WO2022212668A1

WO2022212668A1 - Methods and compositions related to tnfrsf25/dr3 agonists

Info

Publication number: WO2022212668A1
Application number: PCT/US2022/022774
Authority: WO
Inventors: Neil Goldstein; Justine ALEXANDER; John Prendergast; Matthew Seavey; Karla FRIETZ-MILLER; Joshua WAYNE
Original assignee: Heat Biologics, Inc.
Priority date: 2021-03-31
Filing date: 2022-03-31
Publication date: 2022-10-06

Abstract

The disclosure is directed to compositions that specifically bind to the TNT Receptor Superfamily Member 25 (TNFRSF25/DR3), and related methods or use.

Description

METHODS AND COMPOSITIONS RELATED TO TNFRSF25/DR3 AGONISTS

FIELD OF THE DISCLOSURE

The disclosure is directed to compositions that specifically bind to the TNF Receptor Superfamily Member 25 (TNFRSF25/DR3), and related methods.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to and the benefit of U.S. Provisional Patent Application No. 63/168,357, filed on March 31, 2021, the entire content of which is hereby incorporated herein by reference in its entirety.

DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY

This application contains a Sequence Listing in ASCII format submitted electronically herewith via EFS-Web. Said ASCII copy, created on March 29, 2022, is named SKX- 001_SequenceListing_ST25.txt and is 24,576 bytes in size. The Sequence Listing is incorporated herein by reference in its entirety.

BACKGROUND

Stimulation of tumor necrosis factor receptor superfamily, member 25 (TNFRSF25)/ death receptor 3 (DR3) in vivo with its natural ligand TNFSF15 (also known as TL1A), facilitates selective proliferation of regulatory T cells (Tregs). Therapeutic agonists of TNFRSF25 can be used to stimulate Treg expansion, which can reduce inflammation in experimental models of asthma, allogeneic solid organ transplantation, and ocular keratitis. Modulating Treg cell populations also has a significant impact on treatments of various diseases such as cancer or autoimmune disorders.

However, there are numerous challenges with manufacturing a stable TNFRSF25 agonist. There is a need for a stable composition or method for stimulating TNFRSF25.

SUMMARY

Accordingly, in aspects, the present disclosure relates to a composition which specifically binds to TNF Receptor Superfamily Member 25 (TNFRSF25/DR3), wherein the composition comprises: (a) a single chain antibody, or fragment thereof comprising CDR1, CDR2, and CDR3, wherein: CDR1 is RFFSAWMWWL (SEQ ID NO: 1) or INDGDIFESL (SEQ ID NO: 5), or FSKISDWLPR (SEQ ID NO: 9), or TTLRHLHYHH (SEQ ID NO: 13), or FKNGLFIMTSW (SEQ ID NO: 17), or a variant thereof; CDR2 is AHRMTTLPVQ (SEQ ID NO: 2) or QPNTSTWIQV (SEQ ID NO: 6), or IYLGKRAVYD (SEQ ID NO: 10), or DMAWNKNVNN (SEQ ID NO: 14), or NHHKERNPIN (SEQ ID NO: 18), or a variant thereof; and CDR3 is KSPNYNEAMEHHHEDDVL (SEQ ID NO: 3) or LMFGKFNPWGPLMTTRHM (SEQ ID NO: 7), or NPKPKYAKNVVFHHQMKR (SEQ ID NO: 11), or AYLPSMSWMVNMPVARTI (SEQ ID NO: 15), or SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof; or (b) a peptide, the peptide is selected from: YSYDSKSPLSNIWSILERFS (SEQ ID NO: 21), or a variant thereof; DIVINHLWQYVHFLFSQGMR (SEQ ID NO: 22), or a variant thereof;

KEDMPRRLFSFLSSQMYSCC (SEQ ID NO: 23), or a variant thereof;

DFQWSQLTSILASDISWFSL (SEQ ID NO: 24), or a variant thereof;

FLPRFF QWLCEPHWS ADIVD (SEQ ID NO: 25), or a variant thereof; and

KEDMPRRLFSFLSSQMYSCCGGGSGFLPRFFQWLCEPHWSADIVD (SEQ ID NO: 33), or a variant thereof.

In embodiments, CDR1 is RFFSAWMWWL (SEQ ID NO: 1), or a variant thereof, CDR2 is AHRMTTLPVQ (SEQ ID NO: 2), or a variant thereof, and CDR3 is KSPNYNEAMEHHHEDDVL (SEQ ID NO: 3), or a variant thereof, wherein the variant has about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, CDR1 is INDGDIFESL (SEQ ID NO: 5), or a variant thereof, CDR2 is QPNTSTWIQV (SEQ ID NO: 6), or a variant thereof, and CDR3 is

LMFGKFNPWGPLMTTRHM (SEQ ID NO: 7), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, CDR1 is FSKISDWLPR (SEQ ID NO: 9), or a variant thereof, CDR2 is IYLGKRAVYD (SEQ ID NO: 10), or a variant thereof, and CDR3 is

NPKPKYAKNVVFHHQMKR (SEQ ID NO: 11), or a variant thereof, wherein the variant has about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions. In embodiments, CDR1 is TTLRHLHYHH (SEQ ID NO: 13), or a variant thereof, CDR2 is DMAWNKNVNN (SEQ ID NO: 14), or a variant thereof, and CDR3 is AYLPSMSWMVNMPVARTI (SEQ ID NO: 15), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, CDR1 is FKNGLFIMTSW (SEQ ID NO: 17), or a variant thereof, CDR2 is NHHKERNPIN (SEQ ID NO: 18), or a variant thereof, and CDR3 is SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof, wherein the variant has about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the single chain antibody, or fragment thereof, further comprises variable region framework (FW) sequences juxtaposed between the CDRs according to the formula (FW1)-(CDR1)-(FW2)-(CDR2)-(FW3)-(CDR3)-(FW4), wherein the variable region FW sequences in the heavy chain variable region are heavy chain variable region FW sequences, and wherein the variable region FW sequences in the light chain variable region are light chain variable region FW sequences.

In embodiments, the variable region FW sequences are human.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASRFFSAWMWWLWFRQAPGKEREFVAAHRMT TLPVQYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARKSPNYNEAMEHH HEDDVLWGQGTLVTVSSGPGGQ (SEQ ID NO: 4), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 4.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASINDGDIFESLWFRQAPGKEREFVAQPNTSTWI QVYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARLMFGKFNPWGPLMT TRHMWGQGTLVTVSSGPGGQ (SEQ ID NO: 8), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 8.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASFSKISDWLPRWFRQAPGKEREFVAIYLGKRAV YDYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARNPKPKYAKNVVFHH QMKRWGQGTLVTVSSGPGGQ (SEQ ID NO: 12), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 12.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASTTLRHLHYHHWFRQAPGKEREFVADMAWNK NVNNYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARAYLPSMSWMVN MPVARTIWGQGTLVTVSSGPGGQ (SEQ ID NO: 16), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 16.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASFKNGLFIMTSWFRQAPGKEREFVANHHKERN PINYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARSEGWIHENAKMMTS TPALWGQGTLVTVSSGPGGQ (SEQ ID NO: 20), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 20.

In embodiments, the peptide is: YSYDSKSPLSNIWSILERFS (SEQ ID NO: 21), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the peptide is: DIVINHLWQYVHFLFSQGMR (SEQ ID NO: 22), or a variant thereof; wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the peptide is: KEDMPRRLFSFLSSQMYSCC (SEQ ID NO: 23), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the peptide is: DFQWSQLTSILASDISWFSL (SEQ ID NO: 24), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the peptide is: FLPRFFQWLCEPHWSADIVD (SEQ ID NO: 25), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions. In embodiments, the peptide is:

KEDMPRRLFSFLSSQMYSCCGGGSGFLPRFFQWLCEPHWSADIVD (SEQ ID NO: 33), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the peptide further comprises an additional peptide.

In embodiments, the composition comprises a dimer of peptides, and in embodiments, the composition comprises a trimer of peptides. In embodiments, peptides are joined with a linker which is substantially comprised of glycine and serine residues. In embodiments, the linker is (GGS)_n, wherein _nis 1, or 2, or 3, or 4, or 5. For example, in embodiments, the linker is GGSGGSGGSG (SEQ ID NO: 26), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the composition further comprises a targeting moiety. For example, in embodiments, the targeting moiety is directed to a tumor cell. In embodiments, the targeting moiety is directed to a tumor-associated antigen (TAA), such as HER2, PSA, TRP-2, EpCAM, GPC3, mesothelin (MSLN), and EGFR.

In embodiments, the present disclosure provides a polynucleotide comprising a nucleic acid sequence encoding the single chain antibody, or a fragment thereof or a peptide.

In embodiments, the present disclosure provides a vector, or a host cell, comprising the polynucleotide having a nucleic acid sequence encoding the single chain antibody, or a fragment thereof or a peptide.

In aspects, the present disclosure provides a pharmaceutical composition comprising the composition of any of the preceding embodiments, and a pharmaceutically acceptable excipient or carrier.

In aspects, the present disclosure provides a method for treating or preventing cancer, comprising administering an effective amount of composition of any one of the preceding embodiments to a patient in need thereof. In embodiments, the cancer is a solid tumor or a blood cancer. In embodiments, the cancer is selected form one or more a cancer of a blood vessel, an eye tumor, of basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer (including gastrointestinal cancer); glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer (e.g., small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung); melanoma; myeloma; neuroblastoma; oral cavity cancer (lip, tongue, mouth, and pharynx); ovarian cancer; pancreatic cancer; prostate cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; cancer of the respiratory system; salivary gland carcinoma; sarcoma (e.g., Kaposi's sarcoma); skin cancer; squamous cell cancer; stomach cancer; testicular cancer; thyroid cancer; uterine or endometrial cancer; cancer of the urinary system; vulvar cancer; lymphoma including Hodgkin's and non-Hodgkin's lymphoma, as well as B-cell lymphoma (including low grade/follicular non-Hodgkin's lymphoma (NHL); small lymphocytic (SL) NHL; intermediate grade/follicular NHL; intermediate grade diffuse NHL; high grade immunoblastic NHL; high grade lymphoblastic NHL; high grade small non-cleaved cell NHL; bulky disease NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom's Macroglobulinemia; chronic lymphocytic leukemia (CLL); acute lymphoblastic leukemia (ALL); Hairy cell leukemia; chronic myeloblastic leukemia; as well as other carcinomas and sarcomas; and post-transplant lymphoproliferative disorder (PTLD), as well as abnormal vascular proliferation associated with phakomatoses, edema (e.g. that associated with brain tumors), and Meigs' syndrome.

