METHODS AND COMPOSITIONS FOR TUSC2 COMBINATION THERAPY WITH

PDKI INHIBITION

[00011 The present invention was made with government support under Grant No. C A- 016672, CA-070907, U54CA-224065, R01CA204302, U54CA224081, R0ICA169338, and R01CA211052 from the National Institutes of Health/ National Cancer Institute. The government has certain rights in the invention.

[0002] This application claims benefit of priority to U. S. Provisional Application Serial No. 63/158/717 filed March 9, 2021, the entire contents of which are hereby incorporated by reference.

BACKGROUND

1, Field

[0003] The present embodiments provided herein relate generally to the fields of molecular biology, oncology and cancer therapy. More specifically, it relates to the use of PDKI inhibitors in combination with a TUSC2 therapy to treat cancers, particularly those with EGFR-inhibitor resistant cancers.

2, Description of Related Art

[0004] Tyrosine kinase inhibitors (TKIs) targeting the epidermal growth factor receptor (EGFR) have become the standard of care for NSCLC patients with EGFR driver mutations (Gelatti et al., 2019; Kalemkerian et at 2018). Osimertinib (AZD9291) is the first FDA- approved third-generation EGFR TKI, which irreversibly binds to EGFR proteins with T790M drug resistance mutations (Janne et al, 2015; Govindan, 2015; Yun et al, 2008; Sos et al. , 2010), Not all patients respond initially, and responses, when they occur, are variable, typically incomplete, and temporary due to acquired drug resistance (Ramaligam et a!., 2018; Ettinger et al, 2017; Goss et a!., 2016; Whi eiaL, 2018, Lim etal, 2018; Papdimitrakopoulou etal, 2018; Leonetti etal. , 2019; Oxnard et al., 2018). This obstacle to long-termpatient survival highlights the need to identify acquired resistance mechanisms. Acquired drug resistance is a complex problem as multiple downstream effector proteins in bypasspathways can drive tumor regrowth, progression, and ultimately drug resistance (Fumarola et al, 2014; Heavey et al., 2014; Tan, 2020; Iksen & Pongrakhananon, 2021). [0005] The PBK/AKT/mTOR has been implicated in N8CLC acquired resistance, but therole of AKT -independent signaling downstream of PBK is not well-characterized (Lien et al, 2017, Faes & Dormond, 2015). One protein that transduces PBK signaling, is the serine/threonine kinase 3-phosphoinositide-dependent protein kinase 1 (PDKI also known as PDPK1). PDK I is a pleotropic regul atorof 60 serine/threonine kinase proteins classified into 14 families of the AGC kinase superfamily (Arencibiaeia/., 203). It has multifunctional oncogenic activity, concurrently activating pro-survivalprotein kinases (Scheid et al , 2005; Hossen et al, 2015), and suppressing apoptosis in lung cancer (Hann etal, 2013). PDKI is also implicatedin tumors driven by KRAS genetic alterations, and regulates immune cell development, including T and B cells, and their functions in the tumor microenvironment (TME) (Ferro & Falasca, 2014; Caron etal., 2005; Lee etal, 2005; Yagi et al., 2009). NSCLC sera compared to healthy samples were reported to have significantly higher levels of PDKI mRNA expression (Han et al, 2014). Recently, PDKI started to gain a wide interest as a drug target, which has so far led to the filing of more than 50 patents (Hossen et al. , 2015).

[0006] The validity of current preciinieal modeling of osimertinib acquired resistance has been questioned because of inaccuracy in predicting clinical benefit. Studies have reliedon mouse tumor biology, which is useful to certain degree, but cannot provide an accurate recapitulation of osimertinib interact! ons with a highly complex and heterogeneous humantumor microenvironment (TME). There is still a need for a reliable preciinieal platform tomodel osimertinib acquired resistance. The inventor recently published on a humanized mousemodel using irradiated NOD.Cg -Prkdc ^sad (NSG) mice injected with fresh, non- cultured, human CD34 ^" stem cells with rapid and prolonged reconstitution of multiplefimctional human immune cell subpopulations. This model a) replicates human tumor response to checkpoint blockade, b) mounts an immune response to tumor-associated antigens and not alioantigens, and c) is not stem cell donor-dependent for its immune response (Meraz et al, 2019). SUMMARY

[0007] in a first embodiment, there is provided a method of treating a subject having a cancer comprising administering a tumor suppressor therapy (e.g, a TUSC2 therapy) in conjunction with PDK1 inhibition. Thus, a method is provided for treating a subject having a cancer, wherein the subject is being treated with (or was previously administered) may have been treated or is currently being treated with an EGFR inhibitor, and the cancer may be EGFR inhibitor resistant. For example, a subject to be treated with a TUSC2 therapy can be a subject who was administered a PDK1 inhibitor less that one hour, 6 hours, 12 hours, l day, 3 days, one week or two weeks before administration of the TUSC2 therapy. As used herein, a TUSC2 therapy can be any type of therapy that provides or causes expression of a TUSC2 polypeptide in a cancer ceil (see, e.g., U.S. Patent No. 7,902,441, incorporated herein by reference). For example, a TUSC2 therapy may comprise delivery' of a TUSC2 polypeptide or TUSC2 expression vector to cancer cell A therapy may, for instance, be delivered via nanoparticles, or in the case of nucleic acid expression vectors, through the use of a viral vector.

[0008] In certain embodiments, a method is provided for treating a subject having a cancer, comprising administering to the subject a TUSC2 therapy in conjunction with at least one PDK1 inhibitor. For instance, the TUSC2 therapy can be administered, before, after or essentially concomitantly with the at least one PDK1 inhibitor. Thus, in some embodiments, a composition is provided comprising a TUSC2 therapeutic and a PDK1 inhibitor in a therapeutically effective amount to treat a cancer.

[0009] In some aspects, the PDK1 inhibitor is dichloroacetate (DCA), AR-12, BX795, BX912, Dicumaro!, GSK2334470, JX06, radicicol, or combinations thereof.

[0010] In certain embodiments, administration of a T1..SC2 therapy comprises administration of a TUSC2 expression vector, such a DNA plasmid encoding TUSC2. An expression vector for use according to the embodiments provided herein will generally comprise control elements for the expression of the TUSC2 coding sequence. For example, a vector can comprise a promoter and enhancer element that are effective for expression in cancer cell of interest. In certain aspects, for instance, TUSC2 expression is provided by a CMV promoter or recombinant version thereof, such as the CMV promoter construct described in U.S. Patent Publication No. 20070092968, incorporated herein by reference. In certain embodiments, a vector provided herein comprises a modified CMV promoter. In certain erabodiraents, a vector provided herein comprises a mini -CM V promoter. Additional expression control elements can be included such as, for example, an intron, a drug response element, a RNA stabilizing or destabilizing sequence, a cellular localization signal, a polyadenyiation signal sequence and/or an optimized translation start codon. Plasmid DNA vectors may also comprise sequences that help facilitate DNA production, such as, a bacterial origin of replication and/or a drug resistance marker. In certain specific aspects, the TUSC2 expression vector is the pLJ 143/KGB 2/FUS 1 plasmid,

[0011] Methods for delivery of an expression vector to cells (e.g., in vivo delivery) are well known in the art and include, without, limitation, nanoparticles (e.g., liposome nanoparticles), lipid conjugates and viral vectors. In certain aspects, a TU8C2 expression vector is administered in a nanoparticle, such as N-[l-(2,3-dioleoyioxy)propyl]-N,N,N- trimethylammonium chloride (DOTAP): cholesterol liposome nanoparticle. A skilled artisan will recognize that various properties of liposomes can be adjusted to optimize vector delivery' . For example, the liposomes may be adjusted to have a certain size range and/or a particular ratio of DNA to lipid; DNA to cholesterol, or lipid to cholesterol. For instance, in the case of a DOTAP: cholesterol liposome, the DOTAP: cholesterol ratio can be defined as between about 1.5:1 and 1:1.5, such as about 10:9. In further aspects, a TUSC2 expression vector is provided in a liposome nanoparticle, wherein the nanoparticles comprise an average particle size of between about 50 and about 500 nm (e.g., 200-500 nm). In still further aspects, a TUSC2- nanoparticle formulation can be defined by their optical density (OD), such as having OD400 of between about 0.65 and 0.95.

[0012] In still further embodiments, a TUSC2 therapy can comprise administration of a TUSC2 polypeptide. Methods for administration of TUSC2 polypeptide are described for example in U.S. Publication Nos. 20060251726 and 20090023207, incorporated herein by reference. A TUSC2 polypeptide may be modified to enhance its activity and/or ability to enter cancer cells. For instance, the polypeptide can be modified with a lipid moiety (e.g ^· ., myristoylated). In certain aspects a TUSC2 in provided as a nanoparticle (e.g., a lipid-based nanoparticle) such as, a superparamagnetic nanoparticle, a nanoshell, a semiconductor nanocrystal, a quantum dot, a polymer-based nanoparticle, a silicon-based nanoparticle, a silica-based nanoparticle, a metal-based nanoparticle, a fullerene or a nanotube. [0013] A TUSC2 therapy and/or an PDK1 inhibitor according to the embodiments provided herein is typically formulated in a pharmaceutically acceptable carrier. A therapy according to the embodiments may be delivered, for example, intravenously, intradermally, intraart eri ally, intraperitonealiy, intralesionaily, intracranialiy, intraarticularly, intraproslatically, intrapleurally, intratracheaily, intranasally, intravitreally, intravagina!ly, intrarectally, topically, intratum orally, intramuscularly, intraperitonealiy, subcutaneously, subconjunctival, intravesicularly, mucosally, intrapericardially, intraumbilicaily, intraocularly, orally, topically, locally, via inhalation (e.g. aerosol inhalation), by injection or by infusion, and the route of delivery can depend upon the type of cancer to be treated. For example, a TUSC2 expression vector complexed with DOT AP : cholesterol liposome can be administer via intravenous infusion. In certain specific aspects, a TUSC2 therapy is administered intravenously in a dose of from about 0.01 mg/kg to about 0.10 mg/kg, such as a dose of about 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.080.09 or 0.10 mg/kg. In further aspects, a TUSC2 therapy, can be administer two or more times (e.g., 3, 4, 5, 6, 7, 8, 9 or 10 times). The timing between doses of such a therapy can be varied and can include, without limitation, about 1, 2 or 3 days, about 1, 2, or 3 weeks or 1 month or more between doses.

[0014] In yet a further embodiment, there is provided a method for treating a subject having a cancer, comprising administering a TUSC2 therapy to the subject in conjunction at least one PDK1 inhibitor and/or in conjunction with one or more anti-inflammatory agent. For example, the anti-inflammatory agent may he administered before, after or during a TUSC2 therapy. In a further aspect, more than one anti-inflammatory agent is administered, such as administration of an antihistamine and a corticosteroid. Thus, in certain specific aspects the anti-inflammatory for use in conjunction with a TUSC2 therapy is diphenhydramine and/or dexametbasone.

[0015] In further embodiments, a method provided herein further comprises administering a further anticancer therapy. The further anticancer therapy may be, without limitation, a surgical therapy, chemotherapy, radiation therapy, cryotherapy, hyperthermia treatment, phototherapy, radioablation therapy, hormonal therapy, immunotherapy (e.g., checkpoint inhibitor), small molecule therapy, receptor kinase inhibitor therapy, anti- angiogenic therapy, cytokine therapy or a biological therapies such as monoclonal antibodies, siRNA, antisense oligonucleotides, ribozymes or gene therapy. Without limitation the biological therapy may be a gene therapy, such as tumor suppressor gene therapy, a cell death protein gene therapy, a cel! cycle regulator gene therapy, a cytokine gene therapy, a toxin gene therapy, an immunogene therapy, a suicide gene therapy, a prodrug gene therapy, an anti- cellular proliferation gene therapy, an enzyme gene therapy, or an anti -angiogenic factor gene therapy.

[0016] Thus, in yet a further embodiment provided herein are compositions, therapies, and methods for treating a subject having a cancer, comprising administering to the subject a TUSC2 therapy (e.g, a TU8C2 polypeptide or a TUSC2 expression vector) in conjunction with a PDK1 inhibitor and a further anticancer agent, such as a chemotherapeutic. In some aspects the additional chemotherapeutic is an epidermal growth factor receptor (EGFR) inhibitor.

[0017] Thus, in certain embodiments, a method is provided for treating a subj ect having a cancer, comprising administering to the subject a TUSC2 therapy in conjunction with at least one PDK1 inhibitor and, optionally, an immune checkpoint inhibitor. For instance, the TU8C2 therapy can be administered, before, after or essentially concomitantly with the PDK1 inhibitor. Thus, in some embodiments, a composition is provided comprising a TUSC2 therapeutic and a PDK1 inhibitor which are used in a therapeutically effective amount to treat a cancer.

[0018] EGFR-targeted therapies for use in accordance with the embodiments include, but are not limited to, inhibitors of EGFR/ErbB 1 /HER, ErbB2/Neu/FIER2, ErbB3/FIER3, and/or ErbB4/HER4. A wide range of such inhibitors are known and include, without limitation, tyrosine kinase inhibitors active against the receptor(s) and EGFR-binding antibodies or aptamers. For instance, the EGFR inhibitor can be gefitinib, erlotinib, cetuximab, matuzumab, panitumumab, AEE788; CI-IG33, HKI-272, HKI-357 or EKB-569. In certain embodiments, the compositions and therapies provided herein are administered systemically or locally. In one embodiment, the compositions and therapies provided herein are. administered systemically. In certain aspects, an EGFR inhibitor is administered to a patient before, after or essentially concomitantly with a TUSC2 therapy. For example, the therapies may be co-admimstered, such as by co-administration in an intravenous infusion. In certain embodiments, TUSC2 and EGFR inhibitors can be administered in any amount effective to treat cancers. In certain embodiments, the compositions, therapies, and methods provided herein comprise administering TUSC2 and EGFR inhibitors in tower doses than either composition administered alone In certain embodiments, the compositions, therapies, and methods comprise administering TUSC2 and EGFR inhibitors in lower doses that reduce side effects. In certain embodiments, the compositions, therapies, and methods comprise administering a TUSC2 therapy, a PDK1 inhibitor and EGFR inhibitor in doses effective to provide additive, cooperative, or synergistic effect than that provided by either composition administered alone. In certain aspects, cancers for treatment with such therapies can be any of those described herein, such as lung cancers (e.g, non-sma!l cell lung cancer). In certain preferred aspects, a cancer for treatment with a combination therapy is an EGFR-expressing cancer. In certain embodiments, the EGFR-expressing cancer comprises at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% tumor ceils expressing EGFR.

[0019] In yet still a further embodiment provided herein is a method for treating a subject having a cancer, wherein it was previously determined that the cancer expresses an EGFR and is resistant to such therapy, the method comprising administering to the subject a TUSC2 therapy in conjunction with a PDK1 inhibitor. In certain embodiments, provided herein is a method for treating a subject having a cancer comprising the step of determining whether the cancer expresses an EGFR or has a mutated EGFR protein/gene, and administering to the subject a Tl. SC 2, a PDK1 inhibitor and an EGFR inhibitor. Methods for assessing the EGFR-expression status of a cancer have been described, for example in U.S. Patent Publn. No. 20110052570, incorporated herein by reference, in certain aspects, the EGFR-expressing cancer can be a cancer that expresses a mutant EGFR, such as a cancer expressing an EGFR having a L858R and/or T790M mutation. In certain embodiments, the compositions and therapies provided herein are administered to the patient that have an EGFR-expressing cancer that comprises at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% tumor cells expressing EGFR. In still further aspects, the subject for treatment has a cancer that was previously determined to express an EGFR and in which at least 10% of the cells of the cancer are apoptotic. In certain embodiments, the methods provided herein further comprise determining whether at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the cells of the EGFR-expressing cancer are apoptotic.

[0020] In certain embodiments, a cancer for treatment or assessment, may present as a tumor, such as primary or metastatic tumor. A cancer may be an early stage cancer or may be a metastatic or late stage cancer. In certain aspects, the cancer is an oral cancer, oropharyngeal cancer, nasopharyngeal cancer, respiratory cancer, a urogenital cancer, a gastrointestinal cancer, a centra! or peripheral nervous system tissue cancer, an endocrine or neuroendocrine cancer, a hematopoietic cancer, a glioma, a sarcoma, a carcinoma, a lymphoma, a melanoma, a fibroma, a meningioma, brain cancer, oropharyngeal cancer, nasopharyngeal cancer, renal cancer, biliary cancer, prostatic cancer, pheoehromocytoma, pancreatic islet cell cancer, a Li- Fraumeni tumor, thyroid cancer, parathyroid cancer, pituitary tumors, adrenal gland tumors, osteogenic sarcoma tumors, multiple neuroendocrine type I and type II tumors, breast cancer, lung cancer (e.g., a non-small cell lung cancer (N8CLC) or small cell lung cancer (8CLC)), head & neck cancer, prostate cancer, esophageal cancer, tracheal cancer, skin cancer brain cancer, liver cancer, bladder cancer, stomach cancer, pancreatic cancer, ovarian cancer, uterine cancer, cervical cancer, testicular cancer, colon cancer, recta! cancer or skin cancer. In further aspects, a cancer may be defined as a cancer that is resistant to one or more anti cancer therapy, such a chemotherapy resistant cancer. For example, the cancer may be a cancer that is resi stant to a platinum-based chemotherapeutic, such as cisplatin.

[0021] In still further embodiments provided herein is a kit comprising a TUSC2 therapeutic and at least one PDK1 inhibitor For example, in some aspects a kit provided herein comprises a TUSC2 therapeutic, at least one PDK1 inhibitor and a reagent for testing a subject to determine their response for the TU8C2 therapeutic and/or the PDK 1 inhibitor For example, the reagent fortesting a subject to determine their response for the TUSC2 therapeutic can be a reagent for determining the level of apoptosis in cancer cells of the subject. The kit may further comprise an EGFR inhibitor, such as Erlotinib, Gefitinib, Icotinib, Afatinib, Dacomitinib, Osimertinib, Rociletinib, Olmutinib, Lazertinib, or combinations thereof. In further aspects, a kit further comprises one or more anti-inflammatory' agents or a kinase inhibitor. In still further aspect, s the kit may comprise one more additional components including, but not limited to, a pharmaceutically acceptable dilution agent, a syringe, an infusion bag, an infusion line, and/or a set of instruction for use of the kit.

[0022] Also provided is a composition comprising a TUSC2 therapeutic and a 3- phosphoinositide-dependent protein kinase-1 (PDK1) inhibitor in a therapeutically effective amount to treat a cancer. The PDK! inhibitor may be dichloroacetate (DCA), AR-12, BX795, BX912, Dicumarol, G8K2334470, JX06, radicicol, or combinations thereof. The kit may further comprise an EGFR inhibitor, such as Erlotinib, Gefitinib, Icotinib, Afatinib, Dacomitinib, Osimertinib, Rociletinib, Olmutinib, Lazertinib, or combinations thereof. [0023] In yet an additional embodiment, there is provided a method treating a subject having a cancer comprising administering to said subject (i) an EFGR inhibitor; and (ii) a 3- phosphoinositi de-dependent protein kinase-1 (PDKI) inhibitor, wherein the cancer is resistant to epidermal growth factor receptor (EGFR) inhibitor therapy. The method may further comprise identifying said subject as having an EGFR inhibitor resistant cancer. The have not previously received EGFR inhibitor therapy, or may have previously received EGFR inhibitor therapy. The cancer may have an EGFR mutation (EGFRm), such as wherein the EGFRrn is one or more of exon 19 del, L858R, and T790M. The EGFR inhibitor may be Eriotimb, Gefitinib, Icotinib, Afatinib, Dacomitinib, or combinations thereof The EGFR inhibitor may be a selective EGFRm inhibitor, including, for example, Osimertinib, Rociletinib, Olmutinib, Lazertinib, or combinations thereof. The PDKI inhibitor may be dichloroacetate (DCA), AR- 12, BX795, BX912, Dicumaro!, GSK2334470, JX06, radicico!, or combinations thereof. In embodiments, the PDKI inhibitor is BX795.

