lung tissue homogenates can be clarified by centrifugation and the supernatant can be inoculated onto Vero E6 cell cultures for virus titration.
  • Lung histology (hemorrhage and assessment): two different histological assessment tools can be used to quantitate the histological features of lung injury, (i) the American Thoracic Society lung injury scoring tool and (ii) the DAD tool. Both will be used to assess lung histology.
  • Detection of inflammatory cytokines and chemokines cytokines and chemokines in mouse lung homogenates can be measured using a commercial Mouse Cytokine 20-Plex antibody bead kit (Thermo).
  • Neuroendocrine prostate cancer is a lethal form of the disease characterized by loss of androgen receptor (AR) signaling during neuroendocrine transdifferentiation, which results in resistance to AR-targeted therapy. Metastases to the lungs and liver are common and currently undruggable. Generating mouse models for neuroendocrine prostate cancer.
  • AR androgen receptor
  • NCI-H660 H660
  • MSKCC-EF1 Three NEPC cell lines NCI-H660 (H660), MSKCC-EF1, and PARCB2 are established to stably express a luciferase.
  • Cell luciferase signal intensity is examined in vitro before injection into mice.
  • NSG male mice (12 ⁇ 14 week-old) are purchased from Jackson Laboratory (Bar Harbor, ME). Upon receipt, mice are acclimated for one week before the study. All animal experiments are carried out according to a protocol approved by an Institutional Animal Care and Use Committee, or equivalent.
  • Mice are intravenously injected with 0.5 million H660, MSKCC-EF1, or PARCB2 cell lines, respectively, in serum free DMEM or RPMI using insulin syringe (BD). Each cell line is injected into at least 5 mice.
  • Bioluminescence of the full body is monitored using IVIS Lumina XR (Caliper Life Sciences) 1 ⁇ 2 h after cell injection and weekly afterwards until the visceral metastasis is established. Briefly, mice are anesthetized with isoflurane, fixed in the imaging chamber and imaged 15 minutes after Luciferin injection (150 mg/kg, i.p.). Bioluminescence signal is quantified using the Living Image software 4.2 (Caliper Life Sciences). Counteracting NEPC metastasis to the liver and lungs.
  • NEPC cell generally do not express the well-known prostate cancer cell surface marker PSMA, so other membrane markers are targeted, including NCAM1, CHGA, SYP, SNAP25 and CEACAM5. These markers are screened to determine the most effective aptamer-surface marker pair(s) to be used to target aptamer-functionalized LNPs to the NEPC cells. Immunostaining and western blots are used, details for which are described above.

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Abstract

The present application relates to nanoparticles for the targeted delivery of CRISPR/Cas13 systems, and their therapeutic use to treat diseases and disorders such as prostate cancer and COVID-19.

Description

NANOPARTICLE SYSTEMS FOR TARGETED DELIVERY OF CRISPR/CAS13 AND
METHODS OF USING SAME BACKGROUND OF THE INVENTION Cross Reference to Related Applications
[001] This application claims priority to U.S. Provisional Patent Application Serial Number 62/873,295, filed July 12, 2019, the contents of which are hereby incorporated by reference in their entirety. Statement Regarding Federally Sponsored Research or Development
[002] This application was made with United States government support under Federal Grant No. CA014236 awarded by the NIH. The United States government has certain rights in this invention. Incorporation by Reference of Sequence Listing Provided Electronically
[003] This application is being filed electronically via EFS-Web and includes an electronically submitted Sequence Listing in .txt format. The .txt file contains a sequence listing entitled“20-1068-WO_SEQ-LISTING_ST25.txt” created on July 12, 2020 and is 61 kilobytes in size. The Sequence Listing contained in this .txt file is part of the specification and is hereby incorporated by reference herein in its entirety. Field of the Invention
[004] The present application relates to nanoparticles for the targeted delivery of
CRISPR/Cas13 systems, and their therapeutic use to treat diseases and disorders such as prostate cancer and COVID-19. Description of the Related Art
[005] Androgen deprivation therapy is an effective strategy to control androgen-dependent prostate cancer (ADPC) progression. However, the evolution of prostate cancer from an androgen-dependent state (ADPC) to CRPC marks the lethal phase in the progression of the disease (Debes & Tindall N. Engl. J. Med.351: 1488-1490 (2004)). Next generation androgen receptor (AR)-targeted drugs, including abiraterone acetate (Attard et al. J. Clin. Oncol.27: 3742-3748 (2009); Bono et al. N. Engl. J. Med.364: 1995-2005 (2011); Ryan N. Engl. J. Med. 368: 138-148 (2013)) enzalutamide (Tran et al Science 324: 787-790 (2009); Scher et al N Engl. J. Med.367: 1187-1197 (2012)), and darolutamide (Fizazi et al. N. Engl. J. Med.380: 1235-1246 (2019)) have recently demonstrated strong anti-cancer activity and initial clinical benefit. However, these agents have not vastly improved overall survival in CRPC patients, due to the rapid development of resistance (Yuan et al. Oncogene 33: 2815-2825 (2014); Watson et al. Nat. Rev. Cancer 15: 701-711 (2015); Aragon-Ching, Asian J. Androl.,
doi:10.4103/aja.aja_52_19 (2019)). These limited therapeutic options and the inability to clinically counteract other driving transcription factors (TFs) for CRPC demonstrate a need for alternative treatment for advanced prostate cancer.
[006] The emergence of SARS-coronavirus 2 (SARS-CoV-2) has created a global health crisis for which successful treatment has been elusive. Recent studies have demonstrated that SARS-CoV-2 relies on certain host proteases, including TMPRSS2 and Cathepsin L, for S protein priming. (Hoffmann et al. Cell 181: 271-280 (2020); Zhou et al. Nature 579: 270-273 (2020)). Additionally, recent studies found that lung cell entry of SARS-CoV-2 but not SARS- CoV is pre-activated by the proprotein convertase FURIN. (Shang et al. PNAS 117: 11727- 11734 (2020); Hoffmann et al. Mol. Cell 78: 779-784 (2020)). Accordingly, disruption of the relevant host proteases represents a novel therapeutic pathway toward the treatment of COVID- 19.
[007] Gene therapy is a critical alternative strategy for targeting not only AR, but also other undruggable oncogenic transcription factors such as HoxB13, FoxA1, FoxA2, and AR-V7 in CRPC, as well as other diseases like COVID-19. While CRISPR/Cas9 has been a powerful toolbox for targeted gene editing in various cell types and organisms (Barrangou et al., Nat. Biotechnol., 34: 933–941 (2016)), unwanted DNA changes caused by CRISPR/Cas9 gene editing is a major concern. The RNA-editing CRISPR/Cas13d system can knock down RNA with high specificity without altering the genome and without the widespread off-target effects associated with RNA interference (RNAi) strategies due to their key roles in endogenous processes (Konermann et al., Cell, 173: 665-676 (2018); Sigoillo et al., Nat. Methods, 9: 363- 366 (2012)). While the small size of the Cas13d gene makes it easy to package into a low- capacity adeno-associated virus (AAV) vector, clinical application of AAV vectors is limited by mutagenesis, carcinogenesis, and other undesired consequences. (Colella et al. Mol. Ther.
Methods Clin. Dev., 8: 87-104 (2018); Thomas, et al. Nat. Rev. Genet., 4: 346-358 (2003)).
[008] Accordingly, there exists a need in the art for the safe and efficient delivery of the CRISPR/Cas13 system. SUMMARY OF THE INVENTION
[009] In a first aspect, the present invention provides a nanoparticle (NP) for targeted delivery of a CRISPR/Cas13 system comprising a nanoparticle carrier, a first nucleic acid sequence encoding a Cas13, and one or more additional nucleic acid sequences encoding direct repeat RNA sequences and one or more guide RNA or pre-guide RNA sequences. In one embodiment of this aspect of the invention, the Cas13 is Cas13d.
[0010] In one embodiment of the first aspect of the invention, the NP further comprises a cell penetrating peptide. In an additional embodiment of this aspect of the invention, the NP further comprises a nucleic acid aptamer immobilized on the surface of the NP. In a further embodiment of the first aspect of the invention, the aptamer targets certain prostate cancer cells.
[0011] In certain embodiments of the first aspect of the invention, the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences encode gRNAs or pre-gRNAs to a prostate cancer associated transcription factor. In other embodiments of the first aspect of the invention, the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences encode gRNAs or pre-gRNAs to a COVID-19 associated protein.
[0012] In a further embodiment of the first aspect of the invention, the NPs of the invention are formulated with SORT technology to be lung-, liver-, or spleen-selective.
[0013] In a second aspect, the present invention provides a composition comprising the NPs of the invention and a pharmaceutically acceptable carrier or excipient.
[0014] In a third aspect, the present invention provides a method of treating a subject with prostate cancer comprising administering to the subject a therapeutically effective amount of the NPs of the invention.
[0015] In a fourth aspect, the present invention provides a method of treating a subject with COVID-19 comprising administering to the subject a therapeutically effective amount of the NPs of the invention. BRIEF DESCRIPTION OF THE DRAWINGS
[0016] The features, objects and advantages other than those set forth above will become more readily apparent when consideration is given to the detailed description below. Such detailed description makes reference to the following drawings, wherein:
[0017] FIGS.1A-1B illustrate the evaluation of the CRISPR/Cas13d-mediated gene knockdown system. FIG.1A shows a graph illustrating mRNA knockdown through CasRx targeting of four endogenous transcripts. Each transcript is targeted with two guides and a non- targeting (NT) guide in 293FT cells (transcript levels are relative to NT guide control). FIG.1B shows a graph representing mRNA knockdown through CasRx targeting of two additional genes, NF2 and HRAS, in 22RV1 (castration resistant prostate cancer (CRPC)) cells. Transcript levels are relative to NT guide control.
[0018] FIGS.2A-2B. shows graphs representing mRNA knockdown through CasRx targeting of HoxB13 using four guide RNAs and pre-guide RNAs in 293FT cells. Transcript levels are relative to NT guide control. FIG.2B shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 using a single gRNA in 22RV1 cells.
[0019] FIGS.3A-3B illustrates the construction and use of an all-in-one plasmid comprising CasRx and pre-gRNAs. FIG.3A shows a diagram of an all-in-one hU6-pregRNAs-EF1a- CasRx-2AEGFP that can express CasRx and pre-gRNAs. FIG.3B shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 in 22RV1 cells using arrays of three pre-gRNAs. Transcript levels are relative to NT guide control.
[0020] FIG.4 shows a graph of HoxB13 mRNA expression measured after transfection of CasRx mRNA and pre-gRNA oligo targeting the HoxB13 gene at various weight ratios in 22Rv1 cells. Transcript levels are relative to NT guide control.