In aspects, the present disclosure provides a method for treating or preventing an autoimmune disease or disorder, comprising administering an effective amount of the composition of any one of the preceding embodiments to a patient in need thereof. In embodiments, the autoimmune disease or disorder is selected from graft versus host disease, transplantation rejection (e.g., prevention of allograft rejection), multiple sclerosis, diabetes mellitus, lupus, celiac disease, Crohn's disease, ulcerative colitis, Guillain-Barre syndrome, scleroderma, Goodpasture's syndrome, Wegener's granulomatosis, autoimmune epilepsy, Rasmussen's encephalitis, Primary biliary sclerosis, Sclerosing cholangitis, Autoimmune hepatitis, Addison's disease, Hashimoto's thyroiditis, Fibromyalgia, Meniere's syndrome; pernicious anemia, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, Reiter's syndrome, and Grave's disease.

In embodiments, the autoimmune disease or disorder is graft versus host disease.

In aspects, the present disclosure provides a method for treating or preventing an inflammatory eye disease, comprising administering an effective amount of the composition of any one of the preceding embodiments to a patient in need thereof. In embodiments, the inflammatory eye disease is selected from an inflammatory eye disease associated with comeal transplant, diabetic macular edema, diabetic retinopathy, dry eye disease, scleritis, blepharitis, keratitis, conjunctivitis, chorioretinal inflammation, chorioretinitis, iridocyclitis, iritis, posterior cyclitis, and uveitis. In embodiments, the inflammatory eye disease is associated with a comeal allograft, or a comeal allograft rejection. In embodiments, the uveitis is anterior uveitis, panuveitis, intermediate uveitis and posterior uveitis.

In aspects, the present disclosure provides a method for improving a patient response to allogeneic hematopoietic stem cell transplantation (aHSCT), comprising administering an effective amount of composition of any one of the preceding embodiments to a patient in need thereof.

The details of one or more examples of the disclosure are set forth in the description below. Other features or advantages of the present disclosure will be apparent from the following drawings, detailed description of several examples, and also from the appended claims. The details of the disclosure are set forth in the accompanying description below. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, illustrative methods and materials are now described. Other features, objects, and advantages of the disclosure will be apparent from the description and from the claims. In the specification and the appended claims, the singular forms also include the plural unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph showing the results of a Jurkat-DR3 assay for TL1A, a mouse surrogate of human PTX-35 ("PTX-35" or "PTX35", an anti-TNFRSF25 antibody), and peptides 2E ("12920"), 3D ("121030"), and 3D ("12220"). The natural ligand of TNFRSF25, TL1 A, is the positive control in this experiment.

FIG. 2 is a graph showing the results of a P815 Caspase 3/7 assay for TL1A, PTX35, 12920, 121030, and 12220. TL1A is the positive control in this experiment. FIG. 3 is a graph showing the results of a dose response curve for two positive antibodies, P155-3D ("3D 121020" and "3D 12220") and P155-2E ("2E 12920"). TL1A is the positive control in this experiment.

FIG. 4 is an image of a MEME (Multiple EM for Motif Elicitation) analysis of the CDR3 sites from P155-2E and P155-3D single chain antibodies compared to the natural ligand for DR3, TL1A. This image shows motifs expressed in the CDRs that correspond to regions on TL1A.

FIG. 5A-5C show a comparison of CD4+ T cell populations of study PBMCs treated with PTX-35 and bispecific constructs of 155-2E and EGFR. FIG. 5 A is a graph showing the percentages of total lymphocytes in a CD4+ T cell population of PBMC treated with PTX-35, 155-2E, 35-155-2E (no wash), 40-155-2E (no wash), 35-155-2E (wash), and 40-155-2E (wash). FIG. 5B is a graph showing the percentages of CD4 in an activate CD4 T cell population of PBMC treated with PTX-35, 155-2E, 35-155-2E (no wash), 40-155-2E (no wash), 35-155-2E (wash), and 40-155-2E (wash). FIG. 5C is a graph showing the percentages of CD4 in memory CD4 T cells of PBMC treated with PTX-35, 155-2E, 35-155-2E (no wash), 40-155-2E (no wash), 35-155-2E (wash), and 40-155-2E (wash).

FIG. 6A-6C show a comparison of CD8+ T cell populations of study PBMCs treated with PTX-35 and bispecific constructs of 155-2E and EGFR. FIG. 6A is a graph showing the percentage of total lymphocytes in a total CD8+ T cell population of PBMC treated with PTX- 35, 155-2E, 35-155-2E (no wash), 40-155-2E (no wash), 35-155-2E (wash), and 40-155-2E (wash). FIG. 6B is a graph showing the percentages of CD8 in an activate CD8 T cell population of PBMC treated with PTX-35, 155-2E, 35-155-2E (no wash), 40-155-2E (no wash), 35-155-2E (wash), and 40-155-2E (wash). FIG. 6C is a graph showing the percentages of CD8 in cytotoxic CD8 T cells of PBMC treated with PTX-35, 155-2E, 35-155-2E (no wash), 40-155-2E (no wash), 35-155-2E (wash), and 40-155-2E (wash).

FIG. 7 is an image showing human PBMC aggregates expressing different biomarkers when treated with PTX-35 166 ng/ml, and 155-2E 2.7 ug/ml.

FIG. 8 is a series of flow cytometry histograms showing populations of T-effector cells and T-regulatory cells being activated after incubation with PTX-35 at 500 ng/ml, 155-2E at 222 ng/ml, 155-2E at 667 ng/ml, and 155-2E at 2000 ng/ml. FIG. 9 is a series of flow cytometry histograms showing populations of T-effector cells and T-regulatory cells being activated after incubation with TL1 A at 100 ng/ml, 155-2E at 222 ng/ml, 155-2E at 667 ng/ml, and 155-2E at 2000 ng/ml.

FIG. 10A - 10B are images of predictive modeling of full-length DR3 and 155-2E antibody. FIG. 10A is an image of the homology based model of DR3, with topological domains indicated. FIG. 10B is an image of the homology based binding for 155-2E.

FIG. 11A - llC are images of predictive docking for 155-2E antibody and DR3. FIG. 11 A is an image of the full-length ribbon structure of docking of 155-2E on DR3. FIG. 1 IB is an zoomed image at 20 angstroms of the docking of 155-2E on DR3, with key residues identified as direct interactions between molecules. FIG. 11C is an interaction diagram of key interactions between molecules.

FIG. 12A - 12C are images of predictive docking for PTX-35 and DR3. FIG. 12A is an image of the full-length ribbon structure of docking of PTX-35 on DR3. FIG. 12B is a zoomed image at 20 angstroms of docking of PTX-35 on DR3, with key residues identified as direct interactions between molecules. FIG. 12C is an interaction diagram of key interactions between molecules.

FIG. 13A - 13C are images of predictive docking for TL1A and DR3. FIG. 13A is an image of the full-length ribbon structure of docking of TL1A on DR3. FIG. 13B is a zoomed image at 20 angstroms of docking of TL1A on DR3, with key residues identified as direct interactions between molecules. FIG. 13B is an interaction diagram of key interactions between molecules.

FIG. 14A - 14B are images of full length ribbon (FIG. 14 A) and mesh structure (FIG. 14B) of docking comparisons of DR3, 155-2E, PTX-35 and TL1A.

DETAILED DESCRIPTION

The present invention is based, in part, on the surprising discovery of a composition that specifically binds to the TNF Receptor Superfamily Member 25 ("TNFRSF25/DR3"). The composition disclosed herein can be a small protein, or a peptide, or an antibody ( e.g a single chain antibody), that binds to TNFRSF25/DR3. The compositions disclosed herein are capable of functioning as agonists or antagonists. In addition, the present disclosure describes peptide, small protein, and antibody compositions that are interchangeable. The peptide or small protein can be derived from the binding region of an antibody ( e.g ., a single chain antibody), and target specific peptides and small proteins can be incorporated into the binding regions of the antibody (e.g., a single chain antibody). The compositions disclosed herein may be used in a method of treating or preventing cancer (e.g. , a solid tumor, or blood cancer), or an autoimmune disease (e.g., graft versus host disease), and the compositions may be used to improve patient response to allogeneic hematopoietic stem cell transplantation (aHSCT).

To date, immunosuppression remains the primary strategy to prevent GVHD. Because of the central role of T cells in initiating GVHD, approaches have often focused on T-cell depletion and inhibition to prevent GVHD. While treatments targeting T cells, including methotrexate, cyclophosphamide, cyclosporine, and tacrolimus, do reduce GVHD incidence and severity, these treatments are also associated with increased risk of graft failure, disease relapse, and incidence of opportunistic infection. Other GVHD therapies target cytokine/chemokine-receptor interactions and include maravioc (CCR5 agonist), which has had some positive impact, while infliximab and etanercept (IL-1 and TNF-alpha targeting agents, respectively) have failed to demonstrate efficacy in the clinic. The identification of CD4⁺FoxP3⁺ regulatory T cells (Tregs) as a non-redundant cell population essential for the maintenance of peripheral self-tolerance is of interest due to their potential therapeutic application and capability to promote allograft acceptance and ameliorate autoimmune diseases. Accordingly, the fields of transplantation and autoimmunity have converged on a common objective to selectively manipulate the Treg compartment to inhibit conventional T cell ("Tconv") antigen-specific immune responses. Clinical procedures developed to harvest Tregs for therapeutic application have been primarily based on cell surface expression of CD4, CD25, and CD127. Although Tregs can be induced to expand in vitro, size and purity of the initiating culture, the maintenance of FoxP3 expression and functional activity during culture varies and depends on starting cell populations and culture conditions. Consistency of reagents also pose challenges inherent of in vitro manipulations for ultimate clinical application. Generation of a GMP product containing high cell numbers for adoptive therapy requires infrastructure and significant economic investment. Accordingly, routinely generating adequate numbers of functional Tregs ex vivo as a readily available (and cost effective) adoptive therapy remains translationally challenging.

