Peptidic TGF-beta antagonists

Abstract

The present invention provides peptidic TGF-β antagonists capable of inhibiting TGF-β signaling and disrupting the biochemical events that promote fibrosis and the epithelial-mesenchymal transition. The peptidic TGF-β antagonist may contain from 11 to 28 amino acid residues (for instance, may consist of from 12 to 16 amino acid residues) and may have the following structure (II):
NH.sub.2′ETWIWLDTNMG-Xaa.sub.1-Y′COOH  (II)
wherein Xaa.sub.1 is any amino acid and Y is a peptide having from 0 to 9 amino acids. The peptidic TGF-β antagonists can advantageously be used for the prevention, treatment, and/or alleviation of the symptoms of a condition associated with an increase in TGF-β activity, including fibrosis (such as fibrosis of the skin, liver, lungs, and heart, among others) and cancer (including various carcinomas, such as squamous cell carcinoma, sarcomas, and metastatic cancers).

Claims

1. A method of treating or alleviating a symptom of a condition associated with a pathological increase in TGF-β activity in a subject in need thereof, said method comprising administering to the subject a therapeutically effective amount of a transforming growth factor β (TGF-β) antagonist or a pharmaceutical composition comprising said TGF-β antagonist, said TGF-β antagonist comprising a TGF-β-binding peptide comprising i) the amino acid sequence ETWIWLDTNMGX.sub.aa1RIYQ (SEQ ID NO: 26) and ii) fewer than 125 amino acids, wherein X.sub.aa1 is S, T, or Y.

2. The method of claim 1, wherein the subject is a mammal, optionally a human.

3. The method of claim 1, wherein said condition associated with a pathological increase in TGF-β activity is fibrosis, optionally wherein said fibrosis is lung fibrosis, kidney fibrosis, cardiac fibrosis, or liver fibrosis; non-alcoholic steatohepatitis; a pathological skin fibrotic condition, optionally wherein said pathological skin fibrotic condition is a wound or delayed wound healing; scarring, optionally wherein said scarring is hypertrophic scarring, keloid scarring or scarring present on an internal tissue or organ; an external wound caused by a surgical procedure, an internal wound present in an internal organ or tissue, optionally wherein said internal wound is caused by a surgical procedure; a burn, optionally wherein said burn is an epidermal burn, superficial dermal burn, mid-dermal burn, deep dermal burn, or full thickness burn; an autoimmune condition, optionally psoriasis or scleroderma; cancer, optionally wherein the cancer is carcinoma, pancreatic cancer, glioblastoma, myeloid leukemia, head and neck cancer, melanoma, breast cancer, or colorectal cancer; a pulmonary disease, optionally wherein the pulmonary disease is selected from the group consisting of asthma, chronic obstructive pulmonary disease, and fibroproliferative lung disease; or a renal disease, optionally wherein the renal disease is associated with tubular atrophy, glomerulosclerosis, tubulointerstitial fibrosis or diabetic nephropathy.

4. The method of claim 3, said method comprising contacting said wound, said scar, said burn, or said fibrotic tissue of said subject with a topical formulation, optionally a patch or a cream, comprising the therapeutically effective amount of said TGF-β antagonist.

5. The method of claim 3, said method comprising surgically administering a skin graft to said subject at the site of said wound or said burn, wherein said skin graft comprises one or more cells that have been genetically modified so as to express said TGF-β-binding peptide, optionally wherein said skin graft is an autologous, allogeneic, syngeneic, prosthetic, split-thickness and/or full-thickness skin graft.

6. The method of claim 5, wherein said one or more cells that have been genetically modified so as to express said TGF-β-binding peptide comprise one or more fibroblasts, keratinocytes, Merkel cells, melanocytes, or Langerhans cells.

7. The method of claim 5, said method comprising introducing a polynucleotide encoding said TGF-β-binding peptide into said one or more cells.

8. The method of claim 3, said method comprising contacting said wound with a surgical glue, a surgical staple or a surgical suture, said surgical glue, surgical staple and surgical suture comprising a therapeutically effective amount of said TGF-β antagonist.

9. The method of claim 3, said method comprising surgically administering a skin graft to said subject at the site of said wound or said burn, wherein said skin graft is contacted with a solution comprising said TGF-β antagonist prior to surgically administering said skin graft to said subject.

10. The method of claim 3, wherein the carcinoma is selected from the group consisting of squamous cell carcinoma, epidermoid carcinoma, urothelial carcinoma, adenocarcinoma, adrenocortical carcinoma, basal cell carcinoma, ductal carcinoma in situ (DCIS), invasive ductal carcinoma, merkel cell carcinoma, midline tract carcinoma, thymic carcinoma, and renal cell carcinoma.

11. The method of claim 10, wherein the carcinoma is squamous cell carcinoma, optionally wherein said squamous cell carcinoma is vulvar squamous cell carcinoma, epidermal squamous cell carcinoma, oral squamous cell carcinoma, pulmonary squamous cell carcinoma, or head and neck squamous cell carcinoma.

12. The method of claim 3, wherein the condition is scleroderma and the symptom is thickening skin or thickening lining of internal organs and/or blood vessels.

13. The method of claim 1, said method comprising administering said TGF-β antagonist orally, intravenously, intratumorally or by inhalation to said subject.

14. The method of claim 1, wherein the Xaa.sub.1 is S or Y.

15. The method of claim 1, wherein the TGF-β-binding peptide comprises the amino acid sequence selected from the group consisting of ETWIWLDTNMGSRIYQ (SEQ ID NO: 5), ETWIWLDTNMGSRIYQE (SEQ ID NO: 22, ETWIWLDTNMGSRIYQEF (SEQ ID NO: 23), ETWIWLDTNMGSRIYQEFE (SEQ ID NO: 24), ETWIWLDTNMGSRIYQEFEV (SEQ ID NO: 25), ETWIWLDTNMGSRIYQEFEVT (SEQ ID NO: 6), and ETWIWLDTNMGSRIYQEFEVTVPDSITS (SEQ ID NO: 2).

16. The method of claim 1, wherein the TGF-β-binding peptide consists of ETWIWLDTNMGSRIYQ (SEQ ID NO: 5).

17. The method of claim 1, wherein said TGF-β-binding peptide is conjugated to one or more peptides, small molecules and/or proteins, optionally by way of one or more linkers.

18. The method of claim 1, wherein said TGF-β-binding peptide is a linear peptide.

19. The method of claim 1, wherein said TGF-β-binding peptide is a cyclic peptide, optionally a head-to-tail cyclic peptide.

20. The method of claim 1, wherein said TGF-β-binding peptide is covalently bound to a cysteine residue at each of the N-terminus and the C-terminus of said TGF-β-binding peptide, and wherein said cysteine residues are covalently bound to one another by a disulfide bond or by way of a linker, optionally wherein each of said cysteine residues is covalently bound to said linker by a thioether bond.

21. The method of claim 20, wherein said linker comprises an alkyl, aryl, heteroaryl, cycloalkyl or heterocyclolalkyl moiety.

22. The method of claim 1, wherein said TGF-3 antagonist comprises a dimer comprising two copies of said TGF-β-binding peptide.

23. The method of claim 22, wherein each TGF-β-binding peptide consists of ETWI WLDTNMGSRIYQ (SEQ ID NO: 5).

24. The method of claim 22, wherein each of said copies of said TGF-β-binding peptide are covalently bound to one another by a disulfide bond or thioether bond.

25. The method of claim 22, further comprising one or more peptides, small molecules and/or proteins conjugated to at least one of said TGF-β-binding peptide, optionally by way of one or more linkers.

26. The method of claim 22, wherein each copy of said TGF-β-binding peptide is covalently bound to a cysteine residue at the N-terminus or the C-terminus of said TGF-β-binding peptide, and wherein said cysteine residues are covalently bound to one another by a disulfide bond.

27. The TGF-β antagonist of claim 22 further comprising a linker, wherein each copy of said TGF-β-binding peptide is bound to the other via the linker.

28. The TGF-β antagonist of claim 22, wherein each copy of said TGF-β-binding peptide comprises one or more additional amino acids linked to a spacer to form the dimer.

Description

BRIEF DESCRIPTION OF THE FIGURES

(1) FIGS. 1A and 1B illustrate that peptide X but not peptide P16 exhibits aggregation. Peptide X (X, 40 amino acids) and P16 (16 amino acids) were left untreated (−) or treated with 0.5% DMSO (+) for 2 hrs at 4° C. The aggregated and non-aggregated soluble fractions were then separated using a Microcon™ centrifugal filtration device (Millipore), with a molecular weight cut-off of 100 kDa. This device allows passage of molecules <100 kDa through the filter but retains larger molecules (aggregates). The aggregated (FIG. 1A—left panel) and soluble (FIG. 1B—right panel) fractions were then separated by 17% Tricine-SDS gel electrophoresis and peptides detected by silver staining. In the conditions tested, multiple bands with various staining intensities were detected in peptide X aggregated fraction and two of these bands were decreased with DMSO treatment (A—left panel, arrows) leading to an increase in the amount of soluble peptide X (B—right panel, arrow, lane 2 versus 3). In contrast, P16 displayed only a few bands of low intensity in the aggregation fractions which were not altered by DMSO treatment, and no increase in the soluble peptide was noted (B—right panel, lane 4 versus 5). (A-B) Lane 1: Molecular weight marker. Lanes 2-5: samples. As shown in this figure, peptide X existed predominantly in aggregated form and peptide X aggregation was partially reduced by treatment with DMSO, leading to an increase in soluble peptide X.

(2) FIGS. 2A and 2B illustrate the in silico analysis of peptide X aggregation propensity and the design of aggregation-free small molecular weight CD109-based peptides. (FIG. 2A) Aggrescan analysis of peptide X identified amino acids at position 13-18 (ETWIWL, SEQ ID NO: 11) as an aggregation-prone sequence in the 40 amino acid peptide. (FIG. 2B) Amino acid sequence of small molecular weight CD109-based peptides that were designed and tested.

(3) FIGS. 3A and 3B illustrate that, as determined by size-exclusion chromatography, small molecular weight CD109-based peptides X, X-1 and X-3 form aggregates whereas P21, P16, P16-2 (control), P11 and X-4 do not (refer to FIG. 2B for a description of the amino acid sequence of the peptides). Approximately 200 μg of each peptide X (40 amino acids), X-1 (28 amino acids), peptide A (161 amino acids), P11 (11 amino acids), P16 (16 amino acids), P21 (21 amino acids, P16-2 (16 amino acids, scrambled sequence control), X-3 (16 amino acids) and X-4 (11 amino acids) were dissolved in phosphate-buffered saline (PBS) and loaded onto a Superdex Peptide 10/300GL column. The column was eluted with PBS at a flow rate of 0.6 mL/min and eluents were analyzed for peptide content by measuring relative absorbance at a wavelength of 215 nM. (FIGS. 3A and 3B) The data is plotted with relative absorbance (Y-axis) against elution volume (X-axis). Peptides 1-9 are color coded (A—peptides (1) to (5); B (peptides (6) to (9)). As shown on panel A, peptide X (peptide 1, black line) elution profile indicated two major peaks at approximately 8 mL and 11 mL which correspond to molecular weights greater than 12.4 kDa. The theoretical molecular weight of peptide X is 4.7 kDa which is expected to elute from the column at approximately 15 mL. Under the conditions tested, peptide X existed as high molecular weight aggregates with minimal soluble (monomeric) form. On the other hand, P16 (peptide 5, green line) elution profile indicated a broad peak between 14-22 mL which is expected to contain peptides of between 0.1 and 6 kDa and is consistent with its theoretical molecular weight of 2.01 kDa. A standard curve used to determine molecular weights of peptides analyzed by size exclusion chromatography is indicated in FIG. 4.

(4) FIG. 4 illustrates the standard curve used for size-exclusion chromatography of standard peptides using the Superdex Peptide 10/300 GL column (results provided in FIG. 3). A pool of standard peptides of various molecular weights (1. cytochrome c (M.sub.r 12.384 kDa) 1 mg/mL; 2. aprotinin (M.sub.r 6.512 kDa) 2 mg/mL; 3. vitamin B.sub.12 (M.sub.r 1.355 kDa) 0.1 mg/mL; 4. (Gly).sub.3 (M.sub.r 0.189 kDa) 0.1 mg/mL; 5. Gly (M.sub.r 0.075 kDa) 7.8 mg/mL) were subjected to size-exclusion chromatography using the Superdex Peptide 10/300 GL column (flow rate 0.5 ml/min at room temperature, sample volume of 50 μL, eluent 0.05M phosphate, 0.15 M NaCl, ph 7.0). The resulting chromatogram (absorbance at 215 nm (in mAU, left Y axis) and conductivity (in mS/cm, right Y axis, in function of volume of elution (in mL)) indicates the elution profiles of the above peptides with high MW peptides eluting in earlier fractions and lower MW peptides eluting in later fractions as expected. The molecular weights of peptides were plotted against elution volume generating a standard curve (not shown).

(5) FIGS. 5A and 5B illustrate that some small molecular weight CD109-based peptides (Peptide A, P28, P21 and P6) inhibit TGF-β1-induced Smad3-driven transcriptional activity. HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 μM TGF-β1 in the presence or absence of 10 nM (FIG. 5A) or 5 nM (FIG. 5B) of peptide A (Pep A, 161 aa), P28 (28 aa), P21 (21 aa), P16 (16 aa), P16-2 (16 aa, scrambled P16 sequence) or Tris-buffer (buffer control) as indicated. Cell lysates were analyzed for luciferase activity and data are expressed as mean±standard deviation of relative light units (RLU). Asterisks (*) indicate that the values are significantly different from values obtained using TGF-β1 treatment alone (P<0.05). Under the conditions tested, peptide A, P28, P21 and P16 inhibited TGF-β1-induced transcriptional (CAGA.sub.12-lux) activity. Tris buffer alone had no effect indicating that the inhibitory activity of Pep A, P21 and P16 are mediated by the peptides themselves and not from the buffer (Tris) in which they were dissolved. Scrambled peptide also had no effect indicating that the inhibitory effect of P16 (and Peptide A, P28 and P21) was mediated in a sequence specific manner and was not due to amino acid composition or charge of the peptides.

(6) FIG. 6 illustrates that the small molecular weight CD109-based peptide P16 (but not P16-2, P11 or X-4) inhibit TGF-β1-induced Smad3-driven transcriptional activity. HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 μM TGF-β1 in the presence or absence of 10 nM of P16-2 (16 aa scrambled control), P11 (11 aa sequence), P16 (16 aa), X-4 (11 aa) or Tris-buffer (buffer control) as indicated. Cell lysates were analyzed for luciferase activity and data are expressed as mean±standard deviation of luciferase activity. Results are shown as luciferase activity for the peptides used. Asterisks (*) indicate that the values are significantly different from values obtained using TGF-β1 treatment alone (P<0.05). Under the conditions tested, P16 inhibited TGF-β1-induced transcriptional activity whereas P11 and X-4 did not. Tris buffer alone had no effect indicating that the inhibitory activity of P16 is mediated by the peptide itself and not from the buffer (Tris) in which P16 was dissolved. P16-2 (scrambled peptide control) also had no effect indicating that the inhibitory effect of P16 is mediated in a sequence specific manner and is not due to amino acid composition or charge of the peptide.

(7) FIG. 7 illustrates that the small molecular weight CD109-based peptide P16 (but not P11 or P16-1) inhibits TGF-β1-induced PAI-protein production. A431 cells were treated without (lane 1) or with 100 pM of TGF-β1 (lanes 2-6) in the absence (lane 2) or presence of 10 nM of P11 (11 aa peptide, lane 3), P16 (16 aa peptide, lane 4), P16-1 (scrambled peptide of 16 aa, lane 5) or Tris buffer (buffer, lane 6) for 24 hrs. Cell lysates were analyzed by Western blot for PAI-1 (protein activator inhibitor-1) protein levels and normalized to GAPDH protein levels (loading control). In the conditions tested, P16 (but not P11) inhibited TGF-β1-induced PAI-1 expression. Buffer alone had no effect indicating that the inhibitory effect of P16 is mediated by the peptide itself and not due to the buffer in which it was dissolved. Scrambled P16-1 control peptide also had no effect indicating that the inhibitory effect of P16 was mediated in a sequence specific manner and was not due to amino acid composition or charge of the peptide. GAPDH levels were similar for all samples indicating that equal amounts of protein were loaded in each lane.

(8) FIG. 8 illustrates that DMSO treatment enhances the TGF-β inhibitory activity of Peptide X but not P21 or P16. HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of Peptide X (PX), P21 or P16. The peptides were previously dissolved in Tris buffer and left untreated or treated with DMSO prior to addition to the cells. Addition of Tris buffer or DMSO alone served as additional controls. Cell lysates were analyzed for luciferase activity and data are expressed as mean±standard deviation of luciferase activity. Results are shown as luciferase activity. Asterisks (*) indicate that the values are significantly different from values obtained using TGF-β1 treatment alone (P<0.05), whereas NS indicates that the values are not significantly different. Under the conditions tested, peptide X pre-treated with DMSO inhibited TGF-β1-induced transcriptional activity whereas peptide X left untreated (Tris buffer only) did not. P16 and P21 inhibited TGF-β1-induced CAGA.sub.12-lux activity and these effects were not enhanced by DMSO treatment. DMSO alone had no effect on TGF-β1-induced CAGA.sub.12-lux activity indicating that the inhibition of DMSO-treated peptide X is due to the peptide itself and not due to DMSO. Tris buffer alone had no effect on TGF-β1-induced CAGA.sub.12-lux activity indicating that the inhibitory effect of P21 and P16 were mediated by the peptides themselves and not from the buffer (Tris) in which they were dissolved.