[0024] The EGFR inhibitor and the PDKI inhibitor may be administered to the subject simultaneously, in the same or separate pharmaceutical compositions. The EGFR inhibitor and the PDKI inhibitor may be administered to the subject sequentially. The EGRF inhibitor and the PDKI inhibitor may be administered two or more times. The method may further comprise administering an anti-inflammatory agent. The method may further comprise administering a further anti-cancer therapy to the subject, such as chemotherapy, radiotherapy, gene therapy, surgery', hormonal therapy, anti -angiogenic therapy, immunotherapy or cytokine therapy. The immunotherapy may be a checkpoint inhibitor, such as anti -PD- 1 or anti -PD -LI therapy.

[0025] The cancer may be oral cancer, oropharyngeal cancer, nasopharyngeal cancer, respiratory cancer, urogenital cancer, gastrointestinal cancer, central or peripheral nervous system tissue cancer, an endocrine or neuroendocrine cancer or hematopoietic cancer, glioma, sarcoma, carcinoma, lymphoma, melanoma, fibroma, meningioma, brain cancer, oropharyngeal cancer, nasopharyngeal cancer, renal cancer, biliary cancer, pheochromocytoma, pancreatic islet cell cancer, Li-Fraumeni tumors, thyroid cancer, parathyroid cancer, pituitary tumors, adrenal gland tumors, osteogenic sarcoma tumors, multiple neuroendocrine type I and type II tumors, breast cancer, lung cancer, head and neck cancer, prostate cancer, esophageal cancer, tracheal cancer, liver cancer, bladder cancer, stomach cancer, pancreatic cancer, ovarian cancer, uterine cancer, cervical cancer, testicular cancer, colon cancer, rectal cancer or skin cancer. The lung cancer may be a non-small cell lung cancer and/or may be a metastatic lung cancer.

[0026] A further embodiment comprises a kit comprising an EGFR inhibitor and a 3- phosphoinositi de-dependent protein kinase-1 (PDKl) inhibitor. The PDK1 inhibitor may be dichloroacetate (DCA), AR-12, BX795, BX912, Dicumarol, GSK2334470, JX06, radicicoi, or combinations thereof. The EGFR inhibitor may be Erlotinib, Gefitinib, Icotinib, Afatinib, Daeomitinib, Osimertinib, Rociletinib, Olmutinib, Lazertinib, or combinations thereof.

[0027] Additionally, there is provided a composition comprising an EGFR inhibitor and a 3-phosphoinositide-dependent protein kinase-1 (PDKl) inhibitor in a therapeutically effective amount to treat a cancer. The PDKl inhibitor may be dichloroacetate (DCA), AR-12, BX795, BX912, Dicumarol, GSK2334470, JX06, radicicoi, or combinations thereof. The EGFR inhibitor may be Erlotinib, Gefitinib, Icotinib, Afatinib, Daeomitinib, Osimertinib, Rociletinib, Olmutinib, Lazertinib, or combinations thereof.

[0028] It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein. Likewise, aspects of the present embodiments discussed in the context of a method for treating a subject are equally applicable to a method of predicting response in a subject and vice versa,

[0029] The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one,”

[0030] As used herein, “essentially free,” in terms of a specified component, is used herein to mean that none of the specified component has been purposefully formulated into a composition and/or is present only as a contaminant or in trace amounts. The total amount of the specified component resulting from any unintended contamination of a composition is therefore well below 0.01%. Most preferred is a composition in which no amount of the specified component can be detected with standard analytical methods.

[0031] As used herein in the specification and claims, “a” or “an” may mean one or more. As used herein in the specification and claims, when used in conjunction with the word “comprising”, the words “a” or “an” may mean one or more than one. As used herein, in the specification and claim, “another” or “a further” may mean at least a second or more. [0032] As used herein in the specification and claims, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

[0033] Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating certain embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0034] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

[0035] Fig. 1. Effect of osimertinib on survival of NCI-H1975 and NCI- H1975/OSIR cells shown by IC20, IC30 and IC50 values using the SRB assay. Data shown represent themean ± SE of three independent experiments.

[0036] Figs. 2A-E. Effect of osimertinib on humanized H1975 and H1975/OSIR xenografts. (Fig 2 A) Experimental strategy for mouse humanization, tumor cell inoculation, and osimertinib prolonged treatment, (Fig. 2B) Levels of human immune cell repopulation in humanized mice atdifferent time points. (Fig. 2C) Tumor growth comparison between H1975- parental vs HI 975- OsiR and the effect of osimertinib on their growth. (Fig. 2D) Experimental strategy for mouse humanization, tumor cell inoculation, and osimertinib short term treatment. (Fig. 2E) Antitumor effect of osimertinib on tumor growth.

[0037] Figs. 3A-E. TME Immune profile analysis of humanized II1975 and H1975/OSIR tumors: (Fig. 3A) human Ml and M2 macrophages, (Fig 3B) human dendritic cells, (Fig. 3C) human MDSC, (Fig. 3D) human tumor infiltrating lymphocytes (TIL) and (Fig. 3E) human NK ceils.

[0038] Figs. 4A-F. RPPA Gene expression profile analysis in osimertinib treated residual xenograft tumors: (Fig. 4A) treatment strategy, (Fig. 4B) osimertinib response to H1975 parental tumors, (Fig. 4C) Osimertinib response to H1975-OSIR tumors, (Fig. 4D) osimertinib response atD39, (Fig. 4E) Pairwise comparison between HI975 and H1975/OSIR residual tumors treated with osimertinib, (Fig. 4F) Pairwise comparison between H1975-OSIR pre- and post-osimertinib treatment. The criteria of protein selection for each pairwise comparison were: 1. Significant in overall F-test (adjusted p value [FDR q values] <0.05); 2. Significant in pairwise comparison, (adjusted p value [FDR q values] <0.05). Heatmap/Volcano plot: proteins with FDR of 0.0001 and fold change >2.

[0039] Figs. 5A-F. Effect of PDKl knock out and overexpression on cell survival and colony formation. (Fig. 5A) Dose dependent inhibition of pPDKl by the PDKl inhibitor, BX-795; (Fig. 5B) XTT assay shows that BX795 renders NCI-H1975 OS1R sensitive to osimertinih; (Fig. 5C)H1975 OSIRPDK1 knock-out and overexpressor clones; (Fig. 5D) XTT assay shows the effectof PDK1 KO and overexpression on osimertinib response. (Fig. 5E) Colony formation assay shows osimertinib differential sensitivity among all clones. Data shown represent the mean ± SE of three independent experiments.

[0040] Figs. 6A-E, In vivo inhibition of PDKl by PDKl inhibitor, BX795, enhanced osimertinib response in resistant PDXs. (Fig. 6A) pPDKl (S241) expression in TC386-QSIR PDXs treated with BX 795, osimertinib and osimertinib + BX 795. (Fig.6B) Level of pPDKl (S241) expression in osimertinib-sensitive TC386 PDX, and osimertinib-resi stant TC386-G8IR PDX tissuescomparing with H1975-OSIR/PDK-/- and H1975-OSIR/PDK++/++ cells, (Fig. 6C) Osimertinib +BX795 treatment strategies in osimertinib resistant PDXs, (Fig. 6D) Antitumor activity of osimertinib + BX795 combination on TC386-OSIR PDXs, (Fig. 6E) Growth curves of TC386- OSIR PDXs bearing individual mice in different treatment groups.

[0041 ] Figs. 7A-E. PDKl knock-out dysregulates /Akt/niTOR signaling and promotes ceil cyclearrest. (Fig. 7A) Akt, (Fig. 7B) niTQR and (Fig. 7C) PTEN expression in HI 975-OsiR-PDK 1 -/- and HI 975- OsiR-PDK 1 +÷/++ cells and alteration by osimertinib treatment. (Fig. 7C) PTEN expression status among HI 975 -parental, H1975-QsiR, H1975- OsiR-PDKl-/- and H1975-OsiR-PDKl++/++ ceils. (Fig. 7D) Cell cycle analysis of HI 975- parental, H1975-OsiR, H1975-OsiR- PDKl-/- and H1975-OsiR-PDKl++/++ cells after osimertinib treatment. (Fig. 7E) Quantitation ofce!ls in difference phases and its alteration by osimertinib treatment.

[0042] Figs. 8A-E. PDKl knock-out inhibits YAP expression and nuclear translocation. (Fig. 8A) Western blot shows expression of total YAP, pYAP (S127), pYAP (S397) in osimertinib-sensitive 141975, resi stant HI 975-OSiR, PDKl-/- and PDK1++/++ cells, (Fig. 8B) Quantitation of pYAP (SI 27), pYAP (S397) and total YAP in H1975 isogenic cell lines, (Fig 8C) Immunofluorescence images of nuclear translocation of YAP detected by immunostainingwith pYAP (Tyr 357) antibody on osimertinib-sensitive and -resistant cell lines as well as PDKl KO and OE cells, (Fig. 8D) quantitative analysis of nuclear YAP signals in four HI 975 isogenic cell lines, (Fig. 8E) level of YAP and pYAP (8127) in osimertinib sensitive and resistant xenograft tumors (left panel) and osimertinib-treated residual sensitive and resistant tumors (right panel ). [0043] Fig. 9. Whole exome sequencing shows iso new EGFR mutation or loss of T790M imitation. There were 37 new exonic mutations, among them, 0 indels, 27 nonsynonymous single nucleotide variants (SNV), 4 stopgain and 6 synonymous mutations (see list).

100441 Fig. 10. Phospho-proteome analysis by mass spectrometry identifies p- PDK1 significant upregulation in H1975-OS1R compared to H1975 clones,

[0045] Fig. 11, Osimertinib treatment responses on EGFR mutant NSCLC TC386 PDX. Top panel: percentage of tumor volume change on individual mice with starting volume at 200 mm ³ and treatment starting at Day 0. Bottom panel: Tumor volume changes for each individual mouse at Day 21 of treatment.

[0046] Fig. 12. Generation of osimertinib acquired resistance in TC386 PDX, TC386 was treated with osimertinib after regressed tumor grew back to 200 mm ³ . RG1 ~RG4 represent 4 passages of the resistant tumors in NSGmice. Graphs Shown in left panel are tumor volume changes in the first 30 days the mean±SE of each passage. Waterfall plot on right panel shows tumor volume changes for each individual mouse at Day 21 of treatment.

[0047] Figs. 13A-E. Higher level of PDK1 expression in patient samples with progressive disease (PD). Immunohistochemistry (IHC) were performed in EGFR mutant treatment naive and progressive diseases patient samples, (Fig. 13 A) Treatment Naive (TN); EGFR E!9del (E746_A750del); Stage IB NSCLC; Recurrent disease, (Fig. 13B) PD; EGFR L861Q; PD on erlotinib, (Fig. 13C) PD; EGFR mutant (L858R); PD on erlotinib; (Fig 13D) PD ; EGFR E19del (E746_A750del); PD on erlotinib, (Fig. 13E) PDK1 IHC on TN and PD patients.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0048] The development of cancer involves the deregulation of a number of cellular pathways that control normal cell growth. Healthy cells express a number of tumor suppressor genes, which act as molecular gatekeepers and prevent uncontrolled cell division. An important step in the development of a cancer cells, therefore, is disruption of tumor suppressor signaling pathways. In view of this, one promising avenue for cancer therapy involves expression of tumor suppressor genes in cancer ceils to restore normal cellular growth controls.

[0049] In this study, the inventor used a humanized mouse model implanted with the human NSCLC osimertinib sensitive xenograft, NCI-H1975 harboring EGFR T790M and L858Rpoint mutations, and its osimertinib resistant isogenic xenograft, NCI-H1975/QSIR, to model osimertinib acquired resistance. They provide evidence that a) PDK l is a potential driver of osimertinib acquired resistance, b) PDKi genetic and pharmacological targetingrestores osimertinib response in resistant clones and their derived human xenografts andPDXs, c) immune contextures of osimertinib sensitive and resistant humanized xenografts have immunologically distinct TMEs, and d) patient biopsies from EGFR mutant lung adenocarcinoma tumors with the highest PDKI expression associate with patient’s progressive disease following TKI treatment, suggesting they could be responsive to PDKi inhibitors. These and other aspects of the disclosure are set out in detail below.

L EGFR INHIBITION (EGFRi), EGFRI RESISTANCE AND PDKI INHIBITION

A. EGFR

[0050] Epidermal growth factor receptor (EGFR; ErhB-i; HER1 in humans) is a transmembrane protein that is a receptor for members of the epidermal growth factor family (EGF family) of extracellular protein ligands. EGFR is a member of the ErbB family of receptors, a subfamily of four closely related receptor tyrosine kinases: EGFR (ErbB-1), HER2/neu (ErbB-2), Her 3 (ErbB-3) and Her 4 (ErbB-4). In many cancer types, mutations affecting EGFR expression or activity could result in cancer. Interruption of EGFR signaling, either by blocking EGFR binding sites on the extracellular domain of the receptor or by inhibiting intracellular tyrosine kinase activity, can prevent the growth of EGFR-expressing tumours and improve the patient's condition. [0051] The identification of EGFR as an oncogene has led to the development of anticancer therapeutics directed against EGFR (called "EGFR inhibitors", EGFRi), including gefitinib, erlotinib, afatinib, brigatinib and icotinib for lung cancer, and cetuximab for colon cancer. More recently AstraZeneca has developed osimertinih, a third-generation tyrosine kinase inhibitor.

[0052] Many therapeutic approaches are aimed at the EGFR. Cetuximab and panitumumab are examples of monoclonal antibody inhibitors; however, the former is of the IgGl type, the latter of the IgG2 type; consequences on antibody-dependent cellular cytotoxicity can be quite different. Other monoclonals in clinical development are zaiutumumah, nimotuzumab, and matuzumab. The monoclonal antibodies block the extracellular ligand binding domain. With the binding site blocked, signal molecules can no longer attach there and activate the tyrosine kinase.

[0053] Another method is using small molecules to inhibit the EGFR tyrosine kinase, which is on the cytoplasmic side of the receptor. Without kinase activity, EGFR is unable to activate itself, which is a prerequisite for binding of downstream adaptor proteins. Ostensibly by halting the signaling cascade in cells that rely on this pathway for growth, tumor proliferation and migration is diminished. Gefitinib, erlotinib, brigatinib and lapatinib (mixed EGFR and ERBB2 inhibitor) are examples of small molecule kinase inhibitors.

[0054] CimaVax-EGF, an active vaccine targeting EGF as the major ligand of EGF, uses a different approach, raising antibodies against EGF itself, thereby denying EGFR- dependent cancers of a proliferative stimulus: it is in use as a cancer therapy against non-small- cell lung carcinoma (the most common form of lung cancer) in Cuba, and is undergoing further trials for possible licensing in Japan, Europe, and the United States.

[0055] New drugs such as osimertinib, gefitinib, erlotinib and brigatinib directly target the EGFR, Patients have been divided into EGFR-positive and EGFR-negative, based upon whether a tissue test shows a mutation. EGFR-positive patients have shown a 60% response rate, which exceeds the response rate for conventional chemotherapy.

[0056] The most common adverse effect of EGFR inhibitors, found in more than 90% of patients, is a papulopustular rash that spreads across the face and torso; the rash's presence is correlated with the drag's antitumor effect. In 10% to 15% of patients the effects can be serious and require treatment.

[0057] Some tests are aiming at predicting benefit from EGFR treatment, such as Veri strat B, EGFR Inhibitor Resistance

[0058] Many patients develop resistance to EGFR inhibitor therapy. As of 2010 there was no consensus of an accepted approach to combat resistance nor FDA approval of a specific combination. [0059] Two primary sources of resistance are the T790M Mutation and MET oncogene, with over 50% of acquired resistance to EGFR tyrosine kinase inhibitors (TKI) being caused by the T790M mutation in the ATP binding pocket of the EGFR kinase domain involving substitution of a small polar threonine residue with a large nonpolar methionine residue. Clinical trial phase II results reported for brigatinib targeting the T790M mutation, and brigatinib received Breakthrough Therapy designation status by FDA in Feb. 2015.

[Q060] In November 2015, the US FDA granted accelerated approval to osimertinib (Tagrisso) for the treatment of patients with metastatic epidermal growth factor receptor (EGFR) T790M mutation-positive non-small cell lung cancer (N8CLC), as detected by an FDA-approved test, which progressed on or after EGFR TKI therapy. C. PDK1 and PDK1 Inhibitor Therapies

[0061] PDKl refers to the protein 3-phosphoinositi de-dependent protein kinase- 1, an enzyme which is encoded by the PDPKJ gene in humans. It is implicated in the development and progression of melanomas PDPK1 is a master kinase, which is crucial for the activation of AKT/PKB and many other AGC kinases including PKC, S6K, SGK. An important role for PDPK1 is in the signalling pathways activated by several growth factors and hormones including insulin signaling.

[Q062] Mice lacking PDPK1 die during early embryonic development, indicating that this enzyme is critical for transmitting the growth-promoting signals necessary for normal mammalian development. Mice that are deficient in PDPK1 have a ~40% decrease in body mass, mild glucose intolerance, and are resistant to cancer brought about by hyperactivation of the PBK pathway (PTEN+/-).

[0063] The structure of PDPK1 can he divided into two domains: the kinase or catalytic domain and the PH domain. The PH domain functions mainly in the interaction of PDPK1 with phosphatidyl inositol (3,4)-bisphosphate and phosphatidylinositol (3,4,5)- trispbosphate which is important in localization and activation of some of membrane associated PDPKl's substrates including AKT.

[0064] The kinase domain has three ligand binding sites; the substrate binding site, the ATP binding site, and the docking site (also known as PIT pocket). Several PDPK1 substrates including S6K and Protein kinase C, require the binding at this docking site. Small molecule allosteric activators of PDPK1 were shown to selectively inhibit activation of substrates that require docking site interaction. These compounds do not bind to the active site and allow' PDPK1 to activate other substrates that do not require docking site interaction. PDPK1 is constitutive!y active and at present, there is no known inhibitor proteins for PDPK1. The activation of PDPKl’s main effector, AKT, is believed to require a proper orientation of the kinase and PH domains of PDPK i and AKT at the membrane.

[Q065] A variety of PDKi inhibitors are known dichloroacetate (DCA), AR-12, BX795, BX912, Dicumarol, GSK2334470, JX06, radicicoi, , or combinations thereof. Other PDKI inhibitors are listed in U.8. Patents 10,030,016, 9,873,693, 9,546,165, and 8,778,977, the entire contents of which are hereby incorporated by reference.

II. TUSC2 THERAPIES

[0066] In certain aspects, concerns compositions and methods for delivering a nucleic acid or a polypeptide to a cell. In particular, provided herein are nanoparticle-nucleic acid or nanoparti c!e-polypeptide complexes and methods of administering such complexes to a subject. The complexes comprise a TUSC2 polypeptide and/or nucleic acid in association -with a nanoparticle. As used herein, “association” means a physical association, a chemical association or both. For example, an association can involve a covalent bond, a hydrophobic interaction, encapsulation, surface adsorption, or the like.

[0067] Polypeptides and nucleic acids typically have difficulty crossing cellular membranes. Both types of molecules include charged residues, which hinder membrane binding and membrane transport into ceils. The present embodiments overcome this difficulty by, providing nanoparticle complexes that facilitate cellular uptake.

[0068] In accordance with the present embodiments, a polypeptide and/or nucleic acid may be associated with a nanoparticle to form nanoparticle complex. In some embodiments, the nanoparticle is a liposomes or other lipid-based nanoparticle such as a lipid-based vesicle (e.g, a DOTAP: cholesterol vesicle). As used in cancer therapy, liposomes take advantage of the increased fenestrations in the cancer neovasculature to enhance liposome concentration at tumor sites.