Strategies to manipulate Tregs in vivo have and continue to be examined to circumvent the practical and economic considerations that limit the feasibility of in vitro approaches. The observation that a low dose of IL-2 more efficiently stimulates Tregs versus Tconv populations has fostered optimism that selective manipulation of the FoxP3 compartment in situ can be exploited for clinical benefit. Because the production and expansion of effector versus Treg cells is associated with the development of chronic graft-versus-host disease ("cGVHD"), correction of a Treg:Tconv cell imbalance would have therapeutic benefit. Experimentally, a number of molecules expressed on Tregs have been shown to expand natural Treg cells and/or augment their functional activity in vivo, including IL-2, several members of the TNFR family (TNFR2/TNF; TNFRSF25/TL 1 A; OX-40/OX-40L; 4-1BB/4-1BB-L; GITR/GITR-L), as well as CD28 and IL-33, in order to suppress autoimmune responses, allograft rejection and GVHD. Notably, the understanding that IL-2 signaling is crucial for Treg homeostasis has promoted the hypothesis that in vivo IL-2 treatment could provide a strategy to control the compartment. Indeed, a low dose of IL-2 treatment in vivo results in a 2-3-fold increase in Treg frequency within the CD4 cell population and is sufficient to prevent HVG and GVHD.

The tumor necrosis factor receptor superfamily member 25 ("TNFRSF25") is a cell surface receptor of the tumor necrosis factor receptor superfamily that is constitutively expressed on Tregs and upregulated upon activation of CD4⁺ and CD8⁺ T cells. The natural ligand of TNFRSF25 is TNFSF1 /TL1A (referred to hereafter as "TL1A"), and this ligand is primarily expressed on endothelial cells and activated T cells, including Tregs. TNFRSF25 co-stimulation promotes proliferation; effector function and survival; and, dependent on conditions and signal strength, can induce apoptosis. Using either agonistic mAh (clone 4C12), a mouse surrogate of human PTX-35 (mPTX-35), or a TLIA-Ig fusion protein, it has been observed that triggering the TNFRSF25 pathway in the absence of exogenous antigen leads to significant expansion of Tregs in vivo which is dependent on IL-2. Notably, stimulation via TNFRSF25 alone expands Tregs to a greater degree than via CD25 (IL-2) stimulation alone. Interestingly, TNFRSF25 stimulation, when compared to other TNFRSF members, has the strongest in vivo effect on Treg expansion. Disclosed herein are compositions and methods related to the recapitulation of TL1A biological activity.

In embodiments, disclosed herein is a composition that specifically binds to TNF Receptor Superfamily Member 25 (TNFRSF25/DR3).

In embodiments, disclosed herein is a composition which specifically binds to a particular antigen, e.g., TNFRFS25, when it binds to that antigen in a sample, and does not recognize and bind, or recognizes and binds to a lesser extent, other molecules in the sample. In embodiments, the compositions of the present disclosure can selectively bind to an epitope with an affinity (K_d) equal to or less than, for example, about 1 x 10^-6 M (e.g. , equal to or less than about 1 x 10^-9 M, equal to or less than about 1 x 10^-10 M, equal to or less than about 1 x 10^-11 M, or equal to or less than about 1 x 10^-12 M) in phosphate buffered saline. The ability of a compositions of the present disclosure to specifically bind a protein epitope can be determined using any of the methods known in the art or those methods described herein (e.g., by Biacore/Surface Plasmon Resonance). This can include, for example, binding to TNFRSF25 on live cells as a method to stimulate caspase activation in live transformed cells, binding to an immobilized target substrate including human TNFRSF25 fusion proteins as detected using an ELISA method, binding to TNFRSF25 on live cells as detected by flow cytometry, or binding to an immobilized substrate by surface plasmon resonance (including ProteOn).

In embodiments, the composition disclosed herein is a peptide, a small protein, or an antibody (e.g., a single chain antibody), that binds to TNFRSF25/DR3.

In embodiments, a single-chain antibody is a single-chain variable fragment (scFv).

In embodiments, the composition disclosed herein is a single-chain antibody, small protein, or a single polypeptide that contains at least one variable binding domain (e.g., a variable domain of a mammalian heavy or light chain immunoglobulin, a camelid VHH, or a cartilaginous fish (e.g., shark) Ig-NAR domain) that is capable of specifically binding to an antigen. Non-limiting examples of single-chain antibodies include single-domain antibodies.

In embodiments, the term "single-domain antibody" refers to a polypeptide that contains one camelid VHH or at least one cartilaginous fish Ig-NAR domain that is capable of specifically binding to an antigen. Non-limiting examples of single-domain antibodies are described, for example, in U.S. Publication No. 2010/0092470.

In embodiments, the small protein ranges in size from about 2 kDa to about 4 kDa. In embodiments, the small protein ranges in size from about 2 kDa to about 3.5 kDa, from about 2 kDa to about 3 kDa, or from about 2 kDa to about 2.5 kDa.

In embodiments, the peptide or small protein is an agonist. In embodiments, the peptide or small protein is an antagonist. In embodiments, the antibody (e.g., a single chain antibody) is an about 12 kDa fragment.

In embodiments, the antibody ranges in size from about 5 kDa to about 30 kDa, from about 5 kDa to about 25 kDa, from about 5 kDa to about 20 kDa, or from about 5 kDa to about 15 kDa. In embodiments, the antibody retains the biological function of the parent, whole antibody. In embodiments, the small protein and antibody compositions are interchangeable. In embodiments, the peptide or small protein is derived from the binding region of the antibody. In embodiments, the target specific small protein is incorporated into the binding regions of the antibody ( e.g a single chain antibody).

In embodiments, a single-chain antibody is a single-chain variable fragment (scFv). In embodiments, the composition disclosed herein is a single-chain antibody, small protein, or a single polypeptide that contains at least one variable binding domain (e.g., a variable domain of a mammalian heavy or light chain immunoglobulin, a camelid VHH, or a cartilaginous fish (e.g., shark) Ig-NAR domain) that is capable of specifically binding to an antigen. Non-limiting examples of single-chain antibodies include single-domain antibodies.

In embodiments, the composition comprises a single chain antibody, or fragment thereof, having a heavy chain variable domain. The variable domain determines the specificity of the antibody. Each variable region comprises three hypervariable regions also known as complementarity determining regions (CDRs) flanked by four relatively conserved framework regions (FRs). The three CDRs, referred to as CDR1, CDR2, and CDR3, contribute to the antibody binding specificity. In embodiments, the single chain antibody is a chimeric antibody. In embodiments, the single chain antibody is a humanized antibody. In embodiments, the single chain antibody, or fragment thereof comprises a CDR1, CDR2, and CDR3, wherein:

CDR1 is RFFSAWMWWL (SEQ ID NO: 1) or INDGDIFESL (SEQ ID NO: 5), or FSKISDWLPR (SEQ ID NO: 9), or TTLRHLHYHH (SEQ ID NO: 13), or FKNGLFIMTSW (SEQ ID NO: 17), or a variant thereof,

CDR2 is AHRMTTLPVQ (SEQ ID NO: 2) or QPNTSTWIQV (SEQ ID NO: 6), or IYLGKRAVYD (SEQ ID NO: 10), or DMAWNKNVNN (SEQ ID NO: 14), or NHHKERNPIN (SEQ ID NO: 18), or a variant thereof, and

CDR3 is KSPNYNEAMEHHHEDDVL (SEQ ID NO: 3) or

LMFGKFNPWGPLMTTRHM (SEQ ID NO: 7), or NPKPKYAKNVVFHHQMKR

(SEQ ID NO: 11), or AYLPSMSWMVNMPVARTI (SEQ ID NO: 15), or

SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof;

In embodiments, the composition comprises a peptide, and the peptide is selected from:

KEDMPRRLF SFL S S QMY S C C (SEQ ID NO: 23), or a variant thereof; FLPRFFQWLCEPHWS ADIVD (SEQ ID NO: 25), or a variant thereof;

YSYDSKSPLSNIWSILERFS (SEQ ID NO: 21), or a variant thereof;

DIVINHLWQYVHFLFSQGMR (SEQ ID NO: 22), or a variant thereof;

DFQWSQLTSILASDISWFSL (SEQ ID NO: 24), or a variant thereof; and

KEDMPRRLFSFLSSQMYSCCGGGSGFLPRFFQWLCEPHWSADIVD (SEQ ID

NO: 33), or a variant thereof.

NPKPKYAKNVVFHHQMKR (SEQ ID NO: 11), or a variant thereof, wherein the variant has about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, CDR1 is TTLRHLHYHH (SEQ ID NO: 13), or a variant thereof, CDR2 is DMAWNKNVNN (SEQ ID NO: 14), or a variant thereof, and CDR3 is AYLPSMSWMVNMPVARTI (SEQ ID NO: 15), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, CDR1 is FKNGLFIMTSW (SEQ ID NO: 17), or a variant thereof, CDR2 is NHHKERNPIN (SEQ ID NO: 18), or a variant thereof, and CDR3 is SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof, wherein the variant has about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions. In embodiments, the single chain antibody, or fragment thereof, further comprises variable region framework (FW) sequences juxtaposed between the CDRs according to the formula (FW1)-(CDR1)-(FW2)-(CDR2)-(FW3)-(CDR3)-(FW4), wherein the variable region FW sequences in the heavy chain variable region are heavy chain variable region FW sequences, and wherein the variable region FW sequences in the light chain variable region are light chain variable region FW sequences.

In embodiments, the variable region FW sequences are human.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASINDGDIFESLWFRQAPGKEREFVAQPNTSTWI QVYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARLMFGKFNPWGPLMT TRHM (SEQ ID NO: 8), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 8.