[0021] FIG.5 is a schematic representation of a synthesis of nanoparticles (NPs) and plasmid encapsulation strategy. Positively charged TAT and CasRx plasmid and gRNA/pre- gRNA targeting a transcription factor (“TF”) plasmid self-assemble with PLGA in DMF. Polymer cores are then coated with lipid-PEG-COOH. NPs can optionally be conjugated to Alexa Fluor 647-amine-functionalized aptamers by carbodiimide coupling chemistry. In this schematic, an Alexa Fluor labeled aptamer that specifically binds PSMA is used.
[0022] FIGS.6A-6B show the characterization of nanoparticle size distribution with TAT (FIG.6A) or without TAT (FIG.6B).
[0023] FIG.7 shows a graph of HoxB13 mRNA expression measured after incubation of CasRx mRNA-HoxB13 pre-gRNA-LNPs with 22RV1 cells at a weight ratio of 1:1.5
(CasRx:pre-gRNA). Transcript levels are relative to NT guide control.
[0024] FIG.8 shows an immunohistochemical (IHC) analysis of HoxB13 in normal prostate, ADPC and CRPC patient tissues.
[0025] FIG.9 shows a box plot that compares H-scores of HoxB13 nuclear staining in 234 tissue samples as shown in FIG.8 showing increased abundance of HoxB13 during prostate cancer progression from ADPC to CRPC. [0026] FIGS.10A-10B illustrate Assays for Transposase Accessible Chromatin by sequencing (ATAC-seq) results in two CRPC patient tissues and correlated chromatin accessibility with HoxB13 genomic binding in the same tissue from the same patients. FIG. 10A shows UCSC Genome Browser views of representative HoxB13 binding sites and ATAC- seq peaks, showing strong correlation between the two. FIG.10B shows a correlation plot between HoxB13 binding signals and ATAC-seq signal.
[0027] FIGS.11A-11F illustrate Cas13d-mediated mRNA knockdown of human and mouse transcripts for mediating SARS-CoV-2 cell entry. FIG.11A shows graphs representing mRNA knockdown of human TMPRSS2 mRNA with four different pre-gRNAs, with preg2 showing the most effective knockdown. FIG.11B shows graphs representing mRNA knockdown of murine Tmprss2 with four different pre-gRNAs, with preg4 showing the most effective knockdown. FIG.11C shows graphs representing mRNA knockdown of human mRNA with four different pre-gRNAs, with preg4 showing the most effective knockdown CTSL. FIG.11D shows graphs representing mRNA knockdown of murine Ctsl mRNA with four different pre-gRNAs, with preg3 showing the most effective knockdown. FIG.11E shows graphs representing mRNA knockdown of human FURIN mRNA with four different pre-gRNAs, with preg3 showing the most effective knockdown. FIG.11F shows graphs representing mRNA knockdown of murine Furin mRNA with four different pre-gRNAs, with preg4 showing the most effective knockdown. Transcript levels, for both figures, are relative to NT guide control. DETAILED DESCRIPTION OF THE INVENTION
[0028] For the purposes of promoting an understanding of the principles of the present disclosure, reference will now be made to preferred embodiments and specific language will be used to describe the same. It will nevertheless be understood that no limitation of the scope of the disclosure is thereby intended, such alteration and further modifications of the disclosure as illustrated herein, being contemplated as would normally occur to one skilled in the art to which the disclosure relates. Definitions
[0029] Articles“a” and“an” are used herein to refer to one or to more than one (i.e. at least one) of the grammatical object of the article. By way of example,“an element” means at least one element and can include more than one element. [0030] “About” is used to provide flexibility to a numerical range endpoint by providing that a given value may be“slightly above” or“slightly below” the endpoint without affecting the desired result.
[0031] The use herein of the terms "including," "comprising," or "having," and variations thereof, is meant to encompass the elements listed thereafter and equivalents thereof as well as additional elements. As used herein,“and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations where interpreted in the alternative (“or”).
[0032] As used herein, the transitional phrase "consisting essentially of" (and grammatical variants) is to be interpreted as encompassing the recited materials or steps "and those that do not materially affect the basic and novel characteristic(s)" of the claimed invention. Thus, the term "consisting essentially of" as used herein should not be interpreted as equivalent to "comprising."
[0033] Moreover, the present disclosure also contemplates that in some embodiments, any feature or combination of features set forth herein can be excluded or omitted. To illustrate, if the specification states that a complex comprises components A, B and C, it is specifically intended that any of A, B or C, or a combination thereof, can be omitted and disclaimed singularly or in any combination.
[0034] Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise-Indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure.
[0035] As used herein, "treatment,”“therapy” and/or“therapy regimen” refer to the clinical intervention made in response to a disease, disorder or physiological condition manifested by a patient or to which a patient may be susceptible. The aim of treatment includes the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and/or the remission of the disease, disorder or condition.
[0036] The term "effective amount" or“therapeutically effective amount” refers to an amount sufficient to effect beneficial or desirable biological and/or clinical results. [0037] As used herein, the term "subject" and "patient" are used interchangeably herein and refer to both human and nonhuman animals. The term "nonhuman animals" of the disclosure includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dog, cat, horse, cow, chickens, amphibians, reptiles, and the like.
[0038] Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Nanoparticles
[0039] The present invention advantageously provides nanoparticles that allow for the targeted delivery of a CRISPR/Cas13 system for gene therapy, which overcomes shortcomings of prior gene therapy methods such as unwanted DNA changes and difficulties in delivery associated with the use of CRISPR/Cas9 DNA systems, off target effects of interfering RNAs, and clinical shortcomings (e.g., mutagenesis, carcinogenesis) associated with the delivery of gene therapy tools using AAV vectors.
[0040] There are multiple subtypes within the Cas13 family, including at least Cas13a, Cas13b, Cas13c, and Cas13d. Of the subtypes, only Cas13d is small enough for in vivo delivery via an AAV vector. The NPs of the invention, however, are not limited in the same manner, and accordingly the present invention may advantageously be used with any subtype of Cas13, i.e. at least any of Cas13a, Cas13b, Cas13c, and Cas13d. Thus, unless otherwise apparent from the context, any reference to Cas13d within the disclosure is equally applicable to any other Cas13 subtype. It is to be understood then that, unless otherwise apparent from the context, the present disclosure and all inventive aspects disclosed herein are intended to, and do, encompass embodiments in which references to Cas13d are replaced with another Cas13 subtype as though so specifically stated.
[0041] Accordingly, in a first aspect, the present invention provides a nanoparticle (NP) comprising a nanoparticle carrier, a first nucleic acid sequence encoding a Cas13d, and one or more additional nucleic acid sequences encoding direct repeat (DR) RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences.
[0042] As used herein,“a nanoparticle carrier” is any composition comprising one or more materials that can be formulated into nanoparticles that are capable of encapsulating or otherwise retaining (e.g. by adsorption or otherwise) the first and the one or more additional nucleic acid sequences. The NP carrier may be formulated out of any suitable material, including, but not limited to a polymer-lipid, a lipid (to form a lipid nanoparticle (LNP)), or gold. In certain embodiments, the NP carrier is a lipid. [0043] The NPs may comprise a cationic cell penetrating peptide (cpp), examples of which include the transactivator of transcription peptide (TAT) and nuclear localization sequences (NLS). In vivo delivery of plasmid DNA, for example, can be hindered by systemic instability due to excessive size and negative charge. Accordingly, these cpps are used to stably condense plasmids or nucleic acids and deliver them into the nucleus.
[0044] The NPs of the invention may further comprise a nucleic acid aptamer (Apt) immobilized on the surface of the NP. The aptamer serves to achieve cell-specific targeting, including, but not limited to, targeting cancer cells, by recognizing certain cell membrane markers on the desired cells. For example, a prostate-specific membrane antigen (PSMA) aptamer may be utilized to recognize and target PSMA positive castration resistant prostate cancer (CRPC) cells. Similarly, the NPs may be prepared with an Apt to recognize and target neuroendocrine prostate cancer (NEPC) cells. Suitable aptamers for NEPC cell recognition include, but are not limited to, an NCAM1 aptamer, a CHGA aptamer, a SYP aptamer, a SNAP25 aptamer, or a CEACAM5 aptamer.
[0045] In this manner, the NPs of the invention have bi-specific targeting capabilities, i.e. they both target cells of interest by way of an Apt immobilized on the NP surface, and target particular transcription factors or other genes whose knock-down or downregulation is desired by way of the CRISPR/Cas13d system, i.e. the gRNA or pre-gRNA sequences.
[0046] The first nucleic acid sequence encoding a Cas13d may be a plasmid, or it may be an mRNA sequence. Similarly, the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more gRNA or pre-gRNA sequences may be a plasmid, or may be an mRNA sequence. In certain embodiments, both the first nucleic acid sequence and the one or more additional nucleic acid sequences are a plasmid. In this embodiment, the first nucleic acid sequence and the one or more additional nucleic acid sequences may comprise separate plasmids, or they may comprise the same plasmid. In another embodiment, both the first nucleic acid sequence and the one or more additional nucleic acid sequences are an mRNA sequence. In yet a further embodiment, the first nucleic acid sequence is in the form of a plasmid and the one or more additional nucleic acid sequences are an mRNA sequence. In still yet a further embodiment, the first nucleic acid sequence is an mRNA sequence and the one or more additional nucleic acid sequences are a plasmid. Based on studies with Cas9, there may be certain advantages (faster gene editing kinetics and fewer off-target effects) to the co-delivery of the first nucleic acid sequence and the one or more additional nucleic acid sequences by mRNA rather than plasmids. [0047] In certain embodiments, the NPs comprise a core encapsulating a plasmid encoding a Cas 13d and the one or more additional plasmids encoding DR RNA sequences and gRNA or pre-gRNA for the desired target, and a shell surrounding the core. Alternatively the core may encapsulate a plasmid that encodes both the first nucleic acid sequence and the one or more additional nucleic acid sequences. A cpp may be used to encapsulate the plasmids within the core. The cpp to nucleic acid weight ratio may be readily adjusted by one of skill in the art to a suitable level to keep the plasmids from leaching out of the encapsulated core. The core may comprise poly lactic-co-glycolic acid (PLGA), and the shell may comprise a polyethylene glycol (PEG). In certain embodiments, the PEG is carboxy-modified PEG, e.g. lipid-PEG-COOH. The lipid-PEG-COOH may be, for example, m-PEG-DSPE. PLGA and PEG have certain benefits for use with the invention in that they are FDA approved for therapeutic use.
[0048] The first nucleic acid sequence encoding a Cas13d may encode CasRx, a
CRISPR/Cas13d from Ruminococus flavefaciens strain XPD3002 optimized for human use and which has been used for programmable RNA knock down in human cells.