[0069] In other embodiments, the nanoparticle is a non-lipid nanoparticle, such as an iron-oxide based superparamagnetic nanoparticles. Superparamagnetic nanoparticles ranging in diameter from about 10 to 100 nm are small enough to avoid sequestering by the spleen, but large enough to avoid clearance by the liver. Particles this size can penetrate very small capillaries and can be effectively distributed in body tissues. Superparamagnetic nanoparticles complexes can be used as MRI contrast agents to identify and follow those cells that take up the therapeutic complexes. In certain embodiments, the nanoparticle is a semiconductor nanocrystal or a semiconductor quantum dot, both of which can be used in optical imaging. In further embodiments, the nanopartide can be a nanoshell, which comprises a gold layer over a core of silica One advantage of nanoshells is that a polypeptide or nucleic acid can be conjugated to the gold layer using standard chemistry. In other embodiments, the nanoparticle can be a fuilerene or a nanotube (Gupta et al, 2005).

[0070] In accordance with the present embodiments, nanoparticle complexes can be targeted to specific tissues and cells. This can be accomplished by conjugating a cell targeting moiety to the nanoparticle. The targeting moiety can be, but is not limited to, a protein, peptide, lipid, steroid, sugar, carbohydrate or synthetic compound. Ceil targeting moieties such as ligands recognize and bind to their cognate receptors on the surface of cells. Similarly, antibody can act as cell targeting moieties by recognizing their cognate antigens on the cell surface, in certain embodiments, targeted nanoparticle complexes provided herein can enhance the specificity of disease treatment and increase the amount of therapeutic agent entering a targeted cell A. Nanopartides

[0071] As used herein, the tenn “nanoparticle” refers to any material having dimensions in the 1-1,000 nm range. In some embodiments, nanopartides have dimensions in the 50-500 nrn range. Nanoparticles used in the present embodiments include such nanoscale materials as a lipid-based nanoparticle, a superparamagnetie nanoparticle, a nanoshell, a semiconductor nanocrystal, a quantum dot, a polymer-based nanoparticle, a silicon-based nanoparticle, a silica-based nanoparticle, a metal-based nanoparticle, a fullerene and a nanotube (Ferrari, 2005). The conjugation of polypeptide or nucleic acids to nanopartides provides structures with potential application for targeted delivery, controlled release, enhanced cellular uptake and intracellular trafficking, and molecular imaging of therapeutic peptides in vitro and in vivo (West, 2004; Stay ton et a!., 2000; Ballou eta!., 2004; Frangioni, 2003; Dubertret et a! , 2002; Miehalet et al. , 2005; Dwarakanath et al, 2004.

1. Lipid-Based Nanopartides

[0072] Lipid-based nanopartides include liposomes, lipid preparations and lipid-based vesicles (e.g, DOTAPxholesterol vesicles). Lipid-based nanopartides may be positively charged, negatively charged or neutral. In certain embodiments, the lipid-based nanoparticle is neutrally charged (e.g., a DOPC liposome).

[0073] A “liposome” is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Liposomes may be characterized as having vesicular structures with a bilayer membrane, generally comprising a phospholipid, and an inner medium that generally comprises an aqueous composition. Liposomes provided herein include unilamellar liposomes, multilamellar liposomes and mu!tivesicular liposomes. Liposomes provided herein may he positively charged, negatively charged or neutrally charged. In certain embodiments, the liposomes are neutral in charge.

[0074] A multilamellar liposome lias multiple lipid layers separated by aqueous medium. They form spontaneously when lipids comprising phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991). Lipophilic molecules or molecules with lipophilic regions may also dissolve in or associate with the lipid bilayer.

[0075] In specific aspects, a polypeptide or nucleic acids may be, for example, encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the polypeptide/nucleic acid, entrapped in a liposome, complexed with a liposome, or the like.

[0076] A liposome used according to the present embodiments can be made by different methods, as would be known to one of ordinary skill in the art For example, a phospholipid (Avanti Polar Lipids, Alabaster, AL), such as for example the neutral phospholipid dio!eoylphosphatidy!choline (DOPC), is dissolved in tert-butanol. The lipid(s) is then mixed with a polypeptide, nucleic acid, and/or other component(s). Tween 20 is added to the lipid mixture such that Tween 20 is about 5% of the composition's weight. Excess tert- butanol is added to this mixture such that the volume of tert-butanol is at least 95%. The mixture is vortexed, frozen in a dry ice/acetone bath and lyophilized overnight. The lyophilized preparation is stored at -20°C and can be used up to three months. When required the lyophilized liposomes are reconstituted in 0.9% saline.

[0077] Alternatively, a liposome can be prepared by mixing lipids in a solvent in a container, e.g., a glass, pear-shaped flask. The container should have a volume ten-times greater than the volume of the expected suspension of liposomes. Using a rotary' evaporator, the solvent is removed at approximately 40°C under negative pressure. The solvent normally is removed within about 5 min. to 2 hours, depending on the desired volume of the liposomes. The composition can be dried further in a desiccator under vacuum The dried lipids generally are discarded after about 1 week because of a tendency to deteriorate with time.

[0078] Dried lipids can be hydrated at approximately 25-50 m.M phospholipid in sterile, pyrogen-free water by shaking until ail the lipid film is resuspended. The aqueous liposomes can be then separated into aliquots, each placed in a vial, lyophilized and sealed under vacuum.

[0079] The dried lipids or lyophilized liposomes prepared as described above may be dehydrated and reconstituted in a solution of a protein or peptide and diluted to an appropriate concentration with a suitable solvent, e.g,, DPBS. The mixture is then vigorously shaken in a vortex mixer. Unencapsulated additional materials, such as agents including but not limited to hormones, drugs, nucleic acid constructs and the like, are removed by centrifugation at 29,000 x g and the liposomal pellets washed. The washed liposomes are resuspended at an appropriate total phospholipid concentration, e.g., about 50-200 niM The amount of additional material or active agent encapsulated can be determined in accordance with standard methods. After determination of the amount of additional material or active agent encapsulated in the liposome preparation, the liposomes may be diluted to appropriate concentrations and stored at 4°C until use. A pharmaceutical composition comprising the liposomes will usually include a sterile, pharmaceutically acceptable carrier or diluent, such as water or saline solution,

[0080] In other alternative methods, liposomes can be prepared in accordance with other known laboratory procedures (e.g., see Bangham etal, 1965; Gregoriadis, 1979; Deamer and Lister, 198.3; Szoka and Papahadj opoul os, 1978, each incorporated herein by reference in relevant part). Additional liposomes which may be useful with the present embodiments include cationic liposomes, for example, as described in W002/100435A1, U.S Patent 5,962,016, U.S. .Application 2004/0208921, WO03/015757.41, WO04029213A2, U.S. Patent 5,030,453, and U.S. Patent 6,680,068, all of which are hereby incorporated by reference in their entirety without disclaimer. A process of making liposomes is also described in W004/002453A1. Neutral lipids can be incorporated into cationic liposomes (e.g., Farhood et aL, 1995). Various neutral liposomes which may be used in certain embodiments are disclosed in U.S. Patent 5,855,911, which is incorporated herein by reference. These methods differ in their respective abilities to entrap aqueous material and their respective aqueous space-to-lipid ratios.

[00811 The size of a liposome varies depending on the method of synthesis. Liposomes in the present embodiments can be a variety of sizes. In certain embodiments, the liposomes are small, e.g., less than about 100 nni, about 90 nm, about 80 nm, about 70 nm, about 60 nm, or less than about 50 nm in external diameter. For example, in general, prior to the incorporation of nucleic acid, a DOTAPxholesterol liposome for use according to the present embodiments comprises a size of about 50 to 500 nm. Such liposome formulations may also be defined by particle charge (zeta potential) and/or optical density (OD). For instance, a DOTAPxholesterol liposome formulation will typically comprise an OD400 of less than 0.45 prior to nucleic acid incorporation, likewise, the overall charge of such particles in solution can be defined by a zeta potential of about 50-80 mV. [0082] In preparing such liposomes, any protocol described herein, or as would be known to one of ordinary _' skill in the art may be used. Additional non-limiting examples of preparing liposomes are described in U.S. Patents 4,728,578, 4,728,575, 4,737,323, 4,533,254, 4,162,282, 4,310,505, and 4,921,706; International Applications PCT/US85/01161 and PCT/US89/05040; U.K. Patent Application GB 2193095 A, Mayer et al., 1986; Hope et al. , 1985; Mayhew et al. 1987; Mayhew et al., 1984; Cheng et al, 1987; and Liposome Technology, 1984, each incorporated herein by reference).

[0083] In certain embodiments, the lipid-based nanoparticle is a neutral liposome (e.g, a DOPC liposome). "Neutral liposomes” or “non-charged liposomes”, as used herein, are defined as liposomes having one or more lipid components that yield an essentially-neutra!, net charge (substantially non-charged). By “essentially neutral” or “essentially non-charged”, it is meant that few, if any, lipid components within a given population (e.g., a population of liposomes) include a charge that is not canceled by an opposite charge of another component (i.e., fewer than 10% of components include a lion-canceled charge, more preferably fewer than 5%, and most preferably fewer than 1%). In certain embodiments, neutral liposomes may include mostly lipids and/or phospholipids that are themselves neutral under physiological conditions (i.e., at about pH 7).

[0084] Liposomes and/or lipid-based nanoparticles of the present embodiments may comprise a phospholipid. In certain embodiments, a single kind of phospholipid may be used in the creation of liposomes (e.g., a neutral phospholipid, such as DOPC, may be used to generate neutral liposomes) In other embodiments, more than one kind of phospholipid may be used to create liposomes.

[0085] Phospholipids include, for example, phosphatidylcholines, phosphatidylglycero!s, and phosphatidyl ethanol amines; because phosphatidyl ethanolamines and phosphatidyl cholines are non-charged under physiological conditions (i.e., at about pH 7), these compounds may be particularly useful for generating neutral liposomes. In certain embodiments, the phospholipid DOPC is used to produce non-charged liposomes. In certain embodiments, a lipid that is not a phospholipid (e.g., a cholesterol) may be used

[0086] Phospholipids include glycerophospholipids and certain sphingolipids. Phospholipids include, but are not limited to, dioieoylphosphatidylycholine ("DOPC"), egg phosphatidylcholine ("EPC"), dilauryloylphosphatidylcholine ("DLPC"), dimyristoylphosphatidyl choline ("DMPC"), dipalmitoylphosphatidyl choline ("DPPC"), distearoylphosphatidylcholine ("DSPC"), l-myristoyl-2-palmitoyl phosphatidylcholine ("MPPC"), l-palmitoyl-2-myristoyl phosphatidylcholine ("PMPC"), l-palmitoyl-2-stearoyl phosphatidylcholine ("PSPC"), l-stearoyi-2-paimitoyl phosphatidylcholine ("SPPC"), dilauryl oylphosphatidylgly cerol ("DLPG"), dirayri stoylphosphatidylgly cerol ("DMPG"), dipalmitoylphosphatidylglycerol ("DPPG"), distearoylphosphatidylglycerol ("DSPG"), distearoyl sphingomyelin ("DSSP"), distearoyl phophati dyl ethanolamine ("DSPE"), dioieoylphosphatidylglycerol ("DOPG"), dimyristoyl phosphatidic acid ("DMPA"), dipalmitoyl phosphatidic acid ("DPPA"), dimyristoyl phosphatidylethanolamine ("DMPE"), dipalmitoyl phosphatidylethanolamine ("DPPE"), dimyristoyl phosphatidyl serine ("DMPS"), dipalmitoyl phosphatidylserine ("DPPS"), brain phosphatidylserine ("BPS"), brain sphingomyelin ("BSP"), dipalmitoyl sphingomyelin ("DPSP"), dimyristyl phosphatidylcholine ("DMPC"), l,2-distearoyl-sn-glycero-3-phosphocholine ("DAPC"), 1 ,2-diarachidoyl-sn- glycero-3-phosphocholine ("DBPC"), l,2-dieicosenoyl-sn-glycero-3-phosphocholine ("DEPC"), dioleoylphosphatidylethanolamine ("DOPE''), palmitoyloeoyl phosphatidylcholine ("POPC"), palmitoyloeoyl phosphatidylethanolamine ("POPE"), 3 ysophosphati dyl choline, lysophosphatidyiethanolamine, and dilinoleoylphosphatidylcholine.

[0087] Phospholipids may be from natural or synthetic sources. However, phospholipids from natural sources, such as egg or soybean phosphatidylcholine, brain phosphatidic acid, brain or plant phosphatidylinositol, heart cardiolipin and plant or bacterial phosphatidylethanolamine are not used, in certain embodiments, as the primary phosphatide (/. e., constituting 50% or more of the total phosphatide composition) because this may result in instability and leakiness of the resulting liposomes.

2. DOTAP:cholesteroI nanoparticle

[0088] In certain embodiments, the lipid-based vesicle is a DQTAP. cholesterol nanoparticle. DOTAPxholesteroi nanopariicles are prepared by mixing the cationic lipid DQTAP (I,2-bis(oleoyloxy)-3-(trimethylammonio)-propane) with cholesterol. Vesicles prepared with DNA can form a structure (called a “sandwich’) where the DNA appears to be condensed between two lipid bilayers (U.S. Patents 6,770,291 and 6,413,544).

[0089] A DOTAP: cholesterol-nucleic acid complex can be prepared as in the following non-limiting example. The DOTAPxhoiesterol (DC) nanoparticfes (sized 50 to 500 nni) are synthesized as described previously (U.S. Patents 6,770,291 and 6,413,544; Templeton, 1997). Briefly, 420 mg ofDOTAP and 208 mg of cholesterol are measure and mixed together with 30 ml of chloroform. Mixture is then allowed to dry on a rotary evaporator for 30 minutes and freeze dry for 15 minutes. The dried mixture is reconstituted in 30 ml of D5W by swirling at 50°C for 45 minutes and 37°C for 10 minutes. The mixture is ten subjected to low frequency sonication for five minutes to form liposomes. DOTAP: cholesterol liposome are then heated to 50°C and sequentially filtered through 1.0, 0.45, 0 2 and 0.1 pm sterile Whatman filters. The synthesized nanoparticles are stored at 4°C and used for preparing nanoparticle complexes. The formulated DOTAP: cholesterol liposome should be evenly dispersed with a particle size of 50-250 nm, an OD400 of less than 0.45 and zeta potential of 50-80 mV. Residual CHCh levels should be less than 60 ppm.

[0090] To prepare DOTAP:cholesterol-nucieic acid nanoparticles, 240 mΐ of liposomes (see above) are diluted in 360 pi D5W at room temperature. DNA (-5 mg/m!) is added to the mixture to a total volume of 600 pi. The mixture is moved up and down in a pipet to mix. Once settled the mixture should have an OD400 of between 0.65 and 0.95, a particle size of 200- 500 nm and be confirmed gram stain negative. The liposome complexes are stored at between 3°C and 28°C and agitated as little as possible.

B, Targeting of Nanopartides

[0091] Targeted delivery is achieved by the addition of ligands without compromising the ability of nanopartides to deliver their payloads. It is contemplated that this will enable delivery to specific cells, tissues and organs. The targeting specificity of the ligand-based delivery systems are based on the distribution of the ligand receptors on different cell types. The targeting ligand may either be non-covalenlly or covalently associated with a nanoparticle, and can be conjugated to the nanopartides by a variety of methods as discussed herein.

[0092] Examples of proteins or peptides that can be used to target nanopartides include transferin, lactoferrin, TGF-ot, nerve growth factor, albumin, HIV Tat peptide, RGD peptide, and insulin, as well as others (Gupta etal, 2005; Ferrari, 2005).

€, TUSC2 Expression Vectors

[0093] The term “vector” is used to refer to a carrier nucleic acid molecule into which a nucleic acid sequence can be inserted for introduction into a cell where it can be replicated. A nucleic acid sequence can be “exogenous,” which means that it is foreign to the cell into which the vector is being introduced or that the sequence is homologous to a sequence in the ceil but in a position within the host ceil nucleic acid in which the sequence is ordinarily not found. Vectors include plasmids, cosmids, viruses (bacteriophage, animal viruses, and plant viruses), and artificial chromosomes (e.g., YACs). One of skill in the art would be well equipped to construct a vector through standard recombinant techniques (see, for example, Maniatis et ah, 1989 and Ausubel etai, 1994, both incorporated herein by reference).

[0094] The term “expression vector” refers to any type of genetic construct comprising a nucleic acid coding for a RNA capable of being transcribed. In some cases, KNA molecules are then translated into a protein, polypeptide, or peptide. In other cases, these sequences are not translated, for example, in the production of antisense molecules or ribozymes. Expression vectors can contain a variety of “control sequences,” which refer to nucleic acid sequences necessary for the transcription and possibly translation of an operably linked coding sequence in a particular host ceil. In addition to control sequences that govern transcription and translation, vectors and expression vectors may contain nucleic acid sequences that serve other functions as well and are described infra.

[0095] In certain embodiments, provided herein is the use of nucleic acids TUSC2 coding sequence. For example, such vector can be used for recombinant production of a TUSC2 polypeptide and/or for the expression of 1TJSC2 in vivo in a subject. The sequences may be modified, given the ability of several different codons to encode a single amino acid, while still encoding for the same protein or polypeptide. Optimization of codon selection can also be undertaken in light of the particular organism used for recombinant expression or may be optimized for maximal expression in human cell {e.g., a cancer cell). Vector for use in accordance with the present embodiments additionally comprise elements that control gene expression and/or aid in vector production and purification.

1. Promoters and Enhancers

[0096] A “promoter” is a control sequence that is a region of a nucleic acid sequence at which initiation and rate of transcription are controlled It may contain genetic elements at which regulatory proteins and molecules may bind, such as RNA polymerase and other transcription factors, to initiate the specific transcription a nucleic acid sequence. The phrases “operatively positioned,” “operatively linked,” “under control,” and “under transcriptional control” mean that a promoter is in a correct functional location and/or orientation in relation to a nucleic acid sequence to control transcriptional initiation and/or expression of that sequence.

[0097] A promoter generally comprises a sequence that functions to position the start site for RNA synthesis. The best known example of this is the TATA box, but in some promoters lacking a TA TA box, such as, for exampl e, the promoter for the mammalian terminal deoxynucleotidyl transferase gene and the promoter for the SV40 late genes, a discrete element overlying the start site itself helps to fix the place of initiation. Additional promoter elements regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have been shown to contain functional elements downstream of the start site as well. To bring a coding sequence “under the control of’ a promoter, one positions the 5' end of the transcription initiation site of the transcriptional reading frame “downstream” of (i.e.. 3' of) the chosen promoter. The “upstream” promoter stimulates transcription of the DNA and promotes expression of the encoded RNA.

[0098] The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the tk promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either cooperatively or independently to activate transcription, A promoter may or may not be used in conjunction with an “enhancer,” which refers to a cis-acting regulatory sequence involved in the transcriptional activation of a nucleic acid sequence.

[0099] A promoter may be one naturally associated with a nucleic acid sequence, as may be obtained by isolating the 5' non-coding sequences located upstream of the coding segment and/or exon. Such a promoter can be referred to as “endogenous” or “homologous.” Similarly, an enhancer may be one naturally associated with a nucleic acid sequence, located either downstream or upstream of that sequence. Alternatively, certain advantages will be gained by positioning the coding nucleic acid segment under the control of a recombinant, exogenous or heterologous promoter, which refers to a promoter that is not normally associated with a nucleic acid sequence in its natural environment. A recombinant or heterologous enhancer refers also to an enhancer not normally associated with a nucleic acid sequence in its natural environment. Such promoters or enhancers may include viral promoter and enhancers such as the CMV promoter.

[00100] Naturally, it will be important to employ a promoter and/or enhancer that effectively directs the expression of the DNA segment in the organelle, cell, tissue, organ, or organism chosen for expression. Those of skill in the art of molecular biology generally know the use of promoters, enhancers, and cell type combinations for protein expression, (see, for example Sambrook etal 1989, incorporated herein by reference). The promoters employed may be constitutive, tissue-specific, inducible, and/or useful under the appropriate conditions to direct high level expression of the introduced DM A segment, such as is advantageous in the large-scale production of recombinant proteins and/or peptides. The promoter may be heterologous or endogenous.

[00101] Additionally, any promoter/enhancer combination (as per, for example, the Eukaryotic Promoter Data Base EPDB, www.epd.isb-sib.ch/) could also be used to drive expression. Use of a T3, T7 or 8P6 cytoplasmic expression system is another possible embodiment. Eukaryotic cells can support cytoplasmic transcription from certain bacterial promoters if the appropriate bacterial polymerase is provided, either as part of the delivery' complex or as an additional genetic expression construct.

2o Translation Initiation Signals

[00102] A specific initiation signal also may be required for efficient translation of coding sequences. These signals include the ATG initiation codon or adjacent sequences. Exogenous translational control signals, including the ATG initiation codon, may need to be provided. One of ordinary' skill in the art would readily be capable of determining this and providing the necessary' signals. It is well known that the initiation codon must be “in-frame” with the reading frame of the desired coding sequence to ensure translation of the entire insert. The exogenous translational control signals and initiation codons can be either natural or synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements.

3. Multiple Cloning Sites

[00103] Vectors can include a multiple cloning site (MC8), which is a nucleic acid region that contains multiple restriction enzyme sites, any of which can be used in conjunction with standard recombinant technology to digest the vector (see, for example, Carbonelli et ah, 1999, Levenson et ah, 1998, and Cocea, 1997, incorporated herein by reference). “Restriction enzyme digestion” refers to catalytic cleavage of a nucleic acid molecule with an enzyme that functions only at specific locations in a nucleic acid molecule. Many of these restriction enzymes are commercially available. Use of such enzymes is widely understood by those of skill in the art. Frequently, a vector is linearized or fragmented using a restriction enzyme that cuts within the MCS to enable exogenous sequences to be ligated to the vector. “ligation” refers to the process of forming phosphodiester bonds between two nucleic acid fragments, which may or may not be contiguous with each other. Techniques involving restriction enzymes and ligation reactions are well known to those of skill in the art of recombinant techn oi ogy .

4. Splicing Sites

[00104] Most transcribed eukaryotic RNA molecules will undergo RNA splicing to remove introns from the primary' transcripts. Vectors containing genomic eukaryotic sequences may require donor and/or acceptor splicing sites to ensure proper processing of the transcript for protein expression (see, for example, Chandler et ah, 1997, herein incorporated by reference). Inclusion of such splice sites also can enhance expression by averting non-sense mediated decay of resulting RNA transcripts

5. Termination Signals

[00105] The vectors or constructs of the present embodiments will generally comprise at least one termination signal. A “termination signal” or “terminator” is comprised of the DNA sequences involved in specific termination of an RNA transcript by an RNA polymerase. Thus, in certain embodiments a termination signal that ends the production of an RNA transcript is contemplated. A terminator may be necessary in vivo to achieve desirable message levels.

[00106] Terminators contemplated for use in the present embodiments include any known terminator of transcription described herein or known to one of ordinary skill in the art, including but not limited to, for example, the termination sequences of genes, such as for example the bovine growth hormone terminator or viral termination sequences, such as for example the SV40 terminator In certain embodiments, the termination signal may be a lack of transcrib able or translatable sequence, such as due to a sequence truncation. 6. Polyadenylation Signals

[Q0107] In expression, particularly eukaryotic expression, one will typically include a polyadenylation signal to effect proper polyadenylation of the transcript. The nature of the polyadenylation signal is not believed to be crucial to the successful practice of the present embodiments, and any such sequence may be employed. Preferred embodiments include the SV40 polyadenylation signal or the bovine growth hormone polyadenylation signal, convenient and known to function well in various target cells. Polyadenylation may increase the stability of the transcript or may facilitate cytoplasmic transport.

7. Origins of Replication

[00108] In order to propagate a vector in a host cell, it may contain one or more origins of replication sites (often termed “ori”), which is a specific nucleic acid sequence at which replication is initiated. Alternatively, an autonomously replicating sequence (ARS) can be employed if the host cell is yeast.

8. Selectable and Screenable Markers

[00109] In certain embodiments, cells containing a nucleic acid construct provided herein may be identified in vitro or in vivo by including a marker in the expression vector. Such markers would confer an identifiable change to the cell permitting easy identification of ceils containing the expression vector. Generally, a selectable marker is one that confers a property that allows for selection. A positive selectable marker is one in which the presence of the marker allows for its selection, while a negative selectable marker is one in which its presence prevents its selection. An example of a positive selectable marker is a drag resistance marker.

[00110] Usually the inclusion of a drag selection marker aids in the cloning and identification of transformants, for example, genes that confer resistance to neomycin, puromycin, hygromycin, DHFR, GPT, zeocin and histidinol are useful selectable markers. In addition to markers conferring a phenotype that allows for the discrimination of transformants based on the implementation of conditions, other types of markers including screenable markers such as GFP, whose basis is colorimetric analysis, are also contemplated. Alternatively, screenable enzymes such as herpes simplex virus thymidine kinase (tk) or chloramphenicol acetyltransferase (CAT) may be utilized. One of skill in the art. would also know·' how to employ immunologic markers, possibly in conjunction with FACS analysis. The marker used is not believed to be important, so long as it is capable of being expressed simultaneously with the nucleic acid encoding a gene product. Further examples of selectable and screenable markers are well known to one of skill in the art

9. Plasmid Vectors

[00111] In certain embodiments, a plasmid vector is contemplated for use to transform a host cell. In general, plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts. The vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells. In a non-limiting example, E. coli is often transformed using derivatives of pBR322, a plasmid derived from an E. coli species. pBR322 contains genes for ampicillin and tetracycline resistance and thus provides easy means for identifying transformed cells. The pBR plasmid, or other microbial plasmid or phage must also contain, or be modified to contain, for example, promoters which can be used by the microbial organism for expression of its own proteins.

[00112] In addition, phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as transforming vectors in connection with these hosts. For example, the phage lambda GEM ^iM -l l may be utilized in making a recombinant phage vector which can be used to transform host cells, such as, for example, E. coli LE392.

[00113] Further useful plasmid vectors include pIN vectors (Inouye etal, 1985); and pGEX vectors, for use in generating glutathione S-transferase (GST) soluble fusion proteins for later purification and separation or cleavage. Other suitable fusion proteins are those with b-galactQsidase, ubiquitin, and the like.

[00114] Bacterial host, cells, for example, E. coli, comprising the expression vector, are grown in any of a number of suitable media, for example, LB. The expression of the recombinant protein in certain vectors may be induced, as would be understood by those of skill in the art, by contacting a host cell with an agent specific for certain promoters, e.g., by adding IPTG to the media or by switching incubation to a higher temperature. After culturing the bacteria for a further period, generally of 2-24 hr, the cells are collected by centrifugation and washed to remove residual media. 10, Viral Vectors

[00115] The ability of certain viruses to infect cells or enter cells via receptor-mediated endocytosis, and to integrate into host cell genome and express viral genes stably and efficiently have made them attractive candidates for the transfer of foreign nucleic acids into cells (e.g., mammalian cells). Viruses may thus be utilized that encode and express TUSC2. Non-limiting examples of vims vectors that may he used to deliver a TUSC2 nucleic acid are described below.

[00116] Adenoviral Vectors, A particular method for delivery of the nucleic acid involves the use of an adenovirus expression vector. Although adenovirus vectors are known to have a low capacity for integration into genomic DNA, this feature is counterbalanced by the high efficiency of gene transfer afforded by these vectors. "Adenovirus expression vector" is meant to include those constructs containing adenovirus sequences sufficient to (a) support packaging of the construct and (b) to ultimately express a tissue or cell-specific construct that has been cloned therein. Knowledge of the genetic organization or adenovirus, a 36 kb, linear, double-stranded DNA vims, allows substitution of large pieces of adenoviral DNA with foreign sequences up to 7 kb (Grunhaus and Horwitz, 1992).

[00117] AAV Vectors. The nucleic acid may be introduced into the cell using adenovirus assisted transfection. Increased transfection efficiencies have been reported in cell systems using adenovirus coupled systems (Kelleher and Vos, 1994; Gotten et ai, 1992; Curl el, 1994). Adeno-associated vims (AAV) has a high frequency of integration and it can infect non-dividing cells, thus making it useful for delivery of genes into mammalian cells, for example, in tissue culture (Muzyczka, 1992) or in vivo. AAV has a broad host range for infectivity (Tratschin et ai, 1984; Laughlin e/ ai, 1986; Lebkowski et a!., 1988; McLaughlin et al, 1988). Details concerning the generation and use of rAAV vectors are described in U.8. Patents 5,139,941 and 4,797,368, each incorporated herein by reference.

[Q0118] Retroviral Vectors. Retroviruses have the ability to integrate their genes into the host genome, transferring a large amount of foreign genetic material, infecting a broad spectrum of species and cell types and of being packaged in special cell-lines. In order to construct a retroviral vector, a nucleic acid (e.g., one encoding a protein of interest) is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective. In order to produce virions, a packaging cell line containing the gag, roί, and env genes but without the LTR and packaging components is constructed (Mann et al, 1983). When a recombinant plasmid containing a cDNA, together with the retroviral LTR and packaging sequences is introduced into a special cell line (e.g., by calcium phosphate precipitation for example), the packaging sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media (Nicolas and Rubinstein, 1988; Temin, 1986; Mann et al, 1983). The media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression require the division of host cells (Paskind et al, 1975).

[00119] Lentiviruses are complex retroviruses, which, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural function. Lentiviral vectors are well known in the art (see, for example, Naldini et al, 1996; Zufferey et al, 1997; Blomer et al, 1997; U.S. Patents 6,013,516 and 5,994,136). Some examples of ientivirus include the Human Immunodeficiency Viruses: HIV-1, HIV-2 and the Simian Immunodeficiency Vims: SIV. Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif vpr, vpu and nef are deleted making the vector biologically safe,

[00120] Other Viral Vectors. Other viral vectors may be employed as vaccine constructs in the present embodiments. Vectors derived from viruses such as vaccinia virus (Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al, 1988), sindbis vims, cytomegalovirus and herpes simplex vims may be employed. They offer several attractive features for various mammalian cells (Friedmann, 1989; Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al, 1988; Horwich et al, 1990).

[00121] Modified Viruses. A nucleic acid to be delivered may be housed within an infective virus that has been engineered to express a specific binding ligand. The vims particle will thus bind specifically to the cognate receptors of the target cell and deliver the contents to the cell. A novel approach designed to allow ⁷ specific targeting of retrovirus vectors was developed based on the chemical modification of a retrovirus by the chemical addition of lactose residues to the viral envelope. This modification can permit the specific infection of hepatocytes via sialoglycoprotein receptors. [00122] Another approach to targeting of recombinant retroviruses was designed in which biotinylated antibodies against a retroviral envelope protein and against a specific cell receptor were used. The antibodies were coupled via the biotin components by using streptavidin (Roux ei al, 1989). Using antibodies against major histocompatibility complex class I and class II antigens, they demonstrated the infection of a variety of human cells that bore those surface antigens with an ecotropic virus in vitro (Roux ei al, 1989).

III. PHARMACEUTICAL FORMULATIONS

[00123] Pharmaceutical compositions provided herein comprise an effective amount of one or more TUSC2 therapeutic and/or a PDKl inhibitor and, optionally, an additional agent dissolved or dispersed in a pharmaceutically acceptable carrier. The phrases "pharmaceutical or pharmacologically acceptable” refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate. The preparation of a pharmaceutical composition that contains at least TUSC2 nucleic acid, peptide or a nanoparticle complex or additional active ingredient will be known to those of skill in the art in light of the present disclosure, as exemplified by Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990, incorporated herein by reference. Moreover, for animal {e.g., human) administration, it will be understood that preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biological Standards.

[00124] As used herein, "pharmaceutically acceptable earner" includes any and all solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, such like materials and combinations thereof, as would be known to one of ordinary skill in the art. (see, for example, Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990, pp. 1289-1329, incorporated herein by reference). Except insofar as any conventional earner is incompatible with the active ingredient, its use in the therapeutic or pharmaceutical compositions is contemplated. [00125] In certain embodiments, the pharmaceutical composition may comprise different types of carriers depending on whether it is to be administered in solid, liquid or aerosol form, and whether it need to be sterile for such routes of administration as injection. In certain embodiments, pharmaceutical compositions provided herein can be administered intravenously, intradermally, intraarterially, intrapeiitoneally, intralesionally, intracranial ly, intraarticuJarly, intraprostaticaly, intrapieuraily, intratracheally, intranasaily, mtravitreally, intravaginaily, intrarectally, topically, intratumorally, intramuscularly, intrapeiitoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally, topically, locally, inhalation (e.g. aerosol inhalation), injection, infusion, continuous infusion, localized perfusion bathing target cells directly, via a catheter, via a lavage, in cremes, in lipid compositions (e.g ^· ., liposomes), or by other method or any combination of the forgoing as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990, incorporated herein by reference).

[00126] In certain embodiments, the pharmaceutical composition is administered intraperitoneally. In further embodiments, the pharmaceutical composition is administered intrapeiitoneally to treat a cancer (e.g., a cancerous tumor). For example, the pharmaceutical composition may be administered intraperitoneally to treat gastrointestinal cancer. In certain embodiments it may be desirable to administer the pharmaceutical composition into or near a tumor.

[00127] In certain preferred embodiments, the pharmaceutical composition is administered orally to treat a cancer (e.g., a gastrointestinal cancer).

[00128] In certain embodiments, the actual dosage amount of a composition administered to a patient can be determined by physical and physiological factors such as body weight, severity of condition, the type of disease being treated, previous or concurrent therapeutic interventions, idiopathy of the patient and on the route of administration The practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject.

[00129] In certain embodiments, pharmaceutical compositions may comprise, for example, at least about 0.1% of an active compound. In other embodiments, the active compound may comprise between about 2% to about 75% of the weight of the unit, or between about 25% to about 60%, for example, and any range derivable therein. In other non-limiting examples, a dose may also comprise from about 1 microgram/kg/body weight, about 5 microgram/kg/body weight, about 10 microgram/kg/body weight, about 15 microgram/kg/body weight, about 20 microgram/kg/body weight, about 25 microgram/kg/body weight, about 30 rnicrogram/kg/body weight, about 35 microgram/kg/body weight, about 0.04 milligram/kg/body weight, about 005 milligram/kg/body weight, about 0,06 milligram/kg/body weight, about 0.07 milligram/kg/body weight, about 0.08 milligram/kg/body weight, about 0.09 milligram/kg/body weight, about 0.1 milligram/kg/body weight, about 0.2 milligram/kg/body weight, to about 0.5 mg/kg/body weight or more per administration, and any range derivable therein. In non-limiting examples of a derivable range from the numbers listed herein, a range of about 0.01 mg/kg/body w ^r eight to about 0.1 mg/kg/body weight, about 0.04 microgram/kg/body weight to about 0.08 milligram/kg/body weight, etc., can be administered, based on the numbers described above.

[00130] In any case, the composition may comprise various antioxidants to retard oxidation of one or more component. Additionally, the prevention of the action of microorganisms can be brought about by preservatives such as various antibacterial and antifungal agents, including but not limited to parabens (e.g., methylparabens, propylparabens), chlorobutanol, phenol, sorbic acid, thimerosal or combinations thereof.

[00131] The one or more peptides, nanoparticle complexes or additional agent may be formulated into a composition in a free base, neutral or salt form. Pharmaceutically acceptable salts, include the acid addition salts, e.g., those formed with the free amino groups of a proteinaceous composition, or which are formed with inorganic acids such as for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric or mande!ic acid. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as for example, sodium, potassium, ammonium, calcium or ferric hydroxides; or such organic bases as isopropylamine, trimethyi amine, histidine or procaine.

[00132] In embodiments where the composition is in a liquid form, a carrier can be a solvent or dispersion medium comprising but not limited to, water, ethanol, polyol (e.g., glycerol, propylene glycol, liquid polyethylene glycol, etc.), lipids (e.g., triglycerides, vegetable oils, liposomes) and combinations thereof. The proper fluidity can be maintained. for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size by dispersion in earners such as, for example liquid polyol or lipids; by the use of surfactants such as, for example hydroxypropyi cellulose; or combinations thereof such methods. In many eases, it will be preferable to include isotonic agents, such as, for example, sugars, sodium chloride or combinations thereof.

[00133] In other embodiments, one may use eye drops, nasal solutions or sprays, aerosols or inhalants in the present embodiments. Such compositions are generally designed to be compatible with the target tissue type. In a non-limiting example, nasal solutions are usually aqueous solutions designed to be administered to the nasal passages in drops or sprays. Nasal solutions are prepared so that they are similar in many respects to nasal secretions, so that norma! ciliary action is maintained. Thus, in preferred embodiments the aqueous nasal solutions usually are isotonic or slightly buffered to maintain a pH of about 5.5 to about 6.5. In addition, antimicrobial preservatives, similar to those used in ophthalmic preparations, drugs, or appropriate drug stabilizers, if required, may be included in the formulation. For example, various commercial nasal preparations are known and include drugs such as antibiotics or antihistamines.

[00134] In certain embodiments the one or more polypeptide, nucleic acid or nanoparticle complexes are prepared for administration by such routes as oral ingestion. In these embodiments, the solid composition may comprise, for example, solutions, suspensions, emulsions, tablets, pills, capsules (e.g, hard or soft shelled gelatin capsules), sustained release formulations, buccal compositions, troches, elixirs, suspensions, syrups, wafers, or combinations thereof. Oral compositions may be incorporated directly with the food of the diet Preferred carriers for oral administration comprise inert diluents, assimilable edible carriers or combinations thereof. In other aspects, the oral composition may be prepared as a syrup or elixir. A syrup or elixir, and may comprise, for example, at least one active agent, a sweetening agent, a preservative, a flavoring agent, a dye, a preservative, or combinations thereof.

[00135] In certain preferred embodiments an oral composition may comprise one or more binders, excipients, disintegration agents, lubricants, flavoring agents, and combinations thereof. In certain embodiments, a composition may comprise one or more of the following: a binder, such as, for example, gum tragacanth, acacia, cornstarch, gelatin or combinatioiis thereof; an excipient, such as, for example, di calcium phosphate, mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate or combinations thereof, a disintegrating agent, such as, for example, corn starch, potato starch, alginic acid or combinations thereof; a lubricant, such as, for example, magnesium stearate; a sweetening agent, such as, for example, sucrose, lactose, saccharin or combinations thereof; a flavoring agent, such as, for example peppermint, oil of wintergreen, cherry flavoring, orange flavoring, etc.; or combinations thereof the foregoing. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, carriers such as a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit For instance, tablets, pills, or capsules may be coated with shellac, sugar or both.

[00136] Additional formulations which are suitable for other modes of administration include suppositories. Suppositories are solid dosage forms of various weights and shapes, usually medicated, for insertion into the rectum, vagina or urethra. After insertion, suppositories soften, melt or dissolve in the cavity fluids. In general, for suppositories, traditional carriers may include, for example, poiyalkylene glycols, triglycerides or combinations thereof. In certain embodiments, suppositories may be formed from mixtures containing, for example, the active ingredient in the range of about 0.5% to about 10%, and preferably about 1% to about 2%.

[00137] Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and/or the other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, suspensions or emulsion, the preferred methods of preparation are vacuum-drying or freeze-diving techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered liquid medium thereof. The liquid medium should be suitably buffered if necessary and the liquid diluent first, rendered isotonic prior to injection with sufficient saline or glucose. The preparation of highly concentrated compositions for direct injection is also contemplated, where the use of DMSO as solvent is envisioned to result in extremely rapid penetration, delivering high concentrations of the active agents to a small area. [00138] The composition must be stabl e under the conditions of manufacture and storage, and preserved against the contaminating action of microorganisms, such as bacteria and fungi, it will be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less than 0.5 ng/mg protein.

[00139] In particular embodiments, prolonged absorption of an injectable composition can be brought about by the use in the compositions of agents delaying absorption, such as, for example, aluminum monostearate, gelatin or combinations thereof.

IV. COMBINATION THERAPIES

[00140] In order to increase the effectiveness of a nucleic acid, polypeptide or nanoparticle complex of the present embodiments, it may be desirable to combine these compositions with other agents effective in the treatment of the disease of interest.

[00141] As a non-limiting example, the treatment of cancer may be implemented with TUSC2 therapeutic and/or an PDK1 inhibitor of the present embodiments along with other anti-cancer agents. An “anti-cancer” agent is capable of negatively affecting cancer in a subject, for example, by killing cancer cells, inducing apoptosis in cancer cells, reducing the growth rate of cancer cells, reducing the incidence or number of metastases, reducing tumor size, inhibiting tumor growth, reducing the blood supply to a tumor or cancer cells, promoting an immune response against cancer ceils or a tumor, preventing or inhibiting the progression of cancer, or increasing the lifespan of a subject with cancer. More generally, these other compositions would be provided in a combined amount effective to kill or inhibit proliferation of the cell. This process may involve contacting the cells with the anti-cancer peptide or nanoparticle complex and the agenl(s) or multiple factor(s) at the same time. This may be achieved by contacting the cell with a single composition or pharmacological formulation that includes both agents, or by contacting the cell with two distinct compositions or formulations, at the same time, wherein one composition includes the anti-cancer peptide or nanoparticle complex and the other includes the second agent(s). In particular embodiments, an anti-cancer peptide can be one agent, and an anti-cancer nanoparticle complex can be the other agent.

[00142 j Treatment with the anti-cancer peptide or nanoparticle- complex may precede or follow the other agent treatment by intervals ranging from minutes to weeks. In embodiments where the other agent and the anti-cancer peptide or nanoparticle complex are applied separately to the cell, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent and the anti-cancer peptide or nanoparticle complex would still be able to exert an advantageously combined effect on the cell. In such instances, it is contemplated that one may contact the cell with both modalities within about 12-24 hours of each other and, more preferably, within about 6-12 hours of each other. In some situations, it may be desirable to extend the time period for treatment significantly where several days (e.g., 2, 3, 4, 5, 6 or 7 days) to several weeks (e.g, 1, 2, 3, 4, 5, 6, 7 or 8 weeks) lapse between the respective administrations.

[00143] Likewise, in certain aspects a TUSC2 therapy is administered in conjunction with a PDK1 inhibitor. Various combinations may be employed, where the TLISC2 therapy is ‘74” and the PDK1 inhibitor, is “B”:

A/B/A B/A'B B/B/A A/A/B A'B/B B/A/A A/B/B/B B/A/B/B

B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A B/B/A/A

B/A/B/A B/A'A/B A/A/A/B B/A/A/A A/B/A/A A/A/B/A

[00144] In certain embodiments, administration of the TUSC2 therapy and/or an PDK1 inhibitor of the present embodiments to a patient will follow general protocols for the administration of chemotherapeutics, taking into account the toxicity, if any, of the vector. It is expected that the treatment cycles would be repeated as necessary. It also is contemplated that various standard therapies, as well as surgical intervention, may be applied in combination with the described hyperproliferative cell therapy.

A. Chemotherapy

[00145] Cancer therapies also include a variety of combination therapies. In some aspects a 1TJSC2 therapeutic and/or a PDK 1 inhibitor of the embodiments is administered (or formulated) in conjunction with a chemotherapeutic agent. For example, in some aspects the chemotherapeutic agent is a protein kinase inhibitor such as a EGFR, VEGFR, LKΪ. Erb 1 , Erb2, ErbB, Syk, Ber-Abl, JAK, Src, GSK-3, PI3K, Has, Raf, MAPK, MAPKK, mTOR, c-Kit, eph receptor or BRAF inhibitors. Nonlimiting examples of protein kinase inhibitors include Afatinib, Axitinib, Bevacizumab, Bosutinib, Cetuximab, Crizotinib, Dasatinib, Erlotinib, Fostamatimb, Gefitinib, Imatinib, Lapatinib, Lenvatinib, Mubritinib, Nilotinib, Panitumumab, Pazopanib, Pegaptanib, Ranibizumab, Ruxolitinib, Saracatinib, Sorafenib, Sunitinib, Trastuzumab, Vandetanib, AP23451, Vemurafenib, MK-2206, GSK690693, A-443654, VQD- 002, Miltefosine, Perifosine, CAL101, PX-866, LY294002, rapamycin, temsiroiimus, everolimus, ridaforo!imus, Alvocidib, Genistein, Selumetinib, AZD-6244, Vatalanib, P1446A- 05, AG-024322, ZD1839, P276-00, GW572016 or a mixture thereof.

[00146] Yet further combination chemotherapies include, for example, alkylating agents such as thiotepa and cyc!osphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposu!fan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenirnines and methylamelamines including aitretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topoteean); hryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); ciyptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancrati statin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, ch!omaphazine, cholophosphamide, estramustine, ifosfamide, mechiorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calichearnicin, especially cali cheami tin ganimall and calicheamicin omegall; dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores, aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophiiin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino- doxorubicin, cyanomorpholino-doxorubitin, 2-pyrrolino-doxorubiein and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogaiarnycin, olivomycins, peplomycin, potfiromycin, puromycin, quelaxnycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenirnex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, pteropterin, trimetrexate; purine analogs such as fludarabine, 6- mercaptopurine, tbiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine, androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as mitotane, trilostane; folic acid repienisher such as frolinic acid; acegl atone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; eliiptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; ientinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidamnol; nitraerine; pentostatin; phenarnet; pirambicin; losoxantrone; podopbyllinic acid; 2-ethylhydrazide; procarbazine; PSK polysaccharide complex, razoxane; rhizoxin; sizofiran; spirogermaniurn; tenuazonic acid; triaziquone; 2,2',2”-trichl orotri ethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol, pipobroman; gacytosine, arabinoside (“Ara-C”); cyclophosphamide; taxoids, e.g., paelitaxel and docetaxel gemcitabine; 6-thioguanine; mercaptopurine; platinum coordination complexes such as cisplatin, oxaliplatin and carboplatin; vinblastine, platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomyein; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000; difluorometihyiomithine (DMFO); retinoids such as retinoic acid; capecitabine; carboplatin, procarbazine, pli corny tin, gemcitabien, nave!bine, farnesyl -protein tansferase inhibitors, transplatinum, and pharmaceutically acceptable salts, acids or derivatives of any of the above. In certain embodiments, the compositions provided herein may be used in combination with gefitinib. In other embodiments, the present embodiments may be practiced in combination with Gleevac (e.g., from about 400 to about 800 mg/day of Gleevac may be administered to a patient). In certain embodiments, one or more chemotherapeutic may be used in combination with the compositions provided herein.

B. Radiotherapy

[00147] Other factors that cause DNA damage and have been used extensively include what are commonly known as g-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells. Other forms of DNA damaging factors are also contemplated such as microwaves and UV-irradiation. It is most likely that all of these factors effect abroad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes. Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage ranges for radioisotopes vary widely, and depend on the half- life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.

[00148] The terms “contacted” and “exposed,” when applied to a cell, are used herein to describe the process by which a therapeutic composition and a chemotherapeutic or radiotherapeutic agent are delivered to a target cell or are placed in direct juxtaposition with the target cell . To achieve cell killing or stasis, both agents are delivered to a cell in a combined amount effective to kill the cell or prevent it from dividing.

C. Immunotherapy

[00149] Immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells. The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell. The antibody alone may serve as an effector of therapy or it may recruit other cells to actually effect, cell killing. The antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ricin A chain, cholera toxin, pertussis toxin, etc.) and serve merely as a targeting agent. Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target. Various effector ceils include cytotoxic T cells and NK ceils.

[QQ15Q] Immunotherapy, thus, could be used as part of a combined therapy, in conjunction with a TUSC2 therapy of the present embodiments The general approach for combined therapy is discussed below. Generally, the tumor ceil must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in the context of the present embodiments. Common tumor markers include carcinoembryonic antigen, prostate specific antigen, urinary' tumor associated antigen, fetal antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, FLAP, estrogen receptor, laminin receptor, erb B and p 155.

[00151] A particular type of immunotherapy i s an “immune checkpoint therapy” which refers to a component of the immune system which provides inhibitory signals to its components in order to regulate immune reactions. Known immune checkpoint proteins comprise CTLA-4, PD-1 and its ligands PD-L1 and PD-L2 and in addition LAG-3, BTLA, B7H3, B7H4, TΪM3, KIR. The pathways involving LAG3, BTLA, B7H3, B7H4, TIM3, and KIR are recognized in the art to constitute immune checkpoint pathways similar to the CTLA- 4 and PD-1 dependent pathways (see e.g. Pardol!, 2012, Nature Rev Cancer 12:252-264; Meliman etal, 2011, Nature 480:480- 489).

[00152] The term “PD- 1 axis binding antagonist” refers to a molecule that inhibits the interaction of a PD-1 axis binding partner with either one or more of its binding partners, so as to remove T-cell dysfunction resulting from signaling on the PD-1 signaling axis - with a result being to restore or enhance T-cell function (e.g., proliferation, cytokine production, target cell killing). The term “PD-1” axis” refers to any component of the PD-1 immune checkpoint (e.g., PD-1, PD;-L1, and PD-L2). As used herein, a PD-1 axis binding antagonist includes a PD-1 binding antagonist, a PD-L1 binding antagonist and a PD-L2 binding antagonist.

[00153] The term “PD-1 binding antagonist” refers to a molecule that decreases, blocks, inhibits, abrogates or interferes with signal transduction resulting from the interaction of PD-1 with one or more of its binding partners, such as PD-L1 and/or PD-L2. The PD-1 binding antagonist may be a molecule that inhibits the binding of PD-1 to one or more of its binding partners. In a specific aspect, the PD-1 binding antagonist inhibits the binding of PD- 1 toPD-Ll and/or PD-L2. For example, PD-1 binding antagonists include anti-PD-1 antibodies, antigen binding fragments thereof, immunoadhesins, fusion proteins, oligopeptides and other molecules that decrease, block, inhibit, abrogate or interfere with signal transduction resulting from the interaction of PD-1 with PD-L1 and/or PD-L2. An exemplary PD-1 binding antagonist is an anti-PD-1 antibody. For example, the PD-1 binding antagonist is MDX-1106 (nivolumab), MK-3475 (pembrolizumab), CT-011 (pidiiizumab), or AMP-224.

[00154] The term “PD-L1 binding antagonist” refers to a molecule that decreases, blocks, inhibits, abrogates or interferes with signal transduction resulting from the interaction ofPD-Ll with either one or more of its binding partners, such as PD-1 orB7-l . For example, a PD-L1 binding antagonist is a molecule that inhibits the binding of PD-L1 to its binding partners. In a specific aspect, the PD-L.1 binding antagonist inhibits binding ofPD-Ll to PD-1 and/or B7-1. The PD-L1 binding antagonists may include anti-PD-Ll antibodies, antigen binding fragments thereof, immunoadhesins, fusion proteins, oligopeptides and other molecules that decrease, block, inhibit, abrogate or interfere with signal transduction resulting from the interaction ofPD-Ll with one or more of its binding partners, such as PD-1 or B7-1. For example, a PD-L1 binding antagonist reduces the negative co-stimuiatory signal mediated by or through cell surface proteins expressed on T lymphocytes mediated signaling through PD-L1 so as to render a dysfunctional T-cell less dysfunctional (e.g, enhancing effector responses to antigen recognition). In one example, a PD-Ll binding antagonist is an anti-PD- Ll antibody. The anti-PD-Li antibody may be YW243.55.S70, MDX-1IQ5, MPDL3280A, or MEDI4736.

[00155] The term “PD-L2 binding antagonist” refers to a molecule that decreases, blocks, inhibits, abrogates or interferes with signal transduction resulting from the interaction of PD-L2 with either one or more of its binding partners, such as PD- 1. A PD-L2 binding antagonist may be a molecule that inhibits the binding of PD-L2 to one or more of its binding partners. For example, the PD-L2 binding antagonist inhibits binding of PD-L2 to PD- 1, such as PD-L2 antagonists including anti -PD- L2 antibodies, antigen binding fragments thereof, immunoadhesins, fusion proteins, oligopeptides and other molecules that decrease, block, inhibit, abrogate or interfere with signal transduction resulting from the interaction of PD-L2 with either one or more of its binding partners, such as PD-1.

[00156] An “immune checkpoint inhibitor” refers to any compound inhibiting the function of an immune checkpoint protein. Inhibition includes reduction of function and full blockade. In particular the immune checkpoint protein is a human immune checkpoint protein. Thus the immune checkpoint protein inhibitor in particular is an inhibitor of a human immune checkpoint protein.

[00157] Thus, the present disclosure provides methods of enhancing the efficacy of immune checkpoint blockade by administration of a tumor suppressor agent, such as TU8C2 therapy. As discussed above, immune checkpoints either turn up a signal (e.g., co-stimulatory molecules) or turn down a signal. Inhibitory' immune checkpoint molecules that may be targeted by immune checkpoint blockade include adenosine A2A receptor (A2AR), B7-H3 (also known as CD276), B and T lymphocyte attenuator (BTLA), cytotoxic T -lymphocyte- associated protein 4 (CTLA-4, also known as CD152), indoleamine 2,3-dioxygenase (IDO), killer-cell immunoglobulin (KIR), lymphocyte activation gene-3 (LAG3), programmed death 1 (PD-1), T-cell immunoglobulin domain and mucin domain 3 (TIM-3) and V-domain Ig suppressor of T cell activation (VISTA). In particular, the immune checkpoint inhibitors target the PD-1 axis and/or CTLA-4. [00158] The immune checkpoint inhibitors may be drugs such as small molecules, recombinant forms of ligand or receptors, or, antibodies, such as human antibodies (e.g., International Patent Publication No. WO2Q15016718; Pardoll, Nat Rev Cancer, 12(4): 252-64, 2012; both incorporated herein by reference). Known inhibitors of the immune checkpoint proteins or analogs thereof may be used, in particular chimerized, humanized or human forms of antibodies may be used. As the skilled person will know", alternative and/or equivalent names may be in use for certain antibodies mentioned in the present disclosure. Such alternative and/or equivalent names are interchangeable in the context of the present invention. For example, it is known that lambrolizumab is also known under the alternative and equivalent names MK-3475 and pembrolizumab.

[00159] It is contemplated that any of the immune checkpoint inhibitors that are known in the art to stimulate immune responses may be used. This includes inhibitors that directly or indirectly stimulate or enhance antigen-specific T-lympbocytes. These immune checkpoint inhibitors include, without limitation, agents targeting immune checkpoint proteins and pathways involving PD-L2, LAG3, BTLA, B7H4 and TIM3. For example, LAG3 inhibitors known in the art include soluble LAG3 (IMP321, or LAG3-Ig disclosed in W02009044273, incorporated herein by reference) as well as mouse or humanized antibodies blocking human LAG3 {e.g., IMP701 disclosed in WQ2008132601, incorporated herein by reference), or fully human antibodies blocking human LAG3 (such as disclosed in EP 2320940, incorporated herein by reference). Another example is provided by the use of blocking agents towards BTLA, including without limitation antibodies blocking human BTLA interaction with its ligand (such as 4C7 disclosed in WO2011014438, incorporated herein by reference). Yet another example is provided by the use of agents neutralizing B7H4 including without limitation antibodies to human B7H4 (disclosed in WO 2013025779, and in WO2013067492, each incorporated herein by reference) or soluble recombinant forms of B7H4 (such as disclosed in US20120177645, incorporated herein by reference). Yet another example is provided by agents neutralizing B7-H3, including without limitation antibodies neutralizing human B7-H3 (e.g. MGA271 disclosed as BRCA84D and derivatives in US 20120294796, incorporated herein by reference). Yet another example is provided by agents targeting TIM 3, including without limitation antibodies targeting human TIM3 (e.g. as disclosed in WO 2013006490 A2 or the anti-human TIM3, blocking antibody F38-2E2 disclosed by Jones etal., J Exp Med 2008, 205(12):2763-79, each, incorporated herein by reference). [00160] T cell dysfunction or anergy occurs concurrently with an induced and sustained expression of the inhibitory receptor, programmed death 1 polypeptide (PD-1). Thus, therapeutic targeting of PD-1 and other molecules which signal through interactions with PD- I, such as programmed death ligand 1 (PD-LI) and programmed death ligand 2 (PD-L2) is provided herein. PD-LI is overexpressed in many cancers and is often associated with poor prognosis (Okazaki T et at, Intern. Immun. 2007 19(7):813). Thus, improved methods of treating cancer by inhibiting the PD-Ll/PD-1 interaction in combination with administration of a tumor suppressor agent, such as a TUSC2 therapy.

[00161] For example, PD-1 axis binding antagonists include a PD-1 binding antagonist, a PDLl binding antagonist and a PDL2 binding antagonist. Alternative names for “PD-1” include CD279 and SLEB2. Alternative names for “PDLI” Include B7-H1, B7-4, CD274, and B7-H. Alternative names for “PDL2” include B7-DC, Btdc, and CD273. In some embodiments, PD-1, PDL1, and PDL2 are human PD-1, PDL1 and PDL2.

[00162] In some embodiments, the PD-1 binding antagonist is a molecule that inhibits the binding of PD-1 to its ligand binding partners. In a specific aspect, the PD-1 ligand binding partners are PDL1 and/or PDL2. In another embodiment, a PDLI binding antagonist is a molecule that inhibits the binding of PDL1 to its binding partners. In a specific aspect, PDLI binding partners are PD-1 and/or B7-1. In another embodiment, the PDL2 binding antagonist is a molecule that inhibits the binding of PDL2 to its binding partners. In a specific aspect, a PDL2 binding partner is PD- 1. The antagonist may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide. Exemplary antibodies are described in U.8. Patent Nos. U88735553, US8354509, and US8008449, all incorporated herein by reference. Other PD-1 axis antagonists for use in the methods provided herein are known in the art such as described in U.8. Patent Application No. US20140294898, US2014022021, and US20110008369, all incorporated herein by reference.

[Q0I63] In some embodiments, the PD-1 binding antagonist is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody). In some embodiments, the anti-PD-1 antibody is selected from the group consisting of nivo!umab, pembrolizumab, and CT-011 In some embodiments, the PD-1 binding antagonist is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDLI or PDL2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence). In some embodiments, the PD-1 binding antagonist is AMP- 224. Nivolumab, also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558, and OPDIVO ^® , is an anti- PD-1 antibody described in W02006/121168. Pembroiizumab, also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA ^® , and SCH-900475, is an anti-PD-I antibody described in W02009/114335. CT-011, also known as hBAT or hBAT-1, is an anti-PD-1 antibody described in W02009/101611 AMP-224, also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in WO2010/027827 and WO201 1/066342. Additional PD-1 binding antagonists include Pidilizumab, also known as CT-011, MEDI0680, also known as AMP-514, and REGN2810

[00164] In some embodiments, the immune checkpoint inhibitor is a PD-L1 antagonist such as Durvalumab, also known as MEDI4736, atezolizumab, also known as MPDL328QA, or avelumab, also known as MSB00010118C. In certain aspects, the immune checkpoint inhibitor is a PD-L2 antagonist such as rHIgM12B7. In some aspects, the immune checkpoint inhibitor is a LAG-3 antagonist such as, but not limited to, IMP321, and BMS- 986016. The immune checkpoint inhibitor may be an adenosine A2a receptor (A2aR) antagonist such as PBF-509.

[00165] In some embodiments, the antibody described herein (such as an anti-

PD-1 antibody, an anti-PDLl antibody, or an anti-PDL2 antibody) further comprises a human or murine constant region. In a still further aspect, the human constant region is selected from the group consisting of IgGl, IgG2, IgG2, IgG3, and IgG4, In a still further specific aspect, the human constant region is IgGl. In a still further aspect, the murine constant region is selected from the group consisting of IgGl, IgG2A, IgG2B, and IgG3. In a still further specific aspect, the antibody has reduced or minimal effector function. In a still further specific aspect, the minimal effector function results from production in prokaryotic cells. In a still further specific aspect the minimal effector function results from an “effector-less Fc mutation” or aglycosylation.

[00166] Accordingly, an antibody used herein can be aglycosylated. Glycosy!ation of antibodies is typically either N-linked or O-linked, N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue The tripeptide sequences asparagine- X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain. Thus, the presence of either of these tripeptide sequences in a polypeptide creates a potential glycosylation site. O-iinked glycosylation refers to the attachment of one of the sugars N-aceylgalactosamine, galactose, or xylose to a hydroxy amino acid, most commonly serine or threonine, although 5- hydroxyproline or 5 -hydroxy lysine may also be used. Removal of glycosylation sites form an antibody is conveniently accomplished by altering the amino acid sequence such that one of the above-described tripeptide sequences (for N-linked glycosylation sites) is removed. The alteration may be made by substitution of an asparagine, serine or threonine residue within the glycosylation site another amino acid residue (e.g., glycine, alanine or a conservative substitution).

[00167] The antibody or antigen binding fragment thereof, may be made using methods known in the art, for example, by a process comprising culturing a host cell containing nucleic acid encoding any of the previously described anti-PDLl, anti -PD- 1, or anti-PDL2 antibodies or antigen-binding fragment in a form suitable for expression, under conditions suitable to produce such antibody or fragment, and recovering the antibody or fragment.

[00168] Another immune checkpoint that can be targeted in the methods provided herein is the cytotoxic T -lymphocyte-associated protein 4 (CTLA-4), also known as CD152. The complete cDNA sequence of human CTLA-4 has the Genbank accession number Li 5006 CTLA-4 is found on the surface of T cells and acts as an “off’ switch when bound to CD80 or CD86 on the surface of antigen-presenting ceils. CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T ceils and transmits an inhibitory signal to T ceils. CTLA4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to CD80 and CD86, also called B7-1 and B7-2 respectively, on antigen-presenting cells. CTLA4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal. Intracellular CTLA4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.

[00169] In some embodiments, the immune checkpoint inhibitor is an anti- CTLA-4 antibody {e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.

[00170] Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-C ^’ ILA-4 antibodies can be used. For example, the anti-CTLA-4 antibodies disclosed in: US 8,119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab), U.S. Patent No. 6,207, 156; Hurwitz et al. , 1998; can be used in the methods disclosed herein. The teachings of each of the aforementioned publications are hereby incorporated by reference. Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used. For example, a humanized CTLA-4 antibody is described in International Patent Application No. W02001014424, W02000037504, and U.S. Patent No. US8017114; all incorporated herein by reference

[00171] An exemplary anti-CTLA-4 antibody is ipilimumab (also known as 10D1, MDX- 010, MDX- 101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g., WOO 1/14424). In other embodiments, the antibody comprises the heavy and light chain CDRs or VRs of ipilimumab. Accordingly, in one embodiment, the antibody comprises the CDRI, CDR2, and CDR3 domains of the VH region of ipilimumab, and the CDR1, CDR2 and CDR3 domains of the VL region of ipilimumab. In another embodiment, the antibody competes for binding with and/or binds to the same epitope on CTLA-4 as the above- mentioned antibodies. In another embodiment, the antibody has at least about 90% variable region amino acid sequence identity with the above-mentioned antibodies (e.g., at least about 90%, 95%, or 99% variable region identity with ipilimumab).

[00172] Other molecules for modulating CTLA-4 include soluble CTLA-4 ligands and receptors such as described in U.S. Patent Nos. US5844905, US5885796 and International Patent Application Nos. WO1995G01994 and WO1998042752; all incorporated herein by reference, and immunoadhesins such as described in U.S. Patent No. US8329867, incorporated herein by reference.

[00173] .Another immune checkpoint inhibitor for use in the present disclosure is an anti-KIR antibody. Anti-human-KIR antibodies (or VH/VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.

[00174] Alternatively, art recognized anti-KIR antibodies can be used. The anti- KIR antibody can be cross-reactive with multiple inhibitory KIR receptors and potentiates the cytotoxicity of NK ceils bearing one or more of these receptors. For example, the anti-KIR antibody may bind to each of KIR2D2DL1, KIR2DL2, and KIR2DL3, and potentiate NK ceil activity by reducing, neutralizing and/or reversing inhibition of NK cell cytotoxicity mediated by any or all of these KIRs. In some aspects, the anti-KIR antibody does not bind KIR2DS4 and/or KIR2DS3. For example, monoclonal antibodies 1-7F9 (also known as 1PH2101), 14F1, 1-6F1 and 1-6F5, described in WO 2006/003179, the teachings of which are hereby incorporated by reference, can be used. Antibodies that compete with any of these art- recognized antibodies for binding to KIR also can he used Additional art-recognized anti-KIR antibodies which can be used include, for example, those disclosed in WO 2005/003168, WO 2005/009465, WO 2006/072625, WO 2006/072626, WO 2007/042573, WO 2008/084106, WO 2010/065939, WO 2012/071411 and WO 2012/160448, all incorporated herein by reference.

[00175] An exemplary-’ anti-KIR antibody is liriiumab (also referred to as BMS- 986015 or IPH2102). In other embodiments, the anti-KIR antibody comprises the heavy and light chain complementarity determining regions (CDRs) or variable regions (VRs) of liriiumab. Accordingly, in one embodiment, the antibody comprises the CDRL CDR2, and CDR3 domains of the heavy chain variable (VFI) region of liriiumab, and the CDR1, CDR2 and CDR3 domains of the light chain variable (VL) region of liriiumab. In another embodiment, the antibody has at least about 90% variable region amino acid sequence identity with liriiumab.

D. Gene Therapy

[00176] In yet another embodiment, the secondary treatment is a gene therapy in which a therapeutic polynucleotide is administered before, after, or at the same time as the therapeutic composition. Viral vectors for the expression of a gene product are well known in the art, and include such eukaryotic expression systems as adenoviruses, adeno-associated viruses, retroviruses, herpesviruses, lenti viruses, poxviruses including vaccinia viruses, and papiloma viruses, including SV40. Alternatively, the administration of expression constructs can be accomplished with lipid-based vectors such as liposomes or DOTAP: cholesterol vesicles. All of these methods are well known in the art (see, e.g. Sambrook et al, 1989, Ausubel etaL, 1998; Ausubel, 1996).

[00177] Delivery of a vector encoding one of the following gene products will have a combined anti-hypeiproliferative effect on target tissues A variety of proteins are encompassed within the present embodiments, some of which are described below. h Inhibitors of Cellular Proliferatiosi

[00178] As noted above, the tumor suppressor oncogenes function to inhibit excessive cellular proliferation. The inactivation of these genes destroys their inhibitory activity, resulting in unregulated proliferation.

[00179] Genes that may be employed as secondary treatment in accordance with the present embodiments include p53, pl6, Rb, APC, DCC, NF-1, NF-2, WT-1, MEN-I, MEN- li, zacl, p73, VHL, MMAC1 / PTEN, DBCCR-1, FCC, rsk-3, p27, p27/pl6 fusions, p21/p27 fusions, anti-thrombotic genes (e.g., COX-1, TFPI), PGS, Dp, E2F, ras, myc, mu, raf, erb,fnts, irk, ret, gsp, hst, abl , El A, p300, genes involved in angiogenesis (e.g., YEGF, FGF, thrombospondin, BAI-1, GDAIF, or their receptors), MCC and other genes listed in Table IV.

2. Regulators of Programmed Cell Death

[00180] Apoptosis, or programmed cell death, is an essential process for normal embryonic development, maintaining homeostasis in adult tissues, and suppressing carcinogenesis (Kerr etal, 1972). The Bc!-2 family of proteins and iCE-iike proteases have been demonstrated to be important regulators and effectors of apoptosis in other systems. The Bcl-2 protein, discovered in association with follicular lymphoma, plays a prominent role in controlling apoptosis and enhancing cell survival in response to diverse apoptotic stimuli (Bakhshi el al, 1985; Cleary and Sklar, Proc, Nat’ l, Arad. Sci. USA !, 82(21):7439-43, 1985, Cleary et al, 1986; Tsujimoto et al, 1985; Tsujimoto and Croce, 1986). The evolutionari!y conserved Bcl-2 protein now is recognized to be a member of a family of related proteins, which can be categorized as death agonists or death antagonists.

[00181] Subsequent to its discover}', it rvas shown that Bcl-2 acts to suppress cell death triggered by a variety of stimuli. Also, it now is apparent that there is a family of Bcl-2 cell death regulatory proteins which share in common structural and sequence homologies. These different family members have been shown to either possess similar functions to Bcl-2 (e.g, BCE _CL , BcKy, Bcls, Mcl-1, Al, Bfl-1) or counteract Bcl-2 function ami promote cell death (e.g, Bax, Bak, Bik, Bim, Bid, Bad, Harakiri).

E, Surgery

[00182] Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative and palliative surgery. Curative surgery' is a cancer treatment that may be used in conjunction with other therapies, such as the treatments provided herein, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy and/or alternative therapies.

[00183] Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and miscopicaily controlled surgery (Mohs’ surgery). It is further contemplated that the present embodiments may be used in conjunction with removal of superficial cancers, precancers, or incidental amounts of normal tissue.

[00184] Upon excision of part of all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment may be accomplished by perfusion, direct injection or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or ever _} ' 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.

F. Anti-Inflammatory Agents

[00185] In certain aspects Tl SC 2 therapies and/or a PDK1 inhibitor are administered in conjuction with an anti-inflammatory agent. An anti-inflammatory agent is defined herein to refer to an agent that is known or suspected to be of benefit in the treatment or prevention of inflammation in a subject. Corticosteroids are a major class of antiinflammatory agent The corticosteroids may be short, medium, or long acting, and may be delivered in a variety of methods. A non-limiting list of corticosteroids contemplated in the present embodiments include the oral corticosteroids such as: cortisone, hydrocortisone, prednisone, and dexamethasone.

[00186] Another major class of anti-inflammatory' agents are non-steroidal antiinflammatory agents. Non-steroidal anti-inflammatory agents include a class of drugs used in the treatment of inflammation and pain. The exact mode of action of this class of drugs is unknown. Examples of members of this class of agents include, but are not limited to, ibuprofen, ketoprofen, flurbiprofen, nabumetone, piroxicam, naproxen, diclofenac, indomethacin, sulindac, tolmefin, etodolac, flufenamic acid, diflunisal, oxaprozin, rofecoxib, and celecoxib. One of ordinary skill in the art would be familiar with these agents. Included in this category are salicylates and derivates of salicylates, such as acetyl salicylic acid, sodium salicylate, choline salicylate, choline magnesium salicylate and diflunisal.

[00187] Other anti-inflammatory agents include anti-rheumatic agents, such as gold salts (e.g., gold sodium thioraalate, aurothioglucose, and auranofm), anti -rheumatic agents (e.g., chloroquine, hydroxychloroquine, and penicillamine), antihistamines (e.g, diphenhydramine, chlorpheniramine, clemastine, hydroxyzine, and triprolidine), and immunosuppressive agents (e.g, methotrexate, mechiorethamine, cyclophosphamide, chlorambucil, cyclosporine, and azathioprine). Other immunosuppressive agent contemplated by the present embodiments is tacrolimus and everolimus. Tacrolimus suppresses inter!eukin- 2 production associated with T-cell activation, inhibits differentiation and proliferation of cytotoxic T cells. Today, it. is recognized worldwide as the cornerstone of immunosuppressant therapy. One of ordinary skill in the art would be familiar with these agents, and other members of this class of agents, as well as the mechanism of actions of these agents and indications for use of these agents.

G. Other agents

[00188] It is contemplated that other agents may be used in combination with the compositions provided herein to improve the therapeutic efficacy of treatment. These additional agents include immunomodulatory' agents, agents that affect the upregulation of ceil surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cel! adehesion, or agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers. Immunomodulatory agents include tumor necrosis factor; interferon alpha, beta, and gamma; XL-2 and other cytokines; F42K and other cytokine analogs; or MEM, MEMbeta, MCP-1, 11ANΊΈ8, and other chemokines. It is further contemplated that the upregulation of ceil surface receptors or their ligands such as Fas / Fas ligand, DR4 or DR5 / TRAIL would potentiate the apoptotic inducing abililties of the compositions provided herein by establishment of an autocrine or paracrine effect on hyperproliferative cells. Increases intercellular signaling by elevating the number of GAP junctions would increase the anti- hyperproiiferative effects on the neighboring hyperproliferative cell population. In other embodiments, cytostatic or differentiation agents can be used in combination with the compositions provided herein to improve the anti-hyerproliferative efficacy of the treatments. Inhibitors of cell adhesion are contemplated to improve the efficacy of the present invention. Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cel! to apoptosis, such as the antibody c225, could be used in combination with the compositions provided herein to improve the treatment efficacy.

In certain embodiments, hormonal therapy may also be used in conjunction with the present embodiments or in combination with any other cancer therapy previously described. The use of hormones may be employed in the treatment of certain cancers such as breast, prostate, ovarian, or cervical cancer to lower the level or block the effects of certain hormones such as testosterone or estrogen. This treatment is often used in combination with at least one other cancer therapy as a treatment option or to reduce the risk of metastases. V. Examples

[00189] The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1 [00190] In NSCLC, the inventor believed systemic restoration of TUSC2 expression could overcome T790M-dependent and independent osirnertinib resistance. The combination of the multikinase inhibitor TUSC2 with osirnertinib could target multiple vulnerabilities in lung tumors, thus overcoming osirnertinib resistance. By inhibiting multiple kinases, TUSC2 might block psimertinib bypass pathways, reducing the probability of resistance developing.

[00191] Here, the inventor demonstrated a significant tumor growth inhibition by the TUSC2 and osirnertinib combination in NSG mice implanted with T790M-positive osimertinib-resistant H1975 lung adenocarcinoma cells. Their osimertinib-sensitive isogenic counterparts were used as controls. In particular: * TUSC2 and osimertinib combination did not have any toxic adverse effect on mice.

* Protein expression analysis of treated tumors in NSG mice, using high- throughput quantitative functional proteomics technology (Reverse Phase Protein Array, RPPA), revealed a set of proteins that w ^? ere altered significantly between osimertinib-resistant H1975 xenografts and their sensitive isogenic counterparts. One protein of interest was the the 3 -phosphoinositi de-dependent protein kinase-1, PDKl. PDKl functions as a master upstream kinase controlling the activation of numerous AGC kinase members, including the cAMP-dependent protein kinase (PKA), the cGMP-dependent protein kinase (PKG) and the protein kinase C (PKC) families (Mora etal, 2004; Bauer etal, 2013; Raimondi et al. , 2011). In osimertinib-resistant xenografts, PDKl expression was upregulated by osimertinib. TUSC2 + osimertinib combination, induced a significant increase of PDKl levels, when compared with control and osimertimb, suggesting that PDKl might be involved in osimertinib resistance. PDKl was not found dysregulated in any treatment groups in HI 975 -parental tumors.

* In vitro ceil viability and proliferation assays showed that the PDK1 inhibitor, BX795, sensitized the H1975 osimertinib-resistant cells to osimertinib and osimertimb + TUSC2 combination, which is consistent with the in vivo data. BX795 had no effect on osimertinib-resistant H1975 cells treated with TUSC2 alone. Similarly, BX795 had no effect on HI 975 osimertinib-sensitive parental cells.

[00192] In conclusion, TIJSC2 immunogene therapy combination with osimertinib showed significant anti-tumor efficacy in EGFR mutant osimertinib-resistant NSCLC mouse models. Further, there is an association between TUSC2/osimertinib combination efficacy and upregulation of PDK! expression levels. This suggests that PDKl may be a critical drug target in osimertinib resistance.

Example 2 - Materials & Methods

[00193] Osimertinib resistant cells, cell culture and maintenance. The human parental NCI- H1975 NSCLC cell line, which carries EGFR T790M/L858R mutations, and its osimertin-ibresi slant isogenic clone, NCI-H1975/081R, were obtained from Dr. John Minna’s laboratory (University of Texas Southwestern University, Dallas, TX), and Dr. John Heymach’s laboratory (University of Texas MD Anderson Cancer Center (MDACC), Houston, TX), respectively. NCI-H 1975/0 SIR cells were cultured and maintained in RPMI complete media supplemented with 1 mM osimertinib (Medchemexpress (MCE), NJ, USA), which was dissolved in DMSO, stored at -70°C, and diluted in culture medium for in-vitro experiments.

[00194] Antibodies. Antibodies were purchased from Cell Signaling (Beverly, MA): anti- AKT (CS#4691), p-AKT ί Ser i 75) (CS#9271), p-AKT (Thr308) (CS #4056), mTOR, p-mTOR (Ser2448) (CS#2971), PDK1 (CS#13037), p-PDKl(Tyr373/376) (bs- 3017R), p- PDKl(Ser241) (CS#3061), M.APK (CS#4695), p-MAPK (Thr202/Tyr204) (CS#4370), PTEN (CS#9559), p-PTEN (CS#9549)). Monoclonal anti-p-actin (Sigma#A5449) w¾s purchased from Sigma Aldrich (St Louis, MO).

[00195] Generation of PDKl-knockout and PDK1 overexpression cells, NCI-H1975/OSIR PDKl-knockout clones were generated with CRISPR-Cas9 technology (CRTSPR core lab, Baylor College of Medicine (BCM), Houston, TX). The PDK1 overexpressing clone was generated by the BCM core lab, by stable transfection with Myc- tagged PDK1 overexpressing plasmid (QriGene, Rockville, MD).

[00196] Whole Exome Sequence Analysis. NCI-H1975 and NCI-H1975/OSIR cell s were seeded in triplicates at a cell density of 2 X 10 ⁶ /plate. DNA was i solated and purifi ed usinga Qiagen kit (Germantown, MD). The quality of DNA was evaluated and the whole exome sequenced at the sequencing core lab, MDACC, Houston, TX using a next generation sequencer (NextSeqSOO, Ulumina, USA). Sequencing data were analyzed by the Department of Bioinformatics and Computational Biology, MDACC.

[00197] Drag sensitivity assay. NCI-H1975 and NCI-H1975/OSIR isogeneic ceils were seededat a density of 3 x 10 ³ ceils/well in a 96-well microplate and treated with osimertinib at concentrations ranging from 0.00! to 10 mM in DMSO Cells were incubated in 37°C incubators, 5% CO2, for three days. Cytotoxicity assays were performed using colorimetric XTT (Sigma- Aldrich, USA) and SRB (Sulforhodamine B) Assay Kit (Abeam, USA) reagents according to manufactured protocol. Optical density (OD) was measuredusing a mi crop! ate reader (FLUOstar Omega, BMG Labtech USA) at 570 nm . Cel! viability(%) ^:: = [OD (Drug) - OD (Blank)] / [OD (Control) - OD (Blank)] x 100.

[00198] Development of osimertinib sensitive and resistant tumor xenografts in humanized mice. Ail animal experiments were carried out following approval by the MDACC institutional review board and were performed in accordance with the Guidelines for the Care and Use of Laboratory Animals published by the National Institutes of Health. All measurements quantifying experimental outcomes were blinded to the intervention. After mononuclear cells were separated from human umbilical cord blood, CD34 ⁺ HSPCs were isolated using a CD34 ^÷ MicroBead kit (Miltenyi Biotec). Three- to 4-week-old NSG mice were irradiated with 200 cGy using a ^Ki7 Cs gamma irradiator. Over 90% pure freshly isolated HLA typed CD34 ⁺ HSPCs were injected intravenously, twenty-four hours post irradiation, at a density of 1 to 2 x 10 ^s ( ^' 1)34 cells/mouse. Ten mice per group from multiple umbilical cord blood donors w¾re used. The engraftment levels of human CD45 ⁺ cells were determined in the peripheral blood, as early as 4 weeks post CD34 injection, by flow cytometric quantification, as well as other human immune populations. Mice with 25% human CD45 ^÷ cells were considered as humanized (Hu-NSG mice). The reconstitution levels of human immune cell populations in mice was analyzed throughoutexperiments using a 10-color flow cytometry panel at week 6 post CD34 ⁺ engraftment. These include CD45 ⁺ , CD3 ⁺ , CD4 ⁺ and CD8 ⁺ T cell s, B cells, NK cells, dendritic cells (DC), myeloid derived suppressor cells (MDSC), and macrophages. Hu-NSG mice from different cord blood donors with different levels of engraftment were randomized into every ⁷ treatment group in every ⁷ experiment. All Hu-NSG mice were verified for humanization before tumor implantation. Treatment strategies for different experiments are described in the figures.

[00199] Generation of PDXs with acquired resistance to osimertinib. To develop NSCLC PDXs with acquired resistance for osimertinib, the inventor monitored mice with regressed tumors for tumor re-growth. When those tumors regrew to 200 mm ³ in size, the inventor retreated, until mice w ^? ere euthanized. The tumors were passaged to new NSG mice for osimertinib sensitivity testing. PDX TC386, i s in passage 4, with each generation treated with three or more cycles. Susceptibility to osimertinib was reduced in each passage. The inventor performed whole exome sequencing for two tumors obtained in passage 3(G3) of TC386 that was under constant osimertinib treatment and became less responsive. Both G3R1 and G3R2 had the same EGFR exon 19 deletion as the primarytumor (TC386T) and parental PDX (TC386F2), albeit with increased allele frequencies without novel EGFR mutations including absence of T790M. The PDXs with acquired resistance had new mutations that were not detected in either the primary tumor or parental PDX, including mutations in FAT3 and SETD1B.

[00200] Immune profile analysis by flow cytometry, Harvested fresh tumors were processed for single-cell suspensions by enzymatic digestion (Liberase Enzyme Blend, Roche, USA). Erythrocytes in the peripheral blood were lysed with ACK lysis buffer (Fisher Scientific). Several 10-color flow cytometry _' panels were used for immune profiling of innate and adaptive immune populations. Fiuorochrome-eonjugated monoclonal antibodies to the following human antigens were used: CD45-Alexa Fluor 700 (clone 2DLHI30), CD45- phycoerythrin (PE; clone 2D1, H130), CD3-PerCp/ey5.5 (clone HIT3a), CD19-PE-cyanine 7 (clone HP319), CD8-allophycocyanin-cyanine 7 (clone RPA-T8,HIT8a), CD4-Pacific blue (clone QKT4), CD56-PE/BV510 (clone HCD56), CD69- FITC/APC/PE-Alexa Flour 610 (clone FN50, Thermo fisher), HLA-DR-PerCp/cy5.5 (cloneLN3), CD33-PE (clone WM-53) (Thermo fisher), CD1 Ib-PE-Cy7 (clone lCRF-44) (Thermo fisher), Granzyme B-FITC (clone GBl 1), and IFN-y-APC (clone 4S.B3), CD 103- Super bright 600 (Colne B-LY7; Thermo fisher), CD279 (PD-l)-Super Bright 702 (Clone J 105; Thermo fisher), CCR7-FITC (Clone G043H7), CD45RA-PE (Clone FfflOO), CD25-APC (clone CD25-4E3), Lin-FITC (Biolegend), CD163-APC (clone ebioGHl/61; Thermo fisher), CD! lc-Paeific blue (clone Bul5; Thermo fisher). A mouse CD45-FITC (clone 30-FT 1) antibody was used for gating out murine leukocytes. Antibodies were purchased from Biolegend. All samples were run on Attune NxT flow cytometer (Thermo fisher), anddata were analyzed by Flow' Jo software.

[00201] Development of osimertinih sensitive and resistant tumor xenografts in non- humanized mice, NCI-H1975/OSIR isogenic cells were cultured and expanded in osimertinih (1 mM) containing media. NCI-H1975 and NCI-H1975/08IR. at 5 x 10 ⁶ cel! density were injected subcutaneously into 6-8 weeks old NSG mice. When tumor size reached approximately 100 mm ³ , tumor-bearing mice were randomized and treated with osimertinih, 5mg/kg or iOmg/kg, 5 days a week for 3 weeks. To evaluate the effect of thePDKl selective inhibitor, BX795, 5 tumor bearing mice/group were either left untreated, treated with osimertinib alone (5mg/kg), treated with PDK1 inhibitor BX 795 (25mg/kg) (Seileckchem, Houston, TX), or with the combination. Cells (5 x 10 ⁶ ) were injected subcutaneously into 6-8 week old NSG mice followed by osimertinib treatment starting from the day following tumor cell injection so tumors developed under osimertinib pressure. Mice were treated with osimertinib from the first day of tumor cell injection throughout the entire experiment, and tumor sizes were measured twice a week by caliper. Tumor volume was measured using the formula V=ab ² /2 where a is the largest diameter and b is the smallest. At end of the experiment, residual tumor tissues were harvested for further analysis.

[00202] In vivo inhibition of PDK1 in an osimertinib resistant NSCLC PDX. To evaluate the effect of PDKi, BX 795, the inventor propagated the EGFR mutant TC386R PDX with acquired osimertinib resistance in N8G mice. After 3 weeks, fresh PDXs were harvested and 2 x 2 cm size PDX tissues were re-implanted into 25 NSG mice for the experiment. Large sizePDX bearing mice were randomized into four groups including control, osimertinib alone (lOmg/kg), BX 795 alone (25mg/kg) and an osimertinib + BX 795 combination group. Osimertinib treatment was 5 days a week (oral) and BX 795 treatment was 2 times per week (i.p.). Tumor size was measured twice a week by caliper. Tumor volume was calculated according to the formula V==ab ² /2, where a is the largest diameter and b is the smallest. At the end of the experiment, residual tumor tissues were harvested for analysis.

[QQ203] Western blot analysis. Total protein was harvested using Ripa lysis buffer (Merck, Burlington, MA), and their concentrations were evaluated with BC A™ protein assay kit (Pierce, Rockford, IL, USA). Equal amounts of proteins were separated by 8-15% SDS- PAGE gel, electro-transferred onto a Hybond ECL transfer membrane (Amersham Pharmacia, Piscataway, NJ), and blocked with 2-5% non-fat skim milk. Then, membranes were probed with specific primary' antibodies overnight at 4°C, washed with PBS, and incubated with corresponding secondary antibodies at room temperature for 1 h. The specific protein bands w'ere visualized with an ECL advanced western blot analysis detection kit (GE Health Care Bio-Sciences, NJ, USA).

[00204] Colony formation assay. NCI-H1975, NCI-H1975/OSIR, NCI- H 1975/0 SIR- PDK 1 -/- andNCI-H1975-OSIR/PDKl++/++ cells were seeded into 6-well plates at a density of 300 cells per well, and treated with 0, !OnM, lOOnM, 1 mM, 2.5 mM, and 5 mM concentrationsof osimertinib for 72 h. The media was replaced every 2-3 days with osimertinib dose titration containing medium. After twelve days, colonies were fixed with 4% PFA, stained with crystal violet solution, and photographed. [Q0205] < el! Cycle assay. The cell cycle profiles of osimertinib -resistant and sensitive ceils were determined by staining DNA with fluorescent dye (PI/RNase staining buffer, BD Pharmingen, USA) according to the manufacturer’s protocol, and measuring its intensityby flow cytometry (Attune NxT, Thermofisher Scientific, USA). Briefly, cells were seededat 10 ^b cells in a 100mm dish followed by osimertinib treatment at the designated concentrations. Ceil pellets were suspended in ice cold PBS, fixed with 70-80% ethanol, and stored at -20°C overnight. The ceils were washed twice with ice cold PBS and stained with PI/RNase staining dye for 15 min at room temperature. The samples were analyzedby flow cytometry within an hour.

[00206] Reverse Phase Protein Array (RPPA) analysis. Osimertinib-sensitive and -resistant HI 975 tumors were developed in non-humanized NSG mice and treated with osimertinib under the protocol described above. Residual tumor tissues were snap-frozen and storedin -80°C. RPPA analysis was performed using 400 antibodies at the RPPA core lab at MDACC. Bioinformatics analysis was performed by the Department of Bioinformatics and Computational Biology, MDACC.

[00207] Mass Spectrometry. The samples were denatured and lysed by three cycles of LN2 snap freeze and thaw at 95°C. For global profiling, 10 mg of lysate was trypsinized to obtain 10 mg of digested peptides. After fractionation using a small-scale basic pH reverse phase (sBPRP) step elution protocol with increasing acetonitrile concentrations, fractions were combined into 5 pools that were resolved and sequenced online with Fusion Lumas and timsTOF fleX mass spectrometer. For phospho-proteome profiling, a 100 pg protein lysate was digested with trypsin and dried under vacuum. Global and phospho- proteomic analyses covered over 8000 gene protein products (GPS), and over4Q0Q GPS, respectively, which included the kinome profile. After label-free nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS) analysis using Thermo Fusion Mass spectrometer, the data was processed and quantified againstNCBI RefSeq protein databases in Proteome Discover 2.5 interface with Mascot search engine (Saitzman, Ruprecht). The Skyline program was used to get precise quantification. To decipher phospho- proteome signal pathway analysis the inventor utilized protein external datacontributions for phosphorylation-related data mining sets, including PhosphoSitePlus (world-wide-web at pliosphosite.org/), Phospho.ELM, PhosphoPep, and the Phosphorylation Site Database (PHOSIDA). [00208] Immunofluorescence. Cells were seeded at 5000 cells/chamber well and grown overnight before being treated with osimertinib at 1 mM or 2.5 mM for 24 hours. Then cellswere washed with PBS and fixed in 4% paraformaldehyde in PBS pH7.4 for 10 min at RT. After washing with PBS 3 times, cells were treated with 0.125% Triton-XlOO for 10 min at RT to increase cell permeability. The slides were blocked by !%B8A block in PBS-T (Thermo-Fisher) at RT for 30min, incubated with 1:250 anti -p YAP Y357 (Sigma #Y4646) antibody in 1%BSA overnight at 4°C. After three PBS-T washes, the slides werefurther incubated in 1:1000 secondary Alexa 594 antibody (invetrogen # A32741) at RT for 1 hour, before they were mounted with mounting media containing Dapi (abeam #104139). Immune fluorescence images were captured using an EVOS M5Q00 fluorescence microscope (Thermos-Fisher). For each cell line and each treatment condition, 30 individual cell nuclei w'ere counted and their fluorescent intensities were quantified.

[00209 { Immunohistochemistry. Clinical specimens of NSCLC samples that were obtained frompatients before initiating systemic targeted therapy (TKI naive [TN]), at the residual disease (RD) state, and upon subsequent progressive disease as determined by clinical imaging, at which point the tumors showed acquired drug resistance (progression [PD]). All patients gave informed consent for collection of clinical correlates, tissue collection, research testing under Institutional Review ⁷ Board (IRB [-approved protocols. Patient studies w ⁷ ere conducted according to the Declaration of Helsinki, the Belmont Report, andthe U.8. Common Rule. Formalin-fixed paraffin-embedded (FFPE) tumor blocks w ⁷ ere cutat 4-micron thickness and mounted as sections on positively charged histology slides. Immunohistochemistry staining was performed as described previously. In brief, slides were deparaffmized in xylene, rehydrated and epitope retrieval was induced in a histologypressure cooker using pH 6. i citrate buffer (Dako Denmark A/S, S2369). After endogenous peroxidase, tissue v/as permeabilized in in 0.1% Triton-X/PBS. Non-specificbinding w¾s blocked, and slides w ⁷ ere incubated primary antibody solution overnight at 4°C. The antibody forPDPKl (clone EP569Y, # ab52893) was purchased from Abeam anddiluted 1:150. Then, slides w ^? ere incubated with secondary antibody for 30 minutes EnVision Dual Link Labelled Polymer HRP, Agilent K4065), stained using 3,3-DAB, andcounterstained with hematoxylin. Slides rvere dehydrated and mounted before digitizationusing an Aperio AT2 Slide Scanner (Leica Biosystems) at a 2 OX objective.

[00210] Statistical analysis. WES: The quality of raw ⁷ FASTQ reads was assessed using FastQC and then mapped tohuman reference genome GRCh38, using BWA (Andrews, 2010; Li & Durbin, 2009). The reference genome refers to theb38 version with decoy sequences for human GRCh38 provided in the genome analysistoo!kit (GATK) resource bundle (McKenna et al ., 2010). The mutations were called following GATK bestpractice pipeline. The candidate mutations were be filtered for high confident somatic mutations and annotated for functional changes using ANNOY AR (Wang etai, 2010).

[00211] Cell Survival Assay: The percentage of viable cells was determined by the ratio ofabsorbance of treatment and control groups: ODT/ODC x 100%. Univariate analysis wasperformed to evaluate the distribution of data for each treatment group. To determi newhether SRB % was different between treatment groups, two methods were used: l)ANOVA was performed to compare the variance between treatment groups for all samples within each cell line; and 2) Tukey’s multiple comparisons test w¾s perforraedfor pairwise differences between treatment groups. P<0.05 w¾s considered statistically significant; all tests were two-sided. Analyses were performed using SAS 9.3 (SAS Institute Inc., Cary, NC). Values represent the mean of three independent experiments.

[00212] Colony Formation Assay: Colonies were fixed with glutaraldehyde, stained with erystalviolet, counted with a stereomicroscope, and analyzed with Image-J software. Valuesrepresent the mean of three independent experiments. The statistical significance of differences between treatment groups was calculated by two-tailed t test analysis, P<0.05 was considered significant. The Statistical software S-PLUS 8.0 was used for alt analyses.

[00213] Tumor growth: Statistical analyses w¾re performed with GraphPad Prism 7 software. Tumor intensity change per time point was calculated as a relative level of tumor intensitychange from baseline. Two-way ANOVA with interaction of treatment group and time point was performed to compare the difference of tumor intensity changes from baselinebetween each pair of the treatment groups at each time point. Means ± standard errors of the mean are shown in all graphs. The nonparametric Mann-Whitney U test was appliedto compare cell numbers in different treatment groups. Differences of P < 0.05, P < 0.01 ,and P < 0.001 were considered statistically significant. Statistical analysis of flow cytometry data was done by general linear regression models to compare the data amongthe different treatment groups. CONTRAST statement in PROC GENMOD procedure in SAS was used to compare the data between each pair of the treatment groups with treatment indicator in the models. Both nomP values and multiple testing adjusted P values were reported. SAS version 9.2 and S-Plus version 8.04 were used forthe computations for all analyses.

[00214] Reverse Phase Protein Array (RPPA): Slides were scanned using a CanoScan 9000Fand spot intensities were quantified using ArrayPro Analyzer 6.3 (Media Cybernetics Washington DC). SuperCurve, a software developed in house, was used to estimate relative protein levels (Hu et al., 2007). After SuperCurve fitting, protein measurements were normalized for loading using mediancentering across antibodies. One-way analysis of variance (ANOVA) was used to assess the differences in protein expressions between control and treatment groups on a protein-by-protein basis. An over-all F test was carried out to detect any significant difference among the means of ail groups. Fold change (FC) values between the 2 groups, with thefollowing conventional modification: ratios > 1 (up- regulation), ratios < 1 (down- regulation). The type I error rate of multiple comparison will be controlled by using the false discovery rate (FDR). The criteria of significant protein selection were: 1. Significantin overall F-test (FDR <0.05); 2. Significant in pairwise comparison (FDR <0.05).

[00215] In vivo inhibition of PDK1 in an osimertinib-resistant PDX: The inventor evaluated the potential synergistic effect of the drug combination osimertinib + BX795 under the Highest SingleAgent framework (Berenbaum, 1989), where the synergistic effect of a drug combination is declared if the combination effect is greater than that of the more effective individual component. The combination index (Cl) under the HSA and the corresponding standard error were approximated by the Delta method (Huang et al, 2021). The declared the synergistic effect under the significance level of 5% at day 33.

[00216] Mass Spectrometry: Statistical analysis was performed using R software. (R version 4.0.1). The log2 transformation was applied to the iFOT Half Min proteomic data. The Student’s t-test was used to compare expression values between the groups. P values obtained from multiple tests were adjusted using FDR. Statistical significance was defmedas FDR < 0.05. The enriched pathways and hallmarks were identified by pre-ranked GSEA using the gene list ranked by log-transformed P values with signs set to positive/negative for a fold change of>l or <l, respectively.

[00217] Immunohistochemistrv : To investigate the relations of YAP expression and PDPK1 groups, and PDPK1 %Cases and TN/PD, the inventor used a Bayesian hypothesis testing the differences in protein expressions between control and treatment groups on a protein-by-protein basis. An over-all F test was carried out to detect any significant difference among the means of all groups Fold change (FC) values between the 2 groups, with the following conventional modification: ratios > 1 (up-regulation), ratios < 1 (down- regulation). The type I error rate of multiple compari son will be controlled by using the false discovery^ rate (FDR). The criteria of significant protein selection were: 1. Significant!!! overall F-test (FDR <0.05), 2 Significant in pairwise comparison (FDR <0.05).

Example 3 - Results

[00218] Osimerthiih sensitivity assay. The human NSCLC NCI-H1975 cell line harbors two EGFR point mutations, T790M and L858R, in exons 20 and 21, respectively and is highlysensitive to Osimertinib (Papa Pandolfi, 2019), NCI-H1975 was continuously exposed to osimertinib dose escalation (0.5 mM -2.5 mM) until the emergence of the osimertinib resistant clone, NCI- H1975/OSIR, which has less longitudinal ceil morphology and a faster doubling time than the parental sensitive clone (33 hrs versus 42 hrs). An osimertinib sensitivity assay using Sulforhodamine B (SRB) to measure cell proliferation showed that NCI- H1975/08IR cells were 100-200 fold more resistant to osimertinib than their NC1-H1975 counterparts, as shown by IC 20, 30 and 50 values (Fig. 1).

[00219] Whole Exome Sequence (WES) analysis shows there are no new EGFR mutations or loss of the EGFR L858R and T79QM mutations in NCI-H1975/OSIR, WES analysis was performed to identify any acquired or lost EGFR mutation during osimertinib treatment in the entire protein-coding regions of the genome of NC1-H1975/OSIR. clones. The results showed there were no new EGFR mutations or loss of the EGFR L858R and T790M mutations. However, there were 37 new exonic mutations, including 0 indels, 27 nonsynonymous single nucleotide variants (SNV), 4 stopgain, and 6 synonymous mutations. The list of these new mutations and their projected pathways are shown in Fig. 9.

[00220] Modeling osimertinib acquired resistance in the humanized mouse model. The major limitation of current experimental rodent models is that many functional aspects ofhuman innate and adaptive immunity" cannot be recapitulated with mouse models. This improved humanized mouse model is better suited to model osimertinib acquired resistance and provides insight into the complex interaction of osimertinib with variable contextures of the tumor microenvironment (TME) (Meraz ei ciL, 2019). The inventor found, as have others, that anti-tumor responses are independent of HLA status in humanized mice. In addition, when the inventor used HLA-matched human bronchial endothelial cells in co-culture experiments, no allogenic responses were observed. NCI-H1975 and NCI-H 1975/0 SIR xenografts were implanted with fresh CD34 ⁺ -derived humanized mice from different donors with partial HLA compatibility. The humanization protocol, the levels of human immune reconstitutionin humanized mice, growth characterization of turn or xenografts and osimertinib treatmentare illustrated in Figs. 2A-C. The level of human CD45 ⁺ and reconstituted T, B, and NKcells were high 78 days post CD34 engraftment. The general standard for mouse humanization is a minimum level of 25% of reconstituted human CD45 ceils. The improved humanization protocol achieved almost two-fold that level in less than six weeks. Results from two independent experiments with long (78 days) and short term (27 days) osimertinib treatment (5mg/kg), (Figs. 2C and 2E), respectively, show eel that growth of NCI-H1975 tumors were significantly inhibited. In contrast, NCI-H1975/OSIR treated with osimertinib showed initial growth stabilization followed, after a short time, bytumor regrowth. Because NCI- H1975/QSIR xenograft tumors were developed under constant osimertinib (5mg/kg) pressure, twenty-four hours post implantation, their growthwas slower than their untreated NCI-H1975 counterparts. The osimertinib effect in this humanized mouse model was reproducible in multiple experiments (data not shown).

[00221] Analysis of the tumor microenvironment showed distinct immune contextures between osimertinib sensitive and resistant tumors. Fresh osimertinib- sensitive and resistant tumor xenografts grown in humanized mice were processed into single cell suspensions and analyzed by multiple flow cytometry to identify differences in the immune contextures of both tumor microenvironments. Reconstituted human lymphoid and myeloid cell populations were investigated. Sensitive tumors had a higher number of CDllb ^÷ CD163 ^' HLA-DR ⁺ Ml macrophages than their resistant counterparts, which wereinfiltrated with a higher number of GDI lb ⁺ CD163 ⁺ HLA-DR ^’ M2 macrophages (Fig. 3 A). Osimertinib treatment significantly altered the ratio of M2 to Ml, favoring the Ml population. The number of HLA- DR dendritic ceils (DC) were higher in sensitive tumors, and osimertinib treatment enhanced their levels significantly, to the same extent in both sensitive and resistant tumors (Fig. 3B). Surprisingly, CD33 ^÷ MDSC levels were higher insensitive tumors, and were significantly reduced by osimertinib in both sensitive and resistant tumors (Fig. 3C). The percentage of tumor infiltrating lymphocytes, CD3 ^‘h TILs were moderately higher in sensitive tumors compared to their resistant counterparts and were significantly increased in both tumors following osimertinib treatment (Fig. 3D). Natural Killer cells (CD56 ^÷ NK) w ⁷ ere higher in resistant tumors and osimertinib enhanced their levels significantly more in resistant tumors (Fig. 3E).

{002221 Reverse Phase Protein Array (RPPA) shows upregulation of PDKl in NCI- H1975/O8IR xenografts. To understand the underlying mechanisms of osimertinib acquired resistance, NCI-H1975 and NCI-H1975/OSIR xenografts were grown in N8G mice untreated or treated with 5 or lOmg/kg osimertinib. Tumors were grown under constant osimertinib pressure according to the treatment strategy shown in Fig, 4A, A dose dependent osimertinib response w¾s observed in H1975-parental tumors (Figs. 4B and 4D), which was completely lost in H1975-OSIR. tumors (Figs. 4C-D). Untreated and osimertinib- treated residual tumors were harvested for proteomic analysis using an antibody-based functional proteomic analysis, RPPA, consisting of a 400 antibody panel, which indudesserine/threonine and tyrosine kinases. Heat map analysis of pairwise comparison of protein expression profiles between NCI-H1975 and NCI-H1975/OSIR osimertinib treated residual tumors, and NCI- H1975/OSIR osimertinib treated and untreated groups showedupregulation of two distinct protein signatures, respectively. Interestingly in both signatures, PDKl was a highly significant outlier and upregulation w ^r as highest in the osimertinib-resistant tumors. In the former pairwise comparison, PDKl expression level increased by 2.783 fold (Fig. 4E), and in the latter by 2.4 fold loglO scale (Fig. 4F). This suggests that PDKl differential expression between NCI- HI975 and NCI-H1975/OSIR might play a potential role in the latter’s acquisition of resistance to osimertinib. PDKl regulates a number of serine/threonine protein kinases of the AGC kinase superfamily, activating multiple pro-survival and oncogenic pathways, and suppressing apoptosis in lung cancer ^22'25 .

[00223] Mass spectrometry-based proteonsk analysis confirms significant upregulation in PDKl activity in osimertinib-resistant NO-H1975/OSIR clones. To further investigatethe potential role of PDKl in mediating osimertinib acquired resistance, as suggested by RPPA analysis, the inventor profiled osimertinib proteins in the global and phospho-proteome of NCI-H1975 and NCI-H1975/GSIR isogenic clones using an unbiased robust mass spectrometry (MS)-based proteomics workflow _^ (Ferro & Falasca, 2014; Caron et al, 2005). Global and phospho-proteomic analyses covered over 8000 gene protein products (GPS), and over 4000 GPS, respectively. After label-free nanoscale liquid chromatography coupled to tandem massspectrometry (nanoLC-MS/MS) analy sis using a Thermo Fusion Mass spectrometer, thedata was processed and quantified against NCBI RefSeq protein databases in a Proteome Discover 2.5 interface with Mascot search engine (Saltzman, Ruprecht). The level of PDK1 phosphorylation in NCI-H1975/08IR, was fourteen fold higher than in the NCI- H1975 osimertinib sensitive cells (Fig. 10). These results are compatiblewith those of RPPA, validating PDK1 differential expression and activity between NCI- H1975 and NCI- H1975/OSIR. cells and identifying PDK1 as a potential driver of osimertinib acquired resistance.

[00224] Pharmacological inhibition assd genetic knock-out of PDKI sensitizes NCI- H1975/08IR clones to osimertinib. Next, the inventor validated the functional role of PDKI in osimertinib acquired resistance in vitro and in vivo. NCI- H1975/OSIR clones were left untreated, treated with osimertinib, the PDKI selective inhibitor BX-795, or the combination of both, and assayed for survival by XTT assay NCI- H1975 cells were used as controls. Fig. 5A shows dose-dependent inhibition of pPDKl expression by BX795 in both isogenic clones by western blot analysis. The osimertinib and BX-795 combination had no effect on the survival of NCI-H1975, whereas it rendered NCI- H1975/QSIR. sensitive to osimertinib, as shown by a significant increase in ceil death (Fig. 5B). Next, to definitively implicate PDKI as mediator of osimertinib acquired resistance and eliminate drug off-target effects, CRISPR PDKl knockout (H1975-OsiR~PDKl-/-) andNCI- H1975/OSIR stably overexpressing PDKI (HI 975-OsiR-PDK 1 ++/++) cells were generated (Fig. 5C) and assayed for survival and colony formation following osimertinib treatment. PDKI knockout sensitized NC1-H1975/OSIR to osimertinib, whereas PDKI overexpression enhanced their resistance to osimertinib (Fig. 5D). Similarly, in dose titration experiments, at nanomolar and micromolar osimertinib concentrations, PDKI knockout and overexpression significantly reduced and enhanced NCI-H1975/OSIRcolony formation, respectively (Figs. 51· ^' .-! )

[00225] In vivo inhibition of PDKI enhanced osimertinib response in resistant PDXs. To evaluate the antitumor effect of PDK1 inhibition, the inventor developed EGFR mutant osimerti nib-resistant TC386 isogenic PDXs. The parental TC386 PDX was highly sensitive toosimertinib (Fig. 11). The resistant TC386R PDX was generated through continuous treatment of osimertinib over a prolonged period of time and subsequent passages to four generations (Fig. 11 ). Later generation (RG4) showed significantly more resistance than an earlier generation (RG l) without the acquisition or loss of EGFR mutations identified in the parental PDX. When the pPDKl level was compared between parental and resistant PDXs, higher levels of pPDKl were found in TC386R PDXs as compared with parental TC386 PDXs (Figs. 6A-B). To evaluate the effectof the PDK1 inhibitor (PDKi), BX 795 on resistant PDXs, the inventor treated TC386R PDXs according to the treatment strategy shown in Fig. 6C treating with BX 795 with or without osimertinib. The combination treatment inhibited the tumor growth significantly andsynergistically compared to the single agents (Figs. 6D-E). BX 795 greatly reduced pPDKl in the BX 795 tumors compared to untreated or osimertinib alone treated tumors (Fig. 6A). Taken together, the in vitro and in vivo evidence support PDKi as a driver of osimertinibacquired resistance in two independent models.

[00226] PDKI knock-out alters activation of the AKT/mTOR pathway. Activation of theoncogenic PI3K/ AKT/mTOR pathway mediates tumorigenesis and resistance to EGFR TKIs in N8CLC (Fumarola et al , 2014; Heavey et a!., 2014; Tan, 2020; Iksen & Pongrakhananon, 2021). Since PDKI represents a pivotal node in this important signaling axis, the inventor analyzed the phosphorylation status of its major signaling effectors in NCI- H1975, NCI-H 1975/OSIR, H1975-OsiR-PDK-/- and M975-OsiR-PDKl++/++ clones. Fig. 7A shows that AKT expression was similar in both H 1975-OsiR-PDK 1 -/- and H1975- OsiR-PDKl++/++ clones. Osimertinib treatment had no effect on its level. In H1975-OsiR- PDK1 ÷+/'++ clone, osimertinib reduced AKT phosphorylation at threonine 308 (T308) residue, whi ch i s known to be the site activated by PDK 1 (Scheid et al. , 2005) PDK 1 knock-outhad no effect on AKT (8473) phosphorylation, which can be catalyzed by multiple proteinsbut not PDKI. Although the level of AKT expression in OsiR-PDKl-/- cells was similar tothat of H1975-OsiR-PDKl++/++, there was no detected phosphorylation of AKT (T308) in the former. The level of phosphorylation of AKT (S473) in HI975-GsiR-PDK" ^'' was higherthan that of HI 975-OsiR-PDKl ÷+/++ ceils. Osimertinib had no effect on this activity. The level of mTOR expression was similar in HI 975-OsiR-PDK ^'/' and HI 975-OsiR-PDK 1++/++ clones, but its phosphorylation level was higher in the latter, and osimertinib had no effecton mTOR or pmTOR levels (Fig. 7B). PTEN is a tumor suppressor that regulates the PI3K/AKT/PTEN pathway important in senescence and apoptosis (Papa & Pandolfi, 2019). Analysis of PTEN total expression showed that the expression of PTEN was downregulated in NCI-H1975/OSIR compared with NCI-H1975 (Fig. 7C). Phosphorylation of PTEN was upregulated by osimertinib treatment only in NCI-H 1975. [00227] PDKl knock-out promotes cell cycle arrest at GL Cell cycle analysis showed that osimertinib promoted cell cycle arrest at G1 in NCI-H1975 sensitive cells. In contrast, a large number of NCI-H1975/OSIR cells accumulated at G2 and G2/M after osimertinib treatment (Figs. 7D-E). The PDKl knock out also promoted cell cycle arrest at the G! phase, to the same extent as in NCI-H1975 sensitive ceils. NCI-H1975 OSIR-PDK++/++ cells were not arrested at G1 post osimertinib treatment, which is similar to NCI-H1975/OSIR cells. These results suggest that PDKl knock-out renders the resistant ceils more sensitive to osimertinib through ceil cycle arrest at Gl .

[00228] PDKl knock-out inhibits pYAP expression and nuclear translocation of YAP phosphorylated at ¥357, H1975-QsiR-PDK ^" ' ^' downreguiaied YAP and pYAP whereas NCI-H1975 OSIR.-PDK++/++ had increased levels of YAP and pYAP expression (Figs. 8A-B). in osimertinih-sensitive cells, NCI-H1975, osimertinib treatment downregu!ated YAP and pYAP. However, no osimertinib effect on YAP was noted for NCI- H1975/OS1R cells (Figs 8A-B). NCI- H1975/OSIR and NCI-H1975 OSIR-PDK++/++ had higher levels of pYAP than HI 975- QsiR-PDK ^"7' . Phosphorylation of YAP at Y357 is activating and promotes translocation ofYAP to the nucleus. An anti-pYAP ^{Y3:5 /} antibody was used to localize YAP ^Y¾7 by immunofluorescence. Osimertinib treatment of H1975 osimertinib- sensitive cells reducednuclear localization of pYAP ^Yi57 . NCI-H1975/OSIR and NCI-H1975 OSIR-PDK++/++ cells showed a high level of nuclear localization of pYAP ^Y ’ ⁵⁷ , HI 975-OsiR- PDK-/- cells showed significantly reduced nuclear localization of pYAP ^V357 (Figs. 8C-D). The level ofYAP and pYAP was upreguiated in osimertinib-resi slant xenograft tumors as well as in residual tumor tissues following osimertinib treatment (Fig. 8E).

[002291 Immunohistochemical analysis shows an association between high

PDKl expression level and progressive disease in EGFR mutant NSCLC patients. Formalin-fixed paraffin-embedded (FFPE) tumor blocks from EGFR mutant NSCLC tumors obtained prior to initiation of treatment or after tumor progression during treatmentw¾re stained with anti-PDKl antibody for IPIC analysis. The highest levels of PDKl expression were only- observed in the progressive disease patients, suggesting they could be responsive to an osimertinib and PDKl inhibitor combination (Figs, 13A-E). Example 4 - Discussion

[0Q23Q] Responses to osimertinib and other TKIs are transient, and acquired resistance is inevitable. The majority of EGFR mutant NSCLC patients treated initially with osimertinib will eventually progress after only 19 months of treatment (Soria ei al., 2018). Although acquired new mutations in EGFR account for some clinical acquired resistance to both osimertinib andother TKIs, the majority of resistant phenotypes cannot be explained by acquisition of these mutations. Delaying and treating tumors with acquired resistance requires an understanding of multiple complex resistance mechanisms mediated by alternative bypass pathways. In this study, the inventor used the extensively molecular!y characterized human NSCLC NCI-H1975 cell line which harbors two common EGFR point mutations, T790Mand L858R, in exons 20 and 21 respectively, which is very' sensitive to osimertinib, and its isogenic derivative osimertimb-resistant done as a model system, to first develop a relevant humanized mouse model that models Osimertinib acquired resistance accurately, and second, decipher cellular and molecular mechanisms for its acquiredresistance. The NCI-H1975 resistant done, NCI-H1975/QSIR, is 100-200-fold more resistant to osimertinib Whole exome sequencing eliminated the acquisition of newEGFR mutations or loss of T790M and L858R in the resistant done, suggesting theexistence of alternative mechanisms of resistance acquired during osimertinib treatment

[00231] Osimertinib sensitive and resistant humanized xenografts had different responsesto short and long-term treatment, with the latter having initial ly a slowing of growth followed by aggressive tumor regrowth. Sensitive tumors had very long regression, beforetumors started to regrow slowly similar to responses seen in the clinic. When compared to current mouse models, this humanized mouse model replicates human EGFR mutant tumor growth physiology, pathology, immunology, and response to osimertinib treatment. In a recent published report, the inventor showed that HLA matching between CD34 stem-cell donors and inoculated tumors or implanted PDXs, was not necessary for an antigen- specific antitumor response (Meraz et al , 2019). Using this model, the inventor investigated differences between reconstituted human immune contextures in the TME of osimertinib sensitive and resistant xenografts in humanized mice. The results showed that osimertinib sensitive tumors had a higher number of Ml macrophages, dendritic cells, and infiltrating lymphocytes, all of which are strong immunostimulatory contributors to the TME. Osimertinib treatment enhanced their intratumor levels significantly in both sensitive and resistant tumors. On the other hand, the level of M2 macrophages was higher in resistanttumors, and osimertinib decreased their levels significantly. This immune cell populationis a strong contributor to the immunosuppressive tumor microenvironment, and itspreponderance is an obstacle for immunotherapy. Osimertinib significantly altered the ratio of Ml to M2, favoring the Ml population which has an immunostimulatory phenotype. Unexpectedly, the immunosuppressive level of CD33 ⁺ MDSC levels were slightly higher in sensitive compared to resistant tumors and were markedly decreased after osimertinib treatment.

[00232] Pairwise comparison analysis of protein expression profiles of residual tumors in osimertinib treated NSG mice, using reverse phase protein array (RPPA), between NCI-H1975 compared to NCI-H1975/OSIR, and NCI-Hl 975/OSIR osimertinib treated versus untreated groups, showed two distinct protein signatures. The inventor found unexpectedly that both signatures were led by upregulation of PDK1, a master regulator the AGC kinase superfamily (Arencibia et al, 2013). PDK1 regulates the oncogenic PI3k/AKT/mTOR pathway, which is involved in tumori genesis and progression of N8CLC. Next, global and phospho- proteome based mass spectrometry (MS Spec) analyses between NCI-H1975 and NCI-H1975/OSIR clones did not find any detectable increase in PDK1 expression level but indicated a highly significant fourteen fold increase of phosphorylated PDKl in the resistant clone. Pharmacological and genetic suppression of PDKl sensitized NCI- HI 975/OSIR cells to osimertinib. Cell survival and colony formation assays showed that NCI-H1975/Q8IR clones treated with the specific PDKl inhibitor, BX795, or PDKl knockout by €RJSPR/Cas9, recovered their sensitivity to osimertinib treatment. In addition, NCI-H1975/OSIR PDKl knockout clone H1975-OsiR-PDK-/-, with restored overexpression of PDKl was more resistant to osimertinib than its parental clone, validating the role of PDKl in mediating osimertinib resistance in this model. Treatment with a combination ofosimertinib and BX795 in a second model of acquired osimertinib resistance utilizing a PDX showed that, the addition of BX795 to osimertinib resulted in synergistic tumor regression whereas BX795 treatment did not differ from untreated control growth and osimertinib slowed growth but did not cause regression in the drug resistant PDX. This PDX model with acquired osimertinib resistance without a T790M mutation replicates a common clinical scenario that suggests a combination of osimertinib with a PDKl inhibitormay be effective after progression on first-line osimertinib.

[00233] PDKl is a pivotal node in the oncogenic PI3K/AKT/mTOR pathway (Lien et al, 2017; Faes & Dromond, 2015), which mediates lumorigenesis and resistance to EGFR tyrosine kinase inhibitors in NSCLC (Fumarola et a!., 2014; Heavey eta!., 2014; Tan, 2020; Iksen & Pongrakhananon, 2021). Osimertinib had no effect on AKT expression levels, which was similar in both PDK1 knock out and overexpressing clones. In the later, osimertinib reduced AKTphosphorylation at the threonine 308 (T308) residue, which is known to be the site activated by PDK1. The level of mTOR expression was also similar in PDK1 knock out and overexpressing clones, but its phosphorylation level was higher in the later indicatingthat PDKl knock out can downreguiate mTOR activation. A previous study by the inventor’s group implicated mTOR as a mediator of TKI resistance (Dai et aί,, 2015). In this study, three NSCLC ceil lines became sensitive to erlotinib following treatment with the mTOR inhibitor rapamycin.

[00234] PDKl is also a mediator of yes-associated protein (YAP) activation (Emmanouilidi & Falasca, 2017), PBK and PDKl mediate YAP phosphorylation and nuclear accumulation, and thus it is the PI3K- PDKl signal that links EGFR with the Hippo pathway. Phosphorylation of YAP at Y357 motivating, resulting in YAP nuclear translocation (Li et a!,, 2019). Overexpression of PDKl significantly increased YAP Y357 nuclear translocation in H1975 cells when compared to the PDKl knockout, H 1975-OsiR-PDK-/-, implicating YAP as a downstream mediator of osimertinibacquired drug resistance. This is supported by studies implicating YAP activation in persister cells after EGFR TKI treatment, (Kurppa et aί,, 2020). The inventor recently reported YAP-driven transcriptional adaptation as a functional mechanism of TKI drug tolerance (Haderk et ai, 2021). In this study, the inventor found in experiments in humanized mice that YAP reduced treatment sensitivity to osimertinib and enhanced an immunosuppressive tumor microenvironment supportingtumor growth. Thus, PDKl is a central upstream regulator of two critical drug resistance pathways: PI3K/AKT/mTGR and YAP. This suggests that drugs targeting PDKl could bebeneficial in delaying the onset of acquired drug resistance and treating acquired drug resistance at its onset.

[00235] Cell cycle analysis showed that both osimertinib treatment of sensitive cells and PDKl knock out promoted cell cycle arrest at the G1 phase, whereas resistant and PDK 1 overexpressors were not arrested at Gl . PDKl is known to have a critical role in cell proliferation and cell cycle progression (Nakamura et al, , 2008). Finally, the inventor showed that high expression of PDKl was associated with progressive disease in EGFR mutant NSCLC patients, as shown by immunohistochemistry (IHC), suggesting they could be responsive to osimertinib and PDKl inhibitor combination therapy. [Q0236] In conclusion, the inventor presented multiple iines of evidence for PDK1 as a driver of osimertinib acquired resistance in T790M/L858R mutant NSCLC using the most relevant preclinical mouse models, capable of modeling osimertinib acquired resistance, and interrogating its interaction with the microenvironments of sensitive and resistant tumors. The inventor showed that pharmacological and genetic targeting of PDK1 could restore osimertinib responsiveness in celi lines and PDXs with acquired osimertinib resistance thusprovidingsupport for clinical translation.

>H H< %

[00237] Ail of the methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

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