Patent Application
20220378890
Pursuant to the EFS-Web legal framework and 37 CFR §§ 1.821-825 (see MPEP § 2442.03(a)), a Sequence Listing in the form of an ASCII-compliant text file (entitled “Sequence_Listing_3000072-001977_ST25.txt” created on 22 Sep. 2020, and 243,949 bytes in size) is submitted concurrently with the instant application, and the entire contents of the Sequence Listing are incorporated herein by reference.
The present invention relates generally to the field of immunology and medicine. More particularly, it concerns cancer-specific peptides that bind to HLA class I and HLA class II molecules.
T cell based therapies have shown significant promise as a method for treating many cancers; unfortunately, this approach has also been hindered by a paucity of immunogenic antigen targets for common cancers and potential toxicity to non-cancerous tissues. These T cell based therapies can include ACT (adoptive cell transfer) and vaccination approaches. ACT generally involves which involves infusing a large number of autologous activated tumor-specific T cells into a patient, e.g., to treat a cancer. Generally, to develop effective anti-tumor T cell responses, the following three steps are normally required: priming and activating antigen-specific T cells, migrating activated T cells to tumor site, and recognizing and killing tumor by antigen-specific T cells. The choice of target antigen is important for induction of effective antigen-specific T cells.
Neoantigen peptides derived from protein-coding tumor mutations that are displayed at the tumor cell surface by human leukocyte antigen (HLA) molecules could serve as promising antigens for generating an effective immune response. However, as a consequence of HLA diversity and the private nature of most tumor-associated mutations, few neoantigens are shared between patients, and vaccine-induced clinical responses have remained rare event. Thus, method for identification and validation of novel epitopes for cancers expressing neoantigens is needed.
In some embodiments, the present disclosure provides methods of treating a subject having a EGFR-mutant cancer comprising administering to the subject at least a first HLA-binding peptide from EGFR and at least a first EGFR inhibitor, said peptide comprising a mutated amino acid sequence relative to wild type human EGFR that matches the mutation in the cancer of the subject. In some aspects, the HIA-binding peptide from EGFR binds to a HLA class I molecule. In some aspects, the HLA class I-binding peptide is 8, 9, 10, 11, 12 or 13 amino acids in length. In further aspects, the HLA class I-binding peptide is 9, 10 or 11 amino acids in length. In some aspects, the HLA-binding peptide from EGFR binds to a HLA class II molecule. In some aspects, the HLA class II-binding peptide is 13-30 amino acids in length. In further aspects, the HLA class II-binding peptide is 15-23 amino acids in length.
In some aspects, the methods comprise administering at least a first and a second HLA-binding peptide from EGFR, wherein said peptides each comprise a mutated amino acid sequence relative to wild type human EGFR that matches the mutation in the cancer of the subject. In some aspects, the first HLA-binding peptide from EGFR binds to a HLA class I molecule and the second HLA-binding peptide from EGFR binds to a HLA class II molecule. In some aspects, the methods comprise administering a plurality of HIA-binding peptides from EGFR, wherein said peptides each comprise a mutated amino acid sequence relative to wild type human EGFR that matches the mutation in the cancer of the subject. In some aspects, the plurality of HLA-binding peptides comprises peptides that bind to both HLA class I and HLA class II molecules. In some aspects, the methods comprise administering 2 to 30 different HLA-binding peptides to the subject. In further aspects, the methods comprise administering 5 to 30 different HLA-binding peptides to the subject.
In some aspects, the HLA genotype of the subject has been determined. In some aspects, the HLA-binding peptide from EGFR is predicted to bind to a HLA type carried by the subject. In some aspects, HLA-binding peptide from EGFR is predicted to bind to a HLA type carried by the subject using an automated analysis program. In some aspects, the EGFR-mutant cancer expresses an EGFR polypeptide having an amino acid substitution, deletion or insertion relative to wild type EGFR. In some aspects, the EGFR-mutant cancer comprises a mutation selected from the group consisting of E709K, E709A, E709H, G719A, G719S, G719C, S768I, H773L, T790M, L858R, L861Q, 709_710del>D, 745_749del, 745_750del, 746_750del, 746_751del, 746_751del>A, 746_752del>V, 747_750del, 747_751del, 747_751del>P, 747_753del, 747_753del>S, 747_753del>Q, 747_750del>P, 747_752del, 751_759del>N, 752_759del, 744_745ins>KIPVAI, 745_746ins>IPVAIK, 745_746ins>VPVAIK, 745_746ins>TPVAIK, 763_764ins>FQEA, 764_765ins>HH, 766_767ins>AI, 768_770dupSVD, 769_770ins>ASV, 770_771ins>G, 770_771ins>NPG, 770.771ins>SVD, 771_772ins>N, 771_772ins>H, 772_773ins>NP, 772_773ins>PR, 773_774ins>H, 773_774ins>PH, 773_774ins>NPH, 773_774ins>AH, 774_775ins>HV, and 775_776ins>YVMA. In some aspects, the EGFR-mutant cancer comprises a mutation selected from the group consisting of G719A, G719S, G719C, S768I, H773L, T790M, L858R, L861Q, 709_710del>D, 746_750del, 746_752del>V, 747_751del, 747_751del>P, 747_753del>S, 747_750del, 747_752del, 744_745ins>KIPVAI, 745_746ins>IPVAIK, 763_764ins>FQEA, 768_770dupSVD, 769_770ins>ASV, 770_771ins>SVD, 772_773ins>PR, 773_774ins>H, 773_774ins>PH, 773_774ins>NPH, and 773_774ins>AH. In some aspects, the EGFR-mutant cancer comprises a mutation selected from the group consisting of L858R, H773L, T790M, E709V, 747_751Del, V774M and S768I.
In some aspects, the EGFR inhibitor is administered before said HLA-binding peptide from EGFR. In other aspects, the EGFR inhibitor is administered after or essentially simultaneously with said HLA-binding peptide(s) from EGFR. In some aspects, the HLA-binding peptide(s) from mutant EGFR are administered in conjunction with TLR ligand. In some aspects, the TLR ligand is a TLR2, TLR3, TLR4, TLR7, TLR8 or TLR9 agonist. In some aspects, the TLR ligand is a TLR7 agonist. In some aspects, the TLR7 agonist is CL075, CL097, CL264, CL307, GS-9620, Poly(dT), imiquimod, gardiquimod, resiquimod (R848), loxoribine or a ssRNA oligonucleotide. In some aspects, the TLR7 agonist is imiquimod. In some aspects, the EGFR inhibitor is a tyrosine kinase inhibitor. In some aspects, the EGFR inhibitor is an EGFR binding antibody. In some aspects, the EGFR inhibitor is osimertinib, erlotinib, gefitinib, cetuximab, matuzumab, panitumumab, AEE788, CI-1033, HKI-272, HKI-357 or EKB-569.
In some aspects, the cancer is lung cancer. In some aspects, the lung cancer is non-small cell lung cancer. In some aspects, the lung cancer is a metastatic lung cancer. In some aspects, the lung cancer is a lung adenocarcinoma. In some aspects, the cancer is EGFR inhibitor resistant.
In another embodiment, the present disclosure provides immunogenic compositions comprising at least a first and a second HLA-binding peptide from EGFR, said first and second peptides comprising a mutated amino acid sequence relative to wild type human EGFR that matches a mutation in a human EGFR-mutant cancer, wherein the first HLA-binding peptide from EGFR binds to a HLA class I molecule and the second HLA-binding peptide from EGFR binds to a HLA class II molecule. In some aspects, the HLA-binding peptides are formulated in a pharmaceutically acceptable carrier. In some aspects, the pharmaceutically acceptable carrier is an aqueous carrier. In some aspects, the pharmaceutically acceptable carrier is a salt solution. In some aspects, the pharmaceutically acceptable carrier is a saline solution, preferably an isotonic saline solution. In some aspects, the HLA class I-binding peptide is 8, 9, 10, 11, 12 or 13 amino acids in length. In further aspects, the HLA class I-binding peptide is 9, 10 or 11 amino acids in length. In some aspects, the HLA class II-binding peptide is 13-30 amino acids in length. In further aspects, the HLA class I-binding peptide is 15-23 amino acids in length. In some aspects, the compositions comprise a plurality of HLA-binding peptides from EGFR wherein said peptides each comprise a mutated amino acid sequence relative to wild type human EGFR that matches a EGFR mutation in a human EGFR-mutant cancer. In some aspects, the compositions comprise 2 to 30 different HLA-binding peptides to the subject. In some aspects, the compositions comprise at least two HLA class I-binding peptides and at least one HLA class II-binding peptide. In some aspects, the compositions comprise at least one HLA class I-binding peptide and at least two HLA class II-binding peptides. In some aspects, the compositions comprise at least two HLA class I-binding peptides and at least two HLA class II-binding peptides. In some aspects, the compositions comprise at least 3 HLA class I-binding peptides and at least 3 HLA class II-binding peptides.