In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASTTLRHLHYHHWFRQAPGKEREFVADMAWNK NVNNYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARAYLPSMSWMVN MPVARTIWGQGTLVTVSSGPGGQ (SEQ ID NO: 16), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 16. In embodiments, the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASFKNGLFIMTSWFRQAPGKEREFVANHHKERN PINYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARSEGWIHENAKMMTS TPALWGQGTLVTVSSGPGGQ (SEQ ID NO: 20), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 20.

In embodiments, the peptide is: FLPRFFQWLCEPHWSADIVD (SEQ ID NO: 25), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the peptide is:

In embodiments, the peptide further comprises an additional peptide. In embodiments, the composition comprises a dimer of peptides. In embodiments, the composition comprises a trimer of peptides.

In embodiments, the peptides are joined with a linker which is substantially comprised of glycine and serine residues. In embodiments, the linker is (GGS)n, wherein n is 1, or 2, or 3, or 4, or 5. In embodiments, the linker is GGSGGSGGSG (SEQ ID NO: 26), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

In embodiments, the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences of any one of SEQ ID NOs: 15, 16, 17, 18, 19, and 20, provided in Table 1, or a codon-optimized version thereof.

In embodiments, the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequence of SEQ ID NO:

27, provided in Table 1, or a codon-optimized version thereof.

28, provided in Table 1, or a codon-optimized version thereof.

29, provided in Table 1, or a codon-optimized version thereof.

30, provided in Table 1, or a codon-optimized version thereof.

31, provided in Table 1, or a codon-optimized version thereof.

32, provided in Table 1, or a codon-optimized version thereof. In embodiments, the present compositions comprise one or more amino acid or nucleic acid sequence of Table 1.

In embodiments, the amino acid mutations are amino acid substitutions, and may include conservative and/or non-conservative substitutions. "Conservative substitutions" may be made, for instance, on the basis of similarity in polarity, charge, size, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the amino acid residues involved. The 20 naturally occurring amino acids can be grouped into the following six standard amino acid groups: (1) hydrophobic: Met, Ala, Val, Leu, lie; (2) neutral hydrophilic: Cys, Ser, Thr; Asn, Gin; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; and (6) aromatic: Trp, Tyr, Phe.

As used herein, "conservative substitutions" are defined as exchanges of an amino acid by another amino acid listed within the same group of the six standard amino acid groups shown above. For example, the exchange of Asp by Glu retains one negative charge in the so modified polypeptide. In addition, glycine and proline may be substituted for one another based on their ability to disrupt a-helices.

As used herein, "non-conservative substitutions" are defined as exchanges of an amino acid by another amino acid listed in a different group of the six standard amino acid groups (1) to (6) shown above.

In embodiments, the composition further comprises a targeting moiety. In embodiments, the targeting moiety is directed to a tumor cell. In embodiments, the targeting moiety is directed to a tumor-associated antigen (TAA). In embodiments, the TAA is selected from EGFR, HER2, PSA, TRP-2, EpCAM, GPC3, and mesothelin (MSLN).

In embodiments, the present disclosure provides a polynucleotide comprising a nucleic acid sequence encoding the single chain antibody, or a fragment thereof, or peptide described in any of the preceding embodiments.

In embodiments, the polynucleotide is RNA or DNA. In embodiments, the RNA is a messenger RNA (mRNA) or a modified mRNA.

In embodiments, a vector comprising the polynucleotide is provided. In embodiments, a host cell comprising the vector is provided. Cells may be cultured in vitro or genetically engineered, for example. Host cells can be obtained from normal or affected subjects, including healthy humans, cancer patients, and patients with an infectious disease, private laboratory deposits, public culture collections such as the American Type Culture Collection, or from commercial suppliers.

In embodiments, the present disclosure provides a pharmaceutical composition comprising the composition of any of the embodiments disclosed herein, and a pharmaceutically acceptable excipient.

Methods of Treating or Preventing Cancer

In embodiments, the methods disclosed herein treat or prevent cancer by administering an effective amount of the composition that specifically binds to TNF Receptor Superfamily Member 25 (TNFRSF25/DR3). In embodiments, the composition comprises a single chain antibody, or fragment thereof, having a heavy chain variable domain. In embodiments, the single chain antibody, or fragment thereof comprises a CDR1, CDR2, and CDR3, wherein: CDR1 is RFFSAWMWWL (SEQ ID NO: 1) or INDGDIFESL (SEQ ID NO:

5), or FSKISDWLPR (SEQ ID NO: 9), or TTLRHLHYHH (SEQ ID NO: 13), or FKNGLFIMTSW (SEQ ID NO: 17), or a variant thereof,

CDR2 is AHRMTTLPVQ (SEQ ID NO: 2) or QPNTSTWIQV (SEQ ID NO:

6), or IYLGKRAVYD (SEQ ID NO: 10), or DMAWNKNVNN (SEQ ID NO:

14), or NHHKERNPIN (SEQ ID NO: 18), or a variant thereof, and

CDR3 is KS PNYNEAMEHHHEDD VL (SEQ ID NO: 3) or LMFGKFNPWGPLMTTRHM (SEQ ID NO: 7), or

NPKPKY AKNV VFHHQMKR (SEQ ID NO: 11), or

AYLP S MS WMVNMP V ARTI (SEQ ID NO: 15), or

SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof.

In embodiments, the composition comprises a peptide, and the peptide is selected from: YSYDSKSPLSNIWSILERFS (SEQ ID NO: 21), or a variant thereof; DIVINHLWQYVHFLFSQGMR (SEQ ID NO: 22), or a variant thereof; KEDMPRRLF SFL S S QMY S C C (SEQ ID NO: 23), or a variant thereof; DFQWSQLTSILASDISWFSL (SEQ ID NO: 24), or a variant thereof;

FLPRFF QWLCEPHWS ADIVD (SEQ ID NO: 25), or a variant thereof; and KEDMPRRLFSFLSSQMYSCCGGGSGFLPRFFQWLCEPHWSADIVD (SEQ ID NO: 33), or a variant thereof.

In embodiments, the methods disclosed herein prevent an onset or progression of cancer by administering an effective amount a composition disclosed herein ( e.g a single chain antibody or peptide) to the subject.

As a non-limiting example, the prevention of an onset, the presence, and/or the evaluation of the progression of a cancer in a subject can be assessed according to the Tumor/Nodes/Metastases (TNM) system of classification (International Union Against Cancer, 6th edition, 2002), or the Whitmore- Jewett staging system (American Urological Association). Typically, cancers are staged using a combination of physical examination, blood tests, and medical imaging. If tumor tissue is obtained via biopsy or surgery, examination of the tissue under a microscope can also provide pathologic staging. In embodiments, the stage or grade of a cancer assists a practitioner in determining the prognosis for the cancer and in selecting the appropriate modulating therapy.

In embodiments, the prevention of an onset, or progression, of cancer is assessed using the overall stage grouping as a non-limiting example: Stage I cancers are localized to one part of the body, typically in a small area; Stage II cancers are locally advanced and have grown into nearby tissues or lymph nodes, as are Stage III cancers. Whether a cancer is designated as Stage II or Stage III can depend on the specific type of cancer. The specific criteria for Stages II and III can differ according to diagnosis. Stage IV cancers have often metastasized or spread to other organs or throughout the body. The onset or progression of cancer can be assessed using conventional methods available to one of skill in the art, such as a physical exam, blood tests, and imaging scans (e.g., X-rays, MRI, CT scans, ultrasound etc.).

As disclosed herein, administering, or administering a treatment/therapy, refers to a treatment/therapy from which a subject receives a beneficial effect, such as the reduction, decrease, attenuation, diminishment, stabilization, remission, suppression, inhibition or arrest of the development or progression of cancer, or a symptom thereof.

In embodiments, the treatment/therapy that a subject receives, or the prevention in the onset of cancer results in at least one or more of the following effects: (1) the reduction or amelioration of the severity of cancer and/or a genetic disease or disorder, and/or a symptom associated therewith; (2) the reduction in the duration of a symptom associated with cancer and/or a genetic disease or disorder; (3) the prevention in the recurrence of a symptom associated with cancer and/or a genetic disease or disorder; (4) the regression of cancer and/or a genetic disease or disorder, and/or a symptom associated therewith; (5) the reduction in hospitalization of a subject; (6) the reduction in hospitalization length; (7) the increase in the survival of a subject; (8) the inhibition of the progression of cancer and/or a genetic disease or disorder and/or a symptom associated therewith; (9) the enhancement or improvement the therapeutic effect of another therapy; (10) a reduction or elimination in the cancer cell population, and/or a cell population associated with a genetic disease or disorder; (11) a reduction in the growth of a tumor or neoplasm; (12) a decrease in tumor size; (13) a reduction in the formation of a tumor; (14) eradication, removal, or control of primary, regional and/or metastatic cancer; (15) a decrease in the number or size of metastases; (16) a reduction in mortality; (17) an increase in cancer-free survival rate of a subject; (18) an increase in relapse- free survival; (19) an increase in the number of subjects in remission; (20) a decrease in hospitalization rate; (21) the size of the tumor is maintained and does not increase in size or increases the size of the tumor by less 5% or 10% after administration of a therapy as measured by conventional methods available to one of skill in the art, e.g., X-rays, MRI, CAT scan, ultrasound etc.; (22) the prevention of the development or onset of cancer and/or a genetic disease or disorder, and/or a symptom associated therewith; (23) an increase in the length of remission for a subject; (24) the reduction in the number of symptoms associated with cancer and/or a genetic disease or disorder; (25) an increase in symptom-free survival of a cancer subject and/or a subject associated with a genetic disease or disorder; and/or (26) limitation of or reduction in metastasis. In embodiments, the treatment/therapy that a subject receives does not cure cancer, but prevents the progression or worsening of the disease. In certain embodiments, the treatment/therapy that a subject receives does not prevent the onset/development of cancer, but may prevent the onset of cancer symptoms.

In embodiments, "preventing" an onset or progression of cancer in a subject in need thereof, is inhibiting or blocking the cancer or disorder. In embodiments, the methods disclosed herein prevent, or inhibit, the cancer or disorder at any amount or level. In embodiments, the methods disclosed herein prevent or inhibit the cancer or genetic disease or disorder by at least or about a 10% inhibition (e.g., at least or about a 20% inhibition, at least or about a 30% inhibition, at least or about a 40% inhibition, at least or about a 50% inhibition, at least or about a 60% inhibition, at least or about a 70% inhibition, at least or about a 80% inhibition, at least or about a 90% inhibition, at least or about a 95% inhibition, at least or about a 98% inhibition, or at least or about a 100% inhibition).

In embodiments, disclosed herein is a method for treating or preventing cancer, comprising administering an effective amount of the composition of any one of the above claims to a patient in need thereof. In embodiments, the cancer is a solid tumor. In embodiments, the cancer is a blood cancer. In embodiments, the cancer is selected form one or more of a cancer of a blood vessel, an eye tumor, basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer (including gastrointestinal cancer); glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer (e.g., small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung); melanoma; myeloma; neuroblastoma; oral cavity cancer (lip, tongue, mouth, and pharynx); ovarian cancer; pancreatic cancer; prostate cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; cancer of the respiratory system; salivary gland carcinoma; sarcoma (e.g., Kaposi's sarcoma); skin cancer; squamous cell cancer; stomach cancer; testicular cancer; thyroid cancer; uterine or endometrial cancer; cancer of the urinary system; vulvar cancer; lymphoma including Hodgkin's and non- Hodgkin's lymphoma, as well as B-cell lymphoma (including low grade/follicular non- Hodgkin's lymphoma (NHL); small lymphocytic (SL) NHL; intermediate grade/follicular NHL; intermediate grade diffuse NHL; high grade immunoblastic NHL; high grade lymphoblastic NHL; high grade small non-cleaved cell NHL; bulky disease NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom's Macroglobulinemia; chronic lymphocytic leukemia (CLL); acute lymphoblastic leukemia (ALL); Hairy cell leukemia; chronic myeloblastic leukemia; as well as other carcinomas and sarcomas; and post-transplant lymphoproliferative disorder (PTLD), as well as abnormal vascular proliferation associated with phakomatoses, edema (e.g. that associated with brain tumors), and Meigs' syndrome.

In embodiments, disclosed herein is a method for treating or preventing an autoimmune disease or disorder, comprising administering an effective amount of the composition of any one of the above claims to a patient in need thereof. In embodiments, the autoimmune disease or disorder is selected from graft versus host disease, transplantation rejection (e.g., prevention of allograft rejection), multiple sclerosis, diabetes mellitus, lupus, celiac disease, Crohn's disease, ulcerative colitis, Guillain-Barre syndrome, scleroderma, Goodpasture's syndrome, Wegener's granulomatosis, autoimmune epilepsy, Rasmussen's encephalitis, Primary biliary sclerosis, Sclerosing cholangitis, Autoimmune hepatitis, Addison's disease, Hashimoto's thyroiditis, Fibromyalgia, Meniere's syndrome; pernicious anemia, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, Reiter's syndrome, and Grave's disease. In embodiments, the autoimmune disease or disorder is graft versus host disease.

In embodiments, the present disclosure provides a method for treating or preventing an inflammatory eye disease, comprising administering an effective amount of the composition of any one of the preceding embodiments to a patient in need thereof. In embodiments, the inflammatory eye disease is selected from an inflammatory eye disease associated with comeal transplant, diabetic macular edema, diabetic retinopathy, dry eye disease, scleritis, blepharitis, keratitis, conjunctivitis, chorioretinal inflammation, chorioretinitis, iridocyclitis, iritis, posterior cyclitis, and uveitis. In embodiments, the inflammatory eye disease is associated with a comeal allograft, or a comeal allograft rejection. In embodiments, the uveitis is anterior uveitis, panuveitis, intermediate uveitis and posterior uveitis.

In embodiments, disclosed herein is a method for improving a patient response to allogeneic hematopoietic stem cell transplantation (aHSCT), comprising administering an effective amount of the composition of any one of the above claims to a patient in need thereof.

In addition, this document also provides pharmaceutical compositions that comprise compositions as described herein, in combination with a pharmaceutically acceptable carrier. A "pharmaceutically acceptable carrier" (also referred to as an "excipient" or a "carrier") is a pharmaceutically acceptable solvent, suspending agent, stabilizing agent, or any other pharmacologically inert vehicle for delivering one or more therapeutic compounds to a subject (e.g., a mammal, such as ahuman, non-human primate, dog, cat, sheep, pig, horse, cow, mouse, rat, or rabbit), which is nontoxic to the cell or subject being exposed thereto at the dosages and concentrations employed. Pharmaceutically acceptable carriers can be liquid or solid, and can be selected with the planned manner of administration in mind so as to provide for the desired bulk, consistency, and other pertinent transport and chemical properties, when combined with one or more of therapeutic compounds and any other components of a given pharmaceutical composition. Typical pharmaceutically acceptable carriers that do not deleteriously react with amino acids include, by way of example and not limitation: water, saline solution, binding agents (e.g., polyvinylpyrrolidone or hydroxypropyl methylcellulose), fillers (e.g., lactose and other sugars, gelatin, or calcium sulfate), lubricants (e.g., starch, polyethylene glycol, or sodium acetate), disintegrates (e.g., starch or sodium starch glycolate), and wetting agents (e.g., sodium lauryl sulfate). Pharmaceutically acceptable carriers also include aqueous pH buffered solutions or liposomes (small vesicles composed of various types of lipids, phospholipids and/or surfactants which are useful for delivery of a drug to a mammal). Further examples of pharmaceutically acceptable carriers include buffers such as phosphate, citrate, and other organic acids, antioxidants such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins such as serum albumin, gelatin, or immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acids such as glycine, glutamine, asparagine, arginine or lysine, monosaccharides, disaccharides, and other carbohydrates including glucose, mannose or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™. Pharmaceutical compositions can be formulated by mixing one or more active agents with one or more physiologically acceptable carriers, diluents, and/or adjuvants, and optionally other agents that are usually incorporated into formulations to provide improved transfer, delivery, tolerance, and the like. A pharmaceutical composition can be formulated, e.g., in lyophilized formulations, aqueous solutions, dispersions, or solid preparations, such as tablets, dragees or capsules. A multitude of appropriate formulations can be found in the formulary known to all pharmaceutical chemists: Remington's Pharmaceutical Sciences (18th ed, Mack Publishing Company, Easton, PA (1990)), particularly Chapter 87 by Block, Lawrence, therein. These formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LIPOFECTIN™), DNA conjugates, anhydrous absorption pastes, oil-in-water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax. Any of the foregoing mixtures may be appropriate in treatments and therapies as described herein, provided that the active agent in the formulation is not inactivated by the formulation and the formulation is physiologically compatible and tolerable with the route of administration. See, also, Baldrick, Regul Toxicol Pharmacol 32:210-218, 2000; Wang, Int J Pharm 203:1-60, 2000; Charman J Pharm Sci 89:967-978, 2000; and Powell et al. PDA J Pharm Sci Technol 52:238-311, 1998), and the citations therein for additional information related to formulations, excipients and carriers well known to pharmaceutical chemists.

Pharmaceutical compositions include, without limitation, solutions, emulsions, aqueous suspensions, and liposome-containing formulations. These compositions can be generated from a variety of components that include, for example, preformed liquids, self- emulsifying solids and self-emulsifying semisolids. Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other; in general, emulsions are either of the water-in-oil (w/o) or oil-in- water (o/w) variety. Emulsion formulations have been widely used for oral delivery of therapeutics due to their ease of formulation and efficacy of solubilization, absorption, and bioavailability.

Compositions and formulations can contain sterile aqueous solutions, which also can contain buffers, diluents and other suitable additives (e.g., penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers). Compositions additionally can contain other adjunct components conventionally found in pharmaceutical compositions. Thus, the compositions also can include compatible, pharmaceutically active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or additional materials useful in physically formulating various dosage forms of the compositions provided herein, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. Furthermore, the composition can be mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings, and aromatic substances. When added, however, such materials should not unduly interfere with the biological activities of the polypeptide components within the compositions provided herein. The formulations can be sterilized if desired.

In embodiments, a composition containing a composition as provided herein can be in the form of a solution or powder with or without a diluent to make an injectable suspension. The composition may contain additional ingredients including, without limitation, pharmaceutically acceptable vehicles, such as saline, water, lactic acid, mannitol, or combinations thereof, for example.

Any appropriate method can be used to administer a composition as described herein to a mammal. Administration can be, for example, parenteral (e.g., by subcutaneous, intrathecal, intraventricular, intramuscular, or intraperitoneal injection, or by intravenous drip). Administration can be rapid (e.g., by injection) or can occur over a period of time (e.g., by slow infusion or administration of slow release formulations). In embodiments, administration can be topical (e.g., transdermal, sublingual, ophthalmic, or intranasal), pulmonary (e.g., by inhalation or insufflation of powders or aerosols), or oral. In addition, a composition containing a composition as described herein can be administered prior to, after, or in lieu of surgical resection of a tumor.

As used herein, the word "include," and its variants, is intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the materials, compositions, devices, and methods of this technology. Similarly, the terms "can" and "may" and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features. Although the open-ended term "comprising," as a synonym of terms such as including, containing, or having, is used herein to describe and claim the disclosure, the present technology, or embodiments thereof, may alternatively be described using more limiting terms such as "consisting of' or "consisting essentially of' the recited ingredients. Unless defined otherwise, all technical and scientific terms herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials, similar or equivalent to those described herein, can be used in the practice or testing of the present disclosure, the preferred methods and materials are described herein. All publications, patents, and patent publications cited are incorporated by reference herein in their entirety for all purposes.

This disclosure is further illustrated by the following non-limiting examples.

EXAMPLES

Example 1: Identification of Peptides, Small Proteins and Antibodies that bind to TNFRSF 25/DR3

The experiments of this example identify peptides, small proteins, and single chain antibodies that bind to TNFRSF25/DR3. These small proteins are capable of serving as agonists, as demonstrated in a functional assay through a process called "panning". In the experiments of this example, the target (DR3) and an irrelevant protein, are each coated on high capacity microtiter plates. Plates are incubated overnight; the next day at 4°C, and unbound antigen is removed, and the coated wells are blocked using nonfat milk in PBS at room temperature. A peptide, small protein, or antibody phage library is added to the irrelevant antigen-coated wells, and the plates are incubated at room temperature (negative pan). Unbound phage are then added to the DR3 wells, and the plates incubated at room temperature for 2 hours. Each well is washed thirteen times with PBS, and the bound phage are eluted with a glycine/HCl buffer (pH 2.2) following a 3-min incubation. The eluted phage from each library are pooled, neutralized with 1 M Tris/HCl (pH 8.0), added to a log-phase E. coli TGI, and amplified in 2 YT-glucose medium. Helper phage (CM13; ADL) and carbenicillin are added, and the cells are incubated for an additional hour. The cells are pelleted and resuspended in 2 YT-CK medium (YT medium containing carbenicillin and kanamycin), and incubated overnight. The next day the infected bacterial cells are centrifuged and the pellet is discarded. The supernatant containing the phage is precipitated with one-fourth volume of 20% polyethylene glycol-8000 in 2.0 M NaCl by incubation on ice for 60 minutes. The precipitate is centrifuged and the phage pellet resuspended in approximately 1 ml of PBS. The phage is then used for the next round of panning. In some experiments, 3 rounds of panning is sufficient to obtain target-specific phage, and 96 random clones are picked from round 3 and are grown in 96-well cluster plates as a master stock. A phage enzyme-linked immunosorbent assay ("ELISA") is used to determine those peptides and antibodies which bind specifically to DR3. Here, 50 μL of master stock is transferred from each master plate to another set of cluster tubes containing 2 YT medium plus glucose, carbenicillin and helper phage. The tubes are incubated for 2-3 hours with constant shaking. The cultures are centrifuged, the supernatant is discarded, and the bacterial pellet is resuspended in 2X YT medium containing carbenicillin and kanamycin and incubated overnight at 37°C. The cells are removed by centrifugation, and the supernatants are used in an ELISA assay. Each well of a Maxisorp plate is coated with either DR3 or an irrelevant antigen (0.5-1 μg/well) overnight at 4°C. The wells are blocked with NFM-PBS for one hour at room temperature, phage are added, and the plates incubated at room temperature for 2 hours. After washing three times with PBS-Tween 20, plates are probed with an anti-M13 antibody and conjugated to horseradish peroxidase (Sino Biological; 1:10000) at room temperature for 60 minutes. The plates are washed 3x in PBS-Tween 20 followed by an addition of TMB for 15-30 minutes at room temperature. The reaction is stopped by the addition of IN HC1 and the OD is measured using a microplate spectrophotometer at 450 nm. Positive binders are sent out for sequencing. All binders are compared to the cognate ligand for DR3 (TLla) using the MEME/MAST algorithms to determine whether any motifs or consensus amino acids which might suggest peptides with the best chance of reproducing the biological response of the ligand.

For preparing soluble peptides, small molecules, and antibodies for the functional assays, rescued phage (50 μl) is added to 150 μl of the non-amber suppressive bacterial strain SS320, and incubated for 2-3 hours at 37°C. 200 μl of 2X YT medium containing 400 mM IPTG is then added to the cultures, which are incubated overnight at 30°C with shaking. The final concentration of IPTG is 200 mM. Plates are pelleted and the supernatants tested in a DR3 functional assay.

For the DR3 functional assay (also referred herein as the "DR3-Jurkat assay", or "Jurkat-DR3 assay"), DR3 overexpressing Jurkat cells with an NF kappa-B luciferase reporter (DR3-Jurkat) are grown in RPMI containing 10% FBS, hygromycin and blasticidin and harvested by centrifugation (FIG. 1). Cells are washed in Hanks Balanced Salt Solution and resuspended in RPMI containing 5% FBS (R-5) at a concentration of 2x10⁶ cells/ml. 25 μl of the test supernatants and controls are added to 96 well white microtiter plates, followed by 50ul of the Jurkat-DR3 cell suspension (e.g., a total volume of 75ul/well). Negative controls included R-5, fas ligand (1 μg/ml in R-5) 2xYT medium and 2x YT medium plus 200 mM IPTG. The positive control is TL1 A in R-5, tittered 1:3, with a starting concentration of lug/ml. In the initial experiments, the samples are tested as single points on two separate plates. In later studies, positive samples are tested for a dose response versus DR3-Jurkat. Treated cells are incubated for 6 hours at 37°C at 5% C02, and assayed for luminescence using a Promega Glo Max Navigator, and the results in these experiments are expressed as Relative Light Units ("RLU") (FIG 1).

For the P815 Caspase 3/7 assay (FIG. 2), P815 cells were grown in IMDM with 10% FBS, and 25,000 cells/well were plated in 50 pi IMDM- 10 in a white 96 well microtiter plate. Plates were then incubated 2-3 hours at 37°C, and 50 μl of each sample was added to the appropriate wells and the plates incubated overnight 37°C. 100 μl of Caspase 3/7 reagent (Promega) was then added to each well and the plates shaken for 30 seconds. Luminescence and fluorescence were determined after 1 hour in a Promega GloMax Explorer. Results are expressed as RLU (FIG. 2).

The results of the experiments in this example demonstrate that two antibodies, and several peptides, were found to bind to DR3 in the ELISA assay, and activate DR3 in the DR3- Jurkat functional assay. The sequences are shown in Table 1 below.

In the case of the peptides in disclosed in Table 1, two of the peptides were synthesized as dimers, "1H5" (SEQ ID NO: 23) and "3D" (SEQ ID NO: 25), because each of the individual peptides had regions of homology with the natural DR3 ligand, TL1A.

Initially, the peptides and antibodies were tested as bacterial supernatants. In these experiments, SS320 and TGI A cells were infected with phage containing the various peptide and antibody inserts. The individual samples were secreted into the bacterial supernatant after treatment with IPTG (200 mM for SS320 and 1 mM for TG1A), overnight at 30°C. The cells were then pelleted, and the aliquots of the supernatants were tested in the DR3-Jurkat assay. Those showing an agonist response were either synthesized ( e.g peptides) or produced in SS320 cells (2E and 3D), as described above. In the latter case, the two antibodides were further purified using a poly -His purification kit (ThermoFisher).

A dose response curve for two positive antibodies, P155-3D and P155-2E is shown in FIG. 3. As shown in FIG. 3, the activity can be tracked with TL1A, although a direct comparison of the EC50s may have to await purification of the samples. These data suggest that novel DR3 agonists can be generated by phage display, as either 20mer peptides or single chain antibodies. The individual peptides, P155-3D and P155-2E, are capable of activating the insulin receptor by working through "hotspots", or the regions involved in protein-protein interactions. In some experiments, dimers or trimers may be generated to develop a DR-3 agonist.

The MEME analysis in FIG. 4 shows the CDR3 sites from P155-2E and P155-3D single chain antibodies compared to the natural ligand for DR3, TL1A. FIG. 4 shows motifs expressed in the CDRs that correspond to regions on TL1A.

In some experiments of this example, it is expected that a dimer or trimer may be necessary to achieve the necessary level of agonist activity. In the case of the peptides, binders can be synthesized as multimers (two or three peptides) with a short glycine/serine linker (GGSGGSGGSG) (SEQ ID NO: 26). The expected length of the peptide trimer may be ~70 amino acids, and can be produced synthetically. The antibodies can be generated as dimers ( e.g bi-specific antibodies or antibody fragments) where two binding fragments will be cloned 3' to 5' with a 5-10 glycine/serine linker. Another approach in these experiments is to synthesize the CDR3 regions of an antibody DR3 binder, and use those peptides as building blocks for synthetic trimers, as the CDR3 region is the prime region involved in antigen binding by an antibody.

Example 2: Cloning of Antibody Monomers and Dimers

In the experiments of this example, the inserts 2E and 3D were cloned into a PCDNA3.1 (+) vector, and a TGEX-SC blue Mammalian Expression Vector. Inserts were prepared at 500 ng in solid form. The inserts were spun down and 17.375μL molecular grade water added. The stock was further diluted 1 : 10 in molecular grade water. In these experiments, the vectors were added in equal volume to the insert in the ligation mix. The restriction digestion mix was set up as follows: (1) both vectors and inserts were digested in 50 μL total volume. For the vectors, 2 μL of DNA was digested with 1 μL Bgll (NEB) in 5 μL 10x NEBuffer, with 42 μL of water added. For the inserts, 3.5 μL of DNA was digested with 1 μL Bgll (NEB) in 5 μL 10x NEBuffer, with 40.5 μL of water added; (2) both vectors and inserts were digested at 37°C in a thermocycler for 12 minutes. The enzyme was then heat inactivated in the thermocycler at 65°C for 20 minutes. Both inserts and vectors were automatically phosphorylated after digestion. The vectors were then de-phosphorylated after digestion to ligate with the phosphorylated insert, and to avoid the vector self-ligating. Shrimp Alkaline Phosphatase (SAP) was used on both vectors after digestion with Bgll. 1 μL SAP was added to each vector reaction mixture, 30 minutes at 37°C, followed by 65°C for 15 minutes to deactivate. For ligation, a T4 DNA Ligase Master Mix was used to perform 15-minute ligation of each phosphorylated insert with overhanging ends into each dephosphorylated vector for cloning. The reagent volume for each reaction was as follows: for both the 1: 1 and 3:5 vector: insert ratio, the reaction volume totaled 20 μL. All vector and insert reactions from the previous steps were diluted 1: 10 before use in the ligation reaction. For the 1 : 1 vector: insert ratio, the reaction consisted of 1 μL vector, 3 μL DNA insert, 5 μL Anza T4 DNA ligase master mix, and 11 μL water. For the 3:5 vector:insert ratio, the reaction consisted of 1 μL vector, 5 μL DNA insert, 5 μL Anza T4 DNA ligase master mix, and 9 μL water. The GC5 bacterial strain (Genesee Scientific) was then transduced with the vector. 100 μL of bacteria were incubated with 1 μL of ligation mix on ice for 5 minutes. The bacteria/DNA mix was shaken at 37°C in glass test tubes for one hour before streaking the warmed GC plates. Plates were stored at 37°C overnight. In addition to the above procedure, an electroporation protocol was also used. In these experiments, DH5a A. coll ( endA recA mutants) (ElectroMAX; Invitrogen) bacteria were electroporated using the Biorad micropulser (ECl setting at 1.8kv). 25 μL of DH5a of E. coli. bacteria were warmed to room temperature until melted, and then moved to ice. Each sample was diluted 1:10, and 1 μL of this mix was added to 25 μL of bacteria per cuvette. After pulsing, 1 mL SOC was added directly to the cuvette, and the mixture was transferred to a new, sterile, glass test-tube which already contained 3 mL LB each. The mixture was then shaken at 37°C for one hour, and then streaked onto warm GC 2-YT plates.

The experiments of these examples demonstrate the surprising discovery that compositions that bind to TNFRSF25/DR3 can be used in a method of treating or preventing cancer ( e.g ., a solid tumor, or blood cancer), or an autoimmune disease (e.g., graft versus host disease), and the compositions may be used to improve patient response to allogeneic hematopoietic stem cell transplantation (aHSCT).

Table 1

Example 3: Bispecific Constructs of 155-2E Antibody and EGFR

Bispecific T Cell engager molecules were constructed with 155-2E antibody and EGFR. Two constructs, 35-1552E and 40-155-2E were analyzed for T cell activation patterns. Briefly, A431 epidermoid carcinoma cells were plated in 24-well plates and grown to confluency. Cells were treated with mitomycin C to stop growth, followed by treatment as outlined below. After additions, frozen isolated human PBMCs were thawed and added to each well in StemPro™ (Invitrogen) media containing 4ng/mL IL-2. Cell plate was incubated at 37°C for 72 hrs. See Table 2 for experimental design.

Table 2

PBMCs were harvested at 72 hours and washed 2x in FACS buffer. Cells were resuspended in 50μL viability dye and incubated on ice 15 minutes. Cells were then washed lx in FACS buffer and stained with 50μL of antibody stain mix as described below for 30 minutes. After staining cells were washed lx and resuspended in FACS buffer. Samples were collected on a CytoFlex flow cytometer. See Table 3 for T cell panel.

Table 3

CD25+/CD62L- markers were used to determine naive T cells subset vs. activated T cell subsets; CD4+CD45RA-CD45RO+ markers were used to assess memory T cells; CD8+ CD45RA-CD45RO+ markers were used to assess cytotoxic CD8+ T cells. (FIG. 5A - FIG. 6C).

The CD4+ T cell populations of study PBMCs are shown in FIG. 5A - FIG. 5C, and CD8+ cell populations of study PBMCs are shown in FIG. 6A - FIG. 6C. In summary, EGFR- 155-2E bispecific constructs showed similar T cell activation patterns compared to mono- specific constructs. Therefore, results from this study demonstrate that the 35-155-2E and 40- 155-2E bispecific constructs result in marked increase in anti-cancer immune cell responses. Results also showed that 155-2E is bioactive as a single chain antibody. Without wishing to be bound by theory, 155-2E activity is as good as or better than PTX35 for some sub-populations of T cells. 155-2E remained active as part of a bi-specific BiTE (Bispecific T Cell Engager) molecule. The EGFR-2E BiTE retained DR3 agonist activity after binding to the overexpressing EGFR cell line. This was shown by adding the BiTE to A431 epidermoid carcinoma cells and washing extensively.

Example 4: DR3 Flow study CDR3s of 155-2E (SEQ ID NO: 4) and 155-3D (SEQ ID NO: 8) share motifs with

TL1A (SEQ ID NO: 37). See Table 4. A flow cytometry study was conducted to analyze the responses of T cell populations after treatment of 155-2E, PTX-35, and TL1A at various dosages (FIG. 8 - FIG. 9).

Table 4:

24 well plates were coated with lOOng/ml OKT3 in carbonate buffer overnight at 4C. Wells were washed once with Hanks Balanced Salt Solution and PBMCs (4-5x10e5 cells per well) were added in 500ul of StemPro 34 containing 2ng/ml IL-2 and 5ng/ml TGF-beta 1. Samples were added at different concentrations in 500ul of the above medium. Plates were incubated for 5 days at 37C in a 5% C02 atmosphere. Cells were processed, incubated with antibodies to various CD markers and read in a CytoFlex Flow cytometer. Images of the cells treated with PTX-35 at 166 ng/ml and 155-2E at 2.7 ug/ml were taken at day 5 and compared for biomarkers such as CD4, CD8, and CD49d (FIG. 7). Complexed to bΐ or b integrins, CD49d is not only involved in cell adhesion to fibronectin and vascular cell adhesion molecule 1 (VCAM-1), but also in intercellular leucocyte interactions. CD49d is expressed by monocytes, lymphocytes, eosinophils, thymocytes and Langerhans cells.

Results showed that 155-2E (155-2E) induces enhanced T-effector and T-regulatory cell proliferation as shown in Table 5. When the cells were treated with 155-2E at various dosages, the percentage of T-effector cells and the percentage of T-regulatory cells increased compared to PTX-35 treatment (FIG. 8). When the cells were treated with 155-2E at various dosages, the percentage of T-regulatory cells increased compared to TL1A treatment (FIG. 9). Without wishing to be bound by theory, 155-2E is a single chain antibody with an Fc, while PTX-35 is a full antibody with two Fc's, which may cause the differential induction of T- regulatory cells.

Table 5

Example 5: Predictive Modeling of 155-2E, PTX-35 and TL1A binding to DR3

Predictive modeling of DR3 was done using "Cyrus Bench: Protein Design and Structure Prediction, Powered By Rosetta". Cyrus bench utilizes homology based modeling to build structures followed by full atom Talaris2013 energy function to score protein conformations. The homology based model of DR3 and 155-2E are shown in FIG. 10A - FIG. 10B. The topological domains have been color coded. The signal peptide is in red, the extracellular domain is green, transmembrane domain is highlighted in blue, and the cytoplasmic domain containing the death receptor domain is highlighted in cyan (FIG. 10A). Homology based binding for 155-2E was also performed using Cyrus Bench computer aided design. Antibody backbone is in blue and CDRs are in red (FIG. 10B).

Predictive modeling of docking for 155-2E and DR3 was also constructed using PIPER (FIG. 11A - FIG. 11C). The full length ribbon structure of docking of 155-2E is shown (blue with CDRs colored in red) on DR3 (green) (FIG. 11 A). A zoomed in image at 20 angstroms with key residues identified as direct interactions between molecules are also labled in FIG. 11B. An interaction diagram of key interactions identified by PIPER is shown in FIG. 11C. Table 6 lists key interaction residues of 155-2E (Setl) and DR3 (Set2).

Table 6

Predictive modeling of docking for PTX-35 and DR3 was also constructed using PIPER (FIG. 12A - FIG. 12C). The full length ribbon structure of docking of PTX-35 is shown (red- orange) on DR3 (green) (FIG. 12A). A zoomed in image at 20 angstroms with key residues identified as direct interactions between molecules are also labeled in FIG. 12B. An interaction diagram of key interactions identified by PIPER is shown in FIG. 12C. Table 7 lists key interaction residues of PTX-35 (Setl) and DR3 (Set2).

Table 7

Predictive modeling can be used to predict binding sites. Table 8 shows a side by side comparison of binding sites of PTX-35 and DR3 as determined by XL-MS and PIPER docking.

Table 8

Predictive modeling of docking for TL1A and DR3 was also constructed using PIPER (FIG. 13A - FIG. 13C). The full length ribbon structure of docking of TL1 A is shown (yellow) on DR3 (green) (FIG. 13 A). A zoomed in image at 20 angstroms with key residues identified as direct interactions between molecules are also labeled in FIG. 13B. An interaction diagram of key interactions identified by PIPER is shown in FIG. 13C. FIG. 14A - 14B show the predictive modeling of a full length ribbon (FIG. 14 A) and mesh structure (FIG. 14B) of docking sites for 155-2E (blue), PTX-35 (red-orange), and TL1A (yellow) on DR3 (green). Table 9 shows docking sites of 155-2E, PTX-35, and DR3 as determined by PIPER.

Table 9

All of the features disclosed herein may be combined in any combination. Each feature disclosed in this specification may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, each feature disclosed is only an example of a generic series of equivalent or similar features. From the above description, one skilled in the art can easily ascertain the essential characteristics of the present disclosure, and without departing from the spirit and scope thereof, can make various changes and modifications of the disclosure to adapt it to various usages and conditions. Thus, other embodiments are also within the claims.

Claims

CLAIMS What is claimed is:

1. A composition which specifically binds to TNF Receptor Superfamily Member 25

(TNFRSF25/DR3), wherein the composition comprises:

(a) a single chain antibody, or fragment thereof comprising CDR1, CDR2, and CDR3, wherein:

CDR3 is KSPNYNEAMEHHHEDD VL (SEQ ID NO: 3) or

LMF GKFNPW GPLMTTRHM (SEQ ID NO: 7), or

NPKPKYAKNVVFHHQMKR (SEQ ID NO: 11), or

AYLPSMSWMVNMPVARTI (SEQ ID NO: 15), or

SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof; or

(b) a peptide, and the peptide is selected from:

KEDMPRRLFSFLSSQMYSCC (SEQ ID NO: 23), or a variant thereof;

FLPRFFQWLCEPHWSADIVD (SEQ ID NO: 25), or a variant thereof;

YSYDSKSPLSNIWSILERFS (SEQ ID NO: 21), or a variant thereof;

DIVINHLWQYVHFLFSQGMR (SEQ ID NO: 22), or a variant thereof;

DFQWSQLTSILASDISWFSL (SEQ ID NO: 24), or a variant thereof; and

KEDMPRRLFSFLSSQMYSCCGGGSGFLPRFF QWLCEPHW S ADIVD (SEQ

ID NO: 33), or a variant thereof.

2. The composition of claim 1, wherein:

CDR1 is RFFSAWMWWL (SEQ ID NO: 1), or a variant thereof,

CDR2 is AHRMTTLPVQ (SEQ ID NO: 2), or a variant thereof, and

CDR3 is KSPNYNEAMEHHHEDDVL (SEQ ID NO: 3), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

3. The composition of claim 1, wherein

CDR1 is INDGDIFESL (SEQ ID NO: 5), or a variant thereof,

CDR2 is QPNTSTWIQV (SEQ ID NO: 6), or a variant thereof, and CDR3 is LMF GKFNPW GPLMTTRHM (SEQ ID NO: 7), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

4. The composition of claim 1, wherein:

CDR1 is FSKISDWLPR (SEQ ID NO: 9), or a variant thereof,

CDR2 is IYLGKRAVYD (SEQ ID NO: 10), or a variant thereof, and CDR3 is NPKPK Y AKN VVFHHQMKR (SEQ ID NO: 11), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

5. The composition of claim 1, wherein:

CDR1 is TTLRHLHYHH (SEQ ID NO: 13), or a variant thereof,

CDR2 is DMAWNKNVNN (SEQ ID NO: 14), or a variant thereof, and CDR3 is AYLPSMSWMVNMPVARTI (SEQ ID NO: 15), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

6. The composition of claim 1, wherein:

CDR1 is FKNGLFIMTSW (SEQ ID NO: 17), or a variant thereof,

CDR2 is NHHKERNPIN (SEQ ID NO: 18), or a variant thereof, and CDR3 is SEGWIHENAKMMTSTPAL (SEQ ID NO: 19), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

7. The composition of claim 1, wherein the single chain antibody, or fragment thereof, further comprises variable region framework (FW) sequences juxtaposed between the CDRs according to the formula (FW1)-(CDR1)-(FW2)-(CDR2)-(FW3)-(CDR3)-(FW4), wherein the variable region FW sequences in the heavy chain variable region are heavy chain variable region FW sequences, and wherein the variable region FW sequences in the light chain variable region are light chain variable region FW sequences.

8. The composition of claim 7, wherein the variable region FW sequences are human.

9. The composition of claim 1, wherein the single chain antibody comprises an amino acid sequence of:

QVQLVESGGGVVQPGRSLRLSCAASRFFSAWMWWLWFRQAPGKEREFVAAHR MTTLPVQYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARKSP NYNEAMEHHHEDD VLWGQGTLVTVSSGPGGQ (SEQ ID NO: 4), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 4.

10. The composition of claim 1, wherein the single chain antibody comprises an amino acid sequence of:

QVQLVESGGGVVQPGRSLRLSCAASINDGDIFESLWFRQAPGKEREFVAQPNTST WIQVYADS VKGRFTISRDN SKNTLYLQMNSLRAEDTAVYYCARLMFGKF NPWGPLMTTRHMWGQGTLVTVSSGPGGQ (SEQ ID NO: 8), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 8.

11. The composition of claim 1, wherein the single chain antibody comprises an amino acid sequence of:

QVQLVESGGGVVQPGRSLRLSCAASFSKISDWLPRWFRQAPGKEREFVAIYLGK RAVYDYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARNPKPK YAKNVVFHHQMKRWGQGTLVTVSSGPGGQ (SEQ ID NO: 12), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 12.

12. The composition of claim 1, wherein the single chain antibody comprises an amino acid sequence of: QVQLVESGGGVVQPGRSLRLSCAASTTLRHLHYHHWFRQAPGKEREFVADMA WNKNVNNYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARAY LPSMSWMVNMPVARTIWGQGTLVTVSSGPGGQ (SEQ ID NO: 16), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 16.

13. The composition of claim 1, wherein the single chain antibody comprises an amino acid sequence of:

QVQLVESGGGVVQPGRSLRLSCAASFKNGLFIMTSWFRQAPGKEREFVANHHKE RNPINYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARSEGWIH ENAKMMTSTPALWGQGTLVTVSSGPGGQ (SEQ ID NO: 20), or an amino acid sequence having at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity with SEQ ID NO: 20.

14. The composition of claim 1, wherein the peptide is:

YSYDSKSPLSNIWSILERFS (SEQ ID NO: 21), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

15. The composition of claim 1, wherein the peptide is:

DIVINHLWQYVHFLFSQGMR (SEQ ID NO: 22), or a variant thereof; wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

16. The composition of claim 1, wherein the peptide is:

KEDMPRRLFSFLSSQMYSCC (SEQ ID NO: 23), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

17. The composition of claim 1, wherein the peptide is:

DFQWSQLTSILASDISWFSL (SEQ ID NO: 24), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

18. The composition of claim 1, wherein the peptide is:

FLPRFF Q WLCEPHWSADIVD (SEQ ID NO: 25), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

19. The composition of claim 1, wherein the peptide is:

KEDMPRRLF SFLS SQMYSCCGGGSGFLPRFF QWLCEPHW S ADIVD (SEQ ID NO: 33), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

20. The composition of any one of claims 1 or 14-19, wherein the peptide further comprises an additional peptide.

21. The composition of claim 20, wherein the composition comprises a dimer of peptides.

22. The composition of claim 20, wherein the composition comprises a trimer of peptides.

23. The composition of any one of claims 20-22, wherein the peptides are joined with a linker which is substantially comprised of glycine and serine residues.

24. The composition of claim 23, wherein the linker is (GGS)_n, wherein _nis 1, or 2, or 3, or 4, or 5.

25. The composition of claim 23, wherein the linker is GGSGGSGGSG (SEQ ID NO: 26), or a variant thereof, wherein the variant comprises about 1, or about 2, or about 3, or about 4, or about 5 mutations, the mutations selected from substitutions or deletions.

26. The composition of any of the above claims, further comprising a targeting moiety.

27. The composition of claim 26, wherein the targeting moiety is directed to a tumor cell.

28. The composition of claim 26, wherein the targeting moiety is directed to a tumor-associated antigen (TAA).

29. The composition of claim 26, wherein the TAA is selected from EGFR, HER2, PSA, TRP- 2, EpCAM, GPC3, and mesothelin (MSLN).

30. A polynucleotide comprising a nucleic acid sequence encoding the single chain antibody, or a fragment thereof, or peptide of any of the above claims.

31. A vector comprising the polynucleotide of claim 30.

32. A host cell comprising the vector of claim 31.

33. A pharmaceutical composition comprising the composition of any of claims 1-29, and a pharmaceutically acceptable excipient or carrier.

34. A method for treating or preventing cancer, comprising administering an effective amount of the composition of any one of claims 1-29 to a patient in need thereof.

35. The method of claim 34, wherein the cancer is a solid tumor.

36. The method of claim 34, wherein the cancer is a blood cancer.

37. The method of any one of claims 34-36, wherein the cancer is selected form one or more of a cancer of a blood vessel, an eye tumor, basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer (including gastrointestinal cancer); glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer ( e.g ., small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung); melanoma; myeloma; neuroblastoma; oral cavity cancer (lip, tongue, mouth, and pharynx); ovarian cancer; pancreatic cancer; prostate cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; cancer of the respiratory system; salivary gland carcinoma; sarcoma (e.g., Kaposi's sarcoma); skin cancer; squamous cell cancer; stomach cancer; testicular cancer; thyroid cancer; uterine or endometrial cancer; cancer of the urinary system; vulvar cancer; lymphoma including Hodgkin's and non-Hodgkin's lymphoma, as well as B-cell lymphoma (including low grade/follicular non-Hodgkin's lymphoma (NHL); small lymphocytic (SL) NHL; intermediate grade/follicular NHL; intermediate grade diffuse NHL; high grade immunoblastic NHL; high grade lymphoblastic NHL; high grade small non-cleaved cell NHL; bulky disease NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom's Macroglobulinemia; chronic lymphocytic leukemia (CLL); acute lymphoblastic leukemia (ALL); Hairy cell leukemia; chronic myeloblastic leukemia; as well as other carcinomas and sarcomas; and post-transplant lymphoproliferative disorder (PTLD), as well as abnormal vascular proliferation associated with phakomatoses, edema (e.g. that associated with brain tumors), and Meigs' syndrome.

38. A method for treating or preventing an autoimmune disease or disorder, comprising administering an effective amount of the composition of any one of claims 1-29 to a patient in need thereof.

39. The method of claim 38, wherein the autoimmune disease or disorder is selected from graft versus host disease, transplantation rejection (e.g, prevention of allograft rejection), multiple sclerosis, diabetes mellitus, lupus, celiac disease, Crohn's disease, ulcerative colitis, Guillain-Barre syndrome, scleroderma, Goodpasture's syndrome, Wegener's granulomatosis, autoimmune epilepsy, Rasmussen's encephalitis, Primary biliary sclerosis, Sclerosing cholangitis, Autoimmune hepatitis, Addison's disease, Hashimoto's thyroiditis, Fibromyalgia, Meniere's syndrome; pernicious anemia, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, Reiter's syndrome, and Grave's disease.

40. The method of claim 39, wherein the autoimmune disease or disorder is graft versus host disease.

41. A method for treating or preventing an inflammatory eye disease, comprising administering an effective amount of the composition of any one of claims 1-29 to a patient in need thereof.

42. The method of claim 41, wherein the inflammatory eye disease is selected from an inflammatory eye disease associated with corneal transplant, diabetic macular edema, diabetic retinopathy, dry eye disease, scleritis, blepharitis, keratitis, conjunctivitis, chorioretinal inflammation, chorioretinitis, iridocyclitis, iritis, posterior cyclitis, and uveitis.

43. The method of claim 42, wherein the inflammatory eye disease is associated with a corneal allograft, or a corneal allograft rejection.

44. The method of claim 42, wherein the uveitis is anterior uveitis, panuveitis, intermediate uveitis and posterior uveitis.

45. A method for improving a patient response to allogeneic hematopoietic stem cell transplantation (aHSCT), comprising administering an effective amount of the composition of any one of claims 1-29 to a patient in need thereof.