[0049] The one or more additional nucleic acid sequences encoding DR RNA sequences and gRNA or pre-gRNA for the desired target may comprise any suitable gRNA or pre-gRNA for that target, including traditionally“undruggable” oncogenic transcription factors. Specific sequences for use with the invention can be derived by one of skill in the art, and may include certain modifications to improve functionality, e.g. modifications to avoid degradation in vivo. Target regions having low secondary structure are ideal targets for gRNA or pre-gRNA. In certain embodiments of the invention, the gRNA or pre-gRNA targets prostate cancer associated transcription factors. In this embodiment, exemplary transcription factors include, but are not limited to, AR, AR-V7, HoxB13, FoxA1, FoxA2, and GATA2. The gRNA or pre-gRNA sequences of this embodiment may, for example, comprise any one of SEQ ID NOs: 1-4, 55-58, and 62 (HOXB13).
[0050] Recent studies have found that SARS-CoV-2 uses the host receptor ACE2 for cell entry and the serine protease TMPRSS2 and/or the cysteine protease Cathepsin L (CTSL) for S protein priming. Hoffmann et al. Cell 181: 271-280 (2020); Zhou et al. Nature 579: 270-273 (2020). Additionally, recent studies found that lung cell entry of SARS-CoV-2 but not SARS- CoV is pre-activated by the proprotein convertase FURIN. Shang et al. PNAS 117: 11727- 11734 (2020); Hoffmann et al. Mol. Cell 78: 779-784 (2020)). Accordingly, in certain embodiments of the invention, the gRNA or pre-gRNA targets COVID-19 associated proteins including, but not limited to, TMPRSS2, Cathepsin L (CTSL), and Furin. The gRNA or pre- gRNA (preg) sequences of this embodiment may, for example, comprise the various pre-guide 1, pre-guide 2, pre-guide 3, and pre-guide 4 sequences as disclosed herein, infra, or any one of SEQ ID NOs: 5-8, 13-16, 63, and 65 (TMPRSS2), SEQ ID NOs: 9-12, 17-20, 64, and 66 (CTSL), and SEQ ID NOs: 21-24, 25-28, 68, and 69 (Furin).
[0051] The NPs of the invention may have a size of 10 nm to 900 nm, or any individual value or range of values within, inclusive of the upper and lower values, whether specifically recited or not. The NPs may, for example, have a size of 50-500 nm, of 100-200 nm, or 150-200 nm. The average size may be, for example, about 100 nm, about 125 nm, about 150 nm, about 175 nm, or about 200 nm.
[0052] The NPs of the invention may have a zeta potential of about 2.25 mV.
[0053] In embodiments where the first nucleic acid sequence and the one or more additional nucleic acid sequences are mRNA, the weight ratio of the first nucleic acid sequence to the additional nucleic acid sequences within the NPs may be between 1:1 and 1:2, inclusive, including about 1:1.5.
[0054] The NPs of the invention may have a cpp to plasmid or RNA weight ratio of about 0.1 to about 20, or any individual value or range of values within, inclusive of the upper and lower values, whether specifically recited or not. The NPs may, for example, have a cpp to plasmid or RNA weight ratio of about 1 to about 18, of about 3 to about 16, or of about 5 to about 15.6.
[0055] The NPs of the invention may be prepared by any suitable mechanism which can be readily ascertained by one of skill in the art. For example, the NPs may be prepared by self- assembled nano-precipitation. Apt may be immobilized on the NP surface by way of, e.g., carbodiimide coupling chemistry between the–COOH group of carboxy modified PEG and the amino group at the end of the PSMA Apt. Additionally, one of skill in the art can optimize the nano-precipitation time and weight ratio of cpp to plasmid/nucleic acid to help minimize any batch-to-batch variability.
[0056] In certain embodiments of the invention, the NPs may be formulated with selective organ targeting (SORT) technology, as disclosed in Cheng et al. Nat. Nanotechnol.15: 313-320 (2020), the contents of which are incorporated herein by reference. Briefly, SORT enables the selective delivery of NPs comprising CRISPR/Cas9 to lungs, spleens and livers. While lipid NPs (LNPs) typically comprise ionizable cationic lipids, amphipathic phospholipids, cholesterol and PEG lipids, the addition of charge-modifying agents results in targeted delivery of the LNPs to particular organs. Formulating the NPs of the invention with SORT technology allows targeted therapeutic delivery to specific organs in need thereof, with minimal off-target effects. For example, NPs of the invention for the treatment of COVID-19 may be delivered to the lungs, whereas NPs of the invention for the treatment of prostate cancer patients having metastases to the lungs and/or liver may be delivered to the lungs and/or liver.
[0057] As used herein,“formulated with SORT technology” means the NP carrier is a LNP that comprises a charge-modifying agent in accordance with Cheng et al. The particular LNP formulation for use with the invention may be as disclosed in Cheng et al., or it may be a modification thereof within the purview of one of skill in the art. In certain embodiments of the invention, the NP carrier is formulated with SORT technology to be lung-selective, i.e. for the NPs to be delivered to the lungs. In this embodiment, the NP carrier may comprise 1,2-dioleoyl- 3-trimethylammonium-propane (DOTAP), dimethyldioctadecylammonium (DDAB), or 1,2- dimyristoyl-sn-glycero-3-ethylphosphocholine (EPC). In a further embodiment, the NP carrier may be formulated with SORT technology to be liver-selective. In this embodiment, the NP carrier may comprise 1,2-dioleoyl-3-dimethylammonium-propane (DODAP) or 5A2-SC8. In another embodiment, the NP carrier may be formulated with SORT technology to be spleen- selective. In this embodiment, the NP carrier may comprise 1,2-dioleoyl-sn-glycero-3- phosphate (18PA), 1,2-dimyristoyl-snglycero-3-phosphate (14PA), or sn-(3-oleoyl-2-hydroxy)- glycerol-1-phospho-sn-3'-(1',2'-dioleoyl)-glycerol (18BMP).
[0058] In certain embodiments of the invention where the NPs are formulated with SORT technology to be lung-selective, the LNPs may comprise, in a non-limiting example, DLin- MC3-DMA, DSPC, cholesterol, DMG-PEG2000 and DOTAP in a 25/5/19.3/0.5/50 ratio. Pharmaceutical Compositions Comprising and Administration of Nanoparticles
[0059] The NPs of the invention may be administered by any suitable technique, including, but not limited to oral, aerosol, intranasal, injection, systemic, parenteral, subcutaneous, intravenous, intramuscular, intrathecal, intraperitoneal and rectal. In certain embodiments, the NPs are administered by intravenous injection, intratumoral injection, or by oral administration.
[0060] The NPs may be administered at a frequency established based on NP half-life, which can readily be assessed by one of skill in the art.
[0061] The NPs provided herein can be administered to a subject, either alone or in combination with a pharmaceutically acceptable excipient and/or carrier, in an amount sufficient to induce an appropriate biological response (e.g., knock down of the desired target).
[0062] An effective amount of the NPs described herein may be given in one dose, but is not restricted to one dose. Thus, the administration can be two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or more, administrations of the NPs. Where there is more than one administration in the present methods, the administrations can be spaced by time intervals of one minute, two minutes, three, four, five, six, seven, eight, nine, ten, or more minutes, by intervals of about one hour, two hours, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 hours, and so on. In the context of hours, the term "about" means plus or minus any time interval within 30 minutes. The administrations can also be spaced by time intervals of one day, two days, three days, four days, five days, six days, seven days, eight days, nine days, ten days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, and combinations thereof. The present disclosure is not limited to dosing intervals that are spaced equally in time, but encompass doses at non-equal intervals, such as a priming schedule consisting of administration at 1 day, 4 days, 7 days, and 25 days, just to provide a non-limiting example.
[0063] The NPs disclosed herein may be administered with a pharmaceutically or diagnostically acceptable excipient. A "pharmaceutically acceptable excipient" or
"diagnostically acceptable excipient" includes but is not limited to, sterile distilled water, saline, phosphate buffered solutions, amino acid-based buffers, or bicarbonate buffered solutions. An excipient selected and the amount of excipient used will depend upon the mode of administration. Administration may in certain instances comprise an injection, infusion, or a combination thereof.
[0064] An effective amount for a particular subject/patient may vary depending on factors such as the condition being treated, the overall health of the patient, the route and dose of administration and the severity of side effects. Guidance for methods of treatment and diagnosis is available (see, e.g., Maynard, et al. (1996) A Handbook of SOPs for Good
[0065] Clinical Practice, Interpharm Press, Boca Raton, Fla.; Dent (2001) Good Laboratory and Good Clinical Practice, Urch Publ., London, UK).
[0066] A dosing schedule of, for example, once/week, twice/week, three times/week, four times/week, five times/week, six times/week, seven times/week, once every two weeks, once every three weeks, once every four weeks, once every five weeks, and the like, is available for the present disclosure. The dosing schedules encompass dosing for a total period of time of, for example, one week, two weeks, three weeks, four weeks, five weeks, six weeks, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, eleven months, and twelve months.
[0067] Provided are possible cycles of the above dosing schedules. The cycle can be repeated about, e.g., every seven days; every 14 days; every 21 days; every 28 days; every 35 days; 42 days; every 49 days; every 56 days; every 63 days; every 70 days; and the like. An interval of non-dosing can occur between a cycle, where the interval can be about, e.g., seven days; 14 days; 21 days; 28 days; 35 days; 42 days; 49 days; 56 days; 63 days; 70 days; and the like. In this context, the term "about" means plus or minus one day, plus or minus two days, plus or minus three days, plus or minus four days, plus or minus five days, plus or minus six days, or plus or minus seven days.
[0068] The NPs according to the present disclosure may also be administered with one or more additional therapeutic agents (e.g., small molecule therapeutics, anti-cancer agents, etc.). The NPs may be functionalized with the one or more additional therapeutic agents, or the one or more additional therapeutic agents may be co-administered with the NPs. Methods for co- administration with an additional therapeutic agent are well known in the art (Hardman, et al. (eds.) (2001) Goodman and Gilman's The Pharmacological Basis of Therapeutics, 10th ed., McGrawHill, New York, N.Y.; Poole and Peterson (eds.) (2001) Pharmacotherapeutics for Advanced Practice:A Practical Approach, Lippincott, Williams & Wilkins, Phila., Pa.; Chabner and Longo (eds.) (2001) Cancer Chemotherapy and Biotherapy, Lippincott, Williams & Wilkins, Phila., Pa.).
[0069] Co-administration need not refer to administration at the same time in an individual, but rather may include administrations that are spaced by hours or even days, weeks, or longer, as long as the administration of multiple therapeutic agents is the result of a single treatment plan. The co-administration may comprise administering the NPs according to the present disclosure before, after, or at the same time as the one or more additional therapeutic agents. In one exemplary treatment schedule, the NPs of the present disclosure may be given as an initial dose in a multi-day protocol, with one or more additional therapeutic agent given on later administration days; or the one or more additional therapeutic agents given as an initial dose in a multi-day protocol, with the NPs of the present disclosure given on later administration days. On another hand, one or more additional therapeutic agents and the NPs of the present disclosure may be administered on alternate days in a multi-day protocol. In still another example, a mixture of one or more additional therapeutic agents and the NPs of the present disclosure may be concurrently. This is not meant to be a limiting list of possible administration protocols.