In some aspects, the HLA-binding peptides from EGFR comprise an amino acid substitution, deletion or insertion relative to wild type EGFR. In some aspects, the HLA-binding peptides from EGFR comprise an amino acid substitution relative to wild type EGFR. In some aspects, the HLA-binding peptides comprises a mutation selected from the group consisting of E709K, E709A, E709H, G719A, G719S, G719C, S768I, H773L, T790M, L858R, L861Q, 709_710del>D, 745_749del, 745_750del, 746_750del, 746_751del, 746_751del>A, 746_752del>V, 747_750del, 747_751del, 747_751del>P, 747_753del, 747_753del>S, 747_753del>Q, 747_750del>P, 747_752del, 751_759del>N, 752_759del, 744_745ins>KIPVAI, 745_746ins>IPVAIK, 745_746ins>VPVAIK, 745_746ins>TPVAIK, 763_764ins>FQEA, 764_765ins>HH, 766_767ins>AI, 768_770dupSVD, 769_770ins>ASV, 770_771ins>G, 770_771ins>NPG, 770_771ins>SVD, 771_772ins>N, 771_772ins>H, 772_773ins>NP, 772_773ins>PR, 773_774ins>H, 773_774ins>PH, 773_774ins>NPH, 773_774ins>AH, 774_775ins>HV, and 775_776ins>YVMA relative to wild type human EGFR. In some aspects, the HLA-binding peptides comprises a mutation selected from the group consisting of G719A, G719S, G719C, S768I, H773L, T790M, L858R, L861Q, 709_710del>D, 746_750del, 746_752del>V, 747_751del, 747_751del>P, 747_753del>S, 747_750del>P, 747_752del, 744_745ins>KIPVAI, 745_746ins>IPVAIK, 763_764ins>FQEA, 768_770dupSVD, 769_770ins>ASV, 770_771ins>SVD, 772_773ins>PR, 773_774ins>H, 773_774ins>PH, 773_774ins>NPH, and 773_774ins>AH relative to wild type human EGFR. In some aspects, the HLA-binding peptides comprises a mutation selected from the group consisting of L858R, H773L, T790M, E709V, 747_751Del, V774M and S768I relative to wild type human EGFR.
In some aspects, the compositions further comprise an EGFR inhibitor. In some aspects, the compositions further comprise a TLR ligand. In some aspects, the TLR ligand is a TLR2, TLR 2, TLR4, TLR7, TLR8 or TLR9 agonist. In some aspects, the compositions further comprise a TLR-7 agonist. In some aspects, the TLR7 agonist is CL075, CL097, CL264, CL307, GS-9620, Poly(dT), imiquimod, gardiquimod, resiquimod (R848), loxoribine or a ssRNA oligonucleotide. In further aspects, the TLR7 agonist is imiquimod. In some aspects, the HLA-binding peptides are in complex with HLA class I and/or HLA class II molecules. In some aspects, the compositions further comprise an antigen presenting cell. In some aspects, the antigen presenting cell comprises a dendritic cell. In some aspects, the HLA-binding peptides are comprised in a liposome, lipid-containing nanoparticle, or in a lipid-based carrier. In some aspects, the compositions further comprise an adjuvant component.
In still another embodiment, the present disclosure provides methods of treating a subject comprising administering an effective amount of a composition of the present disclosure to the subject (e.g., a composition comprising), wherein the subject has an EGFR-mutant cancer and wherein the HLA-binding peptide from EGFR in the composition comprising mutations matching those from the EGFR-mutant cancer in the subject. In some aspects, the methods further comprise sequencing the EGFR gene in the cancer of the subject. In some aspects, the HLA genotype of the subject has been determined. In some aspects, HLA-binding peptides from EGFR are predicted to bind to a HLA class I or HLA class II type carried by the subject. In further aspects, EGFR-mutant peptides included in the composition are selected using an algorithm that predicts HLA binding to HLA types expressed in the subject. In some aspects, the peptides included in the composition are selected based on predicted HLA affinity and/or predicted HLA ranking. In further aspects, the peptides included in the composition are selected based on predicted HLA affinity and predicted HLA ranking. In further aspects, the algorithm used for selecting HLA-binding peptides is selected from NetMHC4.0, NetMHCpan3.0, NetMHCpan4.0, NetMHCII2.2 and/or NetMHCII2.3. (See, e.g., Andreatta et al., 2015 and Jensen et al., 2018, each of which is incorporated herein by reference).
In some aspects, the methods further comprise administering an EGFR inhibitor to the subject. In some aspects, the EGFR inhibitor is administered before said HLA-binding peptides from mutated EGFR. In some aspects, the EGFR inhibitor is administered after or essentially simultaneously with said HLA-binding peptides from mutated EGFR. In some aspects, the EGFR inhibitor is an EGFR binding antibody. In some aspects, the EGFR inhibitor is Osimertinib, erlotinib, gefitinib, cetuximab, matuzumab, panitumumab, AEE788; CI-1033, HKI-272, HKI-357 or EKB-569. In some aspects, the EGFR inhibitor is a tyrosine kinase inhibitor. In some aspects, the HLA-binding peptide from EGFR is administered in conjunction with a TLR ligand. In some aspects, the TLR ligand is a TLR2, TLR 2, TLR4, TLR7, TLR8 or TLR9 agonist, preferably a TLR7 agonist. In some aspects, the TLR7 agonist is CL075, CL097, CL264, CL307, GS-9620, Poly(dT), imiquimod, gardiquimod, resiquimod (R848), loxoribine or a ssRNA oligonucleotide. In further aspects, the TLR7 agonist is imiquimod.
In some aspects, the cancer is lung cancer. In some aspects, the lung cancer is non-small cell lung cancer. In some aspects, the lung cancer is a metastatic lung cancer. In some aspects, the lung cancer is a lung adenocarcinoma. In some aspects, the cancer is EGFR inhibitor resistant. In some aspects, the composition is administered by parenteral administration, intravenous injection, intramuscular injection, inhalation, or subcutaneous injection. In some aspects, the composition is formulated in an aqueous carrier. In some aspects, the aqueous carrier is a salt solution. In some aspects, the aqueous carrier is an isotonic saline solution. In some aspects, the composition is administered at least two, three, four or five times. In some aspects, there are 2, 3, 4, 5, 6 or 7 days between administrations. In some aspects, the methods further comprise administering a further anti-cancer therapy. In some aspects, the further anti-cancer therapy is selected from the group consisting of a chemotherapy, a radiotherapy, an immunotherapy, or a surgery. In some aspects, the immunotherapy comprises at least one immune checkpoint inhibitor. In some aspects, the immune checkpoint inhibitor is an anti-PD1 or anti-CTLA-4 monoclonal antibody. In some aspects, the immunotherapy is a combination of immune checkpoint inhibitors.
In yet another embodiment, the present disclosure provides methods of producing EGFR-mutant cancer-specific immune effector cells comprising obtaining a starting population of immune effector cells and contacting the starting population of immune effector cells with a composition of the present disclosure, thereby generating EGFR-mutant cancer-specific immune effector cells. In some aspects, contacting is further defined as co-culturing the starting population of immune effector cells with antigen presenting cells (APCs), wherein the APCs present the HLA-binding peptides of the present disclosure on their surface. In some aspects, the APCs are dendritic cells. In some aspects, the immune effector cells are T cells, peripheral blood lymphocytes, NK cells, invariant NK cells, NKT cells. In some aspects, the immune effector cells have been differentiated from mesenchymal stem cell (MSC) or induced pluripotent stem iPS) cells. In some aspects, the T cell is a CD8+ T cell, CD4+ T cell, or γδ T cell. In some aspects, the starting population of T cells are CD8+ T cells or CD4+ T cells. In some aspects, the T cells are cytotoxic T lymphocytes (CTLs). In some aspects, obtaining comprises isolating the starting population of immune effector cells from peripheral blood mononuclear cells (PBMCs).
In still another embodiment, the present disclosure provides EGFR-mutant cancer-specific T cells produced by a method of the present disclosure.
In yet another embodiment, the present disclosure provides pharmaceutical compositions comprising the EGFR-mutant cancer-specific T cells produced by a method of the present disclosure.
In still another aspect, the present disclosure provides methods of treating cancer in a subject comprising administering an effective amount of the EGFR-mutant cancer-specific T cells of the present disclosure to the subject.
In yet another aspect, the present disclosure provides compositions comprising an effective amount of the EGFR-mutant cancer-specific T cells of the present disclosure for the treatment of cancer in a subject.
As used herein, “essentially free,” in terms of a specified component, is used herein to mean that the specified component has not been purposefully formulated into a composition and/or is present only as a contaminant or in trace amounts.
As used herein, “a” or “an” may mean one or more than one.
As used herein, the term “or” means “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” As used herein “another” may mean at least a second or more.
Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.
Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.
In some aspects, peptides derived from mutated EGFR neoantigens are provided that are recognized by, and bind to, HLA class I and/or HLA class II molecules. In particular, peptides are identified that are predicted to bind to specific HLA molecules carrier by a cancer patient having a given EGFR mutant cancer. These peptides, or a cocktail of such peptides (e.g., including both HLA class I and HLA class II-binding peptides), may be employed to stimulate an effective immune response against the EGFR mutant cancer. Thus, such peptides and peptide cocktails may be administered directly to a subject to simulate an immune response in vivo in a subject having an EGFR-mutant cancer, such as a lung cancer. Alternatively, peptides of the embodiments can be used to activate and expand immune effector cells (such as T-cells) ex vivo for use in anti-cancer immunotherapy composition.
As used herein, “essentially free,” in terms of a specified component, is used herein to mean that none of the specified component has been purposefully formulated into a composition and/or is present only as a contaminant or in trace amounts. The total amount of the specified component resulting from any unintended contamination of a composition is therefore well below 0.01%. Most preferred is a composition in which no amount of the specified component can be detected with standard analytical methods.
As used herein the specification, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising,” the words “a” or “an” may mean one or more than one.
The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” As used herein “another” may mean at least a second or more.
Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.
“Treatment” and “treating” refer to administration or application of a therapeutic agent to a subject or performance of a procedure or modality on a subject for the purpose of obtaining a therapeutic benefit of a disease or health-related condition. For example, a treatment may include administration of a T cell therapy.
“Subject” and “patient” are used interchangeably to refer to either a human or non-human, such as primates, mammals, and vertebrates. In particular embodiments, the subject is a human.
