WO2012038825A2 - Methods of increasing radiosensitivity using inhibitors of trefoil factor 1 (tff1) - Google Patents

Abstract

The invention relates generally to the use of inhibitors of TTF1 to increase radiosensitivity of tumors and other cells. The invention provides methods of inhibiting proliferation or survival of a tumor cell; methods of treating, delaying the progression of, preventing a relapse of, or alleviating a symptom of a cancer or other neoplastic condition; methods increasing sensitivity of a tumor cell to radiotherapy; methods of enhancing or supplementing an anti-cancer therapy in a subject that is receiving or has been administered radiotherapy; and methods of inhibiting one or more activity or function of a TFF1 - stimulated cancer stem cell.

Description

METHODS OF INCREASING RADIOSENSITIVITY USING INHIBITORS OF

TREFOIL FACTOR 1 (TFF1)

RELATED APPLICATIONS

[001] This patent application claims the benefit of U.S. Provisional Patent

Application Serial No. 61 /384,972 filed September 21 , 2010 and U.S. Provisional Patent Application Serial No. 61 /392,969 filed October 14, 2010, which are hereby incorporated by reference in their entirety.

FIELD OF THE INVENTION

[002] The invention relates generally to the use of inhibitors of TTF 1 to increase radiosensitivity of tumors. The invention provides methods of inhibiting proliferation or survival of a tumor cell; methods of treating, delaying the progression of, preventing a relapse of, or alleviating a symptom of a cancer or other neoplastic condition; methods increasing sensitivity of a tumor cell to radiotherapy; methods of enhancing or

supplementing an anti-cancer therapy in a subject that is receiving or has been administered radiotherapy; and methods of inhibiting one or more activity or function of a TFF 1 - stimulated cancer stem cell.

BACKGROUND OF THE INVENTION

[003] Radiotherapy is commonly used in the treatment of variety of tumors. The therapy uses ionizing radiation (IR) to, through production of reactive free radicals or direct deposition of energy into cells, damage the DNA of the exposed tissues. The responsiveness of cancerous cell types to IR (i.e., their radiosensitivity) varies. Some cells (e.g., localized lymphoid tumors) can regress dramatically and rapidly after the IR treatment, whereas other require higher IR doses and the IR therapy takes effects over extended periods of time.

[004] The innate or IR-induced ability of cells to resist the lethal effect of IR

(radioresistance) is a major clinical obstacle. There is a need to understand better the causes of cellular resistance to IR therapy in cancer and specifically, to identify the methods of countering the radioresistance formation in order to increase the efficacy of IR therapy in tumors.

SUMMARY OF THE INVENTION

[005] It has been previously shown that inhibition of TFF l expression or function in tumor cells is useful in methods of treating a variety of cancers and proliferation disorders (see e.g., PCT US2005/046634, published as WO 2006/069253;

PCT/US2007/021355, published as WO 2008/042435). In the studies described herein, it has been discovered that TFF l promotes radioresistance in tumor cells. The TFF l -induced reduction of cell sensitivity to radiation may be caused by DNA repair promoting effects of TFF l and/or its effects in protecting cells from apoptotic cell death. In addition, it has been observed in the studies described herein that TFF l has a regulatory effect on stem cell markers. The aberrant expression of TFF l in tumor cells may contribute to abnormal stem cell activation resulting in ionizing radiation (IR) resistance.

[006] The present invention provides methods of inhibiting proliferation or survival of a tumor cell by contacting the tumor cell with an inhibitor to TFF l and exposing the tumor cell to IR. The present invention also provides methods of inhibiting proliferation or survival of a cell associated with a proliferation disorder by contacting the cell with an inhibitor to TFF l and exposing the cell to IR.

[007] The present invention also provides methods for treating, delaying the progression of, preventing a relapse of, or alleviating a symptom of a cancer or other neoplastic condition or proliferation disorder by administering a combination therapy by exposing the subject to radiotherapy and administering a subject in need thereof in an inhibitor that binds to trefoil factor 1 (TFF l ). The inhibitor is administered to the subject in an amount sufficient to treat, delay the progression of, prevent a relapse of, or alleviate the symptom of the cancer or other neoplastic condition or proliferation disorder in the subject.

[008] The present invention provides methods of increasing the efficacy of IR therapy by increasing the cellular sensitivity to IR therapy (radiosensitivity) in tumor cells, cancers, neoplastic conditions and other proliferative disorders. The invention provides methods for increasing tumor cell radiosensitivity by administering to the subject an inhibitor of TFF l . [009] The methods described herein include inhibition of one or more activity or function of a TFF 1 -stimulated cancer stem cell by contacting the TFF 1 -stimulated cancer stem cell with an inhibitor of TFF 1 and exposing the TFF 1 -stimulated cancer stem cell to radiotherapy.

[0010] The methods described herein may be carried out by administration of an antibody or an immunologically active fragment thereof {e.g. , an antigen-binding fragment) that binds to TFF 1. TFF 1 specific antibodies include those that: bind to domains or residues that are exposed (e.g., outer loop structure residues in the tertiary structure of the protein in solution), participate in TFF 1 dimerization or aggregation, as well as bind to the domains responsible for promoting cellular proliferation, survival, and oncogenicity. For example, the epitope binding specificity of the antibody includes a TFF1 sequence that contains a domain involved in stimulation of cell proliferation, survival and oncogenicity. For example, an antibody binds to an epitope containing residue 20, 21 , 42, 43, or 58 of TFF 1 (SEQ ID NO: 6). The anti-TFF l antibody is a polyclonal antibody or monoclonal antibody or a derivative of either of those. The invention encompasses not only an intact monoclonal antibody, but also an immunological ly-active antibody fragment, e.g. , a Fab or (Fab)2 fragment; an engineered single chain Fv molecule; or a chimeric molecule, e.g. , an antibody which contains the binding specificity of one antibody, e.g., of murine origin, and the remaining portions of another antibody, e.g. , of human origin. Other TFF 1 -binding antibodies are used to directly target TFF 1 -over-expressing cells for destruction. In the latter case, the antibody, or fragment thereof, activates complement in a patient treated with the antibody. Preferably, the antibody mediates antibody-dependent cytotoxicity of tumor cells in the patient treated with the antibody. The antibody is optionally conjugated to a radiochemical, or a chemical tag which sensitizes the cell to which it is bound to radiation or laser-mediated killing.

[0011] The methods of this invention may be carried out by administering antibodies that bind TFF 1 , wherein the antibody binds to a conformation epitome on TFF 1 polypeptide monomer. For example, antibodies that bind a conformation epitope (CE) selected from the CEs shown in Table 1. Suitable antibodies may also bind to at least a portion of an antigenic determinant selected from the antigenic determinants shown in Table 2. Other antibodies useful for carrying out the methods disclosed in this invention include antibodies that bind to a conformation epitope on a human TFF 1 polypeptide homodimer. For example, antibodies that bind a CE selected from the CEs shown in Table 3. Other antibodies useful in performing this invention may include antibodies that bind to at least a portion of an antigenic determinant selected from the antigenic determinants shown in Table 4.

[0012] Inhibition of TFF l may be achieved by the use of any of a variety of TFF l inhibitors, also referred to herein as anti-TFFl inhibitors, TFFl antagonists, anti-TFF l antagonists and/or anti-TFF l agents. For example, TFF l can be inhibited using polyclonal or monoclonal antibodies, for example mouse, chimeric, humanized, or fully human monoclonal antibodies. A TFF l specific antibody produced by a hybridoma cell line selected from 1 C6 (ATCC Accession No. PTA-8668), 3F6 (ATCC Accession No. PTA- 8665), 2C5 (ATCC Accession No. PTA-8666), 2D7 (ATCC Accession No. PTA-8664), 2B 10 (ATCC Accession No. PTA-8892), and 1 F9 (ATCC Accession No. PTA-8893) may also be used.

[0013] The methods of the present invention may also be carried out by inhibiting

TFF l using a peptide antagonist, a nucleic acid TFF l inhibitor or a small molecule TFF l inhibitor.

[0014] The TFF l peptide antagonist is a peptide antagonist such as, for example, (a)

TFF l mutant including one or more mutations at a position selected from amino acid residue 20, 21 , 42, 43, and 58 of the amino acid sequence of SEQ ID NO: 6; (b) TFF l mutant including one or more of the following mutations of the amino acid sequence of SEQ ID NO: 6: P20R, G21 , P42R, W43R, C58F or any combination thereof; (c) a chimera of a whole or fragment or mutant of the TFF l of SEQ ID NO: 6 fused with another protein of interest (e.g. , a protein other than a TFF protein such as human serum albumin protein, beta casein); (d) a TFF l deletion mutant of the amino acid sequence of SEQ ID NO: 7, where one of the following groups of amino acids of SEQ ID NO: 7 are deleted: (i) aa 1 - 16; (ii) aa 1 -26; (iii) aa 1 -3 1 ; (iv) aa 1 -32; (v) aa 1 -43 or (vi) aa 1 -57 of SEQ ID NO: 7. The peptide antagonist inhibits binding of an endogenous TFF l to a TFF l receptor; prevents or inhibits aggregation of the TFF l receptor in the cell or inhibits association of TFF l polypeptides, e.g. , TFF l dimerization or aggregation. The TFF l mutant preferably inhibits a function of endogenous TFF l such as oncogenicity and/or potentiation of tumor cell proliferation.

[0015] The TFF l inhibitors useful in carrying out the methods of the present invention include one or more nucleic acid TFFl inhibitor, i.e., one or more iRNAs or one or more DNA molecules encoding one or more iRNAs, wherein the expressed iRNAs interfere with the mRNA of the TFF1 gene and inhibit expression of the TFF1 gene. For example, the iRNA is selected from the group consisting of: (a) iRNA that targets SEQ ID NO: 8 or SEQ ID NO: 9; (b) iRNA has a nucleotide sequence selected from SEQ ID NO: 10 or SEQ ID NO: 1 1.

[0016] Tumors to be targeted by the methods of the invention include tumors characterized as expressing increased levels of TTF l compared to normal, non-cancerous cells. Examples of such include an epithelial tumor such as, e.g. , lung cancer, colorectal cancer, breast cancer, pancreatic cancer, ovarian cancer, prostate cancer, hepatic carcinoma, gastric carcinoma, endometrial carcinoma, renal carcinoma, thyroid cancer, biliary duct cancer, esophageal cancer, brain cancer, melanoma, multiple myeloma, hematologic tumor, and lymphoid tumor.

[0017] The methods of this invention include administering TFF 1 in an amount that is sufficient to: (a) reduce the dosage of IR that is needed to produce the desired therapeutic outcome; (b) decrease the frequency of administration of IR that is needed to produce the desired therapeutic outcome; or (c) reduce the period of cancer regression in the subject treated with IR.

[0018] The TFF1 inhibitor may be administered simultaneously with the exposure to radiotherapy or in a sequential manner.

[0019] The methods of the invention further include the step of the administration of a second chemotherapeutic or anti-neoplastic agent.

[0020] The subject is a mammal, preferably a human suffering from tumor or cancer or proliferative disorder, where the tumor, cancer or proliferative disorder is non- responsive, less responsive or has stopped responding to radiotherapy. The compositions and methods are also useful for veterinary use, e.g. , in treating, cats, dogs, and other pets in addition to livestock, horses, cattle and the like.

[0021] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting. [0022] Other features and advantages of the invention will be apparent from the following detailed description and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0023J Fig. 1 A is a photograph of a blot demonstrating forced expression of TFF l mRNA in mammary carcinoma cells: T47D and MDA-MB-231. The level of TFF l mRNA was determined by semi-quantitative RT-PCR. β-Actin was used as loading control. The cells were stably transfected with either the empty vector (T47D-Vec or MDA-Vec) or the vector containing TFF l cD A (T47D-TFF 1 or MDA-TFF 1 ). Fig. I B is a Western blot showing increased TFF l protein secreted into the medium by stably transfected mammary carcinoma cells compared to the vector transfected control.

[0024] Fig. 2 is a graph illustrating that the forced expression of TFFl mRNA in mammary carcinoma cells: T47D (Fig. 2A) and MDA- MB-231 (Fig. 2B) enhances mammary carcinoma cell viability after exposure to IR.

[0025] Fig. 3 is a graph illustrating that the forced expression of TFFl mRNA increases mammary carcinoma cell number after IR treatment (4Gy ionizing radiation). Fig.3A and B show the results for T47D-vec and T47D-TFF 1 cell lines. Fig. 3C and 3D show the results for MDA-vec and MDA-TFF 1 cell lines.

[0026] Fig. 4 is a graph illustrating that the forced expression of TFF l mRNA protects mammary carcinoma cells T47D (Fig. 4A) and MDA-MB-231 (Fig. 4B) from IR- mediated apoptosis in serum free conditions.

[0027] Fig. 5 is a graph illustrating that the forced expression of TFFl mRNA in mammary carcinoma cells T47D (Fig. 5A) and MDA-MB-231 (Fig. 5B) enhances mammary carcinoma cell clonogenic survival after IR treatment.

[0028] Fig. 6 is a graph and a photograph of cells showing that the forced expression of TFF l enhances mammary carcinoma cell viability following treatment with 4Gy ionizing radiation in 3D Matrigel™ T47D-vec/T47D-TFFl (Fig. 6A) and MDA- vec MDA-TFF l (Fig. 6B).

[0029] Fig. 7 is a graph illustrating that forced expression of TFFl protects T47D and MDA-MB-231 cells against IR mediated DNA double stranded breaks (DSBs) and may enhance repair of DNA DSBs in the cells. [0030] Fig. 8 is a graph illustrating that functional inhibition of TFF 1 with TFF 1 pAb reduces mammary carcinoma cell numbers after IR treatment (T47D (Fig. 8A and 8B) or ZR-751 (Fig. 8C and 8D)).

[0031) Fig. 9 is a graph illustrating that functional inhibition of TFF 1 with TFF 1 pAb enhances IR mediated induction of apoptosis in mammary carcinoma cells.

[0032] Fig. 10 is a graph illustrating that functional inhibition of TFF 1 with TFF1 pAb reduces clonogenic survival of T47D cells mammary carcinoma cells after IR treatment when compared to IgG treated cells.

[0033] Fig. 1.1 is a graph and a photograph of cells showing that functional inhibition of TFF 1 with TFF 1 pAb reduces mammary carcinoma growth in 3D atrigel™ after exposure to IR; T47D cells (Fig. 1 1 A) and ZR-751 cells (Fig. 1 I B).

[0034] Fig. 12 is a graph illustrating that TFF 1 siRNA mediated TFF 1 depletion reduces T47D cell number (Fig. 12A) and survival (Fig. 12B) after IR treatment.

[0035] Fig. 13 is a graph illustrating that functional inhibition of TFF 1 with TFF 1 pAb enhances DNA DSB induction following IR treatment.

[0036] Fig. 14 is a graph and photograph of cells showing that the forced expression of TFF 1 mRNA in mammary carcinoma cell lines MCF7, T47D and MDA-MB-231 enhances mammosphere formation and self-renewal in vitro.

[0037] Fig. 15 is a graph and a photograph of cells showing that inhibition of TFF 1 in cell lines MCF7 (above, black filled columns) and T47D (below, white filled columns) significantly reduces spheroid formation and abrogates mammosphere growth in the respective cell cultures in comparison to controls treated with non-specific IgG.

[0038] Fig. 16 is a graph illustrating that forced expression of TFF 1 in mammary carcinoma cell line MCF7 leads to an increase in the side population as determined by Hoechst 33342 dye efflux.

[0039] Fig.17 is a graph illustrating that forced expression of TFF 1 in MCF7 and

T47D cells increased the size of the CD44+CD24-/low population by five-fold in MCF7 and 4.2-fold in T47D cell lines.

[0040] Fig.18: is a graph illustrating that forced expression of TFF 1 in T47D (Fig.

18A left and B left) and MDA-MB-231 cells (Fig. 18A right and 18B right) was found to significantly enhance resistance to ionizing radiation in T47D and MDA-MB-231 cells as measured by formation of colonies in soft agar (Fig. 18A) and generation of

mammospheres (Fig. 18B). [0041] Fig. 19A is a graph illustrating the response of T47D-vec and MCF-vec to different doses of paclitaxel determined using a cell viability assay. Fig. 19B is a graph illustrating that forced expression of TFF 1 significantly increases MCF-7 and T47D total cell number following both vehicle (DMSO) and 1 nM paclitaxel (PTX) treatments.

Moreover, forced expression of TFF 1 significantly increased formation of colonies in soft agar by MCF7 cells following administration of 5 nM paclitaxel (Fig 19C).

[0042] Fig. 20 is a graph illustrating that TFF 1 modulates mRNA expression of stem cell-associated markers: NOTCH3, DVLl and SUFU in MCF7-TFF 1 cells (Fig. 20 A) as well as GLI3 and ABCG2 in T47D cells (Fig. 20B)

DETAILED DESCRIPTION OF THE INVENTION

[0043] Exposure of tumor cells to ionizing radiation (IR) promotes cell death through the induction of DNA damage and results in a range of lesions including single strand breaks (SSBs) and highly lethal double strand breaks (DSBs) (Jeggo et al. 2006 Radiat Prot Dosimetry 122: 124- 127). Generation of DNA lesions activates DNA damage checkpoint pathways and subsequent DNA repair networks which are central to the cellular response to IR (Branzei et al. 2008 Nat Reb Mol Cell Biol 9:297-308). Intrinsic resistance to radiation therapy is a major clinical obstacle and the response to radiation can vary considerably, even in tumors displaying similar pathology. Numerous extrinsic and intrinsic factors contribute to reduced cellular sensitivity to IR. One well established mechanism is tumor hypoxia; viable cells in hypoxic areas are more resistant to IR-induced cell death than normoxic cells (Brizel et al. 1999 Radiother Oncol 53 : 1 13- 1 17; Dumont et al. 2009 Expert Opin Ther Pat 19:775-799; Nordsmark et al. 1996 Radiother Oncol 41 :31 -39), a consequence of reduced DNA damage to hypoxic regions. Enhanced capacity of cells to repair DNA damage, through alteration in the expression or activity of enzymes involved in such repair is another mechanism contributing to radioresistance (Dumont et al. 2009 Expert Opin Ther Pat 19:775-799). Increased expression in tumor cells of autocrine growth factors and growth factor receptors such as vascular endothelial growth factor (VEGF-A), insulin-like growth factor I receptor (IGF- I R) and members of the human epidermal growth factor receptor (HER) family have been demonstrated to promote radioresistance through multiple mechanisms (Dumont et al. 2009 Expert Opin Ther Pat 19:775-799; Jameel et al. 2004 The Breast 13 :452-460). Accordingly, constitutive activation of pro-survival signal transduction pathways such as the phosphatidylinositol 3-kinase (PI-3K) pathway and mitogen-activated protein kinase ( AP ) pathway have also been implicated in this process (Jameel et al. 2004 The Breast 13:452-460).

[0044] The trefoil factor family of proteins is characterized by a 40-amino acid trefoil motif that contains 3 conserved disulfide bonds. The 3 intrachain disulfide bonds form the trefoil motif (TFF domain). The trefoil motif is known in the art, e.g., Taupin and Podolsky, Nat Rev Mol Cell Bio. 4(9):721 -32, 2003; Hoffmann et al., Histol Histopathol 16( 1 ):3 19-34, 2001 ; and Thim, Cell Mol Life Sci 53( 1 1 - 12):888-903, 1997.'In humans, three distinct members of the trefoil peptides have been identified. TFF l or pS2 was first detected in a mammary cancer cell line as an estrogen-inducible gene. In human stomach, it is predominantly located in the foveolar cells of the gastric mucosa. TFF2 (formerly spasmolytic polypeptide or SP) was first purified from porcine pancreas and is expressed in mucous neck cells, deep pyloric glands, and Brunner's glands. TFF3 or intestinal trefoil factor (ITF) was the last to be identified and is predominantly expressed in the goblet cells of the small and large intestine.

[0045] The trefoil peptides are involved in mucosal healing processes and are expressed at abnormal elevated levels in neoplastic diseases. A wide range of human carcinomas and gastrointestinal inflammatory malignancies, including peptic ulceration and colitis, Crohn's syndrome, pancreatitis, and biliary disease, aberrantly express trefoil peptides. Orthologues of these human proteins have been identified in other animals; for example, rats, mice and primates.

[0046] The trefoil family of peptides possess divergent function in the mammary gland with TFF l functioning as a mitogen and TFF2 stimulating branching morphogenesis and cell survival. TFF3 is widely co-expressed with TFF l in malignancies of the human mammary gland whereas TFF2 is not expressed in the mammary epithelial cells.

[0047] Reference herein to "TFF", "TFF protein(s)", or "TFF family of proteins" refers to the group of related proteins including TFF l , TFF2, and TFF3. TFF proteins share at least approximately 28 to 45% amino acid identity within the same species.

[0048] As used herein, the term "antibody" refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e. , molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, F_ab, F_ab' and F_(ab )2 fragments, and an F_ab expression library. By "specifically bind" or "immunoreacts with" is meant that the antibody reacts with one or more antigenic determinants of the desired antigen and does not react (i.e., bind) with other polypeptides or binds at much lower affinity ( _d > 10^"6) with other polypeptides.

[0049] The basic antibody structural unit is known to comprise a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light" (about 25 kDa) and one "heavy" chain (about 50-70 kDa). The amino-terminal portion of each chain includes a variable region of about 100 to 1 10 or more amino acids primarily responsible for antigen recognition. The carboxy-terminal portion of each chain defines a constant region primarily responsible for effector function. Human light chains are classified as kappa and lambda light chains. Heavy chains are classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgA, and IgE, respectively. Within light and heavy chains, the variable and constant regions are joined by a "J" region of about 12 or more amino acids, with the heavy chain also including a "D" region of about 10 more amino acids. See generally, Fundamental Immunology Ch. 7 (Paul, W., ea., 2nd ed. Raven Press, N.Y. ( 1989)). The variable regions of each light/heavy chain pair form the antibody binding site.

[0050] The term "monoclonal antibody" (MAb) or "monoclonal antibody .

composition", as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarity determining regions (CDRs) of the monoclonal antibody are identical in all the molecules of the population. MAbs contain an antigen binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.

[0051] In general, antibody molecules obtained from humans relate to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule. Certain classes have subclasses as well, such as IgG i, IgG2, and others. Furthermore, in humans, the light chain may be a kappa chain or a lambda chain.

[0052] The term "antigen-binding site" or "binding portion" refers to the part of the immunoglobulin molecule that participates in antigen binding. The antigen binding site is formed by amino acid residues of the N-terminal variable ("V") regions of the heavy ("H") and light ("L") chains. Three highly divergent stretches within the V regions of the heavy and light chains, referred to as "hypervariable regions," are interposed between more conserved flanking stretches known as "framework regions," or "FRs". Thus, the term "FR" refers to amino acid sequences which are naturally found between, and adjacent to, hypervariable regions in immunoglobulins. In an antibody molecule, the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen-binding surface. The antigen-binding surface is complementary to the three-dimensional surface of a bound antigen, and the three hypervariable regions of each of the heavy and light chains are referred to as "complementarity-determining regions," or "CDRs." The assignment of amino acids to each domain is in accordance with the definitions of Kabat Sequences of Proteins of Immunological Interest (National Institutes of Health, Bethesda, Md. ( 1987 and 1991)), or Chothia & Lesk J. Mol. Biol. 196:901 -917 ( 1987), Chothia et al. Nature 342:878- 883 ( 1989).

[0053] As used herein, the term "epitope" includes any protein determinant capable of specific binding to an immunoglobulin, an scFv, or a T-cell receptor. The term "epitope" includes any protein determinant capable of specific binding to an immunoglobulin or T- cell receptor. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics. An antibody is said to specifically bind an antigen when the dissociation constant is < 1 μΜ; preferably < 100 nM and most preferably < 10 nM.

[0054] Those skilled in the art will recognize that it is possible to determine, without undue experimentation, if an antibody has the same specificity as a TFF 1 antibody described herein by ascertaining whether the former prevents the latter from binding to a CD3 antigen polypeptide. If the antibody being tested competes with an antibody of the invention, as shown by a decrease in binding by the TFF 1 antibody of the invention, then the two antibodies bind to the same, or a closely related, epitope. Another way to determine whether an antibody has the specificity of an antibody of the invention is to pre-incubate the antibody of the invention with the TFF antigen with which it is normally reactive, i.e. , TFF 1 , and then add the antibody being tested to determine if the antibody being tested is inhibited in its ability to bind the TFF 1 antigen. If the antibody being tested is inhibited then, it is likely to have the same, or functionally equivalent, epitopic specificity as the antibody of the invention. Anti-TFFl agents

[0055] The TFF I inhibitors described herein, also referred to as anti-TFF l agents, anti-TFF l inhibitors, anti-TFF l antagonists and/or TFF I antagonists, are used to inhibit the growth of a tumor cell, to kill the tumor cell, to treat, delay the progression of, prevent a relapse of or alleviate a symptom of a cancer or other neoplastic indications. In addition, the TFF I inhibitors and other antagonists are useful for increasing the sensitivity of a tumor cell to radiotherapy and/or in methods of otherwise supplementing or enhancing an anticancer therapy. The TFF I inhibitors described herein are also useful in inhibiting one or more biological activities and/or functions of a TFFI -stimulated cancer stem cell.

[0056] "Inhibition" of a TFF protein is intended to refer to blocking, lowering or otherwise reducing the production biological activity and/or expression of the protein. While it may be desirable to completely inhibit the activity of a TFF protein, an inhibition of 5, 10, 20, 25, 50, 75, 90 and up to 100% as compared to a pre-treatment level of TFF protein or activity confers a therapeutic benefit. "Inhibition" of a TFF protein may occur at the level of expression and production of a TFF protein (for example the transcriptional or translational level) or by targeting the function of a TFF protein.

[0057] TFF I inhibitors useful in the methods provided herein can be any agent that blocks, lowers or otherwise reduces the activity and/or expression of TFF I . For example, nucleic acid technology including iRNA, antisense and triple helix DNA may be employed to block expression. Further examples include the use of specific antagonists of TFF I proteins, including peptide antagonists, and antibodies directed against TFF I proteins, or functional derivatives of such antibodies. Antibodies and derivatives thereof include for example, intact monoclonal antibodies, polyclonal antibodies, hybrid and recombinant antibodies (including humanized antibodies, diabodies, and single chain antibodies, for example), and antibody fragments so long as they exhibit the desired activity.

[0058] The efficacy or therapeutic benefit of an agent in inhibiting a TFF I is determined by detecting a reduction in tumor load or tumor mass. Efficacy of agents is also determined by detecting of mitogenesis, cell survival, cell numbers, proliferation. Preferred TFF I inhibitors one or more of the following characteristics: 1 ) the ability to prevent, decrease or inhibit mitogenesis; 2) the ability to prevent, decrease or inhibit cell survival; 3) the ability to prevent or inhibit the increase in cell numbers or to decrease cell numbers; 4) the ability to prevent or abrogate anchorage independent growth or encourage or maintain anchorage dependent growth; and, 5) the ability to prevent, inhibit or decrease oncogenic transformation. Preferably suitable agents will exhibit two or more of these characteristics.

[0059] Anti-TFF l antibodies are used as anti-TFF l agents in the methods provided herein. For example, the anti-TFFl antibody binds to a conformational epitope on a human TFF l polypeptide monomer. In some embodiments, the conformational epitope is selected from a conformational epitope shown below in Table 1 :

[0060] In some embodiments, the antibody binds at least a portion of one of the antigenic determinants shown below in Table 2:

[0061] In some embodiments, the antibody binds to a conformational epitope on a human TFFl polypeptide homodimer. For example, the antibody binds to a conformation epitope shown below in Table 3 :

A and B are two TFF l proteins forming the homodimer.

[0062] In some embodiments, the antibody binds at least a portion of one of the antigenic determinants shown below in Table 4:

PREDICTED AD

AD No. Antigenic Determinant

1 A A_l : EAQTETCTVApRErQN : 16 1

2 A A_19 FPGvTPSQcANKG :31 2

3 A A_34 FDDTVRG :40 3

4 A A_46 YPnTIDVPPEEECEF :60 4

5 B B_l : EAQTETcTvAPRErQNcGFPGvTPSQcAN G :31 5

6 B B_34: FdDTVRG :40 3

7 B B_46: YPNTIDVPPEEECEF: 60 4

[0063] Suitable anti-TFF l antibodies used in the methods provided herein include, for example, monoclonal antibodies such as a mouse, chimeric, humanized, or fully human monoclonal antibody. Suitable anti-TFFl antibodies include an antibody produced by a hybridoma cell line selected from 1 C6 (ATCC Accession No. PTA-8668), 3F6 (ATCC Accession No. PTA-8665), 2C5 (ATCC Accession No. PTA-8666), 2D7 (ATCC Accession No. PTA-8664), 2B 10 (ATCC Accession No. PTA-8892), and 1 F9 (ATCC Accession No. PTA-8893). Suitable anti-TFF l antibodies also include an antibody produced by a hybridoma cell line selected from 1 A 12, 3A2, 3A5, 3B8, 3F4, 3F 12, 3G4, 1 A l 1 , 2B3, 3B4, 1 C4, 2C 12, 2A8, 1 E4, 2E2, 2H4, 3F 1 1 , and 3F3 as described in PCT Publication No. WO 2008/042435.

[0064] Nucleic acids are also utilized to inhibit a TFF 1 protein. Such nucleic acids may be DNA, RNA, single-stranded, or double-stranded. Nucleic acids of use in the invention may be referred to herein as "isolated" nucleic acids. "Isolated" nucleic acids are nucleic acids which have been identified and separated from at least one contaminant nucleic acid molecule with which it is associated in its natural state. Accordingly, it will be understood that isolated nucleic acids are in a form which differs from the form or setting in which they are found in nature. It will further be appreciated that "isolated" does not reflect the extent to which the nucleic acid molecule has been purified.

[0065] Isolated nucleic acids of used in the invention may be obtained using a number of techniques known in the art. For example, recombinant DNA technology may be used as described for example in Joseph Sambrook and David W. Russell. Molecular Cloning: A Laboratory Manual (Third Edition), Cold Spring Harbor Laboratory Press, New York, USA. Similarly chemical synthesis (for example, using phosphoramidite and solid phase chemistry) may be used. [0066] Nucleic acids of use in the invention may be designed on the basis of particular TFF l nucleic acid sequence data, the known relative interactions between nucleotide bases, and the particular nucleic acid technology to be employed, as may be exemplified herein after. Exemplary human nucleic acid and amino acid sequence data for TFF l is provided on GenBank under the accession number NM 003225, herein incorporated by reference. Orthologues have also been described in other primates, and in rat and mouse. Exemplary rat sequence data is provided on GenBank under the accession number NM 057129, herein incorporated by reference. Exemplary murine sequence data is provided under the accession number NM 009362, herein incorporated by reference.

[0067] Interference RNA (iRNA) or short interfering RNA (siRNA) are utilized to inhibit TFF l . The iRNA and siRNA are used interchangeably herein. Nucleic acids of use in iRNA techniques will typically have 100% complementarity to their target. However, it should be appreciated that this need not be the case, provided the iRNA retains specificity for its target and the ability to block translation. Exemplary iRNA molecules may be in the form of -18 to 21 bp double stranded RNAs with 3' dinucleotide overhangs, although shorter or longer molecules may be appropriate. In cases where the iRNA is produced in vivo by an appropriate nucleic acid vector, it will typically take the form of an RNA molecule having a stem-loop structure (for example having an approximately 19 nucleotide stem and a 9 nucleotide loop with 2-3 Us at the 3' end). Algorithms of use in designing siRNA are available from Cenix (Dresden, Germany - via Ambion, Texas USA).

[0068] Suitable anti-TFF l nucleic acids include iRNA molecules to a TFF l transcript or a nucleic acid adapted in use to express such iRNA. In some embodiments, DNA molecule(s) encoding one or more iRNAs are transcribed within the cell. For example, in some embodiments, iRNA molecule(s) are transcribed within the cell as siRNAs. An iRNA can be chosen from the group targeting the following sequences:

[0069] 5'-AATGGCCACCATGGAGAACAA-3 ' (SEQ ID NO:8)

[0070] 5'-AAATAAGGGCTGCTGTTTCGA-3 ' (SEQ ID NO:9)

[0071] An iRNA to TFFl can be chosen from the group having the following structures: XXXXAATGGCCACCATGGAGAACAATTCAAGAGATTGTTCTCCAT.GGTGGC ATT.XXXX (SEQ ID NO: 10) I Sense | Loop | antisense

XXXXAAATAAGGGCTGCTGTTTCGATTCAAGAGATCGAAACAGCAGCCCTTATTTXXXX (SEQ ID NO: 1 1 ) I Sense | Loop | antisense

[0072] XXXX indicates additional nucleotides which may be present; for example termination signals and restriction sites which may be of use in cloning and expressing the iRNA. By way of example, the following nucleic acids may be used to clone and express (in desired vectors) iR As:

TFF 1 :

TFF1 :

8an)til H JU

GqATCCCAATGGCCACCATGGAGAACAATTCAAGAGATTGTTCTCC^^

(SEQ ID NO: 12)

I Sense. | Loop | antjjeryje,. | Termination Signal

BenjHJl Hind III

qGATCCCAAATAAGGGCTGCTGTTTCGATTCAAGAGATCGAAACAGCAGCC TTA n-l m LCCAAAAGCTT

(SEQ ID NO: 13)

I Sense. | Loop nii5?H¾. I Termination Signal

[0073] Antisense molecules are used to inhibit TFF 1 production by a tumor cell.

Antisense means any nucleic acid (preferably RNA, but including single stranded DNA) that binds to a TFF transcript to prevent translation thereof. Typically, antisense molecules or oligonucleotides consist of 15-25 nucleotides which are completely complementary to their target mRNA. However, larger antisense oligonucleotides including full-length cDNAs are also inhibitory. Antisense molecules which are not completely complementary to their targets are utilized provided they retain specificity for their target and the ability to block translation.

[0074] Anti-TFF l nucleic acid molecules of use in the invention, including antisense, iRNA, ribozymes and DNAzymes may be chemically modified to increase stability or prevent degradation or otherwise. For example, the nucleic acid molecules may include analogs with unnatural bases, modified sugars (especially at the 2' position of the ribose) or altered phosphate backbones. Such molecules may also include sequences which direct targeted degradation of any transcript to which they bind. For example, a sequence specific for RNase H, may be included. Another example is the use of External Guide Sequences (EGSs), which may recruit a ribozyme (RNase P) to digest the transcript to which an antisense molecule is bound for example.

[0075] Inhibitory nucleic acids are in the form of synthetic nucleic acid molecules produced in vitro (for example single stranded DNA, iRNA, antisense RNA, DNAzymes), or alternatively, they are encoded by sequences in a vector to produce an active inhibitory compound, e.g., antisense molecules, iRNA, ribozymes. Any suitable vector known in the art is within the scope of the present invention. For example, naked plasmids that employ CMV promoters are used. Standard viral vectors such as adeno-associated virus (AAV) and lentiviruses are suitable. Such vectors are known in the art: the use of retroviral vectors is reported in Miller et al., Meth. Enzymol. 217:581 -599, 1993 and Boesen et al., Biotherapy 6:291 -302, 1994; the use of adenoviral vectors is reported for example in Kozarsky and Wilson, Current Opinion in Genetics and Development 3 :499-503, 1993; -Rosenfeld et al., Science 252:431 -434, 1991 ; Rosenfeld et al., Cell 68: 143- 155, 1992; Mastrangeli et al., J. Clin.. Invest. 91 :225-234, 1993; PCT Publication WO 94/12649; and Wang, et al., Gene Therapy 2:775-783, 1995; and, the use of AAV has been reported in Walsh et al., Proc. Soc. Exp. Biol. Med. 204:289-300, 1993; U.S. Patent No. 5,436, 146. Other examples of suitable promoters and viral vectors are provided herein.

[0076] Nucleic acid vectors or constructs of use in the invention may include appropriate genetic elements, such as promoters, enhancers, origins of replication as are known in the art, including inducible, constitutive, or tissue-specific promoters. A vector can comprise an inducible promoter operably linked to the region coding a nucleic acid of the invention (for example antisense TFF3 or suitable siRNA), such that expression of the nucleic acid is controllable by controlling the presence or absence of the appropriate inducer of transcription. Nucleic acid molecules encoding a peptide of the invention can be flanked by regions that promote homologous recombination at a desired site in the genome, thus providing for intrachromosomal integration of the desired nucleic acids (Koller and Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932-8935; Zijlstra et al., 1989, Nature 342:435-438). Of course, the vectors may remain extrachromosomal.

[0077] Peptides and/or proteins are also useful in methods to inhibit a TFF protein in accordance with the invention. A "peptide antagonist" is a peptide having the ability in use to block, lower or reduce biological activity of a TFF1 polypeptide or protein. While it may be desirable to completely inhibit the activity of TFF 1 , this need not be essential. Peptide antagonists include those peptides that compete with native TFF 1 for binding to a TFF 1 receptor, prevent native TFF 1 binding to a TFF 1 receptor, prevent dimerization of TFF 1 or a TFF 1 receptor, or prevent activation of a TFF 1 receptor.

[0078] A peptide or protein is an "isolated" or "purified" peptide. An "isolated" or

"purified" peptide is one which has been identified and separated from the environment in which it naturally resides. It should be appreciated that 'isolated' does not reflect the extent to which the peptide has been purified or separated from the environment in which it naturally resides. Preferably, the peptide of interest is at least 60%, by weight, of the protein in the preparation. Preferably, the protein in the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight. Purity is measured by any appropriate method, e.g. , column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

[0079] Peptide antagonists are designed on the basis of the published amino acid and nucleic acid sequence data in respect of a TFF as described herein. For instance, a peptide antagonist is derived from a native TFF amino acid sequence incorporating one or more mutation therein. Such mutations include for example amino acid insertions, deletions, substitutions and the like. Alternatively, a peptide antagonist is a fragment of the full length native TFF protein, which may or may not include a mutation(s). Peptide antagonists may also include fragments of the native TFF protein fused to a heterologous peptide. For example, the heterologous peptide (e.g. , human serum albumin) serves to increase serum half-life (i.e. , decrease protein degradation) and/or decrease rapid excretion of the construct by the kidneys. The heterologous peptide may also serve a mass effect of preventing or impairing interaction of TFF with its receptor or receptor activation.

[0080] In some embodiments, the peptide antagonist of TFF 1 is a TFF 1 mutant that includes one or more mutations at a position selected from amino acid residue 20, 21 , 42, 43, and 58 of the following sequence:

EAQTETCTVAPRERQNCGFPGVTPSQCANKGCCFDDTVRGVPWCFYPNTIDVPPEE ECEF (SEQ ID NO: 6). For example, the TFF 1 mutant contains one or more of the following mutations: P20R, G21 R, P42R, W43R, C58F or any combination thereof. In some embodiments, the peptide antagonist of TFF 1 is a TFF 1 deletion mutant of the following sequence: AT EN VICALVLVSMLALGTLAEAQTETCTVAPRERQNCGFPGVTPSQCAN G CCFDDTVRGVPWCFYPNTIDVPPEEECEF (SEQ ID NO: 7). For example, the TFF 1 deletion mutant is selected from: deletion of amino acids 1 - 16 of SEQ ID NO: 7; deletion of amino acids 1 -26 of SEQ ID NO: 7; deletion of amino acids 1 -31 of SEQ ID NO: 7;

deletion of amino acids 1-32 of SEQ ID NO: 7; deletion of amino acids 1 -43 of SEQ ID NO: 7; deletion of amino acids 1 -57 of SEQ ID NO: 7 and any combination thereof.

[0081] The methods of generating peptide antagonists of TFF 1 have previously been described in International Patent Application No. PCT /US2005/046634.

Administration of TFF 1 inhibitors and compositions

[0082] The anti-TFF l agent(s) (e.g., peptides, immunoglobulins, small molecules and/or nucleic acids including those described herein) of use in inhibiting TFF 1 may be used on their own, or in the form of compositions in combination with one or more pharmaceutically acceptable diluents, carriers and/or excipients.

[0083] As used herein, the phrase "pharmaceutically acceptable diluents, carriers and/or excipients" is intended to include substances that are useful in preparing a pharmaceutical composition, may be co-administered with an agent in accordance with the invention while allowing same to perform its intended function, and are generally safe, nontoxic and neither biologically nor otherwise undesirable. Examples of pharmaceutically acceptable diluents, carriers and/or excipients include solutions, solvents, dispersion media, delay agents, emulsions and the like. Diluents, carriers and/or excipients may contain minor amounts of additives such as substances that enhance isotonicity and chemical stability.

[0084] A variety of pharmaceutically acceptable diluents, carriers and/or excipients known in the art may be employed in compositions of the invention. As will be appreciated, the choice of such diluents, carriers and/or excipients will be dictated to some extent by the nature of the agent to be used, the intended dosage form of the composition, and the mode of administration thereof. By way of example, in the case of administration of nucleic acids such as vectors adapted to express antisense or iRNA, suitable carriers include isotonic solutions, water, aqueous saline solution, aqueous dextrose solution, and the like.

[0085] In addition to standard diluents, carriers and/or excipients, a pharmaceutical composition of the invention may be formulated with additional constituents, or in such a manner, so as to enhance the activity of the agent or help protect the integrity of the agent.

20

f For example, the composition may further comprise adjuvants or constituents which provide protection against degradation, or decrease antigenicity of an agent, upon administration to a subject. Alternatively, the agent may be modified so as to allow for targeting to specific cells, tissues or tumors.

[0086] Additionally, the anti-TFF l agent(s) is formulated with other ingredients which may be of benefit to a subject in particular instances. For example, optionally, one or more anti-neoplastic agents are co-administered or incorporated into the formulation.

Examples of such agents include: alkylating agents (e.g. , chlorambucil (Leukeran™), cyclophosphamide (Endoxan™, Cycloblastin™, Neosar™, Cyclophosphamide™), ifosfamide (Holoxan™, Ifex™, Mesnex™), thiotepa (Thioplex™, Thiotepa™));

antimetabolites/S-phase inhibitors (e.g., methotrexate sodium (Folex™, Abitrexate™, Edertrexate™), 5-fluorouracil (Efudix™, Efudex™), hydroxyurea (Droxia™, Hydroxyurea, Hydrea™), amsacrine, gemcitabine (Gemzar™), dacarbazine, thioguanine (Lanvis™)); antimetabolites/mitotic poisons (e.g. , etoposide (Etopophos™, Etoposide, Toposar™), vinblastine (Velbe™, Velban™), vindestine (Eldesine™), vinorelbine (Navelbine™), paclitaxel (Taxol™)); antibiotic-type agents (e.g. , doxorubicin (Rubex™), bleomycin (Blenoxane™), dactinomycin (Cosmegen™), daunorubicin (Cerubidin™), mitomycin ( utamycin™)); hormonal agents (e.g. , aminoglutethimide (Cytadren™); anastrozole (Arimidex™), estramustine (Estracyt™, Emcyt™), goserelin (Zoladex™),

hexamethylmelanine (Hexamet™), letrozole (Femara™), anastrozole (Arimidex™), tamoxifen (Estroxyn™, Genox™, Novaldex™, Soltamox™, Tamofen™)); or any combination of any two or more anti-neoplastic agents (e.g., Adriamycin/5- fluorouracil/cyclophosphamide (FAC), cyclophosphamide/methotrexate/5-fluorouracil (CMF)). The anti-TFF l agent(s) may also be formulated with compounds and agents, other than those specifically mentioned herein, in accordance with accepted pharmaceutical practice.

[0087] In accordance with the mode of administration to be used, and the suitable pharmaceutical excipients, diluents and/or carriers mentioned herein before, compositions of the invention are converted to customary dosage forms such as solutions, orally administrable liquids, injectable liquids, tablets, coated tablets, capsules, pills, granules, suppositories, trans-dermal patches, suspensions, emulsions, sustained release formulations, gels, aerosols, liposomes, powders and immunoliposomes. The dosage form chosen will reflect the mode of administration desired to be used, the disorder to be treated arid the nature of the agent to be used. Particularly preferred dosage forms include orally administrable tablets, gels, pills, capsules, semisolids, powders, sustained release formulation, suspensions, elixirs, aerosols, ointments or solutions for topical administration, and injectable liquids.

[0088] Skilled persons will readily recognize appropriate dosage forms and formulation methods. The compositions can be prepared by contacting or mixing specific agents and ingredients with one another. Then, if necessary, the product is shaped into the desired formulation. By way of example, certain methods of formulating compositions may be found in references such as Gennaro AR: Remington: The Science and Practice of Pharmacy, 20th ed., Lippincott, Williams & Wilkins, 2000.

[0089] The amount of an anti-TFF l agent in a composition can vary widely depending on the type of composition, size of a unit dosage, kind of carriers, diluents and/or excipients, and other factors well known to those of ordinary skill in the art. The final composition can comprise from 0.0001 percent by weight (% w) to 100% w of the actives of this invention, preferably 0.001 % w to 10% w, with the remainder being any other active agents present and/or carrier(s), diluent(s) and/or excipient(s).

[0090] Administration of any of the agents or compositions of the invention can be by any means capable of delivering the desired activity (inhibition of tumor cell proliferation) to a target site within the body of a subject. A "target site" may be any site within the body which may have or be susceptible to a proliferative disorder, and may include one or more cells, tissues or a specific tumor.

[0091] For example, administration may include parenteral administration routes, systemic administration routes, oral and topical administration. For example,

administration may be by way of injection, subcutaneous, intraorbital, ophthalmic, intraspinal, intracisternal, topical, infusion (using e.g., slow release devices or minipumps such as osmotic pumps or skin patches), implant, aerosol, inhalation, scarification, intraperitoneal, intracapsular, intramuscular, intratumoral, intranasal, oral, buccal, transdermal, pulmonary, rectal or vaginal As will be appreciated, the administration route chosen may be dependent on the position of the target site within the body of a subject, as well as the nature of the agent or composition being used.

[0092] The dose of an anti-TFF l agent or composition administered, the period of administration, and the general administration regime may differ between subjects depending on such variables as the nature of the condition to be treated, severity of symptoms of a subject, the size of any tumor to be treated, the target site to be treated, the mode of administration chosen, and the age, sex and/or general health of a subject. Persons of general skill in the art to which the invention relates will readily appreciate or be able to determine appropriate administration regimes having regard to such factors, without any undue experimentation. Administration of an anti-TFF l agent is in an amount necessary to at least partly attain a desired response. Administration may include a single daily dose or administration of a number of discrete divided doses as may be appropriate. Administration regimes can combine different modes or routes of administration. For example, intratumoral injection and systemic administration can be combined.

[0093] The method may further comprise further steps such as the administration of additional agents or compositions which may be beneficial to a subject having regard to the condition to be treated. For example, other agents of use in treating proliferative disorders (such as the anti-neoplastic agents mentioned above) could be administered. It should be appreciated that such additional agents and compositions may be administered concurrently with the agents and compositions of the invention, or in a sequential manner (for example the additional agents or compositions could be administered before or after administration of the agents or compositions of the invention. It should be appreciated in relation to sequential delivery of agents or compositions, that sequential administration of one agent or composition after the other need not occur immediately, although this may be preferable. There may be a time delay between delivery of the agents or compositions. The period of the delay will depend on factors such as the condition to be treated and the nature of the compositions or agents to be delivered. However, by way of example, the delay period can be between several hours to several days or months.

[0094] The data described herein were generated using the following materials and methods.

Materials and methods

Cell lines

[0095] The human mammary carcinoma cell lines MDA- B-231 , T47D and ZR-

751 were obtained from the American Type Culture collection (Manassas, VA, USA). MDA-MB-23 1 , MCF-7, T47D and ZR-75- 1 cell lines were cultured in RPMI 1640 media (Gibco) supplemented with 10% heat-inactivated fetal bovine serum, l OOIU/ml penicillin, Ι ΟΟμ πιΙ streptomycin, and 2mM L-glutamine. All cells were cultured in accordance with ATCC recommendations at 37°C in a humidified 5% C0₂ incubator.

[0096] All cell lines were grown in 75cm² culture flasks containing approximately

20ml of recommended growth media until cells were 80-85% confluent, after which a portion was passaged into a new flask to allow continuation of stock cultures. Cells were then passaged by first removing the media and subsequently rinsing the cells with PBS. Trypsin EDTA (2ml) was then added and the flask incubated at 37°C/5% C0₂ for 2-5 min. Cells were checked under the microscope to ensure all had detached from the flask and that the cells were monodisperse. 8ml of media was then added to the flask and the surface rinsed using a plastic pipette. The cells and media were subsequently transferred to a 10ml sterile tube and centrifuged for 5 min at 1 100 rpm. Following centrifugation, the media was aspirated and the pellet resuspended in fresh media. For further culturing of stock cultures, an appropriate cell number was seeded into a fresh culture flask and approximately 15-20ml fresh media added, after which the cells were maintained in a 37°C/5% C0₂ incubator.

[0097] Counting: 20μΙ of the cell suspension (total volume 10 ml media) was transferred to an Eppendorf tube and mixed with 180μ1 of trypan blue dye (0.4%). Cell counts were then carried out using a haemocytometer. The number of cells contained in 4 quadrants of 16 squares was counted (twice). The counted squares were then added together and averaged, upon which the resulting number was used to determine the amount of cells/ml using the following formula:

(Cells per 4 quadrants/4) X 10000 X dilution factor = cells /ml

Cells/ml X final volume = total no. of cells

[0098] Storage: Cells were trypsinized and resuspended in 10 ml media, counted and then centrifugated. Following removal of the supernatant, cells were resuspended in freezing media. Aliquots of the cell suspension (1 ml) were placed into each cryogenic vial (Nalgene, Rochester, NY, USA). All vials were placed into an isopropanol containing freezing chamber (Nalgene, Rochester, NY, USA) and placed into a -80°C freezer for 24h to allow gradual cooling and freezing for cell preservation. Eventually, frozen cells were stored in the vapor phase of liquid nitrogen for long-term storage.

[0099] Revival: Cell aliquots from each cryogenic vial were thawed immediately in

10ml of 37°C serum-supplemented culture media, transferred into a 25cm² tissue culture flask and cultured at 37°C (NAPCO Series 5400 CO² Incubator, Forma Scientific, Marietta, OH, USA). Media was changed the next day (to remove DMSO and dead cells) and every two days to allow growth of revived cells.

RNAi transfection

[00100] The MDA-MB-23 1 and T47D cell lines overexpressing TFF 1 were generated as described in Amiry, N., et al., Trefoil factor-1 (TFF1) enhances oncogenicity of mammary carcinoma cells. Endocrinology, 2009. 150( 10): p. 4473-4483.

[00101] A validated TFF 1 Stealth™ RNAi duplex and Stealth™ RNAi negative control duplex were purchased from Invitrogen. RNAi and control duplexes were transfected into T47D cells using Lipofectamine2000 (Invitrogen®). The final concentration of RNAi when added to cells was 50 nM and "knock down" of TFF1 mRNA expression was measured by quantitative Real Time PCR to identify the most efficient RNAi duplex.

TFF1 polyclonal antibodies (pAB).

[00102] The inhibitory polyclonal antibody targeting TFF 1 was provided in liquid form by Biogenes and stored a 4°C. An equivalent concentration of dialyzed rabbit IgG (Sigma Aldrich, Germany) was added to control experiments.

Antibody dialysis

[00103] As a control molecule for the TFF 1 polyclonal antibody, Anti-Rabbit IgG

(Sigma, Missouri, USA) was ordered and dialysis was performed to remove all small molecules and metals present. The TFF 1 polyclonal antibody was also dialyzed as it was provided in a Tris-HCl solution containing sodium azide preservative. The antibodies were dialyzed into PBS for the use in subsequent assays. Dialysis tubing ( 12- 14kDa cutoff) was cut to the required length to hold the protein solution plus an extra space for closure at both ends. The tubing was then soaked in ddH20, rinsed with a plastic pipette and treated twice for 5 min at 60°C in bicarbonate solution (2% w/w NaHC03, I mM EDTA) and then rinsed again with ddH20. The IgG/TFF l pAb solutions were transferred into the tubing and left 36 h in 100 times volume of dialysis buffer ( I X PBS) at 4°C, with stirring. The dialysis buffer was changed twice over the duration of the dialysis.

[00104] The antibody solutions were transferred into a Vivaspin 15R column with a molecular weight cut off (molecular weight of the protein that is 90% retained by the membrane) of 3kDa (Vivascience), centrifuged at 6000 rpm for 15min until the appropriate volume of IgG/TFF l pAb solution was reached. The protein concentration in the supernatant was then measured using a Bradford Assay (See 2.5.2) and filtered sterilized.

Ionizing radiation total cell number assay

[00105] Cells were trypsinized and seeded into six well cell culture plates at a density of 100,000 cells/well (MDA-vec/TFF 1 , T47D-vec TFF 1 ). Cells were cultured in complete media overnight at 37°C in 5% CO2 to ensure that they attached to the culture surface and then treated with 4Gy ionizing radiation. IR treatment was conducted using a C06O source from an Eldorado G unit (FMHS, University of Auckland). Assays were set up in triplicate and cells were counted every 2-3 days over a 7 day period. Cells were pretreated with IgG/TFF l polyclonal antibody (40μg/100μl) or transfected with Stealth™ RNAi duplexes targeting TFF 1 24h prior to radiation treatment and cultured in media containing inhibitors for the duration of the experiment.

3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay

[00106] Cells were plated at different concentrations (MDA-stables 1000 or 3000 cells/well; T47D-stables 1500 or 4000 cells/well) and left for 24h prior to irradiation.

Subsequent to treatment, cells were cultured for 5 or 10 days and the media was replaced every 2 days. On day 5 or day 10 the cells were washed with PBS and then incubated with 0.45mg/ml MTT (Sigma Aldrich) solution made up in serum free media at 37°C for l -3h depending on the cell line tested. Once the formation of blue formazan crystals was apparent, the MTT solution was aspirated and the cells solubilized in Ι ΟΟμΙ DMSO (Sigma Aldrich). The absorbance was read at 570nm and 690nm.

Wst-1 cell viability assay

[00107]^' Cells were plated in 96 wells and left 24h prior to treatments. Ι ΟμΙ, of Wst- 1. reagent was added per well and the plates developed. at 37^°C for 1.5h. The plates were agitated on an orbital shaker for 1 min and absorbance read at 440nm and 650nm.

Clonogenic assay

[00108] Untreated Clonogenic Assay: 20 x 10⁴ cells were plated in 6 well plates and left to attach overnight. Cells were then trypsinized, counted and replated in triplicate in 6 well plates at 100-800 cells/well and grown in full serum media for 14 days. Colonies with greater than 50 cells were counted and the plating efficiencies (PE) calculated. PE = (number of colonies formed/number of cells seeded) x 100%. Colonies were stained with 0.1 % crystal violet in 20% ethanol and counted.

[001091 Radiation cell survival clonogenic assay: Radiation sensitivities of the cell lines were determined by measuring colony formation after cells were exposed to ionizing radiation. Exponentially growing cells (MDA-vec TFF I or T47D-vec/TFF l ) were irradiated with 4Gy ionizing radiation. 24h post irradiation cells were trypsinized, plated in 6 well plates in triplicate at 100/400 cells per well and cultured in full serum media for 14 days. For TFF l inhibition, wild-type T47D or ZR-75- 1 cells were pretreated with 100μg/500μl of IgG or TFF l polyclonal antibody for 24h prior to irradiation. 24h after radiation treatment, the cells were trypsinized, replated at 400 (T47D) or 2000 (ZR-75- 1 ) cells/ well and cultured for 14 days in full serum media.

Apoptosis assay

[00110] Apoptotic cell death was measured by fluorescent microscopic analysis of cell DNA staining patterns with Hoechst 33258.

[00111] Standard apoptosis assay: Cells were plated at 20 x 10⁴ cells /well in full serum media in 6 well plates and cultured for 24h. Cells were then washed with PBS and the media replaced with serum free media. 24h later the cells were fixed and permeabilized in 4% paraformaldehyde, 1 % Triton-X- 100 and stained with 4μg/ml of the karyophillic dye Hoeschst 33258 in PBS for 15 minutes at room temperature. Cells were washed with PBS and apoptotic nuclear morphology was determined using an inverted UV fluorescence microscope (Olympus). Apoptotic cells were distinguished from viable cells by their nuclear morphology characterized by nuclear condensation and fragmentation as well as the higher intensity of the blue fluorescence of the nuclei. For statistical analysis, at least 200 cells were counted in eight random microscopic fields at ^χ400 magnification.

[00112] Radiation apoptosis assay: Cells were plated as described for the untreated apoptosis assay; however l h after transferring the cells into serum free media/the cells were exposed to 4Gy ionizing radiation. 24h, 48h or 72h after radiation treatment the cells were fixed, permeabilized and stained. For apoptosis assays involving TFF l inhibition (T47D, MDA), the cells were pre-treated with BSA/B2036 ( Ι ΟΟΟηΜ) or IgG/TFF l (50μg/100μl) for 24h prior to radiation. 3D Matrigel¹

[00113] Growth factor reduced Matrigel™ was purchased from BD Biosciences (BD No. 354230) and thawed overnight at 4°C. Once thawed, the matrigel was stored as 1 ml aliquots at -20°C. The Matrigel™ was added to each well (50μ1Λνε1Ι for 96 well plate). The plate was placed in an incubator at 37°C/5% CO2 for 30 min to allow the basement membrane to solidify. Concurrently, cells were trypsinized and resuspended in 2ml of complete media and centrifuged at 1 100 rpm for 5 min. Cells were then resuspended in 1 ml of media and pipetted up and down 30 times to ensure a single-cell suspension. 25,000 cells were mixed with 4% Matrigel™ in 5% serum media (4% matrigel final concentration). 200μ1 of the 4% Matrigel™ solution ( 1000 cells/well) was pipetted onto the solidified Matrigel™ in each well. Cells were cultured in a 5% C0₂ humidified incubator at 37°C for 12 days. Every second day, 4% Matrigel™ in 5% serum media was added to the wells. For assays involving inhibition of TFF 1 , the 4% matrigel solution containing BSA B2036 (Ι ΟΟΟηΜ) or IgG TFF l polyclonal antibody (50μg/welI) was added to the cells on day 4. The cells were treated with radiation (4Gy) on day 5. After 9 day growth, 20μ1 of Wst- 1 reagent was added to each well. The plate was incubated for 2h in a 5% CO² humidified incubator at 37°C following which the plate was read at 440nm (Wst- 1 assay) using a Synergy2 multi-mode microplate reader and Gen5 data analysis software (Biotek).

Neutral comet assay

[00114] A neutral comet assay to detect DNA double stranded breaks induced by radiation treatment was performed. 20 x 10⁴cells (MDA-vec/TFF l and T47D-vec TFF l ) were seeded in 6 well plates in full serum media. Stable cell l ines were treated the next day with 4Gy ionizing radiation. For comet assays involving TFF 1 (using 40μg/100μl rabbit TFF 1 polyclonal antibody), the cells were pretreated for 24h prior to cytotoxic treatments. At designated timepoints (i.e. , 15m repair time, l h repair, 3h repair and 6h repair), the cells were harvested by trypsinization and resuspended in I mL full serum media. The cells were then centrifuged at l OOOrpm for 5minutes and the media removed. The cells were resuspended in I mL PBS. Subsequently, 200μί of the cell solution was mixed with I mL of low melting temperature Seaplaque Agarose (Cambrex Bio Science) and allowed to set onto GelBond film (Lonza Rockland, Inc.). The cells were lysed overnight at 37°C in neutral lysis solution (2% sarkosyl, 0.5M Na2EDTA, 0.5mg/ml proteinase , pH 8.0) and then washed in rinse buffer (90mM Tris buffer, 90mM boric acid, 2mM Na2EDTA , pH 8.5) three times. Slides were subjected to electrophoresis in I X TBE for 25 minutes at 20V. Comets were stained with Ι Ο ^πιΙ propidium iodide for 20 mins and rinsed in 400ml distilled water to remove excess stain. At least 100 comet images from each slide were examined. Comet tail length and tail moment were analyzed using Tritek CometScore software (Version 1.5).

Hoechst 33342 efflux (side population) assay

[00115] Monolayer cells were harvested with trypsin-EDTA and density calculated as described above. 10⁶ cells were resuspended in 1 mL RPMI containing 5% FBS and either 5 μg/mL Hoechst 33342 (Sigma) or Hoechst plus 50 μΜ verapamil (an ATP-binding cassette transported inhibitor, from Sigma). The specimens were incubated at 37°C for 90 minutes, vortexing periodically to ensure uniform exposure to the fluorescence reagent. For each cell type, unstained control specimens were established in parallel. After incubation, the samples were centrifuged and the supernatant discarded. The cell pellets were resuspended in PBS containing 2% FBS and transferred to 12x75 mm FACS tubes by passing the suspension through a 35 μπι nylon filter cap. The specimens were held on wet ice until analysis.

Antigenic phenotype assay: CD44⁺CD24^{" low} population

[00116] Monolayer cells were harvested with trypsin-EDTA and counted as described above. 5 x 10⁵ cells were aliquoted into 15 mL test tubes, centrifuged, and the supernatant discarded. The cell pellets were washed in PBS containing 2% FBS (FBS-PBS), centrifuged, and resuspended in 100 μΐ. FBS-PBS. 5μL fluorescence-conjugated mouse anti-human CD44 / CD24 antibodies (BD Biosciences) were added to the cell suspensions and incubated for 30 minutes at room temperature. For purposes of calibrating the flow cytometry analysis gates, unstained, single-stained, and isotypic antibody-stained control specimens were established for each cell type (Table 1 ). After incubation the cells were washed in 2 mL FBS-PBS and resuspended in 400 μΐ. FBS-PBS. The specimens were then transferred to 12x75 mm FACS tubes by passing the suspension through a 35 μπι nylon filter cap and were held on wet ice until analysis. Functional cell culture assays - Mammosphere culture (stem cell specific cell culture) * (00117] All functional cell culture experiments, excepting mammosphere assays, were performed in full ( 10%) serum conditions.

[00118] Cell viability with alarmarBlue: Quantitation of cell viability was accomplished using the bioreductive fluorescent cell viability indicator alarmarBlue (Invitrogen). At the conclusion of the respective incubations, a volume of 10X alarmarBlue equal to 10% of the assay volume was administered to each well. The plates were then incubated for 4 hours to allow the reaction to proceed, after which time fluorescence (560EX nm/590EM nm) was measured using a plate-reading BioTek Synergy 2 spectrofluorometer. Background fluorescence was evaluated by measuring blank wells containing media and assay reagents without cells.

[00119] Primary mammosphere generation: Monolayer cells were harvested in trypsin-EDTA and resuspended in Dulbecco's modified Eagle's medium (DMEM) F 12 (Invitrogen) supplemented with 20 ng/mL recombinant human epidermal growth factor (EGF), 20 ng/mL recombinant human basic fibroblast growth factor (bFGF), B27 supplement, 0.4% FBS, penicillin-streptomycin, L-glutamine (all from Gibco), and 5 μg/mL bovine insulin (Sigma). The suspensions were passed through a 35 μιτι nylon filter and assessed under a light microscope to confirm cell disaggregation. The cells were then seeded in Costar ultra low-attachment plates (Corning). Based on several optimization experiments performed, clonal density of 5000 cells per mL, 96-well format, and 7 day incubation were chosen as the optimal parameters for the assay. Aggregation of colonies was found to preclude reliable enumeration of spheroid generation by manual counting. Therefore day 7 mammosphere formation was evaluated using the alarmarBlue cell viability indicator as described above and in accordance with published protocols (Pan et al., 2010).

[00120] Mammosphere formation over serial passage: After taking

alarmarBlue fluorescence measurements, primary mammospheres were harvested by gentle centrifugation (250 g, 5 minutes) and disaggregated enzymatically and mechanically using trypsin-EDTA and iterative pipetting, respectively. The cells were then resuspended in mammosphere-specific culture medium and seeded in Costar ultra low-attachment 96-well plates at a density of 5000 cells per mL. The plates were incubated for 7 days and second generation mammosphere formation assessed using alarmarBlue.

[00121] TFF l -pAb-treated primary mammosphere formation assay: MCF7 and T47D wild type cells were seeded for primary mammosphere formation assay in 150 μL· per well of 96-well plates at a density of 5000 cells per mL as described above. At the time of seeding, 80 μg dialyzed TFFl-pAb or rlgG in 25 μί PBS, or empty PBS was added to each well. A second identical dose was administered after 72 hours incubation. Cell viability was measured after 7 days incubation using alarmarBlue and micrographs taken as described above.

[00122] Ionizing radiation treatment: For radiation resistance experiments, cells were administered a dose of 4 Gy (soft agar colony formation assay) or 8 Gy

(mammosphere formation assay) ⁶⁰Co γ-radiation in a single fraction using an Eldorado model G radiotherapy source (Atomic Energy of Canada Ltd.) at a dose rate of -0.4 Gy/min. Cells were irradiated in adherent, full-serum conditions at low density and allowed to recover for 24 hours before seeding for soft agar or mammosphere assays. The LD50 of 4 Gy ionizing radiation for T47D was established from previously generated dose response curves measuring clonogenic survival as the experimental endpoint (NM Bougen, unpublished). This dose was found to be insufficient to induce detectable death of mammosphere initiating cells (data not shown), hence a higher dose of 8 Gy was used for mammosphere assays.

[00123] Paclitaxel anti-proliferation (1C50) assay: Paclitaxel doses for subsequent functional assays were selected based on the results of dose-response assays performed with empty vector transfected cell lines. Cells were seeded into 96-well plates at a density of 104 cells per well and allowed to attach overnight. The growth medium was then replaced with RPMI containing paclitaxel at concentrations varying in a logarithmic fashion from 0.1 nM to 1 μΜ. Untreated cells and cell free blank wells were included. Cell viability was measured at 24, 72 and 120 hours using alarmarBlue (Invitrogen). Viability was also measured immediately following attachment to ensure accuracy of plating. The assay was performed using both 10% and 3% FBS.

[00124] Colony formation in soft agar: TFF 1 expressing cell lines were assayed for formation of colonies in soft agar under various drug and radiation treatments. The base of each well of a 96-well plate was coated with 50 LL 0.5% (w:v) agarose in serum-free RPMI. Cells were trypsinized and resuspended in pre-warmed 0.35% agarose (w:v) in serum-free RPMI. Five thousand cells in a total volume of 150 μL· agarose-RPMI were aliquoted to each well and allowed to solidify. One hundred μL· full-serum RPMI was then applied to each well. The plates were incubated for 7 days and cell viability was then measured with alarmarBlue. Drug doses were administered at the time of seeding. For radiation-treated assays, cells were irradiated in monolayer culture 24 hours prior to embedding into soft agar.

[00125] Total cell number: Cells were harvested and 5 x 10 or 1 x 10^s (for anti- estrogen and paclitaxel treatment, respectively) were seeded into each well of 6-well culture dish. Cells were allowed to attach overnight after which time the growth medium was replaced with 2 mL RPMI containing the indicated drug or vehicle dose. At the appointed intervals thereafter a subset of wells were trypsinized and total cell number counted as described above. Remaining wells were re-dosed at each time point. All drug treatments and time points were performed in triplicate.

Statistics

[00126] The statistics software program Sigma Stat 3.1 was used in conjunction with Microsoft Excel for statistical analyses presented in Examples 1 and 2. The graphical presentations were generated using GraphPad Prism V5 (Mathlab). All experiments were , performed at least three times and a single representative figure is shown. Numerical data were expressed as mean +/- SEM of triplicate determinants. Data were analyzed using the unpaired two-tailed t test or analysis of variance (ANOVA), except for the xenograft data whereby a repeated measures ANOVA was performed.

[00127] In Example 3, data are presented as mean plus one standard error of the mean. Figures are representative of replicate experiments performed. All cell culture experiments were performed at least three times. Flow cytometry experiments and TFF 1 depletion experiments were performed twice with consistent results. Any exceptions are disclosed in the respective figure legends. Statistical significances were calculated using two-tailed non-parametric Student's t-test (* = p < 0.05, ** = p < 0.01 , *** = p < 0.001 ). A linear regression model was fitted to the paclitaxel anti-proliferation assay data using Prism GraphPad software.

EXAMPLES

Example 1 : The effects of forced expression of TFF1 on the radiosensitivity profiles of the T47D and MDA-MB-231 cell lines

1.1 TFF1 increases mammary carcinoma cell survival after exposure to IR

[00128] To determine whether forced expression of TFF 1 enhances breast cancer cell survival after IR treatment, the mammary carcinoma cell lines (T47D and MDA-MB-23 1 ) were stably transfected with an expression vector containing the TFF l gene (pIRES-TFF l ). These cell lines are designated T47D-TFF 1 and MDA-TFF l respectively. A second cell line transfected with an empty pIRES vector was generated in parallel for control purposes (designated T47D-vec respectively and MDA-vec). TFFl mRNA and protein expression was verified by RT-PCR and western blot respectively (Fig. 1 A and I B).

1.2 TFFl enhances mammary carcinoma cell viability after IR treatment

[00129] In order to determine the effect of forced expression of TFF l on the radiosensitivity profiles of the T47D and MDA-MB-231 cell lines, dose response experiments using a MTT cell viability assay were carried out following treatment with 0- 8Gy IR. Forced expression of TFFl expression significantly enhanced viability of T47D and MDA-MB-231 cells at all radiation doses tested (Fig. 2A and B). At an IR dose of 4Gy T47D-TFF 1 cells had greater than 15% (pO.0001) higher viability than T47D-vec cells (Fig. 2A). At an IR dose of 6Gy MDA-TFFl cells had greater than 15% (pO.0001 ) higher viability than MDA-vec cells (Fig. 2B).

1.3 TFFl increases mammary carcinoma cell number after IR treatment

[00130] Forced expression of TFF l significantly increased untreated T47D cell number over 7 days, where as no significant difference was seen in untreated MDA-MB- 23 1 cells (Fig. 3A and C). Treatment with 4Gy IR significantly reduced T47D-vec and T47D-TFF 1 total cell number by day five (Fig. 3 A and B). However, T47D-TFF 1 cells exhibited significantly higher cell number at day 7 following radiation treatment than the T47D-vec cell line when expressed as a percentage of untreated controls (T47D-TFF 1 70.32±3.66% vs. T47D-vec 35.46± 1.48%; <0.0001 ) (Fig. 3 A and B). . Similarly, forced expression of TFF in MDA-MB-231 cells significantly protected these cells from IR induced cell death (MDA-TFF l 50.75±1.29% vs. MDA-vec 36.13±1.78%; 7><0.05) (Fig. 3C and D).

1.4 Forced expression of TFFl protects mammary carcinoma cells from IR mediated apoptotic cell death

[00131] The karyophillic dye Hoeschst 33252 was utilized to determine the effect of forced expression of TFF l on induction of apoptotic cell death in T47D and MDA-MB-23 1 cells after IR treatment. T47D-vec and T47D-TFF 1 (Fig. 4A) and MDA-vec and MDA- TFF l (Fig. 4B) cells were cultured in serum-free RPMI and left untreated or exposed to 4Gy ionizing radiation. Apoptotic nuclei were counted at 24, 48 and 72h. Consistent with previous observations (Amiry et al. 2009 Endocrinology 150), untreated T47D-TFF 1 cells had significantly lower apoptotic cell death when compared to the control cell line T47D- vec, after 24, 48 and 72h in serum-free media (Fig. 4A). However, forced expression of TFF l in MDA-MB-231 cells did not significantly protect from serum deprivation induced apoptosis (Fig. 4B). Following treatment with 4Gy radiation, the control cell lines, MDA- vec and T47D-vec, had significantly higher apoptotic cell death than MDA-TFF 1 and T47D-TFF 1 cells at 24, 48 and 72h (Fig. 4A and B).

[00132] Treatment with 1R increased apoptotic cell death 1.8 fold in T47D.-vec compared with T47D-TFF 1 cells after 48h in serum-free media (Fig. 4A). A similar trend was observed with MDA-MB-23 1 cells: MDA-vec had 1.4 fold higher number of apoptotic nuclei than MDA-TFF 1 cells 48h following treatment with IR (Fig. 4B). Thus, forced expression of TFF l protects T47D and MDA-MB-231 cells from IR-induced apoptotic cell death.

7.5 TFFl enhances mammary carcinoma cell clonogenic survival after IR treatment

[00133] A clonogenic survival assay was used to measure the ability of T47D and MDA-MB-231 stable cells to form colonies after IR treatment. When 400 untreated cells were plated per well, there was no significant difference in the plating efficiencies (PE) between T47D-vec and T47D-TFF 1 cells (Fig. 5A). However, there was a significant difference between untreated MDA-vec and MDA-TFF 1 cell PEs, with MDA-vec cells having a 88.3% lower PE than MDA-TFF 1 cells (Fig. 5B). Following 4Gy IR treatment, T47D-vec cells had a 30.16% lower PE than T47D-TFF 1 cells (p<0.05) and MDA-vec cells had a 46% lower PE than MDA-TFF 1 cells (p<0.05) (Fig. 5A and B).

/.6 TFFl enhances mammary carcinoma cell growth in 3D Matrigel *

[00134] Cells (T47D-vec/T47D-TFF (Fig. 6A) and MDA-vec/MDA-TFF l (Fig. 6B) were treated with 4Gy ionizing radiation and cultured in growth factor reduced Matrigel™ for 9 days. Cell viability was determined using Wst- 1 and expressed as % of untreated controls. Consistent with previous observations (Amiry et al. 2009 Endocrinology), forced expression of TFF l increased T47D mammary carcinoma cell growth in 3D Matrigel™ (Fig. 6A). After treatment with 4Gy IR, T47D-TFF 1 cells continued to have increased viability compared with T47D-vec cells. When expressed as a percentage of untreated cell viability, T47D-TFF 1 cells exhibited a 18.6% increase in viability compared with T47D-vec (p<0.001 ) (Fig. 6A). Similar results were obtained in the MDA-MB-231 model, MDA- TFF l cells had 1 1.98% greater cell viability after IR than MDA-vec (p<0.05) (Fig. 6B).

1.7 TFFl protects against IR mediated DNA DSBs and enhances repair of DNA double stranded breaks (DSBs) in mammary carcinoma cells

[00135] In order to assess the effect of forced expression of TFF l on the DNA repair capacity of T47D and MDA-MB-231 cells, a neutral comet assay was carried out: T47D- vec/T47D-TFF l (Fig. 7A) and MDA-vec/MDA-TFF l (Fig. 7B) cells were treated with 4Gy IR and DNA double stranded breaks were measured using the neutral comet assay. The tail moment correlates with the level of DSBs present in: untreated (UT) cells; cells at 15m repair time ( 15m RP); cells at l h repair ( l h RP); 3h repair (3h RP) or 6h repair (6h RP). Results from the neutral comet assay, which selectively detects DNA DSBs, indicated that endogenous levels of DSBs in untreated T47D-vec and T47D-TFF 1 , and MDA-vec and MDA-TFF l cells were similar. However, after treatment with 4Gy IR, forced expression of TFF l conferred a significant protection against induction of DSBs, in both T47D and MDA-MB-23 1 cells, as measured by the tail moment (Fig. 7A and B). In both T47D-TFF 1 and MDA-TFF l cells, the tail moment had returned to untreated levels l h following treatment with 4Gy, whereas in T47D-vec and MDA-vec cells, the tail moment had not returned to untreated levels after 6h repair (Fig. 7A and B). The observation that DNA DSBs induced in TFF l forced expression cell lines repaired more rapidly than in the control cell lines may be indicative of an enhanced DNA repair capacity in those cells.

Example 2: Functional inhibition of TFFl enhances mammary carcinoma cell radiosensitivity

[00136] The wild type ER positive mammary carcinoma cell lines T47D and ZR-75-

1 , which endogenously express TFF l (Amiry et al. 2009 Endocrinology) were used to determine the effect of specific polyclonal antibody (pAb) inhibition and siRNA-mediated depletion of TFF l on radiation response. The pAb was purified from antisera of ZI A female rabbits that were immunized with recombinant TFF l (Biogenes, Germany). 2.1 Functional inhibition of TFFl reduces mammary carcinoma cell number after treatment with IR

[00137] A total cell number assay performed over 7 days demonstrated that specific antibody inhibition of TFF l significantly reduced both T47D and ZR-75- 1 total cell number compared to control, IgG treated cells (Fig. 8A/B and C/D). T47D (Fig. 8A and 8B) or ZR- 751 (Fig. 8C and 8D) were treated with either the TFF l pAb or IgG control for 24h prior to treatment with ionizing radiation. Total cell number assays were conducted in full serum media over 7 days. Strikingly, combining TFF l antibody treatment with exposure to 4Gy ionizing radiation additively reduced total cell number over 7 days (pO.0001 for both cell lines) (Fig. 8A/B and C D).

2.2 Functional inhibition of TFFl enhances IR mediated induction of apoptosis in mammary carcinoma cells

[00138] T47D wild-type cells were treated with TFF l pAb or IgG prior to ionizing radiation treatment (4Gy). Consistent with previous reports (Amiry et al. 2009

Endocrinology), treatment of T47D cells with TFF l polyclonal antibody increases the percentage of apoptotic nuclei compared with cells treated with IgG (Fig. 9) (p<0.05). In the current study, pre-treatment of T47D cells with TFF l polyclonal antibody enhanced the induction of apoptosis after irradiation compared with IgG treated controls. IgG pre-treated T47D cells had 22.56% apoptotic nuclei 24h after radiation whereas TFF l pAb treated cells had 35.64% apoptotic nuclei (pO.001 ) (Fig. 9).

2.3 Functional inhibition of TFFl reduces clonogenic survival after IR treatment

[00139] The effect of inhibition of TFFl on radiation response of T47D cells was determined using the clonogenic assay. Cells were pre-treated with IgG or TFF l pAb for 24h and subsequently treated with 4Gy IR and then re-plated-24h later. 14 days later colonies were stained and counted. Cells pre-treated with TFF l pAb, but not exposed to IR had a 19.33% lower PE than IgG control treated cells (p<0.05). However, after treatment with 4Gy IR, TFF l pAb pre-treated cells a 52.8% lower PE than IgG treated controls (p<0.001 ) (Fig. 1 OA and B). 2.4 Functional inhibition ofTFFl reduces mammary carcinoma growth in 3D Matrigel after exposure to IR

[00140] Pre-treatment with TFF 1 pAb reduced T47D cell growth in 3D Matrigel™ after treatment with IR (Fig. 1 1 A). The Matrigel™ assay was conducted over 9 days after treatment with 4Gy radiation in 5% FBS media. Radiation reduced IgG treated cell viability by 36% compared with a 50% decrease in those cells pre-treated with TFF 1 antibody (p<0.05). A similar trend was observed using ZR-75- 1 cells, whereby a combined treatment of TFF 1 antibody and radiation reduced cell viability by 22.97% compared with radiation combined with the control IgG (p<0.05) (Fig. 1 I B).

2.5 siRNA mediated TFF1 depletion reduces T47D cell number after IR treatment

[00141] The effect of TFF 1 depletion on radiation response was also investigated using siRNA mediated depletion of TFF 1 utilizing a previously validated Stealth RNAi™ siRNA construct (Invitrogen). Wild-type T47D cells were transfected with either a control siRNA or siRNA specific for TFF 1. 24h later transfected cells were treated with 4Gy IR and total cell number was assessed over the following 5 days. As previously demonstrated (Amiry et al. 2009 Endocrinology), specific depletion of TFF 1 utilizing RNAi reduced T47D cell number compared to cells transfected with control siRNA constructs (Fig. 12A and B). This reduction in cell number was further enhanced by treatment with IR. By day 5, cells transfected with TFF 1 siRNA exhibited a 12.5% lower cell number than control treated cells.

2.6 Functional inhibition of TFF1 in T47D cells enhances DNA DSB induction following IR treatment

[00142] Given that forced expression of TFF 1 protected T47D and MDA-MB-231 cells from the induction of IR mediated DNA DSBs, studies were designed to examine whether functional inhibition of endogenous TFF 1 in T47D cells affected the DNA damage response after IR. T47D cells were pre-treated with a TFF l -pAb (or IgG as control) for 24h prior to treatment with 4Gy IR. Cells were harvested at 15m, l h, 3h and 6h after radiation and DNA DSBs quantified using the neutral comet assay. Functional inhibition of TFF 1 enhanced DNA DSB induction after treatment with IR and slowed repair of these DNA lesions compared with IgG treated controls (Fig. 13). In those cells treated with TFF 1 pAb and IR, an accumulation of DNA DSBs was observed, reaching a maximal level at 3h. In contrast, cells pre-treated with IgG exhibited a small but insignificant increase of DSBs after IR treatment (maximal at l h), and these lesions were repaired by 3h post 1R (Fig. 13).

Example 3: TFFl increases radioresistance through its role as a stem cell factor

[00143] Cancer stem cells (CSCs) play an obligate role in cancer development, progression, dissemination and recurrence. Several biological features of CSCs have been implicated in rendering them less susceptible to radiation and chemical therapy: quiescence (Ishikawa et al., 2007), high drug efflux activity of ATP-binding cassette (ABC) transporter proteins such as ABCG2 and MDR 1 (Zheng et al., 2010), expression of anti-apoptotic peptides such as Bcl-2 and survivin (Di Stefano et al., 2010), metabolic drug inactivation (Magni et al., 1996), upregulation of DNA damage response (Bao et al., 2006), and protective factors relating to the CSC niche (Calabrese et al., 2007). Enhanced resistance of brain, breast, pancreatic and colon CSCs to radiation and/or chemotherapy has been demonstrated in several preclinical and clinical studies (Bao et al., 2006, Phillips. et al., 2006, Hermann et al., 2007, Woodward et al., 2007, Yu et al., 2007, Dylla et al., 2008, Li et al., 2008, Shafee et al., 2008, Tanei et al., 2010). An interesting hypothesis, supported by recent experimental evidence, is that CSCs in estrogen receptor (ER)-positive breast tumors found to lack ER expression may mediate poor response to anti-hormone therapy (Horwitz et al., 2008). A general formulation of this theory is that dormant CSCs that persist after initial therapy may account for cancer recurrence (Kusumbe and Bapat, 2009).

[00144] The studies described herein demonstrate that TFF l has a role as a putative stem cell factor, thereby potentially contributing to the issue of radioresistance. Studies were designed to test if inhibition of TFF l could increase radiosensitivity of tumors through eliminating cancer stem cells.

[00145] The following experiments were conducted to determine the role of TFF l as a stem cell factor (Fig.14-20). The experiments quantified the number of cancer stem cells in breast cancer cell lines using three methods (mammosphere culture, determine of side population by Hoechst 33342 efflux pump, and determination of the CD44⁺CD24^'/low population) and investigated whether TFFl enhances malignant stem cell populations. The experiments then examined the effects of TFFl expression on resistance to radiation and chemotherapy. Finally, a preliminary investigation was conducted to understand a potential mechanism of action. 3.1 TFFl expression enhances mammosphere formation and self-renewal in vitro

[00146] Generation of non-adherent mammospheres in single and serial passages is a commonly used assay for in vitro propagation of breast cancer cells with stem cell-like properties (Dontu et al., 2003). The effects of forced TFF l expression on mammosphere formation and self-renewal were tested in vitro.

[00147] Forced expression of TFFl in mammary carcinoma cell lines MCF7, T47D and MDA- B-231 significantly increased mammosphere formation in stably transfected cell lines in comparison to cell lines transfected with the vector (Fig. 14A and 14B).

3.2 Inhibition of TFFl with polyclonal antibody abrogates mammosphere formation

[00148] Next, studies were designed to examine whether expression of endogenous TFF l is necessary for generation of mammospheres in vitro using polyclonal antibodies raised against rhTFF l . The treatment with TFFl pAb (high TFF l binding affinity, no cross- reactivity with TFF3 (data not shown) significantly reduced mammosphere formation when compared to control cells treated with a non-specific IgG (Fig. 15A). The confirmed pAb was administered to MCF7 and T47D wild type cells in a primary mammosphere assay (Fig. 15B). Formation of mammospheres in both cell lines was significantly reduced. Moreover, the spheroids generated from TFF l -pAb-treated cells were visibly smaller than rlgG-treated controls and displayed extensive blebbing and release of non-viable cells (Fig. 15C).

3.3 TFFl expression enhances Hoechst 33342 efflux

[00149] Cancer stem cells are enriched for efflux of low molecular weight fluorescent dyes, and label exclusion or 'side population' assays have served as surrogate markers for CSC-like phenotype (Hirschmann-Jax et al., 2004). The effects of TFF l expression on efflux of the DNA-binding probe Hoechst 33342 were examined. In agreement with published literature, the MCF7 cell line was found to present a small but discrete side population. Forced expression of TFF l resulted in an increase in the MCF-7 side population as determined by Hoechst 33342 dye efflux (Fig. 16).

3.4 TFFl expression enhances CD44*CD24~^/low immunophenotype

[00150] Studies were designed to investigate whether TFF l expression modulates the

CSC-enriched population defined by the antigenic phenotype CD44⁺CD24^"/low. Forced expression of TFF l increased the size of the CD44+CD24-/low population by five-fold in MCF7 and 4.2-fold in T47D cell lines (Fig 17A). This effect was correlated with significantly elevated presentation of CD44 on CF7 cells (Fig. 17B)

3.5 TFFl enhances resistance to ionizing radiation in vitro

[00151] Forced expression of TFF l in T47D and DA- B-23 1 cells was found to significantly enhance resistance to ionizing radiation in T47D and MDA-MB-231 cells as measured by formation of colonies in soft agar (Fig. 18A) and generation of mammospheres (Fig. 18B). Following treatment with 4Gy and 8Gy radiation, T47D-TFF 1 and MDA-MB- 231 -TFF l cells exhibited significantly higher colony formation than control transfected cells. In addition, following treatment with 4Gy radiation T47D-TFF 1 and MDA-MB-23 1 - TFF 1 cells exhibited significantly higher mammosphere formation than control transfected cells.

3.6 TFF-1 reduces sensitivity to paclitaxel

[00152] Paclitaxel (Sigma, MO, USA) sensitivity was measured using a cell viability does response assay (IC50) (Fig. 19A), total cell number (Fig. 19B) and soft agar colony formation (Fig. 19C) assays.

[00153] Forced expression of TFF l significantly increased MCF-7 and T47D total cell number following both vehicle (DMSO) and 1 nM paclitaxel treatments. Furthermore, forced expression of TFF l significantly increased formation of colonies in soft agar by MCF7 cells following administration of 5 nM paclitaxel. Collectively, the data provides evidence regulation of CSC-related populations by TFF l is correlated with decreased sensitivity to ionizing radiation and paclitaxel.

3.7 TFFl modulates mRNA expression of stem cell-associated markers

[00154] In terms of understanding the potential mechanism of action, it was found that TFF l modulated mRNA expression of stem cell-associated genes. Relative mRNA expression of several genes known to be functionally related to stem cell biology in mammary carcinoma was examined. Real-time PCR analysis revealed that MCF7-TFF 1 (Fig. 20A) cells demonstrated increased expression of NOTCH3, a positive regulator of self-renewal in mammary stem cells and a key driver of proliferation and osteolytic bone metastasis in ERBB2- breast cancer (Sansone et al., 2007, Yamaguchi et al., 2008, Zhang et al., 2010). Furthermore, TFF l increased expression of DVL 1 , an intracellular member of the Wnt signalling pathway frequently amplified or upregulated in mammary carcinoma (Nagahata et al., 2003). Interestingly, increased expression of SUFU, a tumor suppressor gene and negative regulator of Hedgehog signalling (Barnfield et al., 2005) was detected. T47D cells (Fig. 20B) were generally less responsive to TFF l in terms of expression of genes on the interrogated panel, though elevated expression of GLI3, a transcription factor implicated in mammary gland development through suppression of Hedgehog signalling (Hatsell and Cowin, 2006), was detected. Increased expression of ABCG2 (an ATP-binding cassette (ABC) efflux transporter and key determinant of side population and multidrug resistance phenotypes) was detected in both cell lines.

[00155] Thus, the studies described herein demonstrate that forced expression of TFF l in mammary carcinoma cells enhanced malignant stem cell population as determined by mammosphere formation, Hoechst efflux, and determination of the CD44⁺CD24^"/low immunophenotype. Functional inhibition of TFF l in wild-type mammary carcinoma cell lines reduced mammosphere formation. In addition, forced expression of TFF l in mammary carcinoma cell lines reduced sensitivity to treatment with ionizing radiation and paclitaxel.

Claims

What is claimed is:

1. A method of inhibiting proliferation or survival of a tumor cell, comprising contacting the tumor cell with an inhibitor of trefoil factor 1 (TFFl) and exposing the tumor cell to radiotherapy.

2. A method of treating, delaying the progression of, preventing a relapse of, or alleviating a symptom of a cancer or other neoplastic condition, the method comprising administering a combination therapy to a subject in need thereof in an amount sufficient to treat, delay the progression of, prevent a relapse of, or alleviate the symptom of the cancer or other neoplastic condition in the subject, wherein the combination therapy comprises exposing the subject to radiotherapy and administering the subject an inhibitor that binds to trefoil factor 1 (TFFl).

3. A method of increasing sensitivity of a tumor cell to radiotherapy comprising administering to the subject an inhibitor of trefoil factor 1 (TFFl).

4. A method of enhancing or supplementing an anti-cancer therapy in a subject that is receiving or has been administered radiotherapy in an amount that is sufficient to produce a desired therapeutic outcome in the subject, the method comprising administering to the subject an inhibitor of trefoil factor 1 (TFFl).

5. A method of inhibiting one or more activity or function of a TFF 1 -stimulated cancer stem cell comprising contacting the TFFl -stimulated cancer stem cell with an inhibitor of TFFl and exposing the TFF 1 -stimulated cancer stem cell to radiotherapy.

6. The method of any one of claims 1 to 5, wherein the inhibitor of TFFl is an antibody that binds to a human trefoil factor 1 (TFFl) polypeptide.

7. The method of claim 6, wherein the antibody binds to an epitope containing residue 20, 21, 42, 43 or 58 of the amino acid sequence of SEQ ID NO: 6.

8. The method of claim 6, wherein the antibody binds to a conformational epitope on a human TFF1 polypeptide monomer.

9. The method of claim 8, wherein the conformational epitope is selected from a conformational epitope shown in Table 1.

10. The method of claim 8, wherein the antibody binds at least a portion of an antigenic determinant selected from the antigenic determinants shown in Table 2.

11. The method of claim 6, wherein the antibody binds to a conformational epitope on a human TFF1 polypeptide homodimer.

12. The method of claim 1 1, wherein the conformational epitope is selected from a conformational epitope shown in Table 3.

13. The method of claim 1 1, wherein the antibody binds at least a portion of an antigenic determinant selected from the antigenic determinants shown in Table 4.

14. The method of claim 6, wherein the antibody is a monoclonal antibody.

15. The method of claim 6, wherein the antibody is a mouse, chimeric, humanized, or fully human monoclonal antibody.

16. The method of claim 6, wherein the antibody is an antibody produced by a hybridoma cell line selected from 1C6 (ATCC Accession No. PTA-8668), 3F6 (ATCC Accession No. PTA-8665), 2C5 (ATCC Accession No. PTA-8666), 2D7 (ATCC Accession No. PTA-8664), 2B 10 (ATCC Accession No. PTA-8892), and 1F9 (ATCC Accession No. PTA-8893).

17. The method of any one of claims 1 to 5, wherein the inhibitor of TFF1 is a peptide antagonist, a nucleic acid TFF1 inhibitor or a small molecule TFF1 inhibitor.

18. The method of claim 17, wherein the peptide antagonist of TFF1 is TFF1 mutant comprising one or more mutations at a position selected from amino acid residue 20, 21, 42, 43, and 58 of the amino acid sequence of SEQ ID NO: 6.

19. The method of claim 17, wherein the TFF1 mutant comprises one or more of the following mutations of the amino acid sequence of SEQ ID NO: 6: P20R, G21R, P42R, W43R, C58F or any combination thereof.

20. The method of claim 17, wherein the peptide antagonist of TFF1 is a TFF1 deletion mutant of the amino acid sequence of SEQ ID NO: 7.

21. The method of claim 20, wherein the TFF1 deletion mutant is selected from:

deletion of amino acids 1-16 of SEQ ID NO: 7; deletion of amino acids 1-26 of SEQ ID NO: 7; deletion of amino acids 1-31 of SEQ ID NO: 7; deletion of amino acids 1-32 of SEQ ID NO: 7; deletion of amino acids 1-43 of SEQ ID NO: 7; and deletion of amino acids 1-57 of SEQ ID NO: 7.

22. The method of claim 17, wherein the nucleic acid TFF1 inhibitor is one or more iRNAs or one or more DNA molecules encoding one or more iRNAs, wherein the expressed iRNAs interfere with the mRNA of the TFF1 gene and inhibit expression of the TFF1 gene.

23. The method of claim 22, wherein the iRNA targets a nucleotide sequence selected from S^AATGGCCACCATGGAGAACAA-S' (SEQ ID NO: 8) and

5'-AAATAAGGGCTGCTGTTTCGA-3' (SEQ ID NO: 9).

24. The method of claim 22, wherein the nucleic acid TFF1 inhibitor is one or more i R NAs comprising a nucleotide sequence selected from the following nucleotide sequences or one or more DNA molecules encoding one or more iRNAs comprising the following nucleotide sequences:

XXXXAATGGCCACCATGGAGAACAATTCAAGAGATTGTTCTCCATGGTGGCC ATTXXXX (SEQ ID NO: 10)

I Sense | Loop | antisense XXXXAAATAAGGGCTGCTGTTTCGATTCAAGAGATCGAAACAGCAGCCCTTA TTTXXXX (SEQ ID NO: Ϊ i

I Sense | Loop | antisense

25. The method of claim 22, wherein the one or more DNA molecules encoding the one or more iRNAs are transcribed within the cell.

26. The method of claim 25, wherein the one or more iRNAs are transcribed within the cell as siRNAs.

27. The method of any one of the preceding claims, wherein the subject is non- responsive, less responsive or has stopped responding to radiotherapy.

28. The method of claim 2 or claim 4, wherein the cancer is an epithelial cancer.

29. The method of claim 1 or claim 3, wherein the tumor cell is an epithelial tumor cell.

30. The method of claim 28, wherein the epithelial cancer is selected from lung cancer, colon cancer, breast cancer, prostate cancer, and endometrial carcinoma.

31. The method of claim 29, wherein the epithelial tumor cell is from a tumor selected from lung cancer, colon cancer, breast cancer, prostate cancer, and endometrial carcinoma.

32. The method of any one of the preceding claims, further comprising the

administration of a second compound wherein the second compound is a chemotherapeutic or anti-neoplastic agent.

33. The method of claim 3, wherein the inhibitor of TFF1 is administered in an amount that is sufficient to reduce the dosage of radiotherapy that is needed to produce the desired therapeutic outcome in the subject.

34. The method of claim 4, wherein the inhibitor of TFF1 is administered in an amount that is sufficient to decrease the frequency of administration radiotherapy that is needed to produce the desired therapeutic outcome in the subject.

35. The method of claim 4, wherein the inhibitor of TFF1 is administered in an amount that is sufficient to decrease the period of cancer regression in the subject treated with radiotherapy.

36. The method of claim 4, wherein the desired therapeutic outcome is treating, delaying the progression of, preventing a relapse of, or alleviating a symptom of a cancer or other neoplastic condition in the subject.

37. The method of any one of the preceding claims, wherein the radiotherapy is ionizing radiation (IR).

38. The method of claim 1, claim 2 or claim 5, wherein the inhibitor of TFF1 is administered simultaneously with the exposure to radiotherapy.

39. The method of claim 1, claim 2 or claim 5, wherein the administration of the inhibitor of TFF1 and the exposure to radiotherapy are in a sequential manner.

40. The method of any preceding claim, wherein the subject is human.