[0070] An effective amount of a therapeutic agent is one that will knock down the target by at least 10%, more normally by at least 20%, most normally by at least 30%, typically by at least 40%, more typically by at least 50%, most typically by at least 60%, often by at least 70%, more often by at least 80%, and most often by at least 90%, conventionally by at least 95%, more conventionally by at least 99%, and most conventionally by at least 99.9% as compared to no treatment. [0071] Specific dosing regimens are within the purview of one of ordinary skill in the art. Formulations of therapeutic agents may be prepared for storage by mixing with physiologically acceptable carriers, excipients, or stabilizers in the form of, e.g., lyophilized powders, slurries, aqueous solutions or suspensions (see, e.g., Hardman, et al. (2001) Goodman and Gilman's The Pharmacological Basis of Therapeutics, McGrawHill, New York, N.Y.; Gennaro (2000) Remington: The Science and Practice of Pharmacy, Lippincott, Williams, and Wilkins, New York, N.Y.; Avis, et al. (eds.) (1993) Pharmaceutical Dosage Forms: Parenteral Medications, Marcel Dekker, NY; Lieberman, et al. (eds.) (1990) Pharmaceutical Dosage Forms: Tablets, Marcel Dekker, NY; Lieberman, et al. ( eds.) (1990) Pha1maceutical Dosage Farms: Disperse Systems, Marcel Dekker, NY; Weiner and Kotkoskie (2000) Excipient Toxicity and Safety, Marcel Dekker, Inc., New York, N.Y.). Methods of Using Nanoparticles
[0072] The NPs of the invention may be used therapeutically for the treatment of a wide range of diseases and disorders. Of particular interest are those diseases or disorders that are considered“undruggable,” i.e. those that have not responded or have not responded well to traditional small molecule therapeutics. The diseases or disorders that may be treated with the NPs of the invention include, but are not limited to, cancer. Exemplary cancers include prostate cancer, such as androgen dependent prostate cancer (ADPC), castration resistant prostate cancer (CRPC), and neuroendocrine prostate cancer (NEPC), the most aggressive form of prostate cancer.
[0073] Accordingly, the present invention provides a method of treating a subject with prostate cancer comprising administering to the subject a therapeutically effective amount of the NPs of the invention. The prostate cancer may be ADPC, CRPC, NEPC, or AR-7 variant prostate cancer. Further, the present invention provides a method of treating a subject with prostate cancer that has metastasized to the lungs and/or the liver comprising administering to the subject a therapeutically effective amount an NP of the invention that has been formulated with SORT technology to target the lungs and/or the liver. In yet another embodiment, the invention provides a method of treating a subject with COVID-19 comprising administering to the subject a therapeutically effective amount of an NP of the invention that has been formulated with SORT technology to target the lungs. EXAMPLES
EXAMPLE 1
Evaluation of CRISPR/Cas13d RNA targeting system.
[0074] One functional aspect of a bi-targeting Cas13d delivery system is the ability to successfully knock down mRNA levels for gene products implicated in a disease state of interest. In the present example, quantitative reverse transcriptase PCR was utilized to quantify the ability of CasRx (SEQ ID NO: 76), a Cas13d isolated from Ruminococcus flavefaciens by Konermann et al., to knock down mRNA transcript levels. The effect of CasRx mRNA targeting on end protein levels were assessed via western blots.
[0075] Separately, HEK 293FT and human prostatic carcinoma 22RV1 cells were transfected (Lipofectamine) with the CasRx plasmid (SEQ ID NO: 78) and with non-targeting gRNA/pre-gRNA (Konermann et al. Cell, 173: 665-676 (2018)) or with targeting gRNA (using CasRx gRNA cloning backbone (SEQ ID NO: 76)) or pre-gRNA (using CasRx pre-gRNA cloning backbone (SEQ ID NO: 77)) of interest and cultured for 48 hours, then total RNA was isolated with the RNeasy Mini kit (Qiagen, 74104). qRT-PCR was conducted using the MultiScribe Reverse Transcriptase and Power SYBR Green PCR Master Mix reagents (Applied Biosystems) or Taqman Fast Advanced Master Mix (Applied Biosystem), according to the manufacturer’s instructions. Each assay was repeated three to four times, and transcript levels were quantified. Primer sequences were as follows: HOXB13 forward PCR primer, 5'- ACAGAACCCACCAGGTCCCTTT -3' (SEQ ID NO: 29); HOXB13 reverse PCR primer, 5'- TACGGAATGCGTTTCTTGCGGC -3' (SEQ ID NO: 30); Human b-actin forward PCR primer, 5'- AGGCACCAGGGCGTGAT -3' (SEQ ID NO: 45); Human b-actin reverse PCR primer, 5'- GCCCACATAG GAATCCTTCTGAC -3' (SEQ ID NO: 46); NF2 forward PCR primer 5'- TTGCGAGATGAAGTGGAAAGG -3' (SEQ ID NO: 47); NF2 reverse PCR primer, 5'- CAAGAAGTGAAAGGTGACTGGTT-3' (SEQ ID NO: 48); NFKB1 forward PCR primer, 5'- AACAGAGAGGATTTCGTTTCCG-3' (SEQ ID NO: 49); NFKB1 reverse PCR primer, 5'- TTTGACCTGAGGGTAAGACTTCT-3' (SEQ ID NO: 50); PPARG1 forward PCR primer, 5'- GGGATCAGCTCCGTGGATCT-3' (SEQ ID NO: 51); PPARG1 reverse PCR primer, 5'- TGCACTTTGGTACTCTTGAAGTT-3' (SEQ ID NO: 52); NRAS forward PCR primer, 5'- ATGACTGAGTACAAACTGGTGGT-3' (SEQ ID NO: 53); NRAS reverse PCR primer, 5'- CATGTATTGGTCTCTCATGGCAC-3 (SEQ ID NO: 54). The probes ID were used as follows: GAPDH: Hs02758991-g1.
[0076] Guide RNAs comprise the spacer (or recognition, or targeting) sequence of a specific sequence identifier number (SEQ ID NO) and a single direct repeat sequence at the 5’ end of the spacer sequence (SEQ ID NO: 60). Pre-guide RNAs comprise the 30 nucleotide spacer sequence of a specific sequence identifier number (SEQ ID NO) and 36 nucleotide direct repeats flanking each end of the spacer sequence of SEQ ID NO: 61).
[0077] FIG.1A shows a graph illustrating mRNA knockdown through CasRx targeting of four endogenous transcripts, NF2, NFKB1, PPARG, and NRAS. Each transcript is targeted with two guide RNAs and a non-targeting (NT) guide in 293FT cells. Transcript levels are relative to NT guide control. All transcripts were significantly knocked down, with an average knockdown of approximately 60%. FIG.1B shows a graph illustrating CasRx-mediated mRNA knockdown of NF2 and HRAS in 22RV1 cells, with abundance relative to NT guide control. Again, significant knockdown of mRNA was achieved in this human prostatic carcinoma cell line.
[0078] With control experiments completed, the mRNA transcripts for the transcription factor HoxB13 were targeted. Certain variants of HoxB13 are associated with a significantly increased risk of prostate cancer, and HoxB13 has thus far proved undruggable. FIG.2A shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 using four guide RNAs (or gRNA), with guide 1 having the spacer sequence of (SEQ ID NO: 55), guide 2 having the spacer sequence of (SEQ ID NO: 56), guide 3 having the spacer sequence of (SEQ ID NO: 57), and guide 4 having the spacer sequence of (SEQ ID NO: 58), and four pre-guide RNAs (or pre-gRNA), with pre-guide 1 having the spacer sequence of (SEQ ID NO: 1), pre-guide 2 having the spacer sequence of (SEQ ID NO: 2), pre-guide 3 having the spacer sequence of (SEQ ID NO: 3), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 4), all in 293FT cells. Transcript levels are relative to NT guide control. Significant knockdown was achieved with both guide and pre-guide RNAs, with pre-guide 2 and pre-guide 4 offering the most significant knockdown, with pre-guide 4 suppressing HOXB13 mRNA by over 90%. FIG.2B shows a graph representing a similar set of experiments of mRNA knockdown through CasRx targeting of HoxB13 in 22RV1 cells. The most effective gRNA (SEQ ID NO: 58) and pre-gRNA (SEQ ID NO: 4) from Fig.2A were used. Significant knockdown of HOXB13 transcripts were observed with both gRNA 4 and pre-gRNA 4.
[0079] To determine the effect of CasRx mRNA targeting on cellular protein levels, western blotting was utilized. Cells were collected and lysed in RIPA buffer (1% NP-40, 0.1% sodium dodecyl sulfate (SDS), 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% sodium deoxycholate, 1mM ethylenediaminetetraacetic acid (EDTA), 1×proteinase inhibitor cocktail (Roche)) for 20 minutes on ice and the proteins were resolved on 8% SDS-polyacrylamide gels and transferred onto Nitrocellulose membrane (Bio-Rad). The membrane was blocked with 5% milk powder (Bio-Rad) then incubated with specific antibodies (PSMA #ab19071 from Abcam, HOXB13 #SC-66923 from Santa Cruz Biotechnology, b-actin # from ab8227 from Abcam) at 4 ^C overnight. Following incubation with secondary antibodies, immunoblots were visualized using the C-DiGit Chemiluminescent western Blot Scanner (Li-Cor). The results correlated well with the mRNA knockdown experiments, with all four gRNAs and all four pre-gRNAs substantially suppressing final protein levels relative to NT guide controls.
[0080] A plasmid was constructed that comprised both CasRx and three pre-gRNAs, starting with the plasmid AddGene #109049 (SEQ ID NO: 78). Pre-gRNA sequences 2, 3, and 4 ((SEQ ID NO: 2 through SEQ ID NO: 4, respectively), separated by direct repeats (SEQ ID NO: 61), were inserted into the MLUI restriction site. FIG.3A shows a schematic diagram of the hU6- pre-gRNA-EF1^-CasRx-2A-EGFP“all-in-one” plasmid. 22RV1 cells were then transfected with the plasmid (Lipofectamine), and mRNA and protein levels were assessed. FIG.3B shows a graph representing mRNA knockdown through CasRx targeting of HoxB13 in 22RV1 cells using arrays of three pre-gRNAs. mRNA knockdown of approximately 80% was observed. Transcript levels are relative to NT guide control. As described previously, western blots were also performed that showed a near elimination of HoxB13 protein product compared to controls. CasRx mRNA delivery
[0081] Plasmid-based gene therapy faces several obstacles to its clinical application, such as the substantial time requirement for gene editing and the potential to generate small insertions at the target site or large insertions at off-target sites. Co-delivery of Cas9 mRNA with gRNAs into cells has been shown to provide faster gene editing kinetics and fewer off-target effects compared with plasmid-based delivery. 22RV1 Cells were transfected (Lipofectamine) with CasRx mRNA and HoxB13 pre-gRNA-4 oligonucleotide at various weight ratios (1:1, 1:1.2, 1:1.5 and 1:2 CasRx mRNA to pre-gRNA oligos). Results show greater than 80% knockdown for all four weight ratios, with a trend of increased knockdown with increased weight ratio (FIG. 4).
[0082] These data demonstrate that the CasRx system, with the pre-gRNAs and gRNAs provided herein, can successfully target and knockdown mRNA transcripts for a transcription factor implicated in prostate cancer that has heretofore proved undruggable by other means, and do so in a relevant, castration-resistant prostate cancer cell line. Protein end products were also confirmed to be significantly suppressed. Cell culture of Human Embryonic Kidney (HEK) cell line 293FT.
[0083] Human embryonic kidney (HEK) cell line 293FT (Thermo Fisher) was maintained in DMEM (4.5 g/L glucose), supplemented with 10% FBS (GE Life Sciences) and 10 mM HEPES at 37°C with 5% CO2. Upon reaching 80–90% confluency, cells were dissociated using TrypLE Express (Life Technologies) and passaged at a ratio of 1:2. This cell line was purchased directly from the manufacturer and was not otherwise authenticated. Cell culture of human prostatic carcinoma cell line 22RV1.
[0084] Human prostatic carcinoma cell line 22Rv1 (ATCC, Cat. # CRL-2505) were purchased from American Type Culture Collection (ATCC) and were authenticated by short tandem repeat (STR) profiling and karyotyping. Cells were grown in a humidified incubator with 5% CO2 at 37°C. Cells were routinely tested for mycoplasma contamination using MycoAlert™ PLUS Mycoplasma Detection Kit (Lonza, Cat. # LT07). Cell lines were cultured in RPMI 1640 medium (Corning, Cat. # 10-040-CV) supplemented with 10% fetal bovine serum (Corning, Cat. # 35010CV), penicillin-streptomycin (Corning, Cat. # 30001Cl), and gentamicin (Gibco, Cat. # 15710064) as recommended by the supplier.0.2% Normocin (Invivogen, Cat. # ANT-NR-1) was added to the medium to prevent contamination by mycoplasma, bacteria, or fungi. Cells were dissociated using TrypLE Express (Life Technologies) and passaged at a subculture ratio of 1:3-1:6. EXAMPLE 2
Preparation and Characterization of Nanoparticles.
[0085] A schematic representation of the strategy for nanoparticle (NP) synthesis and plasmid encapsulation is shown in FIG.5. Briefly, a nucleic acid of interest, in this case two plasmids, one encoding CasRx and another cloned guide RNA and/or pre-guide RNA to the target of interest, were encapsulated into a poly(lactic-co-glycolic acid) (PLGA) core. CasRx mRNA with pre-gRNA oligonucleotides were also encapsulated in a similar manner. A shell was formed over the core by lipid-PEG with Alexa Fluor 647 dye labeling. PEG can optionally be functionalized to help target the NP to a desired tissue. In certain embodiments, the shell was formed by prostate specific membrane antigen-specific (PSMA) aptamer-modified lipid-PEG with Alexa Fluor 647 dye labeling. PSMA is expressed on the surface of certain prostate cancers and most castration resistant prostate cancer cell lines. This cell-specific binding helps a NP dock and deliver its nucleic acid payload to the appropriate cell type. Additional types of nanoparticle delivery systems can be used, such as DNA nanoclew vectors, nanogold and cationic lipid-assisted NPs. [0086] In vivo delivery of plasmid DNA has been severely hindered by systemic instability due to negative charge and excess size (in part due to charge repulsion). To reduce these negative effects, the positively charged TAT peptide was used for plasmid complexation at varying weight ratios of TAT to CasRx and gRNA (0.1:1, 0.5:1, 1:1, 5:1, 10:1, and 20:1). Agarose gel electrophoresis showed that TAT effectively condensed the two plasmids at a weight ratio of 5 or above with no visible evidence of constituent parts of the NP leaking from the NP as compared to NPs without TAT. This indicated that most plasmids were successfully encapsulated. In addition, the organic solvent DMF had no influence on plasmid properties. Previous evidence has shown that polyethylene glycol (PEG)-functionalized NPs are more protected against systemic clearance than similar NPs without PEG. Aspects of our work utilized lipid-PEG (m-PEG-DSPE, or 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N- [methoxy(polyethylene glycol) to form a shell, and successfully synthesized NPs with average sizes around 188 nm for those with TAT (FIG.6A) and 178 nm for those without TAT (FIG. 6B). Zeta potential was nearly neutral (2.25 mv). Nanoparticle delivery of nucleic acid payload.
[0087] CasRx mRNA and HoxB13 pre-gRNA oligonucleotides were incorporated into lipid- NPs (LNPs) as described above. HoxB13 mRNA expression was measured after incubation of CasRx mRNA- HoxB13 pre-gRNA-LNPs with 22Rv1 cells at a weight ratio of 1:1.5
(CasRx:pre-gRNA). Transcript levels were compared to NT guide control. HoxB13 mRNA levels were knocked down substantially, averaging 89% suppression (FIG.7). Cells were separately transfected with control LNPs encapsulating GFP mRNA, which indicated high efficiency delivery of GFP mRNA into control 22RV1 cells as evidenced by the presence of GFP under fluorescence, verified by bright-field contrast. Plasmid encapsulation method.
[0088] Briefly, poly(lactic-co-glycolic acid) (PLGA) and TAT peptide (SEQ ID NO: 59) were dissolved separately in DMF at concentrations of 5 mg ml-1 and 2.5 mg ml-1, respectively. Then, 250 mg PLGA and 250 mg TAT were mixed in a small glass vial. Plasmid (16 mg at 1 mg ml-1 concentration) in aqueous solution was mixed into the PLGA-TAT organic solution (weight ratio of Plasmid: PLGA: TAT was 1:15:15) to form cationic lipid-Plasmid nanocomplexes. This solution was then quickly nano-precipitated into 10 ml aqueous solution (0.2 mg ml-1 concentration in DNase/RNase-free UltraPure water) of lipid-PEG-COOH, then Alexa Fluor 647-amine-functionalized A10-3 will be modified on the surface of NPs via carbodiimide coupling chemistry. Upon nanoprecipitation, NPs formed instantly and were kept for 30 min at 600 r.p.m. stirring at room temperature. The NPs were then washed three times with 1× PBS using Amicon tubes (molecular weight cut-off, 100 kDa) to remove organic solvent and free compounds and finally concentrated into 1 ml PBS solution. The NPs were used fresh or kept at -80^ to use later for various in vitro and in vivo studies. The plasmid NPs Sizes and Zeta potential were measured by Zetasizer (Malvern), the morphology was visualized by transmission electron microscopy (TEM) at Duke Pathology Research Electron Microscopy Service. Plasmid encapsulation evaluation and complexation ability of TAT.
[0089] To assess the plasmid encapsulation and its stability in organic solvent (DMF), naked plasmids were incubated with or without DMF for 30 min or plasmids complexed with TAT (in varying weight ratios from 0.1 to 20) were detected. To assess complexation ability of TAT, plasmids with (plasmid and TAT at the weight ratio of 1:15.6) or without TAT were detected. The volumes of samples were adjusted with loading dye (New England Biolabs) and run into 1% agarose (Invitrogen) gel for 40 min at 100 V. Finally, the gel was imaged under ultraviolet and the bands were analysed. EXAMPLE 3
HoxB13 as an Exemplary Target for Nanoparticles.
[0090] Previous studies have implicated HoxB13 in promoting or inhibiting full-length androgen receptor (AR) function in androgen dependent prostate cancer (ADPC). However, the genomic function of HOXB13 in castration dependent prostate cancer (CRPC) has only recently been defined through our discovery that HoxB13 acts as a pioneer transcription factor for AR- V7 (an AR splicing variant) and governs AR-V7-positive CRPC growth. To examine the clinical relevance of HoxB13, immunohistochemical (IHC) analyses of HoxB13 were performed in normal prostate, ADPC and CRPC patient tissues. CRPC samples had significantly higher staining of HoxB13 than the ADPC or normal prostate samples (FIG.8), suggesting that HoxB13 expression increases during prostate cancer progression to the lethal phase. FIG.9 shows a box plot of H-scores for normal (n=141), ADPC (n=74), and CRPC (n=19) cell samples that were examined immunohistochemically. A highly statistically significant increase in HoxB13 expression was observed from normal to ADPC and from ADPC to CRPC, as well as normal to CRPC samples.
[0091] Assays for Transposase Accessible Chromatin by sequencing (ATAC-seq) were performed in two CRPC patient tissues and correlated chromatin accessibility with HoxB13 genomic binding in the same tissue from the same patients. Strong HoxB13 binding was observed, correlated with high chromatin accessibility. For example, UCSC Genome Browser views of representative HOXB13 binding sites and ATAC-seq peaks show strong correlation (FIG.10A and FIG.10B), suggesting that HoxB13 may function as a general pioneer factor in opening chromatin. Together with FIG.8 and FIG.9, HoxB13 appears to function as a general, oncogenic pioneer transcription factor to drive CRPC growth and is thus an attractive target for NP as described herein.
[0092] CasRx and associated pre-gRNAs and gRNAs have been shown to effectively reduce the abundance of HoxB13 mRNA and protein. Nanoparticles of the disclosure comprising nucleic acids (plasmids and mRNAs shown herein) have been shown to deliver their nucleic acid payload to cells in their vicinity. However, it is desirable to not only target a specific transcript, but to also target a specific cell type that comprises the specific target transcript(s). That is, dual targeting functionality.
[0093] As briefly mentioned in Example 2, prostate cancer cell types, like 22RV1 and LNCaP95, have not only been shown to transcribe a specific, disease-associated mRNA (HoxB13 in this case), but they have also been shown to express one or more specific moieties on their cell surfaces that are not ubiquitously found in the body. In the case of 22RV1 and LNCaP95, an example is PSMA. PSMA is common to most CRPC cell lines. Thus, targeting a cell surface antigen on the cell type of interest, increases the probability that a nucleic acid payload in a NP will be delivered where it can confer a benefit. Other disease states share similar opportunities for specific targeting, and NP formulations can also be tuned to facilitate tissue-specific targeting.
[0094] To confirm endogenous co-expression of PSMA and HoxB13 in prostate cancer- specific cells, western blotting was again utilized.22RV1 and LNCaP95 cells were collected and lysed in RIPA buffer (1% NP-40, 0.1% sodium dodecyl sulfate (SDS), 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% sodium deoxycholate, 1mM ethylenediaminetetraacetic acid (EDTA), 1×proteinase inhibitor cocktail (Roche)) for 20 minutes on ice and the proteins were resolved on 8% SDS-polyacrylamide gels and transferred onto Nitrocellulose membrane (Bio-Rad). The membrane was blocked with 5% milk powder (Bio-Rad) then incubated with specific antibodies (PSMA #ab19071 from Abcam, HOXB13 #SC-66923 from Santa Cruz Biotechnology, b-actin #ab8227 from from Abcam) at 4 ºC overnight. Following incubation with secondary antibodies, immunoblots were visualized using the C-DiGit Chemiluminescent western Blot Scanner (Li- Cor). The results show that HOXB13 was expressed approximately as abundantly as the b-actin control and PSMA expressed more strongly that b-actin in 22RV1 cells. LNCaP95 cells expressed HoxB13 modestly more than the b-actin control and PSMA approximately 50% as much as the control. Immunohistochemistry (IHC) analysis.
[0095] Tumor microarrays containing normal prostate (141 samples), androgen dependent prostate cancer (74 samples), or castration-resistant prostate cancer (19 samples) were constructed. Immunohistochemical staining of these samples was performed with a HoxB13 antibody (ab53931, Abcam). Briefly, following deparaffinization, antigen retrieval was performed for 40 min using Reveal Decloaker solution (Biocare Medical), followed by 20 minutes cooling. This was followed by application of Protein Block (Biocare Medical) for 15 minutes and Endogenous Peroxidase Quench (Biocare Medical) for 6 minutes. Primary antibody was applied for 60 min at a dilution of 1:250, while secondary antibody detection was performed as part of the MACH 4TM detection system (Biocare Medical). Counterstaining was performed with hematoxylin. Slides were digitally scanned at 20X magnification using a whole slide scanner (Leica). H-scores ranged from 0 to 300 and were calculated as the product of the Intensity Score for the epithelial region of maximum HOXB13 staining intensity in each sample (assigned on a scale from 0 to 3) multiplied by the percentage of epithelial cells in that sample showing maximum staining intensity (0-100%). ATAC-seq Library Preparation and Data Analysis.
[0096] All of the steps were carried out at 4 °C. A frozen tissue fragment ~20 mg was placed into a pre-chilled 2-ml Dounce homogenizer containing 2 ml of cold 1×homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 167 mM b-mercaptoethanol, in water). Tissue was homogenized with approximately ten strokes with the loose‘A’ pestle, followed by 20 strokes with the tight‘B’ pestle. Connective tissue and residual debris were precleared by filtration through an 80-mm nylon mesh filter followed by centrifugation for 1 min at 100 r.c.f. While avoiding the pelleted debris, 400 ml was transferred to a pre-chilled 2-ml round bottom Lo-Bind Eppendorf tube. An equal volume (400 ml) of a 50% iodixanol solution (50% iodixanol in 1× homogenization buffer) was added and mixed by pipetting to make a final concentration of 25% iodixanol.600 ml of a 29% iodixanol solution (29% iodixanol in 1× homogenization buffer containing 480 mM sucrose) was layered underneath the 25% iodixanol mixture. A clearly defined interface should be visible. In a similar fashion, 600 ml of a 35% iodixanol solution (35% iodixanol in 1× homogenization containing 480 mM sucrose) was layered underneath the 29% iodixanol solution. Again, a clearly defined interface should be visible between all three layers. In a swinging-bucket centrifuge, nuclei were centrifuged for 20 min at 3,000 r.c.f. After centrifugation, the nuclei were present at the interface of the 29% and 35% iodixanol solutions. This band with the nuclei was collected in a 300 ml volume and transferred to a pre-chilled tube. Nuclei were counted after addition of trypan blue, which stains all nuclei due to membrane permeabilization from freezing.50,000 counted nuclei were then transferred to a tube containing 1 ml of ATAC-seq RSB with 0.1% Tween-20. Nuclei were pelleted by centrifugation at 500 r.c.f. for 10 min in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed using the two pipetting steps described above. Because the nuclei were already permeabilized, no lysis step was performed, and the transposition mix (25 ml 2× TD buffer, 2.5 ml transposase (100 nM final), 16.5 ml PBS, 0.5 ml 1% digitonin, 0.5 ml 10% Tween-20, 5 ml water) was added directly to the nuclear pellet and mixed by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns.
[0097] Paired‐end sequencing was performed using an Illumina HiSeq 4000 instrument. Nextera-based sequencing primers and reagents were used. Paired-end 50-cycle reads generally provide accurate alignments with reasonable costs. For inferring differences in open chromatin within human samples >50M mapped reads are generally used. Sequence reads were obtained and mapped to the human (hg19) genomes using Bowtie2 with standard parameters and a maximum fragment length of 2,000. Picard was then used to remove duplicate reads. ChIP-exo and Data Analysis.
[0098] CRPC samples were trimmed and chopped into small pieces on ice and fixed immediately with 1% formaldehyde for 20 min at room temperature. Chromatin was sonicated and incubated overnight with 4 µg antibodies against HOXB13 (H-80, Santa Cruz
Biotechnology). T4 DNA polymerase, T4 PNK and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with 1mM dithiothreitol. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25% sodium deoxycholate, 1% NP-40, 0.5 M LiCl) followed by Tris pH 8.0 twice during each step. The library was amplified with only 10-12 cycles and prepared without gel- based size selection. Paired-end sequencing (50 bp) was performed using Illumina HiSeq2500 at the OSUCCC sequencing core. Raw reads were aligned to the human reference genome (hg19) using Bowtie with default parameter settings. The binding locations for AR-V7, AR-FL and HoxB13 were identified by BELT and Genomics Suite (v6.6, Partek) from ChIP-exo Reads 2. ChIP-exo borders were called by the MALD model from ChIP-exo Reads 1, and DNA motifs were precisely defined by the BPMotif approach. Briefly, the enriched DNA motifs were defined by a multi-phase cross-validation procedure. Genomics Suite (v6.6) and MEME Suite v4.9 were used to find the candidate motifs. Initial motif candidates were generated using default program settings (one instance per sequence, less than 40 bp of border extension). Motifs were then clustered with the Pearson correlation coefficient. Exo signal was measured to define border patterns and classify motifs. A set of overrepresented motifs was then used to correct border extension according to the enriched motif position. Motif discovery was repeated twice. Motifs with E <1e-10 or that were found in 10% of sequences were retained as reliable predictions for the next round of analysis. Finally, motifs satisfying the following extensible criteria were identified: 1) Motif similarity compared to ARE or Homeobox motifs in the transcription factor binding databases or between core motifs defined in HoxB13 ChIP-exo data; 2) At least one common protected border exists upstream and downstream of the strand-specific motif; and 3) Same distance from borders to the most conserved nucleotides in variable motifs. For those core motifs that did not meet criteria (1), motif comparison and clustering based on criteria 2) and 3) using the exo-defined matrix were also performed. Immunostaining assays.
[0099] To visualize PSMA in 22RV1 cells, immunostaining assays were performed. In these assays, 22RV1 cells were fixed using 4% paraformaldehyde for 20 minutes at room temperature, then washed twice in PBS. After blocking for 45 min at room temperature in PBS containing 6% BSA and 0.25% Triton X-100, cells were then stained with the PSMA antibody (PSMA #ab19071 from Abcam) for 1 hour at ambient temperature. After extensive washing, cells were then incubated with Goat anti-Mouse Alexa Fluor 488 Secondary Antibody
(Invitrogen) for 1 hour at ambient temperature. Nuclei were stained with Hoechst. Stained samples were visualized under a laser confocal microscope (Leica SP8). PSMA could be visualized lighting up the perimeter of visualized cells, confirming its presence on the cell surface. EXAMPLE 4
Targeting TMPRSS2, CTSL and FURIN for SARS-CoV-2.
[00100] Recent studies have found that SARS-CoV-2 uses the host receptor ACE2 for cell entry and the serine protease TMPRSS2 and/or the cysteine protease Cathepsin L (CatL/CTSL) for S protein priming. The loss of ACE2 leads to acute lung injury. However, RNA editing NP system of the disclosure can be used to target the TMPRSS2 and CatL/CTSL genes in lung with minimized off-target effects. In addition, lung cell entry of SARS-CoV-2, but not SARS-CoV, is pre-activated by the proprotein convertase, furin. Effective pre-gRNAs for guiding CasRx to target furin have been determined and used to target human FURIN and murine Furin mRNA.
[00101] It is notable that while TMPRSS2 knockout mice exhibit no detectable histological or functional abnormalities in organs such as the lungs, liver, or prostate, suggesting that the role of TMPRSS2 in normal physiology may be dispensable (Kim et al. Mol. Cell. Biol. 26: 965-75 (2006)), TMPRSS2 does affirmatively contribute to SARS-CoV spread and immunopathology in the airway of mouse models. (Iwata-Yoshikawa et al. J. Virol. 93 (2019), doi:10.1128/JVI.01815-18).
[00102] As with HoxB13, mRNA transcripts for TMPRSS2 and CatL were targeted with the RNA editing system of the description. FIG.11A shows a graph representing mRNA knockdown of human TMPRSS2 through CasRx targeting using four pre-guide RNAs (or pre- gRNA), with pre-guide 1 having the spacer sequence of (SEQ ID NO: 5), pre-guide 2 having the spacer sequence of (SEQ ID NO: 6), pre-guide 3 having the spacer sequence of (SEQ ID NO: 7), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 8), all in 293FT cells. Knockdown range varied from about 30% for pre-gRNA 1 to about 80%, with pre-gRNA 2 being the most effective. FIG.11B shows a graph representing mRNA knockdown of murine Tmprss2 through CasRx targeting using four pre-guide RNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 13), pre-guide 2 having the spacer sequence of (SEQ ID NO: 14), pre-guide 3 having the spacer sequence of (SEQ ID NO: 15), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 16), all in 293FT cells. Knockdown range varied from about 25% for pre-gRNA 2 to about 75%, with pre-gRNA 4 being the most effective. FIG.11C shows a graph representing mRNA knockdown of human CTSL through CasRx targeting using four pre- gRNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 9), pre-guide 2 having the spacer sequence of (SEQ ID NO: 10), pre-guide 3 having the spacer sequence of (SEQ ID NO: 11), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 12), all in 293FT cells.
Knockdown range varied from about 10% to about 70%, with pre-gRNA 4 being the most effective. FIG.11D shows a graph representing mRNA knockdown of murine Ctsl through CasRx targeting using four pre-guide RNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 17), pre-guide 2 having the spacer sequence of (SEQ ID NO: 18), pre-guide 3 having the spacer sequence of (SEQ ID NO: 19), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 20), all in 293FT cells. Knockdown range varied from about 30% for pre-gRNA 2 to about 70%, with pre-gRNA 3 being the most effective. FIG.11E shows a graph representing mRNA knockdown of human FURIN through CasRx targeting using four pre- gRNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 21), pre-guide 2 having the spacer sequence of (SEQ ID NO: 22), pre-guide 3 having the spacer sequence of (SEQ ID NO: 23), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 24), all in 293FT cells. Knockdown range varied from about 70% to about 90%, with pre-gRNA 3 being the most effective. FIG.11F shows a graph representing mRNA knockdown of murine Furin through CasRx targeting using four pre-guide RNAs, with pre-guide 1 having the spacer sequence of (SEQ ID NO: 25), pre-guide 2 having the spacer sequence of (SEQ ID NO: 26), pre-guide 3 having the spacer sequence of (SEQ ID NO: 27), and pre-guide 4 having the spacer sequence of (SEQ ID NO: 28), all in 293FT cells. Knockdown range varied from about 50% for pre-gRNA 3 to about 85%, with pre-gRNA 4 being the most effective. All transcript levels are relative to Vector controls. As 293FT is a TMPRSS2-negative cell line, a TMPRSS2-encoding vector was co-transfected with the CasRx and pre-gRNA plasmids. When screening murine gRNAs, 293FT were co-transfected with murine the Tmprss2, Ctsl or Furin encoding vector along with the CasRx and pre-gRNA plasmids.
[00103] 22RV1 cells were incubated with LNPs encapsulating GFP-mRNA (GFP mRNA- NP). Fluorescence microscopy revealed high efficiency delivery of GFP mRNA into the 22RV1 cells as evidenced by the presence of robust GFP under fluorescence and verified by bright-field contrast. Similar experiments were conducted in which the surfaces of empty LNPs were modified with the near-IR fluorescent cyanine dye DiR for tracking the location of LNPs. Incubation of the NPs with 22RV1 cells followed by visualization demonstrated co-location of the NPs with the cell surface.
[00104] NPs comprising the CasRx/gRNA system for specific knockdown of TMPRSS2 and CatL can be specifically targeted to the lungs using a recently developed selective organ targeting (SORT) technology (Lee, J. K. et al. Proc Natl Acad Sci USA 115, E4473-E4482, (2018)). Lung-targeting LNPs have been successfully generated, which LNPs have demonstrated high delivery efficiency in vitro (FIG.7). These NPs comprised DLin-MC3-DMA / DSPC / cholesterol / DMG-PEG2000 / DOTAP at a final molar ratio of 25/5/19.3/0.8/50. Organ-specific nanoparticle formation.
[00105] Unless otherwise stated, all lipids with specified molar ratios were dissolved in ethanol and RNA was dissolved in 10 mM citrate buffer (pH 4.0). The two solutions were rapidly mixed at an aqueous to ethanol ratio of 3/1 by volume (3/1, aq./ethanol, vol./vol.) to satisfy a final weight ratio of 40/1 (total lipids/mRNA), then incubated for 10 min at room temperature. As a representative example, a lung-targeted LNPs (50% DOTAP) was prepared as follows. A solution of lipids in ethanol was prepared consisting of DLin-MC3-DMA, DSPC, cholesterol, DMG-PEG2000 and DOTAP to make the final molar ratio of 25/5/19.3/0.8/50. The systematic names for these reagents are as follows: DLin-MC3-DMA is (6Z,9Z,28Z,31Z)- Heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate; DSPC is 1,2-Distearoyl-sn- glycero-3-phosphocholine; DMG-PEG2000 is 1,2-dimyristoyl-rac-glycero-3- methoxypolyethylene glycol-2000; and, DOTAP is 1,2-dioleoyl-3-trimethylammonium-propane.
[00106] To reach a final ratio of 40/1 (wt/wt) of total lipids/total nucleic acids, 1.16 ml lipid solution was used per mg of RNA. For example, to make a final 5-mg nucleic acid formulation, a mixture of 5.8 ml of lipid and 9.2 ml of ethanol were mixed (total 15 ml), and then a 45 ml nucleic acid solution was prepared consisting of 5 mg of nucleic acid RNA in citrate buffer (10 mM, pH 4.0). Then 45 ml of the nucleic acid solution was rapidly combined with 15 ml of the ethanol/lipid solution to form 50% DOTAP LNPs. For CasRx/sgRNA encapsulation, 1× PBS buffer was used for formulation and the molar ratio of CasRx and sgRNA was fixed at 1:1.5. After LNP formation, the fresh LNP formulations were diluted with 1× PBS to 0.5 ng ml-1 mRNA (with a final ethanol concentration < 5%) for in vitro assays and size detection using dynamic light scattering (Malvern MicroV model; He–Ne laser, wavelength = 632 nm). For in vivo experiments, the formulations can be dialysed (Pur-A-Lyzer Midi Dialysis Kits, WMCO 3.5 kDa) against 1× PBS for 2 hours and diluted with PBS to 15 ml g-1 for i.v. injections. Additional COVID-19 studies
[00107] Additional mRNA knockdown experiments investigating the efficiency and toxicity of organ-selective LNPs carrying CasRx mRNA and pre-gRNA targeting for TMPRSS2 can be conducted. Further experiments targeting CTSL and FURIN (or all three genes combined) in multiple human cell lines, including Calu-3, Caco-2, and prostate cancer cell lines (22RV1, LNCaP, C4-2B) can be conducted.
[00108] The effects of organ-selective LNPs carrying CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, Furin or the three genes combined on normal mouse lung histology and function can be assessed. The extent to which organ-selective LNPs carrying CasRx mRNA and pre- gRNA targeting Tmprss2, Ctsl, Furin, or the three genes combined can block SARS-CoV-2 entry can be evaluated in order to determine utility for antiviral intervention. Additional Methods
[00109] Human cells can be incubated with lung-selective LNPs encapsulating 1mg CasRx mRNA and 1.5 mg pre-gRNA oligo targeting TMPRSS2, CTSL and FURIN or combined 3 genes, respectively, at a weight ratio of 1:1.5 in 6-well plate, for different time points: 6, 12, 24, 48, 72 and 96 hours and subjected for analysis as described below.
[00110] For qRT-PCR, total RNA can be extracted from cells using RNeasy mini kit (Qiagen) and reverse transcribed by transcriptase (Thermo). qRT-PCR primer can be ordered from Integrated DNA Technologies (IDT). mRNA expression levels of TMPRSS2, CTSL and FURIN can be determined by SYBR Green gene expression assays (Thermo). Real-time PCR reactions can be carried out in triplicate by using a qTOWER3 system (Analytik Jena). The expression can be calculated with comparative Ct method and the raw data are normalized with the internal control b-actin.
[00111] For western blots, cell lysates can be resolved on 4–15% SDS-PAGE, transferred to PVDF membranes and probed with corresponding antibodies. Antibodies to TMPRSS2 (#ab92323), FURIN (#ab183495) and b-actin (#ab8227) are from Abcam (Boston, MA); to Cathepsin L (#MAB9521) from Novus Biological (Centennial, CO). The protein expression can be quantified by densitometry and normalized to b-actin.
[00112] For testing the toxicity of treatments disclosed herein, flow cytometric experiments will be performed by first washing cells with 1X PBS, treating with 1X Trypsin EDTA and fixing in 1.6% paraformaldehyde in PBS for 10 minutes. Cells will then be washed with FACS buffer (1X PBS, 0.3% BSA, 1mM EDTA). A BD Accuri C6 plus flow cytometer will used to collect raw data. Raw data can be processed with Cytobank (BD) software. Data can be presented as representative flow cytometry plots of forward versus side scatter (FSC versus SSC).
[00113] To examine the knockdown effects of organ-selective LNPs carrying CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, Furin, or all three combined) on normal mouse lung histology and function, the following method can be performed. C57BL/6 male mice (5~6- week-old) can be purchased from Taconic (Albany, NY). Upon receipt, mice are preferably acclimated for one week before the study. All animal experiments are carried out according to a protocol approved by an Institutional Animal Care and Use Committee. Lung-selective LNPs encapsulating CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, furin, or all three combined, can be administered via the tail vein at a dose of 10 mg CasRx mRNA and 15 mg pre- gRNA oligos/10g body weight in a volume of 10 ml/10g body weight. Mice can be sacrificed at the time points of 24, 72 and 120 hours after injection. Each time point should comprise at least 3~4 mice. Lung tissues can be collected immediately, homogenized and subjected for qRT-PCR and WB analysis to determine its mRNA and protein levels of Tmprss2, Ctsl and Furin, as applicable.
[00114] Histology assessment: Lungs are fixed for 7 days in 10% phosphate buffered formalin, paraffin embedded, and sectioned at 4mm. Serial sections are stained with hematoxylin and eosin (H&E). Two different and complementary quantitative histologic tools, American Thoracic Society lung injury scoring tool and DAD tool, can be used to determine whether knockdown of Tmprss2, Ctsl, Furin or all three combined diminish the histopathological features associated with lung injury.
[00115] Testing the extent to which organ-selective LNPs carrying CasRx mRNA and pre- gRNA targeting TMPRSS2 (human)/Tmprss2(mouse), CTSL (human)/Ctsl(mouse),
FURIN(human)/Furin (mouse), or all three combined, can block SARS-CoV-2 entry into human cells in vitro and into mouse lung in vivo, is important to evaluate their utility for antiviral intervention. Method
[00116] For in vitro studies: Calu-3 or Caco-2 cells can be: (1) pre-incubated with lung- selective LNPs encapsulating1mg CasRx mRNA and 1.5 mg pre-gRNA oligo targeting
TMPRSS2, CTSL and FURIN, or all three combined, at a weight ratio of 1:1.5 in 6-well plates, for 24 hours prior to SAS-Cov2 challenge; (2) incubated with lung-selective LNPs encapsulating CasRx mRNA and pre-gRNA targeting TMPRSS2, CTSL, FURIN, or all three combined, for 24 or 48 hours after SAS-Cov2 challenge. Cell supernatant can be collected for testing virus titer and levels of cytokines (IL-6, IL-8, IL-10, TNF-alpha, IFN-gamma) and chemokines (CCL2, CCL3, CCL4). Cells can also be collected for determination of viral copy number and expression levels of TMPRSS2, CTSL and FURIN.
[00117] For in vivo studies: K18-hACE2 mice (Jackson Laboratory) can be treated through tail vein with a single dose of lung-selective LNPs encapsulating CasRx mRNA and pre-gRNA targeting Tmprss2, Ctsl, Furin, or all three combined, respectively, prophylactically at 18 hours prior to infection, therapeutically at 12 hours post infection, and infected with SARS-CoV-2 intranasally. Body weight can be monitored daily. On day 2 post infection, mice can be euthanized by isoflurane overdose and tissue samples can be harvested for analysis. Lung virus titration: lung tissue homogenates can be clarified by centrifugation and the supernatant can be inoculated onto Vero E6 cell cultures for virus titration. Lung histology (hemorrhage and assessment): two different histological assessment tools can be used to quantitate the histological features of lung injury, (i) the American Thoracic Society lung injury scoring tool and (ii) the DAD tool. Both will be used to assess lung histology. Detection of inflammatory cytokines and chemokines: cytokines and chemokines in mouse lung homogenates can be measured using a commercial Mouse Cytokine 20-Plex antibody bead kit (Thermo). EXAMPLE 5
Targeting HoxB13 and FoxA2 for Neuroendocrine Prostate Cancer (NEPC).
[00118] Neuroendocrine prostate cancer is a lethal form of the disease characterized by loss of androgen receptor (AR) signaling during neuroendocrine transdifferentiation, which results in resistance to AR-targeted therapy. Metastases to the lungs and liver are common and currently undruggable. Generating mouse models for neuroendocrine prostate cancer.
[00119] Three NEPC cell lines NCI-H660 (H660), MSKCC-EF1, and PARCB2 are established to stably express a luciferase. Cell luciferase signal intensity is examined in vitro before injection into mice. NSG male mice (12~14 week-old) are purchased from Jackson Laboratory (Bar Harbor, ME). Upon receipt, mice are acclimated for one week before the study. All animal experiments are carried out according to a protocol approved by an Institutional Animal Care and Use Committee, or equivalent. Mice are intravenously injected with 0.5 million H660, MSKCC-EF1, or PARCB2 cell lines, respectively, in serum free DMEM or RPMI using insulin syringe (BD). Each cell line is injected into at least 5 mice. Bioluminescence of the full body is monitored using IVIS Lumina XR (Caliper Life Sciences) 1~2 h after cell injection and weekly afterwards until the visceral metastasis is established. Briefly, mice are anesthetized with isoflurane, fixed in the imaging chamber and imaged 15 minutes after Luciferin injection (150 mg/kg, i.p.). Bioluminescence signal is quantified using the Living Image software 4.2 (Caliper Life Sciences). Counteracting NEPC metastasis to the liver and lungs.
[00120] The ability of organ-selective LNPs carrying CasRx mRNA and gRNA (or pre- gRNA) to target HoxB13 and FoxA2 and to effectively counteract NEPC metastasis to the liver and lungs is assessed. Alexa Fluor 647 signal is examined in lung and liver using IVIS Lumina XR to evaluate LNP ability to target these organs as the dye is functionalized on the surfaces of the LNPs through surface-specific antigen binding aptamers bound to the LNP suface. The knockdown efficiency of HoxB13 and FoxA2 in mouse lung is assessed by qRT-PCR and western blot assays via the methods described above. Metastasis is monitored by
bioluminescence measurement (photons/second) of the full body using IVIS Lumina XR as described elsewhere herein. HoxB13 and FoxA2 IHC is also performed to evaluate the knockdown efficiency as described above. Nucleic acid aptamer surface-functionalized LNPs for NEPC cell-specific targeting.
[00121] Specific binding of aptamers to cell membrane markers expressed on NEPC cells will be utilized to target NEPC cells. NEPC cell generally do not express the well-known prostate cancer cell surface marker PSMA, so other membrane markers are targeted, including NCAM1, CHGA, SYP, SNAP25 and CEACAM5. These markers are screened to determine the most effective aptamer-surface marker pair(s) to be used to target aptamer-functionalized LNPs to the NEPC cells. Immunostaining and western blots are used, details for which are described above. For surface-functionalizing LNPs with Apts, Alexa Fluor 647-amine-functionalized NEPC Aptamers are reacted with lipid-PEG-COOH (carboxy-modified PEG) via carbodiimide coupling chemistry. The reaction product lipid-PEG-Aptamer are then incorporated into LNPs by incubation at 4 °C for 48 hours. SEQUENCES
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[00122] One skilled in the art will readily appreciate that the present disclosure is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The disclosure described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the present disclosure. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the present disclosure as defined by the scope of the claims. In addition, the section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
[00123] No admission is made that any reference, including any non-patent or patent document cited in this specification, constitutes prior art. In particular, it will be understood that, unless otherwise stated, reference to any document herein does not constitute an admission that any of these documents form part of the common general knowledge in the art in the United States or in any other country. Any discussion of the references states what their authors assert, and the applicant reserves the right to challenge the accuracy and pertinence of any of the documents cited herein. All references cited herein are fully incorporated by reference, unless explicitly indicated otherwise.
[00124] The present disclosure shall control in the event there are any disparities between any definitions and/or description found in any cited references or elsewhere.

Claims

We claim: 1. A nanoparticle (NP) for targeted delivery of a CRISPR/Cas13d system comprising:
a nanoparticle carrier;
a first nucleic acid sequence encoding a Cas13d; and
one or more additional nucleic acid sequences encoding direct repeat (DR) RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences.
2. The NP of claim 1 wherein the NP carrier comprises a polymer-lipid, a lipid, or gold.
3. The NP of claim 1 or claim 2 wherein the NP carrier comprises a lipid.
4. The NP of any of claims 1-3, further comprising a cationic cell penetrating peptide (cpp).
5. The NP of claim 4 wherein the cpp is TAT or a nuclear localization sequence (NLS).
6. The NP of any of claims 1-5, further comprising a nucleic acid aptamer (Apt) immobilized on the surface of the NP.
7. The NP of any of claims 1-3 further comprising an Apt mmobilized on the surface of the NP and a cpp.
8. The NP of claim 6 or claim 7 wherein the Apt targets CRPC cells.
9. The NP of claim 8 wherein the Apt is a PSMA aptamer.
10. The NP of claim 6 or claim 7 wherein the Apt targets NEPC cells.
11. The NP of claim 10 wherein the Apt is an NCAM1 aptamer, a CHGA aptamer, a SYP aptamer, a SNAP25 aptamer, or a CEACAM5 aptamer.
12. The NP of any one of claims 1-11 wherein the first nucleic acid sequence is an mRNA sequence and the one or more additional nucleic acid sequences are mRNA sequences.
13. The NP of any one of claims 1-11 wherein the first nucleic acid sequence is a plasmid and the one or more additional nucleic acid sequences is a plasmid.
14. The NP of any one of claims 1-11 wherein the first nucleic acid sequence is a plasmid and the one or more additional nucleic acid sequences are mRNA sequences.
15. The NP of any one of claims 1-11 wherein the first nucleic acid sequence is an mRNA sequence and the one or more additional nucleic acid sequences are a plasmid.
16. The NP of claim 12 wherein the ratio of the first nucleic acid sequence to the one or more additional nucleic acid sequences is between 1:1 and 1:2, inclusive.
17. The NP of any one of claims 1-11 wherein the nanoparticle carrier comprises a core encapsulating the first nucleic acid sequence and the one or more additional nucleic acid sequences, and a shell surrounding the core.
18. The NP of claim 17 wherein the core comprises polylactic-co-glycolic acid (PLGA).
19. The NP of claim 17 or claim 18 wherein the shell comprises polyethyleneglycol (PEG).
20. The NP of claim 19 wherein the PEG is a carboxy modified PEG.
21. The NP of claim 20 wherein the PEG is lipid-PEG-COOH.
22. The NP of claim 21 wherein the lipid-PEG-COOH is m-PEG-DSPE.
23. The NP of claim 17 wherein the core comprises a first plasmid comprising the first nucleic acid sequence encoding the Cas13d and a second plasmid comprising the one or more additional nucleic acid sequences encoding the DR RNA sequences and gRNA or pre-gRNA sequences.
24. The NP of claim 17 wherein the core comprises a plasmid comprising the first nucleic acid sequence encoding the Cas13d and the one or more additional nucleic acid sequences encoding the DR RNA sequences and gRNA or pre-gRNA sequences.
25. The NP of any one of claims 1-24 wherein the Cas13d is CasRx.
26. The NP of any one of claims 1-24 wherein the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre- gRNA) sequences encode gRNAs or pre-gRNAs to a prostate cancer (PC) associated transcription factor (TF).
27. The NP of claim 26 wherein the PC associated TF is selected from the group consisting of AR, AR-V7, HoxB13, FoxA1, FoxA2, and GATA2.
28. The NP of claim 27 wherein the PC associated TF is HoxB13 and the one or more additional nucleic acid sequences comprises any one of SEQ ID NOs: 1-4, 55-58, and 62.
29. The NP of any one of claims 1-24 wherein the one or more additional nucleic acid sequences encoding DR RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences encode gRNAs or pre-gRNAs to a COVID-19 associated protein.
30. The NP of claim 29 wherein the COVID-19 associated protein is TMPRSS2, Cathepsin L, or Furin.
31. The NP of claim 30 wherein the COVID-19 associated protein is TMPRSS2 and the one or more additional nucleic acid sequences comprises any one of SEQ ID NOs: 5-8, 13-16, 63, and 65.
32. The NP of claim 30 wherein the COVID-19 associated protein is Cathepsin L and the one or more additional nucleic acid sequences comprises any one of SEQ ID NOs: 9-12, 17-20, 64, and 66.
33. The NP of claim 30 wherein the COVID-19 associated protein is Furin and the one or more additional nucleic acid sequences comprises any one of SEQ ID NOs: 21-24, 25-28, 68, and 69.
34. The NP of any one of claims 1-16 wherein the NP carrier is formulated with SORT technology to be lung-selective.
35. The NP of claim 34 wherein the NP carrier comprises 1,2-dioleoyl-3-trimethylammonium- propane (DOTAP), DDAB, or EPC.
36. The NP of any one of claims 1-16 wherein the NP carrier is formulated with SORT technology to be liver-selective.
37. The NP of claim 36 wherein the NP carrier comprises 1,2-dioleoyl-3-dimethylammonium- propane (DODAP) or 5A2-SC8.
38. The NP of claim any one of claims 1-16 wherein the NP carrier is formulated with SORT technology to be spleen-selective.
39. The NP of claim 38 wherein the NP carrier comprises 18PA, 14PA, or 18BMP.
40. A composition comprising the NP of any one of claims 1-39 and a pharmaceutically acceptable carrier or excipient.
41. A method of treating a subject with prostate cancer comprising administering to the subject a therapeutically effective amount of the NP of any one of claims 1-28 and 34-39.
42. The method of claim 41 wherein the prostate cancer is androgen dependent prostate cancer, castration resistant prostate cancer, neuroendocrine prostate cancer, or AR-7 variant prostate cancer.
43. A method of treating a subject with prostate cancer that has metastasized to the lungs and/or the liver comprising administering to the subject a therapeutically effective amount of the NP of claim 34 or 36.
44. A method of treating a subject with COVID-19 comprising administering to the subject a therapeutically effective amount of the NP of anyone of claims 29-33.
45. A nanoparticle (NP) for targeted delivery of a CRISPR/Cas13 system comprising:
a nanoparticle carrier; a first nucleic acid sequence encoding a Cas13; and one or more additional nucleic acid sequences encoding direct repeat (DR) RNA sequences and one or more guide RNA (gRNA) or pre-guide RNA (pre-gRNA) sequences.
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