The term “therapeutic benefit” or “therapeutically effective” as used throughout this application refers to anything that promotes or enhances the well-being of the subject with respect to the medical treatment of this condition. This includes, but is not limited to, a reduction in the frequency or severity of the signs or symptoms of a disease. For example, treatment of cancer may involve, for example, a reduction in the size of a tumor, a reduction in the invasiveness of a tumor, reduction in the growth rate of the cancer, or prevention of metastasis. Treatment of cancer may also refer to prolonging survival of a subject with cancer.
An “anti-cancer” agent is capable of negatively affecting a cancer cell/tumor in a subject, for example, by promoting killing of cancer cells, inducing apoptosis in cancer cells, reducing the growth rate of cancer cells, reducing the incidence or number of metastases, reducing tumor size, inhibiting tumor growth, reducing the blood supply to a tumor or cancer cells, promoting an immune response against cancer cells or a tumor, preventing or inhibiting the progression of cancer, or increasing the lifespan of a subject with cancer.
The term “antibody” herein is used in the broadest sense and specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity.
The phrases “pharmaceutical or pharmacologically acceptable” refers to molecular entities and compositions that do not produce an adverse, allergic, or other untoward reaction when administered to an animal, such as a human, as appropriate. The preparation of a pharmaceutical composition comprising an antibody or additional active ingredient will be known to those of skill in the art in light of the present disclosure. Moreover, for animal (e.g., human) administration, it will be understood that preparations should meet sterility, pyrogenicity, general safety, and purity standards as required by FDA Office of Biological Standards.
As used herein, “pharmaceutically acceptable carrier” includes any and all aqueous solvents (e.g., water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles, such as sodium chloride, Ringer's dextrose, etc.), non-aqueous solvents (e.g., propylene glycol, polyethylene glycol, vegetable oil, and injectable organic esters, such as ethyloleate), dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial or antifungal agents, anti-oxidants, chelating agents, and inert gases), isotonic agents, absorption delaying agents, salts, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, fluid and nutrient replenishers, such like materials and combinations thereof, as would be known to one of ordinary skill in the art. The pH and exact concentration of the various components in a pharmaceutical composition are adjusted according to well-known parameters.
The term “unit dose” or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the therapeutic composition calculated to produce the desired responses discussed above in association with its administration, i.e., the appropriate route and treatment regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the effect desired. The actual dosage amount of a composition of the present embodiments administered to a patient or subject can be determined by physical and physiological factors, such as body weight, the age, health, and sex of the subject, the type of disease being treated, the extent of disease penetration, previous or concurrent therapeutic interventions, idiopathy of the patient, the route of administration, and the potency, stability, and toxicity of the particular therapeutic substance. For example, a dose may also comprise from about 1 μg/kg/body weight to about 1000 mg/kg/body weight (this such range includes intervening doses) or more per administration, and any range derivable therein. In nonlimiting examples of a derivable range from the numbers listed herein, a range of about 5 μg/kg/body weight to about 100 mg/kg/body weight, about 5 μg/kg/body weight to about 500 mg/kg/body weight, etc., can be administered. The practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject. In some embodiments, the dosage of antigen-specific T cell infusion may comprise about 100 million to about 30 billion cells, such as 10, 15, or 20 billion cells.
The term “immune checkpoint” refers to a molecule such as a protein in the immune system which provides signals to its components in order to balance immune reactions. Known immune checkpoint proteins comprise CTLA-4, PD1 and its ligands PD-L1 and PD-L2 and in addition LAG-3, BTLA, B7H3, B7H4, TIM3, KIR. The pathways involving LAG3, BTLA, B7H3, B7H4, TIM3, and KIR are recognized in the art to constitute immune checkpoint pathways similar to the CTLA-4 and PD-1 dependent pathways (see e.g. Pardoll, 2012; Mellman et al., 2011.
An “immune checkpoint inhibitor” refers to any compound inhibiting the function of an immune checkpoint protein. Inhibition includes reduction of function and full blockade. In particular, the immune checkpoint protein is a human immune checkpoint protein. Thus, the immune checkpoint protein inhibitor in particular is an inhibitor of a human immune checkpoint protein.
As used herein, a “protective immune response” refers to a response by the immune system of a mammalian host to a cancer. A protective immune response may provide a therapeutic effect for the treatment of a cancer, e.g., decreasing tumor size or increasing survival.
As used herein, the term “antigen” is a molecule capable of being bound by an antibody or T-cell receptor. An antigen may generally be used to induce a humoral immune response and/or a cellular immune response leading to the production of B and/or T lymphocytes.
The terms “tumor-associated antigen,” “tumor antigen” and “cancer cell antigen” are used interchangeably herein. In each case, the terms refer to proteins, glycoproteins or carbohydrates that are specifically or preferentially expressed by cancer cells.
The term “chimeric antigen receptors (CARs),” as used herein, may refer to artificial T-cell receptors, chimeric T-cell receptors, or chimeric immunoreceptors, for example, and encompass engineered receptors that graft an artificial specificity onto a particular immune effector cell. CARs may be employed to impart the specificity of a monoclonal antibody onto a T cell, thereby allowing a large number of specific T cells to be generated, for example, for use in adoptive cell therapy. In specific embodiments, CARs direct specificity of the cell to a tumor associated antigen, for example. In some embodiments, CARs comprise an intracellular activation domain, a transmembrane domain, and an extracellular domain comprising a tumor associated antigen binding region. In particular aspects, CARs comprise fusions of single-chain variable fragments (scFv) derived from monoclonal antibodies, fused to CD3-zeta a transmembrane domain and endodomain. The specificity of other CAR designs may be derived from ligands of receptors (e.g., peptides) or from pattern-recognition receptors, such as Dectins. In certain cases, the spacing of the antigen-recognition domain can be modified to reduce activation-induced cell death. In certain cases, CARs comprise domains for additional co-stimulatory signaling, such as CD3ζ, FcR, CD27. CD28, CD137, DAP10, and/or OX40. In some cases, molecules can be co-expressed with the CAR, including co-stimulatory molecules, reporter genes for imaging (e.g., for positron emission tomography), gene products that conditionally ablate the T cells upon addition of a pro-drug, homing receptors, chemokines, chemokine receptors, cytokines, and cytokine receptors.
A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) has a certain percentage (for example, 80%, 85%, 90%, or 95%) of “sequence identity” or “homology” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel el al., eds., 1987) Supplement 30, section 7.7.18, Table 7.7.1. Preferably, default parameters are used for alignment. A preferred alignment program is BLAST, using default parameters. In particular, preferred programs are BLASTN and BLASTP, using the following default parameters: Genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+SwissProtein+SPupdate+PIR.
Embodiments of the present disclosure concern tumor antigen-specific peptides, such as to the EGFR peptides that include a mutant EGFR sequence (e.g., a peptide having an insertion, substitution or deletion relative to a wildtype EGR sequence). In particular embodiments, the tumor antigen-specific peptides have the amino acid sequence of a EGFR mutant peptides. In some aspects, the peptide is no more than 50, 45, 40, 35, 30, 25, 20 or 15 amino acids in length. In certain aspects, such as any of those in Tables 1-3 is fused to polypeptide having a non-EGFR amino acid sequence (i.e., a heterologous polypeptide). In some aspects the tumor antigen-specific peptide may have an amino acid sequence with at least 80, 85, 90, 95, 96, 97, 98, 99, or 100 percent sequence identity with the peptide sequence of those in Tables 1-3 or a sequence according to those in Tables 1-3, but including 1, 2 or 3 amino acid substitutions or deletions relative to those in Tables 1-3.
As used herein, the term “peptide” encompasses amino acid chains comprising 7-35 amino acids, preferably 8-35 amino acid residues, and even more preferably 8-25 amino acids, or 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 amino acids in length, or any range derivable therein. For example, EGFR mutant peptides of the present disclosure may, in some embodiments, comprise or consist of the sequence of any one of those in Tables 1-3. As used herein, an “antigenic peptide” is a peptide which, when introduced into a vertebrate, can stimulate the production of antibodies in the vertebrate, i.e., is antigenic, and wherein the antibody can selectively recognize and/or bind the antigenic peptide. An antigenic peptide may comprise an immunoreactive EGFR mutant peptides, and may comprise additional sequences. The additional sequences may be derived from a native antigen and may be heterologous, and such sequences may, but need not, be immunogenic. In some embodiments, a tumor antigen-specific peptide (e.g., EGFR mutant peptides) can selectively bind with Specific HLA class I or HLA class II complexes. In certain embodiments, the EGFR mutant peptides are 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 amino acids in length, or any range derivable therein. Preferably, the tumor antigen-specific peptide (e.g., EGFR mutant peptides) is from 8 to 35 amino acids in length. In some embodiments, the tumor antigen-specific peptide (e.g., EGFR mutant peptides) is from 8 to 10 amino acids in length.
As would be appreciated by one of skill in the art, MHC molecules can bind peptides of varying sizes, but typically not full-length proteins. While MHC class I molecules have been traditionally described to bind to peptides of 8-11 amino acids long, it has been shown that peptides 15 amino acids in length can bind to MHC class I molecules by bulging in the middle of the binding site or extending out of the MHC class I binding groove (Guo et al., 1992; Burrows et al., 2006; Samino et al., 2006; Stryhn el al, 2000; Collins et al., 1994; Blanchard and Shastri, 2008). Further, recent studies also demonstrated that longer peptides may be more efficiently endocytosed, processed, and presented by antigen-presenting cells (Zwaveling et al., 2002; Bijker et al., 2007; Melief and van der Burg, 2008; Quintarelli et al., 2011). As demonstrated in Zwaveling el al. (2002) peptides up to 35 amino acids in length may be used to selectively bind a class II MHC and are effective. As would be immediately appreciated by one of skill, a naturally occurring full-length tumor antigen, such as mutant EGFR, would not be useful to selectively bind a class II MHC such that it would be endocytosed and generate proliferation of T cells. Generally, the naturally occurring full-length tumor antigen proteins do not display these properties and would thus not be useful for these immunotherapy purposes.