(9) FIG. 9 illustrates that DMSO treatment enhanced the TGF-β inhibitory activity of peptide X, but not P16. A431 cells were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of Peptide X or P16. The peptides were previously dissolved in Tris buffer and left untreated or treated with DMSO prior to addition to the cells. Cell lysates were analyzed by Western blot for PAI-1 (plasminogen activator inhibitor-1) protein expression (top panel) and GAPDH served as a loading control (bottom panel). PAI-1 was not detected in untreated cells (lane 1). In the conditions tested, TGF-β1 treatment increased PAI-1 production in A431 cells (lane 2 versus lane 1). Under the conditions tested, peptide X treated with DMSO inhibited TGF-β1-induced PAI-1 protein production whereas peptide X left untreated (in Tris) did not (compare lanes 4, 3 and 2). Furthermore, P16 inhibited TGF-β1-induced PAI-1 protein production and pre-treating the peptide with DMSO did not enhance its inhibitory effect (compare lanes 6, 5 and 2).

(10) FIG. 10A and FIG. 10B illustrate that peptides B, E and X-1 inhibit TGF-β-induced cellular migration of A431 cells in vitro. Results are shown prior to treatment (0 hr, top panels) and after treatment (24 hr, bottom panels) for each of the peptides used. (See FIG. 2 and Table 1 for the amino acid sequence identity of the peptides).

(11) FIG. 11A and FIG. 11B illustrate that peptides B, E and X-1 inhibit TGF-β-induced cellular migration of MDA-MB-231 cells in vitro. Results are shown prior to treatment (0 hr, top panels) and after treatment (24 hr, bottom panels) for each of the peptides used.

(12) FIGS. 12A and 12B illustrate that CD109 mRNA expression is decreased in late stage vulvar squamous cell carcinoma. The Cancer Profiling Array II™ (BD Biosciences/Clontech, Mississauga, ON) was hybridized with a .sup.32P-labeled CD109 cDNA probe. Prehybridization, hybridization, and detection were performed using BD Express Hyb™ Solution (BD Biosciences/Clontech) according to the manufacturer's instructions. (FIG. 12A) CD109 mRNA expression is decreased in 5 out of 5 tumors (T) of vulvar squamous cell carcinoma as compared to the adjacent normal tissue (N). (FIG. 12B) Densitometry was performed using Image J™ Software and data are expressed as relative expression. P=0.08.

(13) FIGS. 13A-13J illustrate that CD109 inhibits TGF-β-induced EMT. (FIGS. 13A and 13G) HaCaT stably transfected with CD109 or EV were treated with 100 pM TGF-β1 for 48 hrs, fixed and stained with Rhodamin-Phalloidin (stain for F-actin, 1.sup.st line), E-cadherin (2.sup.nd line) and DAPI (3.sup.rd line). (FIGS. 13B and 13H) HaCaT cells transfected with control or CD109 siRNA were treated with 100 pM TGF-β1 for 36 hrs and stained as in (A). (FIGS. 13C and 13I) A431 stably transfected with CD109 or EV were treated and stained as in (A). (FIGS. 13D and 13J) A431 transfected with CD109 siRNA or a control siRNA were treated with 50 pM TGF-β1 for 48 hrs and stained as in (A). (A-D) Left: representative panels of cells are shown. (G-J) Right panel: Densitometry of actin staining (mean of n=3 experiments±SEM; *: p<0.05). (FIG. 13E) HaCaT cells transfected with control or CD109 siRNA were treated with 100 pM TGF-β1 for 4 hrs. Cell lysates were subjected to western blot using the indicated antibodies. (FIG. 13F) A431 cells stably transfected with CD109 or EV were treated with or without 100 pM TGF-β1 for 3 hrs. Cell lysates were analyzed by western blot for Slug expression. The actin panel demonstrates equal protein loading. All western blots are representative of n=3 experiments.

(14) FIGS. 14A-14H illustrate that CD109 inhibits TGF-β-induced cell migration. (FIGS. 14A and 14E) HaCaT cells stably transfected with CD109 or EV were scratched and treated with or without 100 pM TGF-β1 for 24 hrs. (FIGS. 14B and 14F) HaCaT cells transfected with control or CD109 siRNA were scratched and treated as in (A). (FIGS. 14C and 14G) A431 cells stably transfected with CD109 or EV were scratched and treated as in (A). (FIGS. 14D and 14H) A431 cells transfected with CD109 siRNA or control siRNA were scratched and treated as in (A). Pictures of the wounded area were taken at 0 and 24 hrs and the percentage of the original wound area filled with keratinocytes were calculated. The graphs shows the mean of n≥3 independent experiments±SEM; *: p<0.05. Dotted line: wound margin at 0 hr, regular line: wound margin at 24 hr.

(15) FIGS. 15A and 15B illustrate that CD109 inhibits TGF-β induced cell invasion. (FIG. 15A) 431 cells stably transfected with CD109 or EV were used. (FIG. 15B) A431 cells transfected with CD109 siRNA or control siRNA were used. Cells were left untreated or treated with 100 pM of TGF-β and were plated in the Matrigel®-coated Boyden chambers. Percent-invaded cells in the lower chambers were determined as per the manufacturer's instructions. Each bar represents mean±standard error of the mean. All results are representative of three separate experiments and analyzed by t-test. **P<0.01.

(16) FIGS. 16A and 16B illustrate that CD109 inhibits TGF-β-induced EMT via the SMAD2/3 and MAPK pathways. HaCaT cells transfected with control or CD109 siRNA were treated for 36 hrs with 100 pM TGF-β1, in the presence or absence of 0.5 μM SB431542, 1 μM SB203580 and/or 10 μM U0126. Cells were fixed and stained for F-actin, E-cadherin and with DAPI. (FIG. 16A) Representative panels of cells are shown. (FIG. 16B) Densitometry of F-actin staining (mean of n=3 independent experiments±SEM; *P<0.05).

(17) FIGS. 17A-17D illustrate that CD109 inhibits TGF-β-induced fibronectin and Slug expression via the SMAD2/3 and MAPK pathways. (FIGS. 17A and 17C) HaCaT cells transfected with control or CD109 siRNA were treated for 16 hrs with or without 100 pM TGF-β1, in the presence or absence of 0.5 μM SB431542, 1 μM SB203580 or 10 μM U0126. FIG. 17A: Cell lysates were analyzed by western blot using the indicated antibodies. FIG. 17C: Densitometry of fibronectin (mean of n=3 independent experiments, SEM; *: p<0.05). (FIGS. 17B and 17D) HaCaT cells transfected with control or CD109 siRNA were treated with 100 pM TGF-β1 for 4 hrs, in the presence of absence of 0.5 μM SB431542, 1 μM SB203580 or 10 μM U0126 and analyzed by western blot for Slug expression (FIG. 17B). FIG. 17D: Densitometry of n=4 independent experiments, SEM; *: p<0.05.

(18) FIGS. 18A and B illustrate that CD109 regulates TGF-β-induced migration via the SMAD2/3 and MAPK pathways. (FIG. 18A) HaCaT cells transfected with control or CD109 siRNA were scratched and treated with or without 100 pM TGF-β1, 0.5 μM SB431542, 1 μM SB203580 and/or 10 μM U0126 for 36 hrs. Dotted line: wound margin at 0 hr, regular line: wound margin at 36 hrs. (FIG. 18B) The graph shows the percentage of migration (compared to wound at 0 hr), *: p<0.05, n=5 independent experiments.

(19) FIGS. 19A-19F illustrate that CD109 modulates TGF-β-induced p38 and ERK1/2 phosphorylation. (FIG. 19A) HaCaT cells transfected with CD109 siRNA or control siRNA were treated with 15 pM TGF-β1 for the indicated time. (FIGS. 19B and 19C) HaCaT cells transfected with CD109 siRNA or control siRNA were treated with 0-60 pM TGF-β1 for 10 min. (FIGS. 19D and 19E) A431 cells transfected with control or CD109 siRNA were treated with 15 pM TGF-β1 for the indicated times (D) or with 0-50 pM TGF-β for 10 min (E). (FIG. 19F) HaCaT cells stably transfected with CD109 or its EV were transiently transfected with caveolin-1 siRNA or negative control siRNA. The cells were then treated with 15 pM TGF-β1 for 0-10 min. Cell lysates were then analyzed by western blot.

(20) FIGS. 20A-20C illustrate that CD109 inhibits TGF-β-induced EMT in SCC-13 cells. (FIGS. 20A and 20C) SCC-13 transfected with CD109 siRNA or a control siRNA were treated and stained for F-actin (1.sup.st line), E-cadherin (2.sup.nd line) and DAPI (3.sup.rd line). FIG. 20A: representative panels of cells are shown. FIG. 20C: densitometry of actin-staining (mean of n=3 experiments±SEM; *: p<0.05). (FIG. 20B) SCC-13 cells transfected with CD109 siRNA or a control siRNA were treated with 100 pM TGF-β1 for 2 hrs. Cell lysates were analyzed by western blotting for Slug expression. The actin panel demonstrates equal protein loading.

(21) FIGS. 21A and 21B illustrate that CD109 inhibits TGF-β-induced fibronectin expression in SCC-derived cells. (FIG. 21A) A431 cells stably transfected with CD109 or EV were treated with 0-100 pM TGF-β1 for 16 hrs. (FIG. 21B) SCC-13 cells transfected with control or CD109 siRNA were treated with 50 pM TGF-β1 for 5 hrs. (A-B) Cell lysates were analyzed by western blot for fibronectin expression. The actin blot demonstrates equal protein loading.

(22) FIG. 22 illustrates the specificity of SMAD2/3 and MAPK inhibitors. HaCaT cells were pre-treated for 1 hr with 0.5 μM SB431542 (SMAD inhibitor), 1 μM SB203580 (p38 inhibitor) or 10 μM U0126 (ERK inhibitor) and treated with 15 pM TGF-β1 for 15 min. Cell lysates were analyzed for phospho-SMAD2 (P-SMAD2), phospho-p38 (P-p38) and phospho-ERK (P-ERK) by western blot. The membranes were then stripped and reprobed for total levels of the above-proteins (T-SMAD2, T-p38 and T-ERK, respectively).

(23) FIGS. 23A and 23B illustrate that CD109 modulates TGF-β-induced p38 and ERK MAPK activation in SCC-13 cells. SCC-13 cells transfected with control or CD-109 siRNA were treated with 15 pM TGF-β1. Cell lysates were analyzed by western blot for CD109, phospho-p38 (P-p38) and total p38 (T-p38) (FIG. 23A) or for phospho-ERK1/2 (P-ERK1/2) and total ERK1/2 (T-ERK1/2) (FIG. 23B).

(24) FIGS. 24A-24E are graphs demonstrating the ability of CD109-based peptides to inhibit Smad3-driven transcriptional activity in a dose-dependent manner. HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of various concentrations of P16 (FIGS. 24A and 24D), P18 (FIGS. 24B and 24D), P16.2 (FIGS. 24C and 24D), or PX (FIG. 24E) as indicated. Cell lysates were analyzed for luciferase activity and data are expressed as mean±standard deviation of relative light units (RLU).

(25) FIG. 25 is a graph showing the ability of CD109-based peptides to inhibit TGF-β-induced, Smad3-driven transcriptional activity. HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 pM TGF-b1 in the presence or absence of 10 nM of P16, P16.2, peptide A, P15, P14, P13, P12, P11, peptide X, P21, or 2% NH.sub.4OH buffer (buffer control) as indicated. Cell lysates were analyzed for luciferase activity and data are expressed as mean±standard deviation of luciferase activity. Asterisks (*) indicate that the values are significantly different from values obtained using TGF-β treatment alone (P<0.05).

(26) FIGS. 26A and 26B show the results of immunoblot assays demonstrating the ability of CD109-based peptide P16 to inhibit a TGF-β-induced epithelial-mesenchymal transition (EMT) response in squamous cell carcinoma (A431) cells in a dose-dependent manner. (FIG. 26A) Immunoblot analysis was carried out using cell lysates of A431 cells following incubation with TGF-β, P16, or scrambled control (P16.2) as indicated to determine expression of proteins involved in the EMT response. (FIG. 26B) Densitometry analysis was subsequently performed using the developed immunoblot to illustrate the relative expression of each protein as a function as P16 concentration as indicated.

(27) FIGS. 27A and 27B demonstrate the ability of CD109-based peptide P16 to inhibit squamous cell carcinoma (A431) cell migration in a dose-dependent manner. A431 cells were grown to 80-90% confluence and serum-starved overnight. The next day, cells were scratched with a plastic pipette tip (time 0 hour) and then left untreated or treated for 24 hours with 100 pM TGF-β1 alone or in the presence of P16 as indicated. (FIG. 27A) Digital images were captured at 0 h and 24 h using an EVOS XL Core microscope. (FIG. 27B) Micrographs were subsequently quantitated to determine the percentage of the wound area that had closed following 24 hours in the presence or absence of P16, as indicated.

(28) FIGS. 28A and 28B show the results of wound closure assays performed using human keratinocyte HaCat cells. These data demonstrate the ability of CD109-based peptide P16 to suppress HaCat cell migration in a sequence-dependent manner. (FIG. 28A) Human Keratinocyte HaCat cells were starved for 24 hours, scratched with pipette tips, and then treated with 100 pM TGF-β and 10 nM CD109-based peptides as indicated for 24 hours. Microscopy images were taken at time 0 and 24 hours of treatment. (FIG. 28B) Migration distances were measured using the Image J software platform. Error bars represent mean+/−standard deviation, asterisk designates a P value of <0.05.

(29) FIGS. 29A and 29B demonstrate the ability of CD109-based peptides to inhibit a TGF-β-induced fibrotic response in human fibroblasts. Human primary fibroblasts were starved for 36 hours, then treated with 20 pM TGF-β and 10 nM CD109-based peptide as indicated for 24 hours. (FIG. 29A) Cell lysates were separated by gel electrophoresis, transferred to a membrane, and immunoblotted with antibodies against fibronectin, PAI-1, CTGF, and α-tubulin. (FIG. 29B) The data shown represent the mean expression levels of 3 different biological replicates calculated by densitometry of fibronectin, PAI-1, and CTGF intensity levels normalized to α-tubulin. Error bars represent the standard deviation of the replicate experiments. A single asterisk designates a t test P value of less than 0.05, and a double asterisk indicates a P value of less than 0.01.

(30) FIGS. 30A and 30B demonstrate the ability of CD109-based peptides to inhibit a TGF-β-induced fibrotic response in primary human fibroblasts isolated from scleroderma patients. Fibroblasts were starved for 36 hours, then treated with 20 pM TGF-β and 10 nM CD109-based peptide as indicated for 24 hours. (FIG. 30A) Cell lysates were separated by gel electrophoresis, transferred to a membrane, and immunoblotted with antibodies against the indicated proteins. (FIG. 30B) The data shown represent the mean expression levels of 3 different biological replicates calculated by densitometry of fibronectin, PAI-1, and CTGF intensity levels normalized to α-tubulin. Error bars represent the standard deviation of the replicate experiments. A single asterisk designates a t test P value of less than 0.05.

(31) FIGS. 31A and 31B demonstrate the ability of CD109-based peptide P16 to inhibit a TGF-β-induced fibrotic response in primary human fibroblasts isolated from scleroderma patients in a dose-dependent manner. Fibroblasts were starved for 36 hours, then treated with 20 pM TGF-β and various concentrations of P16 as indicated for 24 hours. (FIG. 31A) Cell lysates were separated by gel electrophoresis, transferred to a membrane, and immunoblotted with antibodies against the indicated proteins. (FIG. 31B) The data shown represent the mean expression levels of 3 different biological replicates calculated by densitometry of fibronectin, PAI-1, and CTGF intensity levels normalized to α-tubulin. Error bars represent the standard deviation of the replicate experiments. A single asterisk designates a t test P value of less than 0.05, and a double asterisk indicates a P value of less than 0.01.

(32) FIGS. 32A and 32B show that CD109 derived peptide P16 and PA inhibit TGF-b-induced phosphorylation of Smad2 in squamous cell carcinoma (A431) cells. A431 cancer cells treated with 10 nM of P16.2 (negative peptide control), P16 or PA in the absence or presence of 100 pM TGF-b, followed by 45 min of incubation at 4 C. Cells lysates were analyzed by Western blot using an anti-phosphoSmad2 antibody. Actin expression was used as loading control.

(33) FIG. 33 shows that CD109 derived peptide P16 and PA (but not P12) inhibit TGF-b induced EMT response in squamous cell carcinoma (A431) cells. A431 cancer cells treated with 10 nM of P16.2 (negative peptide control), P12, P16 or PA in the absence or presence of 100 pM TGF-b, followed by 24 hrs of incubation. Cells lysates were analyzed by Western blot for the expression of Fibronectin (mesenchymal marker), Snail and Twist (EMT markers). Actin expression was used as loading control.

(34) FIGS. 34A and 34B demonstrate the ability of CD109-based peptide P16 to attenuate the TGF-β-induced expression of fibronectin, collagen (COL1A1), plasminogen activator inhibitor-1 (PAI-1), α-smooth muscle actin (α-SMA), and connective tissue growth factor (CTGF). Human fibroblasts were starved for 36 hours, then treated with 100 pM TGF-β and different dosage of P16 for 24 hrs. (FIG. 34A) Cell lysates were separated by gel electrophoresis, transferred to a membrane, and immunoblotted with antibodies against each of the indicated proteins. (FIG. 34B) Densitometry analysis was subsequently carried out to quantitate the expression of each of the indicated proteins as a function of P16 concentration.

(35) FIGS. 35A and 35B demonstrate the ability of CD109-based peptide P16 to inhibit dermal collagen content in bleomycin-induced mouse models of scleroderma. Wild type mice were treated with bleomycin (5 pg) to induce skin fibrosis or PBS (negative control). Mice were treated with CD109 (1 pg), P16 (1 pg), or PBS by 100 μL subcutaneous injection every other day for 28 days for a total of 14 injections. (FIG. 35A) P16 was found to be capable of reducing dermal thickness and collagen content as assessed by trichrome staining. (FIG. 35B) P16 was found to be capable of reducing dermal collagen content as assessed by measuring the ratio of trichrome stain to total skin area.

(36) FIG. 36 shows that Recombinant CD109 or P16 peptide reduces extracellular matrix production in a bleomycin (bleo)-induced skin fibrosis model (scleroderma model) in vivo. Mice were injected intradermally with bleomycin (5 mg) in 100 ml PBS or PBS alone every second day for 28 days. Mice were co-injected without or with 1.0 mg recombinant CD109 protein or P16 peptide every second day for 28 days (14 mg total). Skin tissue was harvested and immunohistochemical analysis was performed for the detection of Fibronectin, α-sma, CTGF and Type-1 Collagen. Representative images of sections of skin derived from CD109 and p16 treated mice on day 28 after initial bleomycin or PBS treatment are shown. A total of 4-6 different mice per treatment group were analyzed. Original magnification x 20.

(37) FIG. 37 shows that Recombinant CD109 or P16 peptide reduces TGF-β expression and SMAD2 phosphorylation while enhancing SMAD1 phosphorylation in a bleomycin (bleo)-induced skin fibrosis model (scleroderma model) in vivo. Mice were injected intradermally with bleomycin (5 mg) in 100 ml PBS or PBS alone every second day for 28 days. Mice were co-injected without or with 1.0 mg recombinant CD109 protein or P16 peptide every second day for 28 days (14 mg total). Skin tissue was harvested and immunohistochemical analysis was performed for the detection of phospho-Smad2, phospho-Smad1 and TGF-β levels. Representative images of sections of skin derived from CD109 and p16 treated mice on day 28 after initial bleomycin or PBS treatment are shown. A total of 4-6 different mice per treatment group were analyzed. Original magnification x 20.

(38) FIGS. 38A and 38B show that CD109 derived peptide P16 and PA significantly inhibit TGF-b induced cellular invasion in vitro in squamous cell carcinoma (A431) cells, as detected by a Matrigel invasion Assay. A431 cancer cells (8000 cells) were seeded on a BioCoat™ Matrigel® Invasion Chamber and treated with 10 nM of P16.2 (negative peptide control), P16 or PA in the absence or presence of 100 pM TGF-b, followed by 24 hrs of incubation. Invasive cells (in the lower chambers) were stained by crystal violet dye, photographed and counted. Representative photos (A) and statistical plots of invasion (B) are shown. The data are shown as mean±SD of the number of invasive cells for three independent experiments. **P<0.01 and ***P<0.001 as compared with controls. Magnification, ×100 FIGS. 39A-39G show that Recombinant CD109 and CD109-derived peptides inhibit the number of cancer stem cells (CD133 positive cells). Squamous cell carcinoma (epidermoid A431 and head and neck FaDu) cells were stimulated with 100 pM of TGF-b1, then treated with 10 nM of peptide 16.2, P16, PA or CD109 for 24 hours. Cells were analysed by Flow cytometry and CD133 positive cell population, which represent cancer stem cell population, were quantified.

(39) FIGS. 40A and 40B show that peptide A exists as both dimeric and monomeric forms. Peptide A was bacterially expressed and purified by affinity chromatography. Purified peptide A was analyzed by SDS-PAGE under reducing and non-reducing conditions and visualized by Coomassie blue staining (FIG. 40A) or Western blot analysis using an anti-His antibody (FIG. 40B). In FIG. 40A, lane 1 of the SDS-PAGE analysis corresponds to 2.00 μg of BSA, land 2 corresponds to 2.00 μg of CD109-derived peptide A (under reducing conditions), and lane 3 corresponds to peptide 2.00 μg of peptide A under non-reducing conditions. In FIG. 40B, lane 4 of the Western Blot corresponds to peptide A under reducing conditions, and lane 5 corresponds to peptide A under non-reducing conditions. The positions of the dimer and monomer are indicated by arrows. The SDS-PAGE was run on 4%-20% gradient gel. M1 and M2 designate protein markers (GENSCRIPT®).

(40) FIG. 41 shows that peptide A dimer inhibits whereas peptide A monomer potentiates TGF-b-dependent Smad3 (CAGA.sub.12-lux) transcriptional activity in 293 cells. HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter construct were incubated with dimeric or monomeric forms of peptide A as indicated and treated with 100 pM TGF-b overnight. Cell lysates were analyzed for luciferase activity. Data are presented as fold-activation compared to TGF-b1 treatment alone (scaled to 1.0). M+D, mixture of monomer and dimer.

(41) FIG. 42 shows that peptide A inhibits TGF-b1 induced migration in A431 cells. Cells were scratched with a pipette tip and treated without or with 100 pM TGF-b1 alone or in the presence of 10 nM Peptide A or Peptide A1 (C31S mutant). Pictures were taken at 0 and 24 hrs. Peptide A but not Peptide A1 inhibits TGF-b-induced migration in A431 cells. Peptide A contains monomeric and dimeric forms whereas Peptide A1 contains a C31S mutation to prevent intermolecular disulfide bond formation so that it forms monomers only.

DETAILED DESCRIPTION

(42) The invention provides TGF-β antagonists containing a low-molecular weight TGF-β-binding peptide. The TGF-β-binding peptides described herein are derived from CD109, a high-molecular weight protein that binds endogenous TGF-β in an inhibitory fashion so as to attenuate TGF-β signaling. The present invention is based in part on the discovery that various low-molecular weight fragments of CD109 are capable of binding TGF-β in solution without the need for flanking N-terminal and C-terminal domains. A motif within CD109 containing a TGF-β-binding pharmacophore, ETWIWLDTNMG (SEQ ID NO: 4), has presently been discovered that imparts TGF-β inhibitory activity to a low-molecular weight peptide. The presence of this motif renders the peptide capable of binding and inhibiting TGF-β signaling, for instance, as observed in the form of reduced expression of genes under the control of transcription factors activated by TGF-β signal transduction, such as Smad3. TGF-β-binding peptides containing this motif, such as a peptide having the amino acid sequence of any one of SEQ ID NOs: 5, 6, 12-15, and 22-25, may be capable of attenuating the expression of proteins involved in the fibrotic response, such as fibronectin, plasminogen activator inhibitor-1 (PAI-1), and connective tissue growth factor (CTGF). Due to their capacity for inhibiting TGF-β activity, the TGF-β-binding peptides described herein can be used as TGF-β antagonists for the treatment of a variety of pathological conditions, including fibrosis, autoimmune diseases, and cancers, among others. The TGF-β antagonists described herein may include a TGF-β-binding peptide and, for example, one or more additional moieties (e.g., peptides, small molecules, or proteins) that do not interfere with binding of the peptide to TGF-β. Alternatively, a TGF-β antagonist may consist of the TGF-β-binding peptide and not contain any additional elements.

(43) An additional discovery underlying the present invention is that, surprisingly, low-molecular weight peptides containing the amino acid sequence of SEQ ID NO: 4 do not aggregate in solution. A barrier that has hindered the development of high-molecular weight proteins and large (e.g., >10 kDa) fragments thereof has been the propensity of various peptides to aggregate in aqueous solution. In accordance with the present disclosure, there is provided peptides capable of antagonizing at least one TGF-β's biological activity while exhibiting a very low propensity to aggregate during storage. The peptides are derived from the CD109 polypeptide and can be used for the prevention, treatment and/or alleviation of symptoms associated with fibrosis.

(44) Peptidic TGF-β Antagonists

(45) As shown herein, peptide X, a 40-amino acid fragment of the CD109 polypeptide (having the amino acid sequence shown in SEQ ID NO: 1) has the propensity to aggregate during storage. In the conditions described in Example 1, peptide X was shown to aggregate when stored for 2 hours at 4° C. (e.g., when dissolved at a concentration of 50 mM in a Tris-HCl (pH=7.0) solution). The aggregation of peptide X reduced its ability to antagonize at least some of TGF-β's biological activity (e.g., reduction of the transcription induced by Smad3, reduction in the expression of PAI-1, etc.). However, it has presently been discovered that the conversion of aggregated peptide X to an un-aggregated form partially restores its ability to antagonize TGF-β's biological activity.

(46) In addition to peptide X, some TGF-β peptide antagonists, such as high-molecular weight TGF-β antagonists, may have a propensity to aggregate. Peptide aggregation is considered a common and troubling manifestation and is encountered in almost all stages of peptide drug development. Peptide aggregation, along with other physical and/or chemical instabilities of proteins, remains one of the major road blocks hindering rapid commercialization of potential peptide drug candidates. Moreover, peptide aggregation is associated with adverse immunogenic side effects underscoring the importance for the design of peptides with a low propensity to (self) aggregate, particularly at the early stages of peptide (drug) development.

(47) To further understand why peptide X has a propensity to aggregate, its amino acid sequence was further analyzed. As discussed in Example 1, the amino acid motif ETWIWL (SEQ ID NO: 11) associated with binding with TGF-β (and presumably involved in antagonizing TGF-β's biological activity) was identified as favoring aggregation of peptide X. Nevertheless, a series of peptides that contain the ETWIWL motif were designed and tested These included Peptide X1/P28, Peptide X2/P21, peptide X3, Peptide X4, Peptide 16/P16, Peptide 11/P11, Peptide 16.1/P16.1 and Peptide 16.2/P16.2.

(48) As also shown herein, some of the fragments of peptide X (referred to herein as peptidic TGF-β antagonists) lack or have a low propensity to aggregate upon storage and exhibit antagonist activity against TGF-β. Unexpectedly, the peptidic TGF-β antagonists contain the hydrophobic, aggregation-prone amino acid motif ETWIWL (SEQ ID NO: 11) but do not have the propensity to aggregate. As such, the peptidic TGF-β antagonists represent a class of therapeutic peptides which will not aggregate and may have increased stability during storage.

(49) The peptidic TGF-β antagonists may have, for instance, up to 28 amino acids. In some embodiments, the peptidic TGF-β antagonists contain from 12 to 28 amino acids, such as from 12 to 27 amino acids, from 12 to 26 amino acids, from 12 to 25 amino acids, from 12 to 24 amino acids, from 12 to 23 amino acids, from as to 22 amino acids, from as to 21 amino acids, from 12 to 20 amino acids, from 12 to 19 amino acids, from 12 to 18 amino acids, from 12 to 17 amino acids, from 12 to 16 amino acids, from 12 to 15 amino acids, from 12 to 14 amino acids, or 13 amino acids. In some embodiments, the TGF-β antagonist peptides contain between 12 and 16 amino acid residues organized in a linear fashion (e.g., absence of amino acid branching). These peptidic TGF-β antagonists can be, for instance, 12, 13, 14, 15 or 16 amino acid residues in length. Some of the peptidic TGF-β antagonists described herein are not shorter than 12 amino acid residues and are not longer than 16 amino acid residues. The peptidic TGF-β antagonists described herein can be provided as a composition comprising a single length of peptidic TGF-β antagonist (each having the same number in amino acids) or a plurality of lengths of peptidic TGF-β antagonists (comprising at least two different peptides each having a different number of amino acids).

(50) The peptidic TGF-β antagonists described herein may comprise the ETWIWL motif (SEQ ID NO: 11) as well as additional amino acid residues (located either at the NH.sub.2 and/or COOH terminus) to have a total of, instance, up to 28 amino acids, such as between 12 and 16 amino acid residues. In an embodiment, the peptidic TGF-β antagonists have a structure of the following formula (III):
NH.sub.2′ETWIWLDTNMG(SEQ ID NO:4)-Xaa.sub.1-Xaa.sub.2-Xaa.sub.3-Xaa.sub.4-Xaa.sub.5′COOH  (III), wherein Xaa.sub.1 is any naturally-occurring amino acid; Xaa.sub.2 is absent or is any naturally-occurring amino acid; Xaa.sub.3 is absent or is any naturally-occurring amino acid, wherein Xaa.sub.3 can only be present when Xaa.sub.2 is present; Xaa.sub.4 is absent or is any naturally-occurring amino acid, wherein Xaa.sub.4 can only be present only when Xaa.sub.3 is present; Xaa.sub.5 is absent or is any naturally-occurring amino acid, wherein Xaa.sub.5 can only be present only when Xaa.sub.4 is present; and “-” represents a peptide bond between two adjacent amino acid residues.

(51) In some embodiments of the peptidic TGF-β antagonists of formula (III), Xaa.sub.2 can be an arginine residue, Xaa.sub.3 can be an isoleucine residue, Xaa.sub.4 can be a tyrosine residue and/or Xaa.sub.5 can be a glutamine residue. The TGF-β antagonist peptide having the structure of formula (III) are also presented in the generic amino acid sequence of SEQ ID NO: 16.

(52) The peptidic TGF-β antagonists of formula (III) can include at least two amino acid residues bearing a net negative charge (when measuring at physiological pH). In some embodiments, the charge of the peptidic TGF-β antagonist is involved in binding to TGF-β. Such negatively-charged amino acid residues can interact, for example, with Arg25 and Arg94 of TGF-β3. These at least two net negative charge are present in the glutamate (E) and aspartate (D) residues of ETWIWLDTNMG (SEQ ID NO: 4).

(53) In the peptidic TGF-β antagonists of formula (III), Xaa.sub.1 can be any naturally-occurring amino acid. In an embodiment, Xaa.sub.1 is an amino acid residue having a polar and uncharged side-chain or an amino acid residue having a hydrophobic side-chain. When Xaa.sub.1 is an amino acid residue having a polar and uncharged side-chain, Xaa.sub.1 can be, for example, a serine residue, a threonine residue, an asparagine residue or a glutamine residue. When Xaa.sub.1 is an amino acid residue having an hydrophobic side-chain, Xaa.sub.1 can be, for example, a tyrosine residue, an alanine residue, a valine residue, an isoleucine residue, a leucine residue, a methionine residue, a phenylalanine residue or a tryptophan residue. In some embodiments, Xaa.sub.1 is a serine residue or a tyrosine residue. When Xaa.sub.1 is present, Xaa.sub.2, Xaa.sub.3, Xaa.sub.4 and Xaa.sub.5 can be present or absent. In one embodiment, Xaa.sub.1 is present and Xaa.sub.2, Xaa.sub.3, Xaa.sub.4 and Xaa.sub.5 are absent. In such embodiment, the TGF-β antagonist peptide can have the amino acid sequence of SEQ ID NO: 12.

(54) In the TGF-β antagonist peptide of formula (III), Xaa.sub.2 is an optional amino acid residue and can be any naturally-occurring amino acid. In some embodiments, Xaa.sub.2 is an amino acid residue having a positively-charged side-chain. In an embodiment, Xaa.sub.2 is an arginine residue, a histidine residue or a lysine residue. In yet another embodiment, Xaa.sub.2 can be an arginine residue. When Xaa.sub.2 is present, Xaa.sub.3, Xaa.sub.4 and Xaa.sub.5 can be present or absent. In one embodiment, Xaa.sub.2 is present and Xaa.sub.3, Xaa.sub.4 and Xaa.sub.5 are absent. In such embodiment, the TGF-β antagonist peptide can have the amino acid sequence of SEQ ID NO: 13.

(55) In the TGF-β antagonist peptide of formula (III), Xaa.sub.3 is an optional amino acid residue and can be any naturally-occurring amino acid. Xaa.sub.3 can only be present when Xaa.sub.2 is present. In some embodiments, Xaa.sub.3 is an amino acid residue having a hydrophobic side-chain. In an embodiment, Xaa.sub.3 can be, for example, an alanine residue, a valine residue, an isoleucine residue, a methionine residue, a phenylalanine residue, a tyrosine residue, or a tryptophan residue. In an embodiment, Xaa.sub.3 is an isoleucine residue. When Xaa.sub.3 is present, Xaa.sub.4 and Xaa.sub.5 can be present or absent. In one embodiment, Xaa.sub.2 and Xaa.sub.3 are present and Xaa.sub.4 and Xaa.sub.5 are absent. In such embodiment, the TGF-β antagonist peptide can have the amino acid sequence of SEQ ID NO: 14.

(56) In the TGF-β antagonist peptide of formula (III), Xaa.sub.4 is an optional amino acid residue and can be any naturally-occurring amino acid. Xaa.sub.4 can only be present when Xaa.sub.2 and Xaa.sub.3 are present. In some embodiments, Xaa.sub.4 is an amino acid residue having a hydrophobic side-chain. In an embodiment, Xaa.sub.4 can be, for example, an alanine residue, a valine residue, an isoleucine residue, a methionine residue, a phenylalanine residue, a tyrosine residue, or a tryptophan residue. In some embodiments, Xaa.sub.4 is a tyrosine residue. When Xaa.sub.2, Xaa.sub.3 and Xaa.sub.4 are present, Xaa.sub.5 can be present or absent. In some embodiments, Xaa.sub.4 is present and Xaa.sub.5 are absent. In such embodiment, the TGF-β antagonist peptide can have the amino acid sequence of SEQ ID NO: 15.

(57) In the TGF-β antagonist peptide of formula (III), Xaa.sub.5 is an optional amino acid residue and can be any naturally-occurring amino acid. Xaa.sub.5 can only be present when Xaa.sub.2, Xaa.sub.3 and Xaa.sub.4 are present. In an embodiment, Xaa.sub.5 is an amino acid residue having a polar and uncharged side-chain. Xaa.sub.5 can be, for example, a serine residue, a threonine residue, an asparagine residue or a glutamine residue. In an embodiment, Xaa.sub.5 is a glutamine residue. In one embodiment, the TGF-β antagonist peptide can have the amino acid sequence of SEQ ID NO: 5.

(58) In some embodiments, the peptidic TGF-β antagonists have a structure of the following formula (II):
NH.sub.2′SEQ ID NO:4-Xaa.sub.1-Y′COOH  (II),
Wherein Xaa.sub.1 is any naturally-occurring amino acid; Y is a peptide having between 0 and 4 amino acid residue; and “-” represents a peptide bond between two adjacent amino acids.

(59) In the peptidic TGF-β antagonists of formula (II), Y is a linear peptide having between 0 and 4 amino acid residues. When present, Y can be represented by the formula (IIa), (IIb), (IIc) or (IId).

(60) In some of the embodiments of the peptidic TGF-β antagonists of formula (II), Xaa.sub.1 can be as defined above for formula (III). When Y is absent (e.g., it has no (0) amino acid residues), Xaa.sub.1 can be any naturally-occurring amino acid and in some embodiments, a serine residue. In the latter, the peptidic TGF-β antagonist consists of the amino acid sequence of SEQ ID NO: 12. When Y is present (e.g., it has between 1 and 4 amino acid residues) Xaa.sub.1 can be any naturally-occurring amino acid and in some embodiments, a serine residue. In the latter, the peptidic TGF-β antagonist has the amino acid sequence of SEQ ID NO: 12.

(61) In some embodiments of the peptidic TGF-β antagonists of formula (II), Y comprises a single amino acid residue. In such embodiment, Y can be of the formula (IIa)
-Xaa.sub.2  (IIa)
wherein “-” represents a peptide bond between Xaa.sub.1 and Xaa.sub.2. In such embodiment, Xaa.sub.2 can be any naturally-occurring amino acid or as defined above for formula (III). In some embodiments, Xaa.sub.2 can be an arginine residue. In some embodiments, when Y has a single (1) amino acid residue and Xaa.sub.2 is an arginine residue, the peptidic TGF-β antagonist consists of the amino acid sequence of SEQ ID NO: 13. In some embodiments, when Y has a more than one amino acid residues and Xaa.sub.2 is an arginine residue, the peptidic TGF-β antagonist has the amino acid sequence of SEQ ID NO: 13.

(62) In some embodiments of the peptidic TGF-β antagonists of formula (II), Y comprises two (2) amino acid residues. In such embodiment, Y can be of the formula (IIb):
-Xaa.sub.2-Xaa.sub.3  (IIb)
wherein “-” represents a peptide bond between two adjacent amino acid residues (Xaa.sub.1 and Xaa.sub.2 as well as Xaa.sub.2 and Xaa.sub.3). In such embodiment, Xaa.sub.2 can be any naturally-occurring amino acid and, in some embodiments, Xaa.sub.2 can be an arginine residue. In such embodiments, Xaa.sub.3 can be any naturally-occurring amino acid (such as defined above for formula (III)) and, in some embodiments, Xaa.sub.3 can be an isoleucine residue. In some embodiments, when Y has two (2) amino acid residues, Xaa.sub.2 is an arginine residue and Xaa.sub.3 is an isoleucine residue, the peptidic TGF-β antagonist consists of the amino acid sequence of SEQ ID NO: 14. In some embodiments, when Y has more than two (2) amino acid residues, Xaa.sub.2 is an arginine residue and Xaa.sub.3 is an isoleucine residue, the peptidic TGF-β antagonist comprises the amino acid sequence of SEQ ID NO: 14.

(63) In some embodiments of the peptidic TGF-β antagonists of formula (II), Y comprises three (3) amino acid residues. In such embodiments, Y can of the formula (IIc):
-Xaa.sub.2-Xaa.sub.3-Xaa.sub.4  (IIc)
wherein “-” represents a peptide bond between two adjacent amino acid residues (between Xaa.sub.1 and Xaa.sub.2, between Xaa.sub.2 and Xaa.sub.3 as well as between Xaa.sub.3 and Xaa.sub.4). In such embodiment, Xaa.sub.2 can be any naturally-occurring amino acid and, in some embodiments, Xaa.sub.2 can be an arginine residue. In such embodiments, Xaa.sub.3 can be any naturally-occurring amino acid and, in some embodiments, Xaa.sub.3 can be an isoleucine residue. In such embodiments, Xaa.sub.4 can be any naturally-occurring amino acid (as provided in the definition above for formula (III)) and, in some embodiments, Xaa.sub.4 can be a tyrosine residue. In some embodiments, when Y has three (3) amino acid residues, Xaa.sub.2 is an arginine residue, Xaa.sub.3 is an isoleucine residue and Xaa.sub.4 is a tyrosine residue, the peptidic TGF-β antagonist consists of the amino acid sequence of SEQ ID NO: 15. In some embodiments, when Y has more than three (3) amino acid residues, Xaa.sub.2 is an arginine residue, Xaa.sub.3 is an isoleucine residue and Xaa.sub.4 is a tyrosine residue, the peptidic TGF-β antagonist has the amino acid sequence of SEQ ID NO: 15.

(64) In some embodiments of the peptidic TGF-β antagonists of formula (II), Y comprises four (4) amino acid residues. In such embodiment, Y can be of the formula (IId):
-Xaa.sub.2-Xaa.sub.3-Xaa.sub.4-Xaa.sub.5  (IId)
wherein “-” represents a peptide bond between two adjacent amino acid residues (between Xaa.sub.1 and Xaa.sub.2, between Xaa.sub.2 and Xaa.sub.3, between Xaa.sub.3 and Xaa.sub.4 as well as between Xaa.sub.4 and Xaa.sub.5). In such embodiment, Xaa.sub.2 can be any naturally-occurring amino acid and, in some embodiments, Xaa.sub.2 can be an arginine residue. In such embodiments, Xaa.sub.3 can be any naturally-occurring amino acid and, in some embodiments, Xaa.sub.3 can be an isoleucine residue. In such embodiments, Xaa.sub.4 can be any naturally-occurring amino acid and, in some embodiments, Xaa.sub.4 can be a tyrosine residue. In such embodiments, Xaa.sub.5 can be any naturally-occurring amino acid (as provided above for formula (III)) and, in some embodiments, Xaa.sub.5 can be a glutamine residue. In some embodiments, when Y has four (4) amino acid residues, Xaa.sub.2 is an arginine residue, Xaa.sub.3 is an isoleucine residue, Xaa.sub.4 is a tyrosine residue and Xaa.sub.5 is a glutamine residue, the peptidic TGF-β antagonist consists of the amino acid sequence of SEQ ID NO: 5.

(65) In some of the TGF-β antagonists described herewith, the amino acid sequence of SEQ ID NO: 4 (found in formulae (II) and (III)) can be replaced by the following amino acid sequence (herein referred to as the peptides having the amino acid sequence of SEQ ID NO: 1 or variants of SEQ ID NO: 4):
Xaa.sub.1-Xaa.sub.2-Xaa.sub.3-Xaa.sub.4-Xaa.sub.5-Xaa.sub.6-Xaa.sub.7-Xaa.sub.8-Xaa.sub.9-Xaa.sub.10-Xaa.sub.11  (SEQ ID NO: 21)

(66) wherein “-” represents a peptide bond between two adjacent amino acid residues (between Xaa.sub.1 and Xaa.sub.2, between Xaa.sub.2 and Xaa.sub.3, between Xaa.sub.3 and Xaa.sub.4, between Xaa.sub.4 and Xaa.sub.5, between Xaa.sub.5 and Xaa.sub.6, between Xaa.sub.6 and Xaa.sub.7, between Xaa.sub.7 and Xaa.sub.8, between Xaa.sub.8 and Xaa.sub.9 as well as between Xaa.sub.9 and Xaa.sub.10). Xaa.sub.1 can be any amino acid having a negatively-charged side-chain (aspartic acid or glutamic acid for example) and, in some embodiments, Xaa.sub.1 can be a glutamic acid residue. Xaa.sub.2 can be any amino acid having a polar uncharged side-chain (serine, threonine, asparagine or glutamine for example) and, in some embodiments, Xaa.sub.2 can be a threonine residue. Xaa.sub.3 can be any amino acid having a hydrophobic side-chain (alanine, isoleucine, leucine, methionine, phenylalanine, tyrosine or tryptophan for example) and, in some embodiments, Xaa.sub.3 can be a tryptophan residue. Xaa.sub.4 can be any amino acid having a hydrophobic side-chain (alanine, isoleucine, leucine, methionine, phenylalanine, tyrosine or tryptophan for example) and, in some embodiments, Xaa.sub.4 can be an isoleucine residue. Xaa.sub.5 can be any amino acid having a hydrophobic side-chain (alanine, isoleucine, leucine, methionine, phenylalanine, tyrosine or tryptophan for example) and, in some embodiments, Xaa.sub.5 can be a tryptophan residue. Xaa.sub.6 can be any amino acid having a hydrophobic side-chain (alanine, isoleucine, leucine, methionine, phenylalanine, tyrosine or tryptophan for example) and, in some embodiments, Xaa.sub.6 can be a leucine residue. Xaa.sub.7 can be any amino acid having a negatively-charged side-chain (aspartic acid or glutamic acid for example) and, in some embodiments, Xaa.sub.7 can be an aspartic acid residue. Xaa.sub.8 can be any amino acid having a polar uncharged side-chain (serine, threonine, asparagine or glutamine for example) and, in some embodiments, Xaa.sub.8 can be a threonine residue. Xaa.sub.9 can be any amino acid having a polar uncharged side-chain (serine, threonine, asparagine or glutamine for example) and, in some embodiments, Xaa.sub.9 can be an asparagine residue. Xaa.sub.10 can be any amino acid having a hydrophobic side-chain (alanine, isoleucine, leucine, methionine, phenylalanine, tyrosine or tryptophan for example) and, in some embodiments, Xaa.sub.10 can be a methionine residue. Xaa.sub.11 can be any amino acid having a neutral non-polar side-chain (alanine, valine or glycine for example) and, in some embodiments, Xaa.sub.10 can be a glycine residue.

(67) Table A provides various embodiments of the contemplated TGF-β antagonist peptides of formulae (II) and (III).

(68) Table A. The TGF-β antagonist peptides described herein can possess the common structure shown in formula (III). Some of the contemplated combinations of the Xaa.sub.1, Xaa.sub.2, Xaa.sub.3, Xaa.sub.4 and Xaa.sub.5 residues are shown below. Amino acid residues are identified using three-letter code. Xaa refers to any naturally-occurring amino acid residue.

(69) TABLE-US-00001 Peptide Xaa.sub.1 Xaa.sub.2 Xaa.sub.3 Xaa.sub.4 Xaa.sub.5 12-A Xaa Absent Absent Absent Absent 12-B Ser Absent Absent Absent Absent 13-A Xaa Xaa Absent Absent Absent 13-B Ser Xaa Absent Absent Absent 13-C Xaa Arg Absent Absent Absent 13-D Ser Arg Absent Absent Absent 14-A Xaa Xaa Xaa Absent Absent 14-B Ser Xaa Xaa Absent Absent 14-C Xaa Arg Xaa Absent Absent 14-D Xaa Xaa Ile Absent Absent 14-E Ser Arg Xaa Absent Absent 14-F Ser Xaa Ile Absent Absent 14-G Xaa Arg Ile Absent Absent 14-H Ser Arg Ile Absent Absent 15-A Xaa Xaa Xaa Xaa Absent 15-B Xaa Xaa Xaa Tyr Absent 15-C Ser Xaa Xaa Xaa Absent 15-D Ser Xaa Xaa Tyr Absent 15-E Xaa Arg Xaa Xaa Absent 15-F Xaa Arg Xaa Tyr Absent 15-G Xaa Xaa Ile Xaa Absent 15-H Xaa Xaa Ile Tyr Absent 15-I Ser Arg Xaa Xaa Absent 15-J Ser Arg Xaa Tyr Absent 15-K Ser Xaa Ile Xaa Absent 15-L Ser Xaa Ile Tyr Absent 15-M Xaa Arg Ile Xaa Absent 15-N Xaa Arg Ile Tyr Absent 15-O Ser Arg Ile Xaa Absent 15-P Ser Arg Ile Tyr Absent 16-A Xaa Xaa Xaa Xaa Xaa 16-B Xaa Xaa Xaa Xaa Gln 16-C Xaa Xaa Xaa Tyr Xaa 16-D Xaa Xaa Xaa Tyr Gln 16-E Ser Xaa Xaa Xaa Xaa 16-F Ser Xaa Xaa Xaa Gln 16-G Ser Xaa Xaa Tyr Xaa 16-H Ser Xaa Xaa Tyr Gln 16-I Xaa Arg Xaa Xaa Xaa 16-J Xaa Arg Xaa Xaa Gln 16-K Xaa Arg Xaa Tyr Xaa 16-L Xaa Arg Xaa Tyr Gln 16-M Xaa Xaa Ile Xaa Xaa 16-N Xaa Xaa Ile Xaa Gln 16-O Xaa Xaa Ile Tyr Xaa 16-P Xaa Xaa Ile Tyr Gln 16-Q Ser Arg Xaa Xaa Xaa 16-R Ser Arg Xaa Xaa Gln 16-S Ser Arg Xaa Tyr Xaa 16-T Ser Arg Xaa Tyr Gln 16-U Ser Xaa Ile Xaa Xaa 16-V Ser Xaa Ile Xaa Gln 16-W Ser Xaa Ile Tyr Xaa 16-X Ser Xaa Ile Tyr Gln 16-Y Xaa Arg Ile Xaa Xaa 16-Z Xaa Arg Ile Xaa Gln 16-AA Xaa Arg Ile Tyr Xaa 16-BB Xaa Arg Ile Tyr Gln 16-CC Ser Arg Ile Xaa Xaa 16-DD Ser Arg Ile Xaa Gin 16-EE Ser Arg Ile Tyr Xaa 16-FF Ser Arg Ile Tyr Gln

(70) The peptidic TGF-β3 antagonists can be provided as a composition. The composition can comprises a single type of peptidic TGF-β3 antagonists having the same amino acid sequence or a plurality of types of peptidic TGF-β3 antagonists in which at least two peptides having different amino acid sequences.

(71) The present disclosure also provides peptidic TGF-β3 antagonists variants, such as cyclic and multimeric variants, for instance, as described below. Exemplary peptides for use with the compositions and methods described herein are summarized in Table B, below. Peptides that can be used with the compositions and methods described herein include those listed in Table B, as well as those having at least 85% sequence identity (e.g., at least 85%, 90%, 95%, 97%, 99%, or greater) relative to each of the listed peptides in Table B.

(72) TABLE-US-00002 TABLE B Summary of select peptides described herein: Peptide Name Amino Acid Sequence P11 ETWIWLDTNMG (SEQ ID NO: 4) P12 ETWIWLDTNMGS (SEQ ID NO: 12) P13 ETWIWLDTNMGSR (SEQ ID NO: 13) P14 ETWIWLDTNMGSRI (SEQ ID NO: 14) P15 ETWIWLDTNMGSRIY (SEQ ID NO: 15) P16 ETWIWLDTNMGSRIYQ (SEQ ID NO: 5) P17 ETWIWLDTNMGSRIYQE (SEQ ID NO: 22) P18 ETWIWLDTNMGSRIYQEF (SEQ ID NO: 23) P19 ETWIWLDTNMGSRIYQEFE (SEQ ID NO: 24) P20 ETWIWLDTNMGSRIYQEFEV (SEQ ID NO: 25) P21 ETWIWLDTNMGSRIYQEFEVT (SEQ ID NO: 6) P28 ETWIWLDTNMGSRIYQEFEVTVVPDSITS (SEQ ID NO: 2)
Peptide Synthesis Techniques

(73) Systems and processes for performing solid phase peptide synthesis are known in the art and have been described, for instance, in U.S. Pat. Nos. 9,169,287; 9,388,212; 9,206,222; 6,028,172; and 5,233,044, among others, the disclosures of each of which are incorporated herein by reference as they pertain to protocols and techniques for the synthesis of peptides on solid support. Solid phase peptide synthesis is a known process in which amino acid residues are added to peptides that have been immobilized on a solid support, such as a polymeric resin (e.g., a hydrophilic resin, such as a polyethylene-glycol-containing resin, or hydrophobic resin, such as a polystyrene-based resin).

(74) Peptides, such as those containing protecting groups at amino, hydroxy, thiol, and carboxy substituents, among others, may be bound to a solid support such that the peptide is effectively immobilized on the solid support. For example, the peptides may be bound to the solid support via their C termini, thereby immobilizing the peptides for subsequent reaction in at a resin-liquid interface.

(75) The process of adding amino acid residues to immobilized peptides can include exposing a deprotection reagent to the immobilized peptides to remove at least a portion of the protection groups from at least a portion of the immobilized peptides. The deprotection reagent exposure step can be configured, e.g., such that side-chain protection groups are preserved, while N-termini protection groups are removed. For instance, an exemplary amino protecting may contain fluorenylmethyloxycarbonyl (Fmoc). A deprotection reagent containing piperidine (e.g., a piperidine solution in an appropriate organic solvent, such as dimethyl formamide (DMF)) may be exposed to the immobilized peptides such that the Fmoc protecting groups are removed from at least a portion of the immobilized peptides. Other protecting groups suitable for the protection of amino substituents include, for instance, the tert-butyloxycarbonyl (Boc) moiety. A deprotection reagent comprising a strong acid, such as trifluoroacetic acid (TFA) may be exposed to immobilized peptides containing a Boc-protected amino substituent so as to remove the Boc protecting group by an ionization process.

(76) In this way, peptides can be protected and deprotected at specific sites, such as at one or more side-chains or at the N- or C-terminus of an immobilized peptide so as to append chemical functionality regioselectively at one or more of these positions. This can be used, for instance, to derivatize a side-chain of an immobilized peptide, or to synthesize a peptide, e.g., from the C-terminus to the N-terminus.

(77) The process of adding amino acid residues to immobilized peptides can include, for instance, exposing protected, activated amino acids to the immobilized peptides such that at least a portion of the activated amino acids are bonded to the immobilized peptides to form newly-bonded amino acid residues. For example, the peptides may be exposed to activated amino acids that react with the deprotected N-termini of the peptides so as to elongate the peptide chain by one amino acid. Amino acids can be activated for reaction with the deprotected peptides by reaction of the amino acid with an agent that enhances the electrophilicity of the carbonyl carbon of the amino acid. For example, phosphonium and uronium salts can, in the presence of a tertiary base (e.g., diisopropylethylamine (DIPEA) and triethylamine (TEA), among others), convert protected amino acids into activated species (for example, BOP, PyBOP, HBTU, and TBTU all generate HOBt esters). Other reagents can be used to help prevent racemization that may be induced in the presence of a base. These reagents include carbodiimides (for example, DCC or WSCDI) with an added auxiliary nucleophile (for example, 1-hydroxy-benzotriazole (HOBt), 1-hydroxy-azabenzotriazole (HOAt), or HOSu) or derivatives thereof. Another reagent that can be utilized to prevent racemization is TBTU. The mixed anhydride method, using isobutyl chloroformate, with or without an added auxiliary nucleophile, can also be used, as well as the azide method, due to the low racemization associated with this reagent. These types of compounds can also increase the rate of carbodiimide-mediated couplings, as well as prevent dehydration of Asn and Gln residues. Typical additional reagents include also bases such as N,N-diisopropylethylamine (DIPEA), triethylamine (TEA) or N-methylmorpholine (NMM). These reagents are described in detail, for instance, in U.S. Pat. No. 8,546,350, the disclosure of which is incorporated herein in its entirety.

(78) Cyclic peptides can be synthesized using solid-phase peptide synthesis techniques. For instance, a side-chain substituent, such as an amino, carboxy, hydroxy, or thiol moiety can be covalently bound to a resin, leaving the N-terminus and C-terminus of the amino acid exposed in solution. The N- or C-terminus can be chemically protected, for instance, while reactions are carried out that elongate the peptide chain. The termini of the peptide can then be selectively deprotected and coupled to one another while the peptide is immobilized by way of the side-chain linkage to the resin. Techniques and reagents for the synthesis of head-to-tail cyclic peptides are known in the art and are described, for instance, in U.S. Pat. Nos. 9,388,212 and 7,589,170, the disclosures of which are incorporated herein by reference in their entirety.

(79) Cyclic and Dimeric Variants of TGF-β Antagonist Peptides

(80) In some embodiments, a TGF-β-binding peptide described herein is a linear peptide, for instance, containing amine and carboxyl substituents at the N- and C-termini of the peptide, respectively, or containing acyl (e.g., acetyl) and carboxamide substituents at the N- and C-termini of the peptide, respectively. In some embodiments, the TGF-β-binding peptide is a cyclic peptide. For instance, the TGF-β-binding peptide may be covalently bound to a cysteine residue at each of the N-terminus and the C-terminus of the TGF-β-binding peptide. The cysteine residues can be covalently bound to one another, for example, by a disulfide bond. In some embodiments, the cysteine residues are covalently bound to one another by way of a linker, for instance, through thioether bonds. In some embodiments, the linker contains an alkyl, aryl, heteroaryl, cycloalkyl, or heterocyclolalkyl moiety. In some embodiments, the TGF-β-binding peptide is a head-to-tail cyclic peptide.

(81) In some embodiments, the peptidic TGF-β antagonists or their variants can be provided as multimers, such as dimers (e.g., in a dimeric form). For example, in some embodiments, the peptidic TGF-β antagonist can be modified to bear (e.g., either at their N- or C-terminus) one or more amino acids (such as one or more lysine residues for example) that can be linked with a spacer to form a dimer. In a further embodiment, the dimeric peptidic TGF-β antagonist comprises two identical TGF-β antagonist having the same amino acid sequence. In such embodiment, the each of the peptidic TGF-β antagonist can be covalently associated by a linker. The section that follows provides a description of chemical bond-forming techniques and linkers that can be used for synthesizing dimeric and cyclic TGF-β antagonist peptides.

(82) Linkers for Peptide Cyclization and Dimerization

(83) A variety of linkers can be used to covalently couple reactive residues within peptidic TGF-β antagonist to one another, for instance, so as to form cyclic or dimeric peptide products. Exemplary linkers include those that may be cleaved, for instance, by enzymatic hydrolysis, photolysis, hydrolysis under acidic conditions, hydrolysis under basic conditions, oxidation, disulfide reduction, nucleophilic cleavage, or organometallic cleavage (see, for example, Leriche et al., Bioorg. Med. Chem., 20:571-582, 2012, the disclosure of which is incorporated herein by reference as it pertains to linkers suitable for chemical coupling). Examples of linkers useful for the synthesis of cyclic TGF-β antagonist peptides and dimeric TGF-β antagonist peptides include those that contain electrophiles, such as Michael acceptors (e.g., maleimides), activated esters, electron-deficient carbonyl compounds, and aldehydes, among others, suitable for reaction with nucleophilic substituents present within antibodies, antigen-binding fragments, and ligands, such as amine and thiol moieties. For instance, linkers suitable for the synthesis of cyclic TGF-β antagonist peptides and dimeric TGF-β antagonist peptides include, without limitation, alkyl, cycloalkyl, and heterocycloalkyl linkers, such as open-chain ethyl, propyl, butyl, hexyl, heptyl, octyl, nonyl, or decyl chains, cyclohexyl groups, cyclopentyl groups, cyclobutyl groups, cyclopropyl groups, piperidinyl groups, morpholino groups, or others containing two reactive moieties (e.g., halogen atoms, aldehyde groups, ester groups, acyl chloride groups, acyl anhydride groups, tosyl groups, mesyl groups, or brosyl groups, among others, that can be displaced by reactive nucleophilic atoms present within a TGF-β antagonist peptide), aryl or heteroaryl linkers, such as benzyl, napthyl, or pyridyl groups containing two halomethyl groups that can be displaced by reactive nucleophilic atoms present within a TGF-β antagonist peptide. Exemplary linkers include succinimidyl 4-(N-maleimidomethyl)-cyclohexane-L-carboxylate (SMCC), N-succinimidyl iodoacetate (SIA), sulfo-SMCC, m-maleimidobenzoyl-N-hydroxysuccinimidyl ester (MBS), sulfo-MBS, and succinimidyl iodoacetate, among others described, for instance, Liu et al., 18:690-697, 1979, the disclosure of which is incorporated herein by reference as it pertains to linkers for chemical conjugation. Additional linkers include the non-cleavable maleimidocaproyl linkers, which are described by Doronina et al., Bioconjugate Chem. 17:14-24, 2006, the disclosure of which is incorporated herein by reference as it pertains to linkers for chemical conjugation.

(84) Pharmaceutical Compositions and Routes of Administration

(85) The peptidic TGF-β antagonists described herein, as well as their variants, can be formulated as a pharmaceutical composition. In the pharmaceutical compositions described herein, the peptidic TGF-β antagonists and/or their variants can be formulated to include a pharmaceutically acceptable carrier or vehicle. The peptidic TGF-β antagonists, dimers and/or their variants may be formulated prior to administration to the mammal using available techniques and procedures. The peptidic TGF-β antagonists and/or their variants as well as their corresponding pharmaceutical compositions can be formulated for administration to the skin of the mammal, including the skin of the human. In the context of the present disclosure, the expression “administration to the skin” includes, but is not limited to topical skin administration, subcutaneous (sc) injection or intra-dermal injection. Exemplary formulations suitable for topical skin administration include, but are not limited to, lotions, creams, pastes, gels as well as solids. Topical skin formulations can be administered using a dressing (such as, for example, an impregnated wound dressing), can be applied directly to the skin area to be treated, can be administered transdermally using a patch, surgical suture, or surgical staple. Such compositions include, for example, lotions, creams, solutions, gels and solids. In some embodiments, suitable carriers for topical administration typically remain in place on the skin as a continuous film and resist being removed by perspiration or immersion in water. The carrier can be organic in nature and capable of having dispersed or dissolved therein the antagonists. The carrier may include pharmaceutically acceptable emollients, emulsifiers, thickening agents, solvents and the like. In some embodiments, the peptidic TGF-β antagonists are formulation as a biodegradable sustained-release composition for cutaneous, subcutaneous or intramuscular administration.

(86) In some embodiments, peptidic TGF-β antagonists, dimers, and/or their variants as well as their corresponding pharmaceutical compositions can be formulated for administration in the vicinity of or inside a cancerous tumor. In the context of the present disclosure, the expression “administration in the vicinity of or inside a cancerous tumor” includes, but is not limited to intra-tumoral administration as well as systemic administration (intravenous, oral, intraarterial, parenteral (including subcutaneous, intra-muscular and intravenous), intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intrathecal, epidural, intracisternal, intraperitoneal, rectal, buccal (including sublingual), pulmonary and intranasal). Exemplary formulations suitable for administration in the vicinity of or inside a cancerous tumor include, but are not limited to, solutions, suspensions and the like.

(87) Therapeutic Uses of the Peptidic TGF-β Antagonists

(88) As shown herein, the peptidic TGF-β antagonists can be used to prevent, limit or, in some instances, treat a pathological condition associated with a pathological increase in TGF-β activity. As used in the context of the present disclosure, a “pathological increase in TGF-β activity” refers to an increase in a subject's level or activity of TGF-β (which can be systemic or local) leading to unwanted biological effects. In some embodiments, a pathological increase in TGF-β activity causes or sustains “a pathological fibrotic condition”, e.g., a condition in which excessive and pathological fibrosis occurs. “Fibrosis” refers in general to the formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process. “Pathological fibrosis” refers to a fibrotic condition in which the excess fibrous tissue will not resorb to a normal healthy state. In the context of the present disclosure, pathological fibrotic conditions include, but are not limited to, skin fibrotic conditions (e.g., hypertrophic scarring, keloids, delayed scarring, etc.) and auto-immune diseases (e.g., scleroderma, psoriasis). In some embodiments, a pathological increase in TGF-β activity causes or sustains cancer maintenance and/or progression by allowing or facilitating cancerous cellular migration (cancer metastasis).

(89) The expression: “prevention, treatment and alleviation of symptoms refer to the ability of the antagonists to limit the development, progression and/or symptomology of the pathological conditions described herein. When a skin fibrotic condition or an auto-immune disease is the pathological condition, the prevention, treatment and/or alleviation of symptoms can encompass the reduction of proliferation of cells (e.g., fibroblasts), the reduction in extracellular matrix production, the reduction in inflammation, and/or the increase in matrix degradation.

(90) When cancer is the pathological condition, the prevention, treatment and/or alleviation of symptoms can encompass the reduction of epithelial-mesenchymal transition of the cells, the reduction in the migration of the cells (which can include, in an embodiment, the reduction in the metastasis of the cells (number, size and/or location of the metastasis) and/or the reduction in the proliferation of the cells (e.g. by reducing the total number of cells in an hyperproliferative state and/or by reducing the pace of proliferation of cells). Symptoms associated with cancer include, but are not limited to: local symptoms which are associated with the site of the primary cancer (such as lumps or swelling (tumor), hemorrhage, ulceration and pain), metastatic symptoms which are associated to the spread of cancer to other locations in the body (such as enlarged lymph nodes, hepatomegaly, splenomegaly, pain, fracture of affected bones, and neurological symptoms) and systemic symptoms (such as weight loss, fatigue, excessive sweating, anemia and paraneoplastic phenomena). The peptidic TGF-β antagonists and/or their corresponding variants can be used to limit, reduce or inhibit epithelial-mesenchymal transition of cancer cells, invasion of cancer cells outside their tissue of origin, motility of cancer cells, limit/reduce the number and proliferation of cancer stem cells, the expression of fibronectin, and the expression of Slug and/or the migration of cancer cells.

(91) Hypertrophic scarring is a pervasive medical problem which often occurs as a result of burn, trauma, or surgical injury. Hypertrophic scarring is characterized by the formation of rigid scar tissue often resulting in significant functional impairment, leading to joint contractures, deformities, and central nervous system dysfunction. Keloid scars are thick, raised, itchy clusters of scar tissue that grow beyond the edges of a wound; they are more frequent in dark-skinned individuals and tend to recur. Hypertrophic scars are raised, red, thick scars that remains within the boundary of the injury. Keloid and hypertrophic scars result from local skin trauma or inflammatory skin disorders like lacerations, burns, skin piercing, surgery, etc.

(92) Scleroderma (also referred to as systemic sclerosis) is a connective tissue disorder characterized by excessive extracellular matrix (ECM) synthesis and deposition in the skin and internal organs, leading to organ dysfunction and failure. Other features of SSc include autoimmunity and inflammation, widespread vasculopathy (blood vessel damage) affecting multiple vascular beds and progressive interstitial and perivascular fibrosis. Depending on its location and extent, localized scleroderma may cause severe cosmetic problems as well as restricted joint motion secondary to contractures.

(93) Psoriasis is a common, chronic, relapsing/remitting, immune-mediated systemic disease characterized by skin lesions including red, scaly patches, papules, and plaques, which usually itch. The skin lesions seen in psoriasis may vary in severity from minor localized patches to complete body coverage. Psoriasis is also linked to cardiovascular diseases.

(94) Cancer, also referred to as a malignant neoplasm, is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. In the context of the present disclosure, the term “cancer” includes, but is not limited to, carcinoma, sarcoma, lymphoma, leukemia, germ cell tumor and blastoma.

(95) The peptidic TGF-β antagonists and their corresponding variants are intended to be administered in a “therapeutically effective amount”. The expression “therapeutically effective amount” refers to the amount of peptidic TGF-β antagonists and/or their corresponding variants, when administered to a mammalian subject for treating or preventing the particular disorders, diseases or conditions described above, is sufficient to effect such treatment or prevention of those disorders, diseases or conditions. Dosages and therapeutically effective amounts may vary for example, depending upon a variety of factors including the activity of the specific antagonist employed, the age, body weight, general health, gender, and diet of the mammalian subject, the time of administration, the route of administration, the rate of excretion, and any drug combination, if applicable, the effect which the practitioner desires the compound to have upon the subject and the properties of the compounds (e.g. bioavailability, stability, potency, toxicity, etc.), and the particular disorder(s) the mammalian subject is suffering from. In addition, the therapeutically effective amount may depend on the mammalian subject's skin condition (e.g. lightly or severely burned, presence of other skin injuries, etc.), the mammalian's cancer stage (e.g., I, II, III and IV), the severity of the disease state, or underlying disease or complications.

(96) The therapeutic uses and methods described herein can also include co-formulation and/or co-administration of at least one antagonists together with another therapeutically effective agent for the prevention and/or treatment of a pathological fibrotic disease or cancer. These other therapeutically effective agents can be administered prior to, at the same time or after the antagonists are administered to the mammalian subject. Examples of such therapeutic agents used for the treatment of pathological fibrosis include, but are not limited to, vitamin D analogs, interferon α and γ, methotrexate, penicillin, corticosteroids, immune suppressants, cyclosporine, anti-TNF antibodies, anti-infectives such as silver and iodine composition, ibuprofen and antibiotics. Examples of therapeutic agents used for the treatment of cancer include, but are not limited to, chemotherapeutic agents, radiation therapy, signaling pathway inhibitors, kinase inhibitors, gene expression blockers and modifiers.

(97) The therapeutic uses and methods described can be used before or after surgery (e.g., removal of a scar or tumor). The therapeutic uses and methods described can be used in conjunction with radiotherapy.

(98) The administration of the peptidic TGF-β antagonists and/or their variants can be conducted in a single unit dosage form with continuous therapy, in a single dose therapy ad libitum or as multiple doses.

(99) Methods for the Delivery of Exogenous Nucleic Acids to Cells

(100) Transfection Techniques

(101) Techniques that can be used to introduce a polynucleotide, such as nucleic acid encoding a TGF-β antagonist peptide describe herein, into a cell (e.g., a mammalian cell, such as a human cell) are well known in the art. Exemplary cells include, for instance, cells of a skin graft (such as fibroblasts, keratinocytes, Merkel cells, melanocytes, or Langerhans cells). By inducing expression of a TGF-β antagonist protein described herein in one or more cells of a skin graft, the graft may be administered to a patient, such as a patient suffering from a fibrotic skin condition, cancer, or burn described herein, so as to attenuate TGF-β expression and alleviate the disease or condition (or one or more symptoms associated with the disease or condition).

(102) For instance, electroporation can be used to permeabilize mammalian cells (e.g., human cells) by the application of an electrostatic potential to the cell of interest. Mammalian cells, such as human cells, subjected to an external electric field in this manner are subsequently predisposed to the uptake of exogenous nucleic acids. Electroporation of mammalian cells is described in detail, e.g., in Chu et al., Nucleic Acids Research 15:1311 (1987), the disclosure of which is incorporated herein by reference. A similar technique, Nucleofection™, utilizes an applied electric field in order to stimulate the uptake of exogenous polynucleotides into the nucleus of a eukaryotic cell. Nucleofection™ and protocols useful for performing this technique are described in detail, e.g., in Distler et al., Experimental Dermatology 14:315 (2005), as well as in US 2010/0317114, the disclosures of each of which are incorporated herein by reference.

(103) Additional techniques useful for the transfection of cells of interest include the squeeze-poration methodology. This technique induces the rapid mechanical deformation of cells in order to stimulate the uptake of exogenous DNA through membranous pores that form in response to the applied stress. This technology is advantageous in that a vector is not required for delivery of nucleic acids into a cell, such as a human cell. Squeeze-poration is described in detail, e.g., in Sharei et al., Journal of Visualized Experiments 81:e50980 (2013), the disclosure of which is incorporated herein by reference.

(104) Lipofection represents another technique useful for transfection of cells. This method involves the loading of nucleic acids into a liposome, which often presents cationic functional groups, such as quaternary or protonated amines, towards the liposome exterior. This promotes electrostatic interactions between the liposome and a cell due to the anionic nature of the cell membrane, which ultimately leads to uptake of the exogenous nucleic acids, for instance, by direct fusion of the liposome with the cell membrane or by endocytosis of the complex. Lipofection is described in detail, for instance, in U.S. Pat. No. 7,442,386, the disclosure of which is incorporated herein by reference. Similar techniques that exploit ionic interactions with the cell membrane to provoke the uptake of foreign nucleic acids include contacting a cell with a cationic polymer-nucleic acid complex. Exemplary cationic molecules that associate with polynucleotides so as to impart a positive charge favorable for interaction with the cell membrane include activated dendrimers (described, e.g., in Dennig, Topics in Current Chemistry 228:227 (2003), the disclosure of which is incorporated herein by reference) and diethylaminoethyl (DEAE)-dextran, the use of which as a transfection agent is described in detail, for instance, in Gulick et al., Current Protocols in Molecular Biology 40:1:9.2:9.2.1 (1997), the disclosure of which is incorporated herein by reference. Magnetic beads are another tool that can be used to transfect cells in a mild and efficient manner, as this methodology utilizes an applied magnetic field in order to direct the uptake of nucleic acids. This technology is described in detail, for instance, in US 2010/0227406, the disclosure of which is incorporated herein by reference.

(105) Another useful tool for inducing the uptake of exogenous nucleic acids by cells is laserfection, a technique that involves exposing a cell to electromagnetic radiation of a particular wavelength in order to gently permeabilize the cells and allow polynucleotides to penetrate the cell membrane. This technique is described in detail, e.g., in Rhodes et al., Methods in Cell Biology 82:309 (2007), the disclosure of which is incorporated herein by reference.

(106) Microvesicles represent another potential vehicle that can be used to modify the genome of a cell according to the methods described herein. For instance, microvesicles that have been induced by the co-overexpression of the glycoprotein VSV-G with, e.g., a genome-modifying protein, such as a nuclease, can be used to efficiently deliver proteins into a cell that subsequently catalyze the site-specific cleavage of an endogenous polynucleotide sequence so as to prepare the genome of the cell for the covalent incorporation of a polynucleotide of interest, such as a gene or regulatory sequence. The use of such vesicles, also referred to as Gesicles, for the genetic modification of eukaryotic cells is described in detail, e.g., in Quinn et al., Genetic Modification of Target Cells by Direct Delivery of Active Protein [abstract]. In: Methylation changes in early embryonic genes in cancer [abstract], in: Proceedings of the 18th Annual Meeting of the American Society of Gene and Cell Therapy; 2015 May 13, Abstract No. 122.

(107) Incorporation of Genes by Gene Editing Techniques

(108) In addition to the above, a variety of tools have been developed that can be used for the incorporation of exogenous genes, e.g., exogenous genes encoding a TGF-β antagonist peptide described herein, into cells, such as a human cell (e.g., fibroblasts, keratinocytes, Merkel cells, melanocytes, or Langerhans cells of a human skin graft). One such method that can be used for incorporating polynucleotides encoding a TGF-β antagonist described herein into cells involves the use of transposons. Transposons are polynucleotides that encode transposase enzymes and contain a polynucleotide sequence or gene of interest flanked by 5′ and 3′ excision sites. Once a transposon has been delivered into a cell, expression of the transposase gene commences and results in active enzymes that cleave the gene of interest from the transposon. This activity is mediated by the site-specific recognition of transposon excision sites by the transposase. In some instances, these excision sites may be terminal repeats or inverted terminal repeats. Once excised from the transposon, the gene encoding a TGF-β antagonist peptide can be integrated into the genome of a mammalian cell by transposase-catalyzed cleavage of similar excision sites that exist within the nuclear genome of the cell. This allows the gene of interest to be inserted into the cleaved nuclear DNA at the complementary excision sites, and subsequent covalent ligation of the phosphodiester bonds that join the gene encoding the TGF-β antagonist peptide to the DNA of the mammalian cell genome (e.g., fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell genome) completes the incorporation process. In some cases, the transposon may be a retrotransposon, such that the gene encoding the TGF-β antagonist peptide is first transcribed to an RNA product and then reverse-transcribed to DNA before incorporation in the mammalian cell genome. Exemplary transposon systems include the piggybac transposon (described in detail in, e.g., WO 2010/085699) and the sleeping beauty transposon (described in detail in, e.g., US 2005/0112764), the disclosures of each of which are incorporated herein by reference as they pertain to transposons for use in gene delivery to a cell of interest, such as a fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell.

(109) Another tool for the integration of genes encoding TGF-β antagonist peptides into the genome of a cell, such as a fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell, is the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, a system that originally evolved as an adaptive defense mechanism in bacteria and archaea against viral infection. The CRISPR/Cas system includes palindromic repeat sequences within plasmid DNA and an associated Cas9 nuclease. This ensemble of DNA and protein directs site specific DNA cleavage of a sequence of interest by first incorporating foreign DNA into CRISPR loci. Polynucleotides containing these foreign sequences and the repeat-spacer elements of the CRISPR locus are in turn transcribed in a host cell to create a guide RNA, which can subsequently anneal to a particular sequence and localize the Cas9 nuclease to this site. In this manner, highly site-specific cas9-mediated DNA cleavage can be engendered in a foreign polynucleotide because the interaction that brings cas9 within close proximity of the DNA molecule of interest is governed by RNA:DNA hybridization. As a result, one can theoretically design a CRISPR/Cas system to cleave any DNA molecule of interest. This technique has been exploited in order to edit eukaryotic genomes (Hwang et al., Nature Biotechnology 31:227 (2013)) and can be used as an efficient means of site-specifically editing cell genomes in order to cleave DNA prior to the incorporation of a gene encoding a gene. The use of CRISPR/Cas to modulate gene expression has been described in, for instance, U.S. Pat. No. 8,697,359, the disclosure of which is incorporated herein by reference as it pertains to the use of the CRISPR/Cas system for genome editing. Alternative methods for site-specifically cleaving genomic DNA prior to the incorporation of a gene of interest in a cell include the use of zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Unlike the CRISPR/Cas system, these enzymes do not contain a guiding polynucleotide to localize to a specific sequence. Sequence specificity is instead controlled by DNA binding domains within these enzymes. The use of ZFNs and TALENs in genome editing applications is described, e.g., in Urnov et al., Nature Reviews Genetics 11:636 (2010); and in Joung et al., Nature Reviews Molecular Cell Biology 14:49 (2013), the disclosure of each of which are incorporated herein by reference as they pertain to compositions and methods for genome editing.

(110) Additional genome editing techniques that can be used to incorporate polynucleotides encoding a TGFβ antagonist peptide into the genome of a cell of interest, such as a fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell, include the use of ARCUS™ meganucleases that can be rationally designed so as to site-specifically cleave genomic DNA. The use of these enzymes for the incorporation of genes encoding a TGF-β antagonist peptide into the genome of a mammalian cell (e.g., a human cell) is advantageous in view of the defined structure-activity relationships that have been established for such enzymes. Single chain meganucleases can be modified at certain amino acid positions in order to create nucleases that selectively cleave DNA at desired locations, enabling the site-specific incorporation of a gene of interest into the nuclear DNA of a cell, such as a fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell. These single-chain nucleases have been described extensively in, for example, U.S. Pat. Nos. 8,021,867 and 8,445,251, the disclosures of each of which are incorporated herein by reference as they pertain to compositions and methods for genome editing.

(111) Vectors for Delivery of Exogenous Nucleic Acids to Cells

(112) Viral Vectors for Nucleic Acid Delivery

(113) Viral genomes provide a rich source of vectors that can be used for the efficient delivery of exogenous genes encoding TGF-β antagonist peptides described herein into the genome of a cell (e.g., a mammalian cell, such as a human cell, e.g., a fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell). Viral genomes are particularly useful vectors for gene delivery because the polynucleotides contained within such genomes are typically incorporated into the genome of a cell by generalized or specialized transduction. These processes occur as part of the natural viral replication cycle, and do not require added proteins or reagents in order to induce gene integration. Examples of viral vectors include AAV, retrovirus, adenovirus (e.g., Ad5, Ad26, Ad34, Ad35, and Ad48), parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g. measles and Sendai), positive strand RNA viruses, such as picornavirus and alphavirus, and double stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, modified vaccinia Ankara (MVA), fowlpox and canarypox). Other viruses useful for delivering polynucleotides encoding TGF-β antagonist peptides described herein to a mammalian cell (e.g., a human cell, such as a fibroblast, keratinocyte, Merkel cell, melanocyte, or Langerhans cell) include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example. Examples of retroviruses include: avian leukosis-sarcoma, mammalian C-type, B-type viruses, D-type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996). Other examples include murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus and lentiviruses. Other examples of vectors are described, for example, in U.S. Pat. No. 5,801,030, the disclosure of which is incorporated herein by reference as it pertains to viral vectors for use in gene delivery.

EXAMPLES

(114) The following examples are put forth so as to provide those of ordinary skill in the art with a description of how the compositions and methods described herein may be used, made, and evaluated, and are intended to be purely exemplary of the invention and are not intended to limit the scope of what the inventor regards as her invention.

Example 1. Characterization of TGF-β Antagonistic Activity

(115) Cell Culture

(116) Cells were grown in Dulbecco's modified Eagle's medium (DMEM) High Glucose with L-Glutamine, 10% fetal bovine serum (FBS), 100 IU/mL penicillin, 100 pg/mL streptomycin. Cells were maintained at 37° C., 95% relative humidity, and 5% CO.sub.2.

(117) Aggregation assay. Soluble peptides were separated from aggregates and precipitates by filtration. The molecular weight cut-off of the filter was chosen such that soluble protein was allowed to pass through the filter, while aggregate forms were retained. Peptide X and P16 previously dissolved in 50 mM Tris-HCl (pH=7.0) were left untreated or treated with 0.5% dimethyl sulfoxide (DMSO) for 2 hours at 4° C. Soluble protein was then separated from aggregated protein using a Microcon™ concentrator (Millipore), with a molecular weight cut-off of 100 kDa. The Microcon was spun in a desktop centrifuge at 16,000×g for 15 min. Aggregated protein retained on the membrane was resuspended in H.sub.2O, pipetting repeatedly across the membrane to ensure that as much protein as possible was removed. Aliquots of soluble protein and aggregated protein were each mixed with 5× sample buffer (250 mM Tris-HCl, 40% glycerol, 140 mM SDS, 0.6 M β-mercaptoethanol, pH 6.8) and heated to 85-90° C. for 10 min prior to Tricine SDS-PAGE. Samples were analyzed by 17% Tricine SDS-PAGE and peptides visualized by silver staining.
Aggrescan Analysis

(118) Aggrescan is a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides [Conchillo-Sole et al. 2007, de Groot et al. 2012]. The website for this program is http://bioinf.uab.es/aggrescan and it is available to the public.

(119) Luciferase Assay

(120) Luciferase reporter assays were performed using a HEK293-(CAGA).sub.12 cell line that stably expresses a TGF-β/Smad3-responsive (CAGA).sub.12-luciferase reporter gene [Cash et al. 2013]. HEK293-(CAGA).sub.12 cells were grown in 24-well plates to 70-80% confluency and serum-starved overnight. Cells were washed with PBS and treated with or without TGF-β1 in presence or absence of various CD109-based peptides as indicated in the figure legends. Cells were then washed twice with cold PBS and solubilized in 100 μl of Passive Lysis Buffer (Promega) for 30 min at 4° C. The cell lysates were assayed for luciferase and β-galactosidase activities using commercially available kits (BD Biosciences).

(121) Western Blotting

(122) A431 cells were grown in 6-well plates to 70-80% confluency and serum-starved overnight. Cells were washed with PBS and treated with or without TGF-β1 in presence or absence of various CD109-based peptides as indicated in the figure legends. Cells were solubilized with 500 μl of lysis buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 50 mM NaF, 50 mM β-glycerophosphate, 1 mM sodium orthovanadate, 1 mM dithiothreitol, 5 mM EDTA, pH 8.0, 1% Nonidet P-40, 10% glycerol, 10 μM phenylmethylsulfonyl fluoride, 200 μg/ml bovine serum albumin, 1 μg/ml leupeptin, 10 pg/ml soybean trypsin inhibitor, 10 μg/ml benzamide, and 2 μg/ml pepstatin) for 30 min at 4° C. with mild agitation. Cell lysates were collected and centrifuged for 10 min at 10,000×g. The supernatants were collected and protein concentrations were determined using the Bio-Rad protein assay kit. Lysates containing equivalent protein concentrations were mixed with 0.2 volume of 5× electrophoresis sample buffer containing 5% β-mercaptoethanol and boiled for 5 min. Samples were resolved on 7.5% SDS-polyacrylamide gels and transferred to nitrocellulose membranes. Membranes were blocked for 3 h in blocking buffer (30 mM Tris, pH 7.5, 150 mM NaCl, and 0.05% (w/v) Tween 20™ (Tris-buffered saline/Tween) containing 5% (w/v) skim milk powder). The blot was incubated overnight at 4° C. with a 1:1000 dilution of anti-PAI-1 antibody (BD Biosciences). Blots were washed with Tris-buffered saline/Tween and incubated for 45 min at room temperature with a 1:5000 dilution of secondary antibody conjugated to horseradish peroxidase (Pierce). Chemiluminescence detection of the immune complexes was performed using the ECL system (Amersham Biosciences) according to the manufacturer's instructions. The membranes were stripped and reprobed with an anti-GAPDH antibody to confirm equal protein loading.

(123) TABLE-US-00003 TABLE 1 Characteristics of the peptides used Peptide Peptide Number (on SEQ Name Figure 3) Aggregation? Amino Acide Sequence ID NO: X 1 Aggregated LGSSPHVRKHFPETWIWLDTNMGSRIYQEFEVTVPDSITS 1 X-1 2 Aggregated ETWIWLDTNMGSRIYQEFEVTVPDSITS 2 A 3 Not aggregated TMENVVHELELTNTGYYLGMFMNSFAVFQECGL 3 WVLTDANLTKDYIDGVYDNAEYAERFMEENE GHIVDIHDFSLGSSPHVRKHPETWIWLDTNM GSRIYQEFEVTVPDSITSWVATGFVISEDLGLGL TTTPVELQAFQPFFIFLNLPSVIRGEEFAL P11 4 Not aggregated ETWIWLDTNMG 4 P16 5 Not aggregated ETWIWLDTNMGSRIYQ 5 P21 or X-2 6 Not aggregated ETWIWLDTNMGSRIYQEFEVT 6 P16-2 7 Not aggregated WINMDTGQLIEQRYTS 7 X-3 8 Aggregated LDTNMGSRIYQEFEVT 8 X-4 9 Not aggregated GSRIYQEFEVT 9 P16-1 Not tested Not tested ILNTWMDSTQIGYRWE 10 Y Not tested Not tested TMENVVHELELYNTGYYLGMFMNSFAVFQECGL 17 WVLTDANLTKDYIDGVYDNAEYAERFMEENE GHIVDIHDFSLGSSPHVRKHPETWIWLDTNMGSRIYQEFEVTVPDSITSWVATGFV Z Not tested Not tested LTKDYIDGVYDNAEYAERFMEENEGHIVIHDFSLG 18 SSPHVRKHFPETWIWLDTNMGSRIYQEFEV TVPDSITSWVATGFVISEDLGLGLTTTPVELQAFQPFFIFLNLPYSVIRGEEFAL B Not tested Not tested TMENVVHELELYNTGYYLGMFMNSFAVFQECGL 19 WVLTDANLTKDYIDGVYDNAEYAERFMEENE GHIVDIHDFSLGSSPHVRKHFPETWIWLDTNMGSRIYQEFEVT E Not tested Not tested LTKDYIDGVYDNAEYAERFMEENEGHIVDIHDFSL 20 GSSPHVRKHFPETWIWLDTNMGSRIYQEFEVTV
Peptide X but not Peptide P16 Exhibited Aggregation

(124) Peptide X (X, 40 amino acids) and P16 (16 amino acids) were left untreated (−) or treated with 0.5% DMSO (+) for 2 hrs at 4° C. The aggregated and non-aggregated (soluble) fractions were then separated using a Microcon centrifugal filtration device (Millipore), with a molecular weight cut-off of 100 kDa. This device allows passage of molecules less than 100 kDa through the filter but retains larger molecules (aggregates). The aggregated and soluble fractions were then separated by 17% Tricine-SDS gel electrophoresis and peptides visualized by silver staining. As shown in FIG. 1, multiple bands with various staining intensities were detected in the peptide X aggregated fraction and the intensities of two of these bands were decreased by 0.5% DMSO treatment (FIG. 1A, arrows) which was associated with an increase in the amount of soluble peptide X (FIG. 1B, arrow). In contrast, P16 displayed only a few bands of low staining intensity in the aggregation fractions indicating that this peptide aggregated only to a minor extent. The data presented in FIG. 1 suggests that peptide X existed predominantly in aggregated form and that peptide X aggregation was partially decreased by DMSO treatment leading to an increase in soluble peptide X.

(125) In Silico Analysis of Peptide X Aggregation Propensity and the Design of Aggregation-Free Small Molecular Weight CD109-Based Peptides

(126) As shown in FIG. 2A, Aggrescan analysis of peptide X identified amino acids at position 13 to 18 (ETWIWL, SEQ ID NO: 11) as an aggregation-prone sequence in the 40 amino acid peptide. Importantly, this sequence was identified as part of the putative TGF-β binding domain. Definition of terms: #=position of the amino acid in peptide X (i.e. #1-40); ‘AA’=identity of the amino acid (single letter nomenclature); ‘a4v’=intrinsic aggregation propensity of each amino acid residue; Hot Spot Area (HSA)=the area of the AP graph, above the hot spot threshold (HST), of a given HS calculated with trapezoidal integration (data not shown). Normalized Hot Spot Area (NHSA) value was calculated as the HSA divided by the number of residues in the input amino acid sequence. α4v average in the Hot Spot (a4vAHS)=a4v average in a given HS.

(127) To design a small molecular weight CD109-based peptide containing the TGF-β binding domain and at the same time having a low propensity for self-aggregation, a series of N- and C-terminal deletions of peptide X were tested to determine whether removing any of these amino acids would alter aggregation properties. Deletion of 1-22 amino acids from the C-terminus of peptide X yielded sequences that were predicted to contain the same aggregation prone segment (ETWIWL, SEQ ID NO: 11) whereas deletion of exactly 12 amino acids from the N-terminus of peptide X gave a 28 amino acid sequence (X-1) that contained the ETWIWL segment but was predicted to have a low propensity to aggregate (‘aggregation-free’). Using X-1 as a starting point, a series of smaller peptides were designed by further deleting N- and/or C-terminal amino acids of X-1 (X-2, X-3, X-4, P16, P11) to determine the minimum sequence required produce an aggregation-free peptide that inhibited TGF-β-signaling (see FIG. 2B). The peptides were analyzed for aggregation by size-exclusion chromatography (see below, FIGS. 3-4) and tested for TGF-β-inhibitory activity in cell-based assays (see below, FIGS. 5-9).

(128) Size-exclusion chromatography of small molecular weight CD109-based peptides indicated that peptide X, X-1 and X-3 formed aggregates whereas P21, P16, P16-2 (control), P11 and X-4 did not (FIG. 3). More specifically, approximately 200 pg of each peptide X (40 amino acids), X-1 (28 amino acids), peptide A (161 amino acids), P11 (11 amino acids), P16 (16 amino acids), P21 (21 amino acids, P16-2 (16 amino acids, scrambled sequence control), X-3 (16 amino acids) and X-4 (11 amino acids) were dissolved in phosphate-buffered saline (PBS) and loaded onto a Superdex Peptide 10/300GL column. The column was eluted with PBS at a flow rate of 0.6 ml/min and eluants were analyzed for peptide content by measuring relative absorbance at a wavelength of 215 nM. The data were plotted with relative absorbance (Y-axis) against elution volume (X-axis). As shown in FIG. 3, peptide X (peptide 1) elution profile indicated two major peaks at approximately 8 mL and 11 mL which correspond to molecular weights greater than 12.4 kDa. The theoretical molecular weight of peptide X is 4.7 kDa which is expected to elute from the column at approximately 15 mL. These results suggest that peptide X existed as high molecular weight aggregates with minimal soluble (monomeric) form under these conditions. P16 (peptide 5) elution profile indicated a peak between 14-22 mL which was expected to contain peptides of between 0.1 and 6 kDa and is consistent with its theoretical molecular weight of 2.01 kDa. A summary of findings for the remaining peptides analyzed in the top and middle panels is provided in Table 1.

(129) The elution pattern of molecular weight standards in size exclusion chromatography is shown in FIG. 4. More specifically, a pool of standard proteins of various molecular weights were subjected to size-exclusion chromatography using the Superdex Peptide 10/300 GL column. The resulting chromatogram indicated the elution profiles of the peptides with high molecular weight peptides eluting in earlier fractions and lower molecular weight peptides eluting in later fractions as expected. The molecular weights of peptides were plotted against elution volume generating a standard curve (not shown) and was used to calculate molecular weights of the CD109-based peptides. The identity of the peptides, their molecular weights and conditions of the analysis are indicated in the bottom panel.

(130) Small Molecular Weight CD109-Based Peptides with Low Propensity to Aggregate Inhibited TGF-β1-Induced Transcriptional (Smad3-Driven CAGA.sub.12-Lux) Activity

(131) HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of 10 nM (FIG. 5A) or 5 nM (FIG. 5B) of peptide A (Pep A, 161 aa), P28 (28 aa peptide), P21 (21 aa peptide), P16 (16 aa peptide), P16.2 scrambled peptide (16 aa, scrambled P16 sequence) or Tris-buffer (negative control for peptides) as indicated. In summary, Peptide A, P28 (X-1), P21 (X-2) and P16 inhibited TGF-β1-induced CAGA.sub.12-lux activity. Tris buffer alone had no effect indicating that the inhibitory activity of Pep A, P21 and P16 were mediated by the peptides themselves and not from the buffer (Tris) in which they were dissolved. The scrambled peptide (P16.2) also had no inhibitory effect indicating that the inhibitory effect of P16 (and Pep A, P28 and P21) was mediated in a sequence specific manner and was not due to amino acid composition or charge of the peptides.

(132) Small Molecular Weight CD109-Based Peptide P16, but not P11 or X-4, Inhibited TGF-β1-Induced Smad3-Driven (CAGA.sub.12-Lux) Transcriptional Activity

(133) HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of 10 nM of P16-2 (16 aa, scrambled P16 sequence), P11 (11 aa peptide), P16 (16 aa peptide), X-4 (11 aa peptide) or Tris-buffer (negative control for peptides) as indicated. As shown in FIG. 6, P16 inhibited TGF-β1-induced CAGA.sub.12-lux activity and P11 and X-4 did not. Tris buffer alone had no effect indicating that the inhibitory activity of Pep A, P21 and P16 were mediated by the peptides themselves and not from the buffer (Tris) in which they were dissolved. P16-2 (scrambled peptide control) also had no effect indicating that the inhibitory effect of P16 was mediated in a sequence specific manner and was not due to amino acid composition or charge of the peptide.

(134) Small Molecular Weight Aggregation-Free CD109-Based Peptide P16 (but not P11 or P16-1 Scrambled Control) Inhibited TGF-β1-Induced PAI-Protein Production

(135) A431 cells were treated without (lane 1) or with 100 pM of TGF-β1 (lanes 2-6) in the absence (lane 2) or presence of 10 nM of P11 (11 aa peptide, lane 3), P16 (16 aa peptide, lane 4), P16-1 (scrambled peptide of 16 aa, lane 5) or Tris buffer (buffer, lane 6) for 24 hrs. Cell lysates were analyzed by Western blot for PAI-1 (protein activator inhibitor-1) protein levels and normalized to GAPDH protein levels (loading control). As shown in FIG. 7, P16 (but not P11) inhibited TGF-β1-induced PAI-1 protein production. Tris buffer alone had no effect indicating that the inhibitory effect of P16 was mediated by the peptide itself and not due to the buffer in which it was dissolved. Scrambled P16-1 control peptide also had no effect indicated that the inhibitory effect of P16 was mediated in a sequence specific manner and was not due to amino acid composition or charge of the peptide. GAPDH levels were similar for all samples indicating that equal amounts of protein were loaded in each lane.

(136) DMSO Treatment Enhanced the TGF-β Inhibitory Activity of Peptide X, but not of P21 or P16

(137) HEK293 cells stably transfected with the Smad3-responsive CAGA.sub.12-lux luciferase reporter were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of Peptide X (PX), P21 or P16. The peptides were previously dissolved in Tris buffer and left untreated or treated with 0.5% DMSO prior to their addition to the cells. Tris buffer and 0.5% DMSO alone served as additional controls. As shown on FIG. 8, Peptide X pre-treated with 0.5% DMSO inhibited TGF-β1-induced CAGA.sub.12-lux activity whereas Peptide X left untreated (Tris buffer only) did not. P16 and P21 inhibited TGF-β1-induced CAGA.sub.12-lux activity and these effects were not enhanced by DMSO treatment. DMSO alone had no effect on TGF-β1-induced CAGA.sub.12-lux activity indicating that the inhibition of DMSO-treated peptide X is due to the peptide itself and not due to DMSO. Tris buffer alone had no effect on TGF-β1-induced CAGA.sub.12-lux activity indicating that the inhibitory effect of P21 and P16 were mediated by the peptides themselves and not from the buffer (Tris) in which they were dissolved.

(138) DMSO Treatment Enhanced the TGF-β Inhibitory Activity of Peptide X, but not of P16

(139) A431 squamous cell carcinoma cells were treated for 18 hours without (−) or with (+) 100 pM TGF-β1 in the presence or absence of Peptide X or P16. The peptides were dissolved in Tris buffer and left untreated or treated with 0.5% DMSO prior to addition to the cells. Cell lysates were analyzed by Western blot for PAI-1 (protein activator inhibitor-1) protein expression (top panel) and GAPDH served as a loading control (bottom panel). As shown in FIG. 9, PAI-1 was not detected in untreated cells (lane 1). TGF-β1 treatment increased PAI-1 production in A431 cells (lane 2 versus lane 1). Peptide X treated with DMSO inhibited TGF-β1-induced PAI-1 protein production whereas peptide X left untreated (in Tris) did not (compare lanes 4, 3 and 2). P16 inhibited TGF-β1-induced PAI-1 protein production and pre-treating the peptide with DMSO did not enhance its inhibitory effect (compare lanes 6, 5 and 2).

(140) The results shown in FIG. 9 also showed that the peptides inhibit PAI-1 production in A431 squamous cell carcinoma cells. Upregulation of PAI-1 production is an indicator of cancer cell migration and invasion.

(141) The results presented in this example indicate that the design of a small molecular weight CD109-based peptide (P16, 16 amino acids) that contains the putative TGF-β binding region of CD109 and inhibits TGF-β signaling cannot be deduced solely on the basis of previous knowledge of sequence information for Peptide A (described in U.S. Pat. No. 7,173,002). Further, results showing that peptide X (in the absence of DMSO treatment) could not inhibit TGF-β signaling were unexpected since peptide X was obtained from N- and C-terminal deletion regions from peptide A and retained the putative TGF-β binding region. In the present example, it is shown that peptide X aggregated in solution and failed to inhibit TGF-β signaling in cell-based assays unless its aggregation is decreased by DMSO treatment. Although treatment with DMSO partially reduces peptide X aggregation and confers it with TGF-β-inhibitory activity, a vast majority of peptide X remains in aggregated form. Using a combination of in silico aggregation analysis together with physicochemical and functional analysis, the problem of peptide aggregation was overcome and resulted in the identification of a novel CD109-based peptide of 16 amino acids (P16) that does not aggregate in solution, retains the putative TGF-β binding region and potently inhibits TGF-β signaling in vitro.

Example 2. Cancer Cell Migration Assay

(142) Material and Methods

(143) Squamous cell carcinoma (A431) or breast cancer (MDA-MB-231) cells were grown to 80-90% confluence and serum-starved overnight. The next day, cells were scratched with a plastic pipette tip (time 0 hour) and then left untreated or treated for 24 hours with 100 pM TGF-β1 alone or in the presence of 10 nM peptide B (100 aa), E (67 aa), or X1 (P28, 28 aa). Digital images were captured at 0 h and 24 h (20× magnification) using an EVOS XL Core microscope.

(144) Cell migration is a process central to the development of multicellular structures. It involves the movement of cells from their site of origin to a new cell site in response to physical and biochemical signals. Cell migration is involved in the invasion of cancer cells into surrounding tissue and the vasculature in the initial step in tumor metastasis. We examined the effect of various CD109-based peptides on cell migration in squamous cell carcinoma (A431) and breast cancer (MDA-MB-231) cells using scratch assay. Results presented in FIGS. 10A and 10B and FIGS. 11A and 11B indicated that peptides B, E and X1/P28 inhibited TGF-β-induced migration in these cells. These results suggested that small molecular weight CD109-based may have application for the treatment of cancer metastasis.

Example 3. The Role of CD109 in the Epithelial-Mesenchymal Transition

(145) Cancer Profiling Array

(146) The expression of CD109 in vulvar squamous cell carcinoma was determined using a Cancer Profiling Array™ (BD BiosciencesClontech, Mississauga, ON, Canada). The Cancer Profiling Array II was hybridized with a .sup.32P-labeled CD109 cDNA probe. Prehybridization, hybridization, and detection were performed using BD Express Hyb™ Solution (BD Biosciences/Clontech) according to the manufacturer's instructions.

(147) Cell Lines

(148) HaCaT clones and A431 cells stably expressing CD109 (or its empty vector, EV) were generated as described in Bizet et al., 2011. The highly differentiated and highly tumorigenic epidermal squamous cell carcinoma SCC-1327 were cultured in Keratinocyte Serum-free Media supplemented with 30 pg/ml Bovine Pituitary Extract, 0.1 ng/ml of recombinant EGF (Invitrogen Carlsbad, Calif., USA) and 100 U/ml penicillin and 50 pg/ml streptomycin.

(149) siRNA transfections. HaCaT, A431 and SCC-13 cells were transfected with CD109 siRNA (ID #129083) or a negative control siRNA (ID #4611) (Ambion, Austin, Tex., USA) using Lipofectamine 2000™ (Invitrogen) according to the manufacturer's instructions. Western blot. Western blot analyses were conducted with the following antibodies: mouse monoclonal anti-CD109, anti-fibronectin (both from BD Biosciences), and anti-p-actin (C4) antibodies (Santa Cruz Biotechnology), rabbit polyclonal anti-p44/42 MAPK (ERK), anti-p38 MAPK, anti-phospho-p38 MAPK (Thr180/Tyr182) and rabbit monoclonal anti-phospho p44/42 MAPK (Thr202/Tyr204), anti-Slug (C19G7) (all from Cell Signaling Technologies, Danvers, Mass., USA).
Immunofluorescence Microscopy

(150) Cells were treated with 0-100 pM TGF-β1, in the presence or absence of 10 μM U0126 (Cell signaling Technologies), 1 μM SB203580, 0.5 μM SB431542 (both from Ascent) for 36-40 hrs. Cells were fixed with 4% paraformaldehyde for 10 min at 37° C. and non-specific sites were blocked with 10% NGS, 0.1% Triton X-100 in PBS. E-cadherin was detected using a FITC-conjugated anti-E-cadherin antibody (BD Biosciences), followed by an AlexaFluor488™-conjugated anti-FITC antibody (Molecular Probes). F-actin was detected using Rhodamin-conjugated phalloidin (Cytoskeleton, Denvers, Colo.) and nuclei were stained with DAPI (Sigma Aldrich). Images were acquired with an Olympus BX60 fluorescent microscope coupled to a QColor3™ camera (Olympus) using Image ProPlus™ 6.0 software.

(151) Scratch Assay

(152) Confluent monolayers of HaCaT or A431 cells were wounded by scrapping the cells with a 200 μl pipette tip. Cells were then incubated with 100 pM TGF-β1, in presence or absence of 10 μM U0126, 1 μM SB203580, 0.5 μM SB431542 in serum free medium for 24-48 hrs. Pictures were taken at the same spot at 0 hr, 24 hrs and 48 hrs. The cell-free area (wound) area was measured using ImageJ™ software and the percentage of original wound area filled with keratinocytes was calculated. At least 3 independents series of experiments were performed in triplicates.

(153) Matrigel™ Invasion Assay

(154) The BD BioCoat Matrigel™ Cell Culture Inserts (BD Biosciences, USA) were used for invasion assays. Briefly, the control inserts or Matrigel™-coated inserts were rehydrated with plain DMEM for 2 hrs before use. These were then filled with cells after transfection and recovery (5×10.sup.4 cells in 0.5 ml of DMEM), and placed in a well of a 24-well plate. At 22 hrs after incubation the cells on the upper side of the filters were removed with cotton-tipped swabs. Migrated and/or invaded cells on the lower side of the filters were fixed and stained with 0.05% Crystal Violet. The cells on the underside of the filters were viewed under a microscope and counted.

(155) Statistical Methods

(156) Numerical results are represented as means of n independent experiments±SEM. A two-tailed Student t test was used to determine statistical significance between two groups. Comparisons within more than two groups were made by Holm-Sidak test following one-way ANOVA using SigmaSTAT.

(157) CD109 expression is decreased in late stage vulvar squamous cell carcinoma. To assess the expression of CD109 in squamous cell carcinoma, the expression of CD109 mRNA in late stage vulvar squamous cell carcinoma was analyzed using a cancer profiling array. As shown in FIG. 12A, CD109 expression is decreased in 5 out of 5 tumors of vulvar squamous cell carcinoma as compared to the corresponding adjacent normal skin tissue.

(158) CD109 Inhibits TGF-β-Induced Epithelial-Mesenchymal Transition

(159) It was previously shown that CD109 is an inhibitor of TGF-β signaling and responses in skin cells, the role of CD109 in regulating TGF-β-induced EMT was investigated, by first looking at two different markers: the appearance of actin stress fibers and the disappearance of E-cadherin from the membrane. HaCaT cells stably overexpressing CD109 show a marked decrease in actin stress fibers formation upon TGF-β treatment (the actin filament appears more cortical) as compared to EV transfected cells (FIGS. 13A and 13G). Quantification of F-actin staining intensity demonstrates that the effect of CD109 on TGF-β-induced actin stress fibers formation is statistically significant (p<0.05) (FIG. 13G). In addition, HaCaT cells overexpressing CD109 also display a decrease in TGF-β-induced loss of membrane E-cadherin, as compared to EV transfected cells (FIG. 13A).

(160) Similarly, knock-down of CD109 expression in HaCaT cells results in a significant (p<0.05) increase of actin stress fibers appearance and an increase of membrane E-cadherin delocalization upon TGF-β treatment, as compared to control siRNA transfected cells (FIGS. 13B and 13H). This result indicates that, in human non-tumorigenic keratinocytes, CD109 can inhibit some of the characteristics of TGF-β-induced EMT.

(161) It was then examined whether CD109 inhibits TGF-β-induced EMT in tumorigenic cell lines, the A431 and SCC-13, which both derived from epidermal squamous cell carcinomas (FIGS. 13C, 13I, 13D, 13J, 20A and 20C). As observed in HaCaT cells, A431 cells stably overexpressing CD109 display less actin stress fibers and reduced loss of membrane E-cadherin after TGF-β treatment as compared to EV transfected cells (FIGS. 13C and 13I). Moreover, A431 and SCC-13 cells transfected with CD109 siRNA show more actin stress fibers (p<0.05) and a more cytoplasmic localization of E-cadherin, than in control siRNA transfected cells after TGF-β treatment (FIGS. 13D, 13J and 19A). These results suggest that exogenous and endogenous CD109 is able to inhibit TGF-β-induced EMT in SCC-derived cells.

(162) Consistent with CD109's ability to inhibit TGF-β-induced EMT, it was shown that CD109 is also able to decrease TGF-β-induced fibronectin expression, in HaCaT cells as well as in SCC cells (FIGS. 20A-20C). Collectively, these results indicate that CD109 is able to inhibit several key features of TGF-β-induced EMT, including production of ECM components, such as fibronectin.

(163) CD109 Inhibits TGF-β-Induced Slug Expression.

(164) Because TGF-β can promote the expression of the transcription factor Slug, that initiates EMT and acts as master regulator of the EMT process, it was determined whether CD109 affects TGF-β-induced Slug expression. Transfection of HaCaT and SCC-13 cells with CD109 siRNA increases TGF-β-induced Slug expression, as compared to control siRNA transfected cells (FIGS. 13E and 19B). In addition, overexpression of CD109 in A431 cells reduces the level of Slug expression, as compared to EV transfection (FIG. 13F). Altogether, these results imply that CD109 can reduce TGF-β-induced Slug expression and this may contribute to inhibition of TGF-β-induced EMT by CD109.

(165) CD109 Inhibits Cell Migration in HaCaT and SCC Cell Lines.

(166) Cells undergoing EMT display enhanced migratory capacity. Thus, in vitro wound healing (scratch) assays were performed to evaluate the role of CD109 in regulating TGF-β-induced cell migration. Results shown in FIGS. 14A-14H demonstrate that TGF-β treatment in HaCaT and A431 cells decreases the wounded area 24 hrs post wounding, as compared to cells left untreated, which is consistent with TGF-β's ability to promote cell migration. Importantly, HaCaT cells stably overexpressing CD109 display a less migratory phenotype, in the absence and in the presence of TGF-β, as compared to EV transfected cells (FIGS. 14A and 14E). This result confirms previous observation showing that CD109S, a shorter, placental version of CD109, inhibits migration of HaCaT cells. The effect of CD109 on cell migration in the absence of TGF-β treatment might be due to inhibition of autocrine TGF-β signaling. The reduction in wound gap closure observed in CD109 overexpressing cells is not the result of reduced cell growth, since CD109 enhances cell proliferation.

(167) In addition, knock-down of CD109 expression enhances TGF-β-induced “wound” closure, as compared to control siRNA transfected cells (FIGS. 14B and 14F), indicating that endogenous CD109 is able to inhibit TGF-β-induced migration.

(168) Moreover, CD109 overexpression inhibits TGF-β-induced migration of A431 cells (FIGS. 14C and 14G) while knock-down of CD109 increases migration (FIGS. 14D and 14H).

(169) Together, these results suggest that CD109 can decrease the migration rate of SCC cells in response to TGF-β and is consistent with a decrease in TGF-β-induced EMT.

(170) CD109 Inhibits Cell Invasion in A431 SCC Cells

(171) In the transwell Matrigel™ invasion assay, as shown in FIG. 15A, TGF-β treatment of A431 cells resulted in increased invasion of these cells. However, A431 cells over expressing CD109 when treated with TGF-β show reduced invasion as compared to empty vector transfected cells. In addition, knockdown of CD109 in A431 cells increases TGF-β mediated invasion compared to control siRNA transfected cells as shown in FIG. 15B. These results suggest that CD109 can decrease the invasion of SCC cells in response to TGF-β.CD109's effects on EMT involves both SMAD and MAPK pathways.

(172) Several studies indicate an important role for both SMAD2/3 and p38 and ERK MAPK pathways in TGF-β-induced EMT. To investigate whether CD109's ability to inhibit TGF-β-induced EMT involves the SMAD or the MAPK pathway, three different inhibitors were used: SB431542, an inhibitor of TGFBR1 shown to inhibit the SMAD2/3 pathway; U0126, an inhibitor of the ERK1/2 pathway and SB203580, an inhibitor of p38 MAPK at concentrations that specifically blocks their respective pathways (FIG. 22) and examined the involvement of each pathway in CD109's ability to inhibit EMT. Treatment with SB431542, U0126 and SB203580 had no effect in the absence of TGF-β (data not shown). Importantly, SB431542, U0126 or SB203580 treatment in the presence of TGF-β reduces (but does not abrogate) the effect mediated by CD109 siRNA transfection on actin stress fibers appearance and relocalization of E-cadherin (FIGS. 16A and B). These findings suggest that, when CD109 levels are reduced, TGF-β induces EMT at least via the SMAD2/3, ERK and p38 pathways. In control siRNA transfected cells, SB431542 totally prevents the appearance of actin stress fibers (FIGS. 16A and B), suggesting that the SMAD2/3 pathway is the principal pathway mediating EMT in these cells. Interestingly, the combination of SB431542+U0126, SB431542+SB203580 totally abrogates the TGF-β-induced appearance of actin stress fibers and relocalization of membrane E-cadherin in both CD109 siRNA and control siRNA transfected cells (FIGS. 16A and B), suggesting that the SMAD and MAPK pathways may cooperate to promote TGF-β-induced EMT. Together, these results suggest that, when CD109 expression is reduced, TGF-β mediates its effect on EMT via both SMAD and MAPK pathways.

(173) Next, the role of the SMAD2/3 and MAPK pathways was examined in CD109's effect on fibronectin and Slug expression. Knock-down of CD109 using siRNA in HaCaT cells dramatically increases TGF-β-induced fibronectin expression (FIGS. 17A and 17C). Fibronectin production is totally abrogated by SB431542 treatment and is reduced by SB203580 and U0126 treatment, suggesting that p38 and ERK participate to a much lesser extent than the SMAD2/3 pathway, in fibronectin production (FIGS. 17A and 17C).

(174) In contrast, the effect of CD109 knock-down on TGF-β-induced Slug expression is abrogated by SB431542 and U0126 treatment, suggesting that SMAD2/3 and ERK contribute to the elevation of Slug expression mediated by CD109 siRNA (FIGS. 17B and 17D). Surprisingly, SB203580 treatment in the absence (data not shown) or in the presence of TGF-β (FIGS. 17B and 17D) increases Slug expression in HaCaT cells transfected with control siRNA and CD109 siRNA transfected cells, suggesting that p38 may inhibit Slug expression in HaCaT cells.

(175) CD109's Effects on Migration Involves Both SMAD and MAPK Pathways

(176) Finally, it was determined whether CD109's effect on migration was also mediated by the SMAD2/3 and MAPK pathways. Knock-down of CD109 increases cell migration, in the presence of TGF-β (FIGS. 18A and B). This increase is partially reversed by SB431542 and U0126 treatment and to a much lesser extent by SB203580 (FIGS. 18A and B). The combination of SMAD2/3 with MAPK inhibitors (SB431542+U0126 or SB431542+SB203580) totally blocks the effect of CD109 siRNA on TGF-β-induced migration (FIGS. 18A and B), suggesting that the MAPK pathways cross-talk with the SMAD2/3 pathway to modulate cell migration. Collectively, these results suggest that CD109 negatively regulates TGF-β-induced cell migration via the SMAD2/3 and MAPK pathways.

(177) CD109 Modulates TGF-β-Induced MAPK Phosphorylation

(178) The results presented so far suggested that CD109 could not only negatively regulate SMAD2/3 signaling in keratinocytes, but also could modulate non-canonical pathways, notably p38 and ERK1/2 MAPK pathways. Thus, CD109's ability to regulate TGF-β-induced p38 and ERK 1/2 phosphorylation was investigated. Treatment of HaCaT cells with 15 pM of TGF-β1 results in rapid phosphorylation of p38 and ERK1/2 (FIG. 19A). Interestingly, knock-down of CD109 leads to a decrease in TGF-β-induced p38 phosphorylation and an increase in TGF-β-induced ERK 1/2 phosphorylation, especially at early (10 min to 1 hr) time points (FIG. 19A). In addition, examination of TGF-β dose response demonstrates that CD109 siRNA transfection decreases p38 phosphorylation (FIG. 19B) and increases ERK phosphorylation (FIG. 19C) at all dose of TGF-β tested, as compared to control siRNA transfection. No change in the levels of total ERK and total p38 were observed. Together, these results indicated that endogenous CD109 is able to promote TGF-β-induced p38 activation while inhibiting TGF-β-induced activation of ERK pathway in HaCaT cells.

(179) Next, CD109's ability to modulate TGF-β-induced MAPK pathways in SCC cell lines was studied. Similar to what was observed in HaCaT cells, CD109 siRNA transfection reduces TGF-β-induced p38 phosphorylation and enhances TGF-β-induced ERK phosphorylation in both A431 (FIGS. 19D and E) and SCC-13 cells (FIGS. 23A and B), as compared to negative control siRNA transfection. Collectively, the results suggested that CD109 is able to inhibit TGF-β-induced SMAD and ERK 1/2 pathways, but promotes TGF-β-induced p38 MAPK pathway in human keratinocytes and in SCC-derived cells.

(180) CD109's Effects on TGF-β-Induced MAPK Activation Involve the Caveolae

(181) Localization of the TGF-β receptors to the caveolar compartment has been implicated in MAPK activation. Because it was previously shown that CD109 promotes the localization of the TGF-β receptors to the caveolae, it was investigated whether CD109's ability to regulate TGF-β-induced p38 and ERK phosphorylation requires the caveolar pathway. Consistent with the above results, overexpression of CD109 in HaCaT cells leads to a reduction in TGF-β-induced ERK phosphorylation and an increase in TGF-β-induced p38 phosphorylation, as compared to EV transfected cells (FIG. 19F). Importantly, the effect of CD109 on ERK and p38 activation is abrogated by caveolin-1 siRNA transfection (FIG. 19F), suggesting that CD109, by promoting TGF-β receptor localization to the caveolae, is able to regulate TGF-β-induced MAPK activation.

(182) CD109 Expression is Deregulated in Many Types of Human Cancers, Particularly in SCCs

(183) The expression of CD109 has been found to be significantly higher in cervical SCCs as compared to endometrial adenocarcinomas and normal cervix and endometrium. CD109 is also more frequently expressed in lung SCC compared with other types of lung carcinomas. In addition, CD109 expression was shown to be up regulated in head and neck SCCs (HNSCCs) and pre-malignant lesions of the oral cavity, but not in normal squamous epithelia. CD109 expression was found to be higher in low grade and non-muscle invasive urothelial carcinoma and associated with better prognosis. In oral squamous cell carcinoma, CD109 expression was found to be higher in well differentiated SCCs compared to moderately and poorly differentiated SCCs. In colorectal cancer, CD109 was shown to be mutated at significant frequency and the CD109 promoter showed higher frequency of methylation as compared to normal healthy subjects.

(184) In the present study, it was found that CD109 expression was down regulated in 5 out of 5 tumors of late stage vulvar carcinoma compared to adjacent normal tissues. These results corroborate with previous findings which also observed decreased expression of CD109 in poorly differentiated vulvar tumors compared to well and moderately differentiated tumors.

(185) It was previously shown that CD109 is a TGF-β co-receptor that inhibits SMAD2/3 pathway, promotes the localization of TGF-β receptor in caveolae and enhances their degradation mediated by SMAD7 and Smurf2. Because TGF-β is a potent inducer of EMT, a program leading to the escape of cancer cells from solid tumors to form metastasis, it was sought to determine whether CD109 could regulate TGF-β-induced EMT in SCC-derived cell lines. In the present example, it was demonstrated that CD109 negatively regulates key features of TGF-β-induced EMT: CD109 inhibited the TGF-β-induced appearance of actin stress fibers, the relocalization of cell-cell adhesion molecule E-cadherin, decreased ECM production and the expression of the initiator of EMT Slug and inhibited TGF-β-induced cell migration, in both HaCaT and SCC derived cell lines. Using specific inhibitors, it was shown that CD109 mediated its diverse effects on TGF-β-induced EMT via both the SMAD2/3 and p38 and ERK1/2 MAPK pathways. Finally, the results indicated that CD109 was able to increase TGF-β-induced p38 phosphorylation, while reducing ERK1/2 activation, probably by targeting the receptor localization to the caveolae. CD109 regulated both TGF-β canonical and non-canonical signaling pathways to inhibit TGF-β-induced EMT.

(186) The results presented herein indicated that CD109 reduced TGF-β-induced SMAD2/3 and ERK1/2 phosphorylation, but increased TGF-β-induced p38 phosphorylation levels. CD109-mediated reduction of ERK1/2 activation levels and CD109's ability to inhibit EMT are consistent with ERK's involvement in cytoskeleton remodeling, disassembly of cell adherent junction and cell motility. The function of ERK and p38 MAPK highly depends on the duration, strength of the signal and on their location. Consistent with previous results demonstrating that CD109 promoted the localization of TGF-β receptor into lipid raft/caveolae and that TGF-β-induced MAPK activation occurred in lipid raft, the results suggest that activation of p38 and downregulation of ERK by CD109 likely occurred in caveolae. It is thus possible that the function of these MAPKs in caveolae differs from their function in other cell compartments, as they may not interact with the same partners.

(187) The result suggested that p38 activation decreases Slug expression, thus CD109, by increasing TGF-β-induced p38 activation may further decrease Slug expression and EMT. While inhibition of p38 pathway increased Slug expression, it is not associated with a reduction of E-cadherin expression, as evidence by immunofluorescence. One possible explanation is that p38 pathway inhibited Slug expression in these cells, but differentially affected other transcription factors, such as Snail and Twist, whose function are known to overlap with Slug's. Interestingly, inhibition of the p38 pathway has only a minor effect on actin stress fibers appearance, E-cadherin relocalization, cell migration and fibronectin expression. This suggests that the increased activation of p38 by CD109 is not directly involved in CD109's inhibition of EMT. In contrast, the effect of CD109 is totally abrogated when SB203580 is used in combination with SMAD2/3 inhibitor, indicating the existence of a cross-talk between the different pathways. Indeed, MAPKs can phosphorylate the SMAD on their linker region to regulate their transcriptional activity. MAPK can also activate transcription factors that synergize or antagonize SMADs function.

(188) Our results show that CD109 inhibited several features of EMT induced by TGF-β. The ability of TGF-β to mediate an EMT-like phenotype (or partial EMT) in HaCaT cells has been reported previously. However, it has been shown that, in addition to TGF-β treatment, Ras activation is required in order to obtain a more mesenchymal phenotype, indicating that synergy between different pathways is necessary for the cells to undergo a full EMT. Although in the presence of TGF-β alone, HaCaT cells do not undergo a full EMT but rather a partial EMT, any changes in cell migration are likely to be of importance during cancer invasion and metastasis. Thus, the finding that manipulation of CD109 expression levels lead to changes in migration of SCC cells may be of critical importance in cancer progression. In agreement with this notion, it has recently been reported that CD109 expression is elevated in premalignant lesional and well-differentiated SCCs as compared to normal epithelia, and that its expression levels decreases as the cells become poorly differentiated. Based on the results showing that CD109 reduces TGF-β-induced growth inhibition in HaCaT cells and that CD109 inhibits TGF-β-induced EMT in HaCaT and SCCs cells, a role for CD109 in cancer progression is herewith suggested. Without wishing to be bound to theory, the upregulation of CD109 may contribute to tumor progression by inhibiting TGF-β-induced growth arrest in the early stage of the disease, while the loss of CD109 expression at later stage of the disease may relieve the inhibition of TGF-β-mediated EMT, thus promoting tumor invasion.

(189) The EMT program is not only employed by cancer cells to become invasive, but can occur also in other diseases, such as fibrosis, to trigger the formation of excess fibrous connective tissue. Therefore, it is possible that CD109, by regulating EMT, may play an important role not only in tumor progression but also during tissue fibrosis.

(190) While the invention has been described in connection with specific embodiments thereof, it will be understood that the scope of the claims should not be limited by the preferred embodiments set forth in the examples, but should be given the broadest interpretation consistent with the description as a whole.

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OTHER EMBODIMENTS

(192) All publications, patents, and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.

(193) While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the invention that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.

(194) Other embodiments are within the claims.