In certain embodiments, a tumor antigen-specific peptide (e.g., EGFR mutant peptides) is immunogenic or antigenic. As shown in the below examples, various tumor antigen-specific peptides (e.g., EGFR mutant peptides) of the present disclosure can promote the proliferation of T cells. It is anticipated that such peptides may be used to induce some degree of protective immunity.
A tumor antigen-specific peptide (e.g., EGFR mutant peptides) may be a recombinant peptide, synthetic peptide, purified peptide, immobilized peptide, detectably labeled peptide, encapsulated peptide, or a vector-expressed peptide (e.g., a peptide encoded by a nucleic acid in a vector comprising a heterologous promoter operably linked to the nucleic acid). In some embodiments, a synthetic tumor antigen-specific peptide (e.g., EGFR mutant peptides) may be administered to a subject, such as a human patient, to induce an immune response in the subject. Synthetic peptides may display certain advantages, such as a decreased risk of bacterial contamination, as compared to recombinantly expressed peptides. A tumor antigen-specific peptide (e.g., EGFR mutant peptides) may also be comprised in a pharmaceutical composition such as, e.g., a vaccine composition, which is formulated for administration to a mammalian or human subject.
A. HLA Class I and H Library Peptides Example Procedures for Peptide Selection
Table 1 below shows an example of a final peptide composition of EGFR mutant peptides predicted to bind to specific HLA class I complexes. The peptides have been ranked based on predicted binding characteristics. In this case, the example patient has a L858R mutation and 2 different specific HLA-A, HLA-B and HLA-C genes.
Example Procedure for Selecting MIA Class I Peptides (HLA Class II Peptides can be Selected Using the Same Procedure):
The HLA Class I Library contains the top 20 EGFR mutations and covers ˜95% of EGFRmut patients (see Table 2 below). There are 364 total EGFR mutant peptides in library, including 342 mutation-specific peptides and 16 peptides shared by 2 mutations. The library contains 100 HLA class I allotypes (HLA-A, 30; HLA-B, 48; and HLA-C, 22)
The HLA Class II Library comes the top 20 EGFR mutations and contains 429 total EGFR mutant peptides in the library (see Table 3 below). The top 20 EFGR mutation are A763_Y764insFQEA, D770_N771insSVD, E746_A750del, E746_S752del>V, G719A, G719C, G719S, H773_V774insH, I744_K745insKIPVAI, L747_A750del>P, L747_P753del>S, L747_S752del, L747_T751del, L747_T751del>P, L858R, L861Q, P772_H773insPR, S768I, T790M, and V769_D770insASV.
B. Cell Penetrating Peptides
In some embodiments, an immunotherapy may utilize a tumor antigen-specific peptide (e.g., EGFR mutant peptides) of the present disclosure that is associated with a cell penetrator, such as a liposome or a cell penetrating peptide (CPP). Antigen presenting cells (such as dendritic cells) pulsed with peptides may be used to enhance antitumour immunity (Celluzzi et al., 1996; Young et al., 1996). Liposomes and CPPs are described in further detail below. In some embodiments, an immunotherapy may utilize a nucleic acid encoding a tumor antigen-specific peptide (e.g., EGFR mutant peptides) of the present disclosure, wherein the nucleic acid is delivered, e.g., in a viral vector or non-viral vector.
A tumor antigen-specific peptide (e.g., EGFR mutant peptides) may also be associated with or covalently bound to a cell penetrating peptide (CPP). Cell penetrating peptides that may be covalently bound to a tumor antigen-specific peptide (e.g., EGFR mutant peptides) include, e.g., HIV Tat, herpes virus VP22, the Drosophila Antennapedia homeobox gene product, signal sequences, fusion sequences, or protegrin I. Covalently binding a peptide to a CPP can prolong the presentation of a peptide by dendritic cells, thus enhancing antitumour immunity (Wang and Wang, 2002). In some embodiments, a tumor antigen-specific peptide (e.g., the EGFR mutant peptide) of the present disclosure (e.g., comprised within a peptide or polyepitope string) may be covalently bound (e.g., via a peptide bond) to a CPP to generate a fusion protein. In other embodiments, a tumor antigen-specific peptide (e.g., EGFR mutant peptides) or nucleic acid encoding a tumor antigen-specific peptide may be encapsulated within or associated with a liposome, such as a mulitlamellar, vesicular, or multivesicular liposome, an exocytic vesicle or exosome.
As used herein, “association” means a physical association, a chemical association or both. For example, an association can involve a covalent bond, a hydrophobic interaction, encapsulation, surface adsorption, or the like.
As used herein, “cell penetrator” refers to a composition or compound which enhances the intracellular delivery of the peptide/polyepitope string to the antigen presenting cell. For example, the cell penetrator may be a lipid which, when associated with the peptide, enhances its capacity to cross the plasma membrane. Alternatively, the cell penetrator may be a peptide. Cell penetrating peptides (CPPs) are known in the art, and include, e.g., the Tat protein of HIV (Frankel and Pabo, 1988), the VP22 protein of HSV (Elliott and O'Hare, 1997) and fibroblast growth factor (Lin et al., 1995).
Cell-penetrating peptides (or “protein transduction domains”) have been identified from the third helix of the Drosophila Antennapedia homeobox gene (Antp), the HIV Tat, and the herpes virus VP22, all of which contain positively charged domains enriched for arginine and lysine residues (Schwarze et al., 2000; Schwarze et al., 1999). Also, hydrophobic peptides derived from signal sequences have been identified as cell-penetrating peptides. (Rojas el al., 1996; Rojas et al., 1998; Du et al., 1998). Coupling these peptides to marker proteins such as β-galactosidase has been shown to confer efficient internalization of the marker protein into cells, and chimeric, in-frame fusion proteins containing these peptides have been used to deliver proteins to a wide spectrum of cell types both in vitro and in vivo (Drin et al., 2002). Fusion of these cell penetrating peptides to a tumor antigen-specific peptide (e.g., EGFR mutant peptides) in accordance with the present disclosure may enhance cellular uptake of the polypeptides.
In some embodiments, cellular uptake is facilitated by the attachment of a lipid, such as stearate or myristilate, to the polypeptide. Lipidation has been shown to enhance the passage of peptides into cells. The attachment of a lipid moiety is another way that the present disclosure increases polypeptide uptake by the cell. Cellular uptake is further discussed below.
A tumor antigen-specific peptide (e.g., EGFR mutant peptides) of the present disclosure may be included in a liposomal vaccine composition. For example, the liposomal composition may be or comprise a proteoliposomal composition. Methods for producing proteoliposomal compositions that may be used with the present disclosure are described, e.g., in Neelapu et al. (2007) and Popescu et al. (2007). In some embodiments, proteoliposomal compositions may be used to treat a melanoma.
By enhancing the uptake of a tumor antigen-specific polypeptide, it may be possible to reduce the amount of protein or peptide required for treatment. This in turn can significantly reduce the cost of treatment and increase the supply of therapeutic agent. Lower dosages can also minimize the potential immunogenicity of peptides and limit toxic side effects.
In some embodiments, a tumor antigen-specific peptide (e.g., EGFR mutant peptides) may be associated with a nanoparticle to form nanoparticle-polypeptide complex. In some embodiments, the nanoparticle is a liposomes or other lipid-based nanoparticle such as a lipid-based vesicle (e.g., a DOTAP:cholesterol vesicle). In other embodiments, the nanoparticle is an iron-oxide based superparamagnetic nanoparticles. Superparamagnetic nanoparticles ranging in diameter from about 10 to 100 nm are small enough to avoid sequestering by the spleen, but large enough to avoid clearance by the liver. Particles this size can penetrate very small capillaries and can be effectively distributed in body tissues. Superparamagnetic nanoparticles-polypeptide complexes can be used as MRI contrast agents to identify and follow those cells that take up the tumor antigen-specific peptide (e.g., EGFR mutant peptides). In some embodiments, the nanoparticle is a semiconductor nanocrystal or a semiconductor quantum dot, both of which can be used in optical imaging. In further embodiments, the nanoparticle can be a nanoshell, which comprises a gold layer over a core of silica. One advantage of nanoshells is that polypeptides can be conjugated to the gold layer using standard chemistry. In other embodiments, the nanoparticle can be a fullerene or a nanotube (Gupta el al., 2005).
Peptides are rapidly removed from the circulation by the kidney and are sensitive to degradation by proteases in serum. By associating a tumor antigen-specific peptide (e.g., EGFR mutant peptides) with a nanoparticle, the nanoparticle-polypeptide complexes of the present disclosure may protect against degradation and/or reduce clearance by the kidney. This may increase the serum half-life of polypeptides, thereby reducing the polypeptide dose need for effective therapy. Further, this may decrease the costs of treatment, and minimizes immunological problems and toxic reactions of therapy.
C. Polyepitope Strings
In some embodiments, a tumor antigen-specific peptide (e.g., EGFR mutant peptides) is included or comprised in a polyepitope string. A polyepitope string is a peptide or polypeptide containing a plurality of antigenic epitopes from one or more antigens linked together. A polyepitope string may be used to induce an immune response in a subject, such as a human subject. Polyepitope strings have been previously used to target malaria and other pathogens (Baraldo et al.. 2005; Moorthy et al., 2004; Baird et al., 2004). A polyepitope string may refer to a nucleic acid (e.g., a nucleic acid encoding a plurality of antigens including EGFR mutant peptides) or a peptide or polypeptide (e.g., containing a plurality of antigens including EGFR mutant peptides). A polyepitope string may be included in a cancer vaccine composition.
D. Biological Functional Equivalents
A tumor antigen-specific peptide (e.g., EGFR mutant peptides) of the present disclosure may be modified to contain amino acid substitutions, insertions and/or deletions that do not alter their respective interactions with an HLA class protein, such as HLA-A*0101, binding regions. Such a biologically functional equivalent of a tumor antigen-specific peptide (e.g., EGFR mutant peptides) could be a molecule having like or otherwise desirable characteristics, e.g., binding of Specific HLA class I or HLA class II complexes. As a nonlimiting example, certain amino acids may be substituted for other amino acids in a tumor antigen-specific peptide (e.g., EGFR mutant peptides) disclosed herein without appreciable loss of interactive capacity, as demonstrated by detectably unchanged peptide binding to HLA. In some embodiments, the tumor antigen-specific peptide has a substitution mutation at an anchor residue, such as a substitution mutation at one, two, or all of positions: 1 (P1), 2 (P2), and/or 9 (P9). It is thus contemplated that a tumor antigen-specific peptide (e.g., EGFR mutant peptides) disclosed herein (or a nucleic acid encoding such a peptide) which is modified in sequence and/or structure, but which is unchanged in biological utility or activity remains within the scope of the compositions and methods disclosed herein.
It is also well understood by the skilled artisan that, inherent in the definition of a biologically functional equivalent peptide, is the concept that there is a limit to the number of changes that may be made within a defined portion of the molecule while still maintaining an acceptable level of equivalent biological activity. Biologically functional equivalent peptides are thus defined herein as those peptides in which certain, not most or all, of the amino acids may be substituted. Of course, a plurality of distinct peptides with different substitutions may easily be made and used in accordance with the present disclosure.
The skilled artisan is also aware that where certain residues are shown to be particularly important to the biological or structural properties of a peptide, e.g., residues in specific epitopes, such residues may not generally be exchanged. This may be the case in the present disclosure, as a mutation in an tumor antigen-specific peptide (e.g., the EGFR mutant peptide) disclosed herein could result in a loss of species-specificity and in turn, reduce the utility of the resulting peptide for use in methods of the present disclosure. Thus, peptides which are antigenic (e.g., bind specifically to HLA class I or HLA class II complexes) and comprise conservative amino acid substitutions are understood to be included in the present disclosure. Conservative substitutions are least likely to drastically alter the activity of a protein. A “conservative amino acid substitution” refers to replacement of amino acid with a chemically similar amino acid, i.e., replacing nonpolar amino acids with other nonpolar amino acids; substitution of polar amino acids with other polar amino acids, acidic residues with other acidic amino acids, etc.
Amino acid substitutions, such as those which might be employed in modifying a tumor antigen-specific peptide (e.g., EGFR mutant peptides) disclosed herein are generally based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. An analysis of the size, shape and type of the amino acid side-chain substituents reveals that arginine, lysine and histidine are all positively charged residues; that alanine, glycine and serine are all a similar size; and that phenylalanine, tryptophan and tyrosine all have a generally similar shape. Therefore, based upon these considerations, arginine, lysine and histidine; alanine, glycine and serine; and phenylalanine, tryptophan and tyrosine; are defined herein as biologically functional equivalents. In some embodiments, the mutation may enhance TCR-pMHC interaction and/or peptide-MHC binding.
The present disclosure also contemplates isoforms of the tumor antigen-specific peptides (e.g., EGFR mutant peptides) disclosed herein. An isoform contains the same number and kinds of amino acids as a peptide of the present disclosure, but the isoform has a different molecular structure. The isoforms contemplated by the present disclosure are those having the same properties as a peptide of the present disclosure as described herein.
Nonstandard amino acids may be incorporated into proteins by chemical modification of existing amino acids or by de novo synthesis of a peptide disclosed herein. A nonstandard amino acid refers to an amino acid that differs in chemical structure from the twenty standard amino acids encoded by the genetic code.
In select embodiments, the present disclosure contemplates a chemical derivative of a tumor antigen-specific peptide (e.g., EGFR mutant peptides) disclosed herein. “Chemical derivative” refers to a peptide having one or more residues chemically derivatized by reaction of a functional side group, and retaining biological activity and utility. Such derivatized peptides include, for example, those in which free amino groups have been derivatized to form specific salts or derivatized by alkylation and/or acylation, p-toluene sulfonyl groups, carbobenzoxy groups, t-butyloxycarbonyl groups, chloroacetyl groups, formyl or acetyl groups among others. Free carboxyl groups may be derivatized to form organic or inorganic salts, methyl and ethyl esters or other types of esters or hydrazides and preferably amides (primary or secondary). Chemical derivatives may include those peptides which comprise one or more naturally occurring amino acids derivatives of the twenty standard amino acids. For example, 4-hydroxyproline may be substituted for serine; and ornithine may be substituted for lysine.
It should be noted that all amino-acid residue sequences are represented herein by formulae whose left and right orientation is in the conventional direction of amino-terminus to carboxy-terminus. Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino-acid residues. The amino acids described herein are preferred to be in the “L” isomeric form. However, residues in the “D” isomeric form can be substituted for any L-amino acid residue, as long as the desired functional properties set forth herein are retained by the protein.
Preferred tumor antigen-specific peptides (e.g., EGFR mutant peptides) or analogs thereof preferably specifically or preferentially bind a Specific HLA class I or HLA class II complexes. Determining whether or to what degree a particular tumor antigen-specific peptide or labeled peptide, or an analog thereof, can bind an Specific HLA class I or HLA class II complexes and can be assessed using an in vitro assay such as, for example, an enzyme-linked immunosorbent assay (ELISA), immunoblotting, immunoprecipitation, radioimmunoassay (RIA), immunostaining, latex agglutination, indirect hemagglutination assay (IHA), complement fixation, indirect immunofluorescent assay (FA), nephelometry, flow cytometry assay, chemiluminescence assay, lateral flow immunoassay, u-capture assay, mass spectrometry assay, particle-based assay, inhibition assay and/or an avidity assay.
E. Nucleic Acids Encoding a Tumor Antigen-Specific Peptide
In an aspect, the present disclosure provides a nucleic acid encoding an isolated antigen-specific peptide comprising a sequence that has at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a peptide selected from those in Tables 1-3, or the peptide may have 1, 2, 3, or 4 point mutations (e.g., substitution mutations) as compared to a peptide selected from those in Tables 1-3. As stated above, such a tumor antigen-specific peptide may be, e.g., from 8 to 35 amino acids in length, or any range derivable therein.
Some embodiments of the present disclosure provide recombinantly-produced tumor antigen-specific peptides (e.g., EGFR mutant peptides) which can specifically bind a Specific HLA class I or HLA class II complexes. Accordingly, a nucleic acid encoding a tumor antigen-specific peptide may be operably linked to an expression vector and the peptide produced in the appropriate expression system using methods well known in the molecular biological arts. A nucleic acid encoding a tumor antigen-specific peptide disclosed herein may be incorporated into any expression vector which ensures good expression of the peptide. Possible expression vectors include but are not limited to cosmids, plasmids, or modified viruses (e.g. replication defective retroviruses, adenoviruses and adeno-associated viruses), so long as the vector is suitable for transformation of a host cell.
A recombinant expression vector being “suitable for transformation of a host cell” means that the expression vector contains a nucleic acid molecule of the present disclosure and regulatory sequences selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid molecule. The terms, “operatively linked” or “operably linked” are used interchangeably and are intended to mean that the nucleic acid is linked to regulatory sequences in a manner which allows expression of the nucleic acid.
Accordingly, the present disclosure provides a recombinant expression vector comprising nucleic acid encoding a tumor antigen-specific peptide, and the necessary regulatory sequences for the transcription and translation of the inserted protein-sequence. Suitable regulatory sequences may be derived from a variety of sources, including bacterial, fungal, or viral genes (e.g., see the regulatory sequences described in Goeddel (1990).
Selection of appropriate regulatory sequences is generally dependent on the host cell chosen, and may be readily accomplished by one of ordinary skill in the art. Examples of such regulatory sequences include: a transcriptional promoter and enhancer or RNA polymerase binding sequence, a ribosomal binding sequence, including a translation initiation signal. Additionally, depending on the host cell chosen and the vector employed, other sequences, such as an origin of replication, additional DNA restriction sites, enhancers, and sequences conferring inducibility of transcription may be incorporated into the expression vector. It will also be appreciated that the necessary regulatory sequences may be supplied by the native protein and/or its flanking regions.
A recombinant expression vector may also contain a selectable marker gene which facilitates the selection of host cells transformed or transfected with a recombinant tumor antigen-specific peptides (e.g., EGFR mutant peptides) disclosed herein. Examples of selectable marker genes are genes encoding a protein such as G418 and hygromycin which confer resistance to certain drugs, β-galactosidase, chloramphenicol acetyltransferase, or firefly luciferase. Transcription of the selectable marker gene is monitored by changes in the concentration of the selectable marker protein such as β-galactosidase, chloramphenicol acetyltransferase, or firefly luciferase. If the selectable marker gene encodes a protein conferring antibiotic resistance such as neomycin resistance transformant cells can be selected with G418. Cells that have incorporated the selectable marker gene will survive, while the other cells die. This makes it possible to visualize and assay for expression of a recombinant expression vector, and in particular, to determine the effect of a mutation on expression and phenotype. It will be appreciated that selectable markers can be introduced on a separate vector from the nucleic acid of interest.
Recombinant expression vectors can be introduced into host cells to produce a transformant host cell. The term “transformant host cell” is intended to include prokaryotic and eukaryotic cells which have been transformed or transfected with a recombinant expression vector of the present disclosure. The terms “transformed with”, “transfected with”, “transformation” and “transfection” are intended to encompass introduction of nucleic acid (e.g. a vector) into a cell by one of many possible techniques known in the art. Suitable host cells include a wide variety of prokaryotic and eukaryotic host cells. For example, the proteins of the present disclosure may be expressed in bacterial cells such as E. coli, insect cells (using baculovirus), yeast cells or mammalian cells.
A nucleic acid molecule of the present disclosure may also be chemically synthesized using standard techniques. Various methods of chemically synthesizing polydeoxy-nucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See e.g., U.S. Pat. Nos. 4,598,049; 4,458,066; 4,401,796; and 4,373,071).
Embodiments of the present disclosure concern obtaining and administering antigen-specific cells (e.g., autologous or allogeneic T cells (e.g., regulatory T cells, CD4 T cells, CD8+ T cells, or gamma-delta T cells), NK cells, invariant NK cells, NKT cells, mesenchymal stem cell (MSC)s, or induced pluripotent stem (iPS) cells) to a subject as an immunotherapy to target cancer cells. In particular, the cells are antigen-specific T cells (e.g., mutant EGFR-specific T cells). Several basic approaches for the derivation, activation and expansion of functional anti-tumor effector cells have been described in the last two decades. These include: autologous cells, such as tumor-infiltrating lymphocytes (TILs); T cells activated ex-vivo using autologous DCs, lymphocytes, artificial antigen-presenting cells (APCs) or beads coated with T cell ligands and activating antibodies, or cells isolated by virtue of capturing target cell membrane; allogeneic cells naturally expressing anti-host tumor T cell receptor (TCR); and non-tumor-specific autologous or allogeneic cells genetically reprogrammed or “redirected” to express tumor-reactive TCR or chimeric TCR molecules displaying antibody-like tumor recognition capacity known as “T-bodies”. These approaches have given rise to numerous protocols for T cell preparation and immunization which can be used in the methods described herein.
B. T Cell Preparation
In some embodiments, the T cells are derived from the blood, bone marrow, lymph, umbilical cord, or lymphoid organs. In some aspects, the cells are human cells. The cells typically are primary cells, such as those isolated directly from a subject and/or isolated from a subject and frozen. In some embodiments, the cells include one or more subsets of T cells or other cell types, such as whole T cell populations, CD4+ cells, CD8+ cells, and subpopulations thereof, such as those defined by function, activation state, maturity, potential for differentiation, expansion, recirculation, localization, and/or persistence capacities, antigen-specificity, type of antigen receptor, presence in a particular organ or compartment, marker or cytokine secretion profile, and/or degree of differentiation. With reference to the subject to be treated, the cells may be allogeneic and/or autologous. In some aspects, such as for off-the-shelf technologies, the cells are pluripotent and/or multipotent, such as stem cells, such as induced pluripotent stem cells (iPSCs). In some embodiments, the methods include isolating cells from the subject, preparing, processing, culturing, and/or engineering them, as described herein, and re-introducing them into the same patient, before or after cryopreservation.
Among the sub-types and subpopulations of T cells (e.g., CD4+ and/or CD8+ T cells) are naive T (TN) cells, effector T cells (TEFF), memory T cells and sub-types thereof, such as stem cell memory T (TSCM), central memory T (TCM), effector memory T (TEM), or terminally differentiated effector memory T cells, tumor-infiltrating lymphocytes (TIL), immature T cells, mature T cells, helper T cells, cytotoxic T cells, mucosa-associated invariant T (MAIT) cells, naturally occurring and adaptive regulatory T (Treg) cells, helper T cells, such as TH1 cells, TH2 cells, TH3 cells, TH17 cells, TH9 cells, TH22 cells, follicular helper T cells, alpha/beta T cells, and delta/gamma T cells.
In some embodiments, one or more of the T cell populations is enriched for or depleted of cells that are positive for a specific marker, such as surface markers, or that are negative for a specific marker. In some cases, such markers are those that are absent or expressed at relatively low levels on certain populations of T cells (e.g., non-memory cells) but are present or expressed at relatively higher levels on certain other populations of T cells (e.g., memory cells).
In some embodiments, T cells are separated from a PBMC sample by negative selection of markers expressed on non-T cells, such as B cells, monocytes, or other white blood cells, such as CD14. In some aspects, a CD4+ or CD8+ selection step is used to separate CD4+ helper and CD8+ cytotoxic T cells. Such CD4+ and CD8+ populations can be further sorted into sub-populations by positive or negative selection for markers expressed or expressed to a relatively higher degree on one or more naive, memory, and/or effector T cell subpopulations.
In some embodiments, CD8+ T cells are further enriched for or depleted of naive, central memory, effector memory, and/or central memory stem cells, such as by positive or negative selection based on surface antigens associated with the respective subpopulation. In some embodiments, enrichment for central memory T (TCM) cells is carried out to increase efficacy, such as to improve long-term survival, expansion, and/or engraftment following administration, which in some aspects is particularly robust in such sub-populations. See Terakura et al., 2012; Wang el al., 2012.
In some embodiments, the T cells are autologous T cells. In this method, tumor samples are obtained from patients and a single cell suspension is obtained. The single cell suspension can be obtained in any suitable manner, e.g., mechanically (disaggregating the tumor using, e.g., a gentleMACS™ Dissociator, Miltenyi Biotec, Auburn, Calif.) or enzymatically (e.g., collagenase or DNase). Single-cell suspensions of tumor enzymatic digests are cultured in interleukin-2 (IL-2). The cells are cultured until confluence (e.g., about 2×106 lymphocytes), e.g., from about 5 to about 21 days, preferably from about 10 to about 14 days.
The cultured T cells can be pooled and rapidly expanded. Rapid expansion provides an increase in the number of antigen-specific T-cells of at least about 50-fold (e.g., 50-, 60-, 70-, 80-, 90-, or 100-fold, or greater) over a period of about 10 to about 14 days. More preferably, rapid expansion provides an increase of at least about 200-fold (e.g., 200-, 300-, 400-, 500-, 600-, 700-, 800-, 900-, or greater) over a period of about 10 to about 14 days.
Expansion can be accomplished by any of a number of methods as are known in the art. For example, T cells can be rapidly expanded using non-specific T cell receptor stimulation in the presence of feeder lymphocytes and either interleukin-2 (IL-2) or interleukin-15 (IL-15), with IL-2 being preferred. The non-specific T cell receptor stimulus can include around 30 ng/ml of OKT3, a mouse monoclonal anti-CD3 antibody (available from Ortho-McNeil®, Raritan, N.J.). Alternatively, T cells can be rapidly expanded by stimulation of PBMCs in vitro with one or more antigens (including antigenic portions thereof, such as epitope(s), or a cell) of the cancer, which can be optionally expressed from a vector, such as an human leukocyte antigen A2 (HLA-A2) binding peptide, in the presence of a T cell growth factor, such as 300 IU/ml IL-2 or IL-15, with IL-2 being preferred. The in vitro-induced T cells are rapidly expanded by re-stimulation with the same antigen(s) of the cancer pulsed onto HLA-A2-expressing antigen-presenting cells. Alternatively, the T cells can be re-stimulated with irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and IL-2, for example.
The autologous T cells can be modified to express a T cell growth factor that promotes the growth and activation of the autologous T cells. Suitable T cell growth factors include, for example, IL-2, IL-7, IL-15, and IL-12. Suitable methods of modification are known in the art. See, for instance, Sambrook et al., 2001; and Ausubel et al., 1994. In particular aspects, modified autologous T cells express the T cell growth factor at high levels. T cell growth factor coding sequences, such as that of IL-12, are readily available in the art, as are promoters, the operable linkage of which to a T cell growth factor coding sequence promote high-level expression.
C. Antigen-Presenting Cells
Antigen-presenting cells, which include macrophages, B lymphocytes, and dendritic cells, are distinguished by their expression of a particular MHC molecule. APCs internalize antigen and re-express a part of that antigen, together with the MHC molecule on their outer cell membrane. The major histocompatibility complex (MHC) is a large genetic complex with multiple loci. The MHC loci encode two major classes of MHC membrane molecules, referred to as class I and class II MHCs. T helper lymphocytes generally recognize antigen associated with MHC class II molecules, and T cytotoxic lymphocytes recognize antigen associated with MHC class I molecules. In humans the MHC is referred to as the HLA complex and in mice the H-2 complex. In some aspects, EGFR mutant peptides of the embodiments are expressed in antigen presenting cells. Such cells provide engineered APCs that can be used to specifically propagate immune effector cells specific for the mutant EGER antigen of interest.
In some cases, aAPCs are useful in preparing therapeutic compositions and cell therapy products of the embodiments. For general guidance regarding the preparation and use of antigen-presenting systems, see, e.g., U.S. Pat. Nos. 6,225,042, 6,355,479, 6,362,001 and 6,790,662; U.S. Patent Application Publication Nos. 2009/0017000 and 2009/0004142; and International Publication No. WO2007/103009.
aAPC systems may comprise at least one exogenous assisting molecule. Any suitable number and combination of assisting molecules may be employed. The assisting molecule may be selected from assisting molecules such as co-stimulatory molecules and adhesion molecules. Exemplary co-stimulatory molecules include CD86, CD64 (FcγRI), 41BB ligand, and IL-21. Adhesion molecules may include carbohydrate-binding glycoproteins such as selectins, transmembrane binding glycoproteins such as integrins, calcium-dependent proteins such as cadherins, and single-pass transmembrane immunoglobulin (Ig) superfamily proteins, such as intercellular adhesion molecules (ICAMs), which promote, for example, cell-to-cell or cell-to-matrix contact. Exemplary adhesion molecules include LFA-3 and ICAMs, such as ICAM-1. Techniques, methods, and reagents useful for selection, cloning, preparation, and expression of exemplary assisting molecules, including co-stimulatory molecules and adhesion molecules, are exemplified in, e.g., U.S. Pat. Nos. 6,225,042, 6,355,479, and 6,362,001.
Provided herein are methods for treating or delaying progression of cancer in an individual comprising administering to the individual an effective amount an antigen-specific cell therapy, such as a mutant EGFR-specific T cell therapy. Adoptive T cell therapies with genetically engineered TCR-transduced T cells (conjugate TCR to other bio reactive proteins (e.g., anti-CD3) are also provided herein. In further embodiments, methods are provided for the treatment of cancer comprising immunizing a subject with a purified tumor antigen or an immunodominant tumor antigen-specific peptide.
The EGFR mutant peptides provided herein can be utilized to develop cancer vaccines or immunogens (e.g., a peptide or modified peptide mix with adjuvant, coding polynucleotide and corresponding expression products such as inactive virus or other microorganisms vaccine). These peptide specific vaccines or immunogens can be used for immunizing cancer patients directly to induce anti-tumor immuno-response in vivo, or for expanding antigen specific T cells in vitro with peptide or coded polynucleotide loaded APC stimulation. These large number of T cells can be adoptively transferred to patients to induce tumor regression.
Examples of cancers contemplated for treatment include lung cancer, head and neck cancer, breast cancer, pancreatic cancer, prostate cancer, renal cancer, bone cancer, testicular cancer, cervical cancer, gastrointestinal cancer, lymphomas, pre-neoplastic lesions in the lung, colon cancer, melanoma, and bladder cancer.
In some embodiments, T cells are autologous. However, the cells can be allogeneic. In some embodiments, the T cells are isolated from the patient themself, so that the cells are autologous. If the T cells are allogeneic, the T cells can be pooled from several donors. The cells are administered to the subject of interest in an amount sufficient to control, reduce, or eliminate symptoms and signs of the disease being treated.
In some embodiments, the subject can be administered nonmyeloablative lymphodepleting chemotherapy prior to the T cell therapy. The nonmyeloablative lymphodepleting chemotherapy can be any suitable such therapy, which can be administered by any suitable route. The nonmyeloablative lymphodepleting chemotherapy can comprise, for example, the administration of cyclophosphamide and fludarabine, particularly if the cancer is melanoma, which can be metastatic. An exemplary route of administering cyclophosphamide and fludarabine is intravenously. Likewise, any suitable dose of cyclophosphamide and fludarabine can be administered. In particular aspects, around 60 mg/kg of cyclophosphamide is administered for two days after which around 25 mg/m2 fludarabine is administered for five days.
In certain embodiments, a T-cell growth factor that promotes the growth and activation of the autologous T cells is administered to the subject either concomitantly with the autologous T cells or subsequently to the autologous T cells. The T-cell growth factor can be any suitable growth factor that promotes the growth and activation of the autologous T-cells. Examples of suitable T-cell growth factors include IL-2, IL-7, IL-15, and IL-12, which can be used alone or in various combinations, such as IL-2 and IL-7, IL-2 and IL-15, IL-7 and IL-15, IL-2, IL-7 and IL-15, IL-12 and IL-7, IL-12 and IL-15, or IL-12 and IL2. IL-12 is a preferred T-cell growth factor.
The T cell may be administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. The appropriate dosage of the T cell therapy may be determined based on the type of disease to be treated, severity and course of the disease, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician.
Intratumoral injection, or injection into the tumor vasculature is specifically contemplated for discrete, solid, accessible tumors. Local, regional or systemic administration also may be appropriate. For tumors of >4 cm, the volume to be administered will be about 4-10 ml (in particular 10 ml), while for tumors of <4 cm, a volume of about 1-3 ml will be used (in particular 3 ml). Multiple injections delivered as single dose comprise about 0.1 to about 0.5 ml volumes.
B. Pharmaceutical Compositions
Also provided herein are pharmaceutical compositions and formulations comprising antigen-specific immune cells (e.g., T cells) or receptors (e.g., TCR) and a pharmaceutically acceptable carrier. A vaccine composition for pharmaceutical use in a subject may comprise a tumor antigen peptide (e.g., a EGFR mutant peptide) composition disclosed herein and a pharmaceutically acceptable carrier.
Pharmaceutical compositions and formulations as described herein can be prepared by mixing the active ingredients (such as an antibody or a polypeptide) having the desired degree of purity with one or more optional pharmaceutically acceptable carriers (Remington's Pharmaceutical Sciences 22nd edition, 2012), in the form of lyophilized formulations or aqueous solutions. Pharmaceutically acceptable carriers are generally nontoxic to recipients at the dosages and concentrations employed, and include, but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride; benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); 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, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g. Zn-protein complexes); and/or non-ionic surfactants such as polyethylene glycol (PEG). Exemplary pharmaceutically acceptable carriers herein further include interstitial drug dispersion agents such as soluble neutral-active hyaluronidase glycoproteins (sHASEGP), for example, human soluble PH-20 hyaluronidase glycoproteins, such as rHuPH20 (HYLENEX®, Baxter International, Inc.). Certain exemplary sHASEGPs and methods of use, including rHuPH20, are described in US Patent Publication Nos. 2005/0260186 and 2006/0104968. In one aspect, a sHASEGP is combined with one or more additional glycosaminoglycanases such as chondroitinases.
C. Combination Therapies
In certain embodiments, the compositions and methods of the present embodiments involve an antigen-specific immune cell population or TCR in combination with at least one additional therapy. The additional therapy may be radiation therapy, surgery (e.g., lumpectomy and a mastectomy), chemotherapy, gene therapy, DNA therapy, viral therapy, RNA therapy, immunotherapy, bone marrow transplantation, nanotherapy, monoclonal antibody therapy, or a combination of the foregoing. The additional therapy may be in the form of adjuvant or neoadjuvant therapy.
In some embodiments, the additional therapy is the administration of small molecule enzymatic inhibitor or anti-metastatic agent. In some embodiments, the additional therapy is the administration of side-effect limiting agents (e.g., agents intended to lessen the occurrence and/or severity of side effects of treatment, such as anti-nausea agents, etc.). In some embodiments, the additional therapy is radiation therapy. In some embodiments, the additional therapy is surgery. In some embodiments, the additional therapy is a combination of radiation therapy and surgery. In some embodiments, the additional therapy is gamma irradiation. In some embodiments, the additional therapy is therapy targeting PBK/AKT/mTOR pathway, HSP90 inhibitor, tubulin inhibitor, apoptosis inhibitor, and/or chemopreventative agent. The additional therapy may be one or more of the chemotherapeutic agents known in the art.
An immune cell therapy may be administered before, during, after, or in various combinations relative to an additional cancer therapy, such as immune checkpoint therapy. The administrations may be in intervals ranging from concurrently to minutes to days to weeks. In embodiments where the immune cell therapy is provided to a patient separately from an additional therapeutic agent, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the two compounds would still be able to exert an advantageously combined effect on the patient. In such instances, it is contemplated that one may provide a patient with the antibody therapy and the anti-cancer therapy within about 12 to 24 or 72 h of each other and, more particularly, within about 6-12 h of each other. In some situations it may be desirable to extend the time period for treatment significantly where several days (2, 3, 4, 5, 6, or 7) to several weeks (1, 2, 3, 4, 5, 6, 7, or 8) lapse between respective administrations.
Various combinations may be employed. For the example below an antigen-specific immune cell therapy, peptide, or TCR is “A” and an anti-cancer therapy is “B”:
Administration of any compound or therapy of the present embodiments to a patient will follow general protocols for the administration of such compounds, taking into account the toxicity, if any, of the agents. Therefore, in some embodiments there is a step of monitoring toxicity that is attributable to combination therapy.
2. Chemotherapy
A wide variety of chemotherapeutic agents may be used in accordance with the present embodiments. The term “chemotherapy” refers to the use of drugs to treat cancer. A “chemotherapeutic agent” is used to connote a compound or composition that is administered in the treatment of cancer. These agents or drugs are categorized by their mode of activity within a cell, for example, whether and at what stage they affect the cell cycle. Alternatively, an agent may be characterized based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis.
Examples of chemotherapeutic agents include alkylating agents, such as thiotepa and cyclosphosphamide; alkyl sulfonates, such as busulfan, improsulfan, and piposulfan; aziridines, such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines, including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide, and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TMI); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards, such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, and uracil mustard; nitrosureas, such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics, such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammaII and calicheamicin omegaII); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores, aclacinomysins, actinomycin, authrarnycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins, such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, and zorubicin; anti-metabolites, such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues, such as denopterin, pteropterin, and trimetrexate; purine analogs, such as fludarabine, 6-mercaptopurine, thiamiprine, and thioguanine; pyrimidine analogs, such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, and floxuridine; androgens, such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, and testolactone; anti-adrenals, such as mitotane and trilostane; folic acid replenisher, such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids, such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSKpolysaccharide complex; razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2″-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; taxoids, e.g., paclitaxel and docetaxel gemcitabine; 6-thioguanine; mercaptopurine; platinum coordination complexes, such as cisplatin, oxaliplatin, and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids, such as retinoic acid; capecitabine; carboplatin, procarbazine, plicomycin, gemcitabine, navelbine, farnesyl-protein transferase inhibitors, transplatinum, and pharmaceutically acceptable salts, acids, or derivatives of any of the above.
3. Radiotherapy
Other factors that cause DNA damage and have been used extensively include what are commonly known as γ-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells. Other forms of DNA damaging factors are also contemplated, such as microwaves, proton beam irradiation (U.S. Pat. Nos. 5,760,395 and 4,870,287), and UV-irradiation. It is most likely that all of these factors affect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes. Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.
4. Immunotherapy
The skilled artisan will understand that additional immunotherapies may be used in combination or in conjunction with methods of the embodiments. In the context of cancer treatment, immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells. Rituximab (RITUXAN®) is such an example. The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell. The antibody alone may serve as an effector of therapy or it may recruit other cells to actually affect cell killing. The antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ricin A chain, cholera toxin, pertussis toxin, etc.) and serve as a targeting agent. Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target. Various effector cells include cytotoxic T cells and NK cells.
Antibody-drug conjugates have emerged as a breakthrough approach to the development of cancer therapeutics. Cancer is one of the leading causes of deaths in the world. Antibody-drug conjugates (ADCs) comprise monoclonal antibodies (MAbs) that are covalently linked to cell-killing drugs. This approach combines the high specificity of MAbs against their antigen targets with highly potent cytotoxic drugs, resulting in “armed” MAbs that deliver the payload (drug) to tumor cells with enriched levels of the antigen. Targeted delivery of the drug also minimizes its exposure in normal tissues, resulting in decreased toxicity and improved therapeutic index. The approval of two ADC drugs, ADCETRIS® (brentuximab vedotin) in 2011 and KADCYLA® (trastuzumab emtansine or T-DM1) in 2013 by FDA validated the approach. There are currently more than 30 ADC drug candidates in various stages of clinical trials for cancer treatment (Leal et al., 2014). As antibody engineering and linker-payload optimization are becoming more and more mature, the discovery and development of new ADCs are increasingly dependent on the identification and validation of new targets that are suitable to this approach and the generation of targeting MAbs. Two criteria for ADC targets are upregulated/high levels of expression in tumor cells and robust internalization.
In one aspect of immunotherapy, the tumor cell must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in the context of the present embodiments. Common tumor markers include CD20, carcinoembryonic antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, laminin receptor, erb B, and p155. An alternative aspect of immunotherapy is to combine anticancer effects with immune stimulatory effects. Immune stimulating molecules also exist including: cytokines, such as IL-2, IL-4, IL-12, GM-CSF, gamma-IFN, chemokines, such as MIP-1, MCP-1, IL-8, and growth factors, such as FLT3 ligand.
Examples of immunotherapies currently under investigation or in use are immune adjuvants, e.g., Mycobacterium bovis, Plasmodium falciparum, dinitrochlorobenzene, and aromatic compounds (U.S. Pat. Nos. 5,801,005 and 5,739,169; Hui and Hashimoto, 1998; Christodoulides et al., 1998); cytokine therapy, e.g., interferons α, β, and γ, IL-1, GM-CSF, and TNF (Bukowski et al., 1998; Davidson el al., 1998; Hellstrand et al., 1998); gene therapy, e.g., TNF, IL-1, IL-2, and p53 (Qin et al., 1998. Austin-Ward and Villaseca, 1998; U.S. Pat. Nos. 5,830,880 and 5,846,945); and monoclonal antibodies, e.g., anti-CD20, anti-ganglioside GM2, and anti-p185 (Hollander, 2012; Hanibuchi et al., 1998; U.S. Pat. No. 5,824,311). It is contemplated that one or more anti-cancer therapies may be employed with the antibody therapies described herein.
In some embodiments, the immunotherapy may be an immune checkpoint inhibitor. Immune checkpoints either turn up a signal (e.g., co-stimulatory molecules) or turn down a signal. Inhibitory immune checkpoints that may be targeted by immune checkpoint blockade include adenosine A2A receptor (A2AR), B7-H3 (also known as CD276), B and T lymphocyte attenuator (BTLA), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4, also known as CD152), indoleamine 2,3-dioxygenase (IDO), killer-cell immunoglobulin (KIR), lymphocyte activation gene-3 (LAG3), programmed death 1 (PD-1), T-cell immunoglobulin domain and mucin domain 3 (TIM-3) and V-domain Ig suppressor of T cell activation (VISTA). In particular, the immune checkpoint inhibitors target the PD-1 axis and/or CTLA-4.
The immune checkpoint inhibitors may be drugs such as small molecules, recombinant forms of ligand or receptors, or, in particular, are antibodies, such as human antibodies (e.g., International Patent Publication WO2015016718; Pardoll, Nat Rev Cancer, 12(4): 252-64, 2012; both incorporated herein by reference). Known inhibitors of the immune checkpoint proteins or analogs thereof may be used, in particular chimerized, humanized or human forms of antibodies may be used. As the skilled person will know, alternative and/or equivalent names may be in use for certain antibodies mentioned in the present disclosure. Such alternative and/or equivalent names are interchangeable in the context of the present disclosure. For example, it is known that lambrolizumab is also known under the alternative and equivalent names MK-3475 and pembrolizumab.
In some embodiments, the PD-1 binding antagonist is a molecule that inhibits the binding of PD-1 to its ligand binding partners. In a specific aspect, the PD-1 ligand binding partners are PDL1 and/or PDL2. In another embodiment, a PDL1 binding antagonist is a molecule that inhibits the binding of PDL1 to its binding partners. In a specific aspect, PDL1 binding partners are PD-1 and/or B7-1. In another embodiment, the PDL2 binding antagonist is a molecule that inhibits the binding of PDL2 to its binding partners. In a specific aspect, a PDL2 binding partner is PD-1. The antagonist may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide. Exemplary antibodies are described in U.S. Pat. Nos. 8,735,553, 8,354,509, and 8,008,449, all incorporated herein by reference. Other PD-1 axis antagonists for use in the methods provided herein are known in the art such as described in U.S. Patent Application No. US20140294898, US2014022021, and US20110008369, all incorporated herein by reference.
In some embodiments, the PD-1 binding antagonist is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody). In some embodiments, the anti-PD-1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and CT-011. In some embodiments, the PD-1 binding antagonist is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDL1 or PDL2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence). In some embodiments, the PD-1 binding antagonist is AMP-224. Nivolumab, also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558, and OPDIVO®, is an anti-PD-1 antibody described in WO2006/121168. Pembrolizumab, also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA®, and SCH-900475, is an anti-PD-1 antibody described in WO2009/114335. CT-011, also known as hBAT or hBAT-1, is an anti-PD-1 antibody described in WO2009/101611. AMP-224, also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in WO2010/027827 and WO2011/066342.
Another immune checkpoint that can be targeted in the methods provided herein is the cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), also known as CD152. The complete cDNA sequence of human CTLA-4 has the Genbank accession number L15006. CTLA-4 is found on the surface of T cells and acts as an “off” switch when bound to CD80 or CD86 on the surface of antigen-presenting cells. CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T cells and transmits an inhibitory signal to T cells. CTLA4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to CD80 and CD86, also called B7-1 and B7-2 respectively, on antigen-presenting cells. CTLA4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal. Intracellular CTLA4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.
In some embodiments, the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-CTLA-4 antibodies can be used. For example, the anti-CTLA-4 antibodies disclosed in: U.S. Pat. No. 8,119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab), U.S. Pat. No. 6,207,156; Hurwitz et al. (1998) Proc Natl Acad Sci USA 95(17): 10067-10071; Camacho et al. (2004) J Clin Oncology 22(145); Abstract No. 2505 (antibody CP-675206); and Mokyr et al. (1998) Cancer Res 58:5301-5304 can be used in the methods disclosed herein. The teachings of each of the aforementioned publications are hereby incorporated by reference. Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used. For example, a humanized CTLA-4 antibody is described in International Patent Application No. WO2001014424, WO2000037504, and U.S. Pat. No. 8,017,114; all incorporated herein by reference.
An exemplary anti-CTLA-4 antibody is ipilimumab (also known as 10D1, MDX-010, MDX-101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g., WO 01/14424). In other embodiments, the antibody comprises the heavy and light chain CDRs or VRs of ipilimumab. Accordingly, in one embodiment, the antibody comprises the CDR1, CDR2, and CDR3 domains of the VH region of ipilimumab, and the CDR1, CDR2 and CDR3 domains of the VL region of ipilimumab. In another embodiment, the antibody competes for binding with and/or binds to the same epitope on CTLA-4 as the above-mentioned antibodies. In another embodiment, the antibody has at least about 90% variable region amino acid sequence identity with the above-mentioned antibodies (e.g., at least about 90%, 95%, or 99% variable region identity with ipilimumab).
Other molecules for modulating CTLA-4 include CTLA-4 ligands and receptors such as described in U.S. Pat. Nos. 5,844,905, 5,885,796 and International Patent Application Nos. WO1995001994 and WO1998042752; all incorporated herein by reference, and immunoadhesins such as described in U.S. Pat. No. 8,329,867, incorporated herein by reference.
5. Surgery
Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative, and palliative surgery. Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed and may be used in conjunction with other therapies, such as the treatment of the present embodiments, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy, and/or alternative therapies. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically-controlled surgery (Mohs' surgery).
Upon excision of part or all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment may be accomplished by perfusion, direct injection, or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.
6. Other Agents
It is contemplated that other agents may be used in combination with certain aspects of the present embodiments to improve the therapeutic efficacy of treatment. These additional agents include agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers, or other biological agents. Increases in intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population. In other embodiments, cytostatic or differentiation agents can be used in combination with certain aspects of the present embodiments to improve the anti-hyperproliferative efficacy of the treatments. Inhibitors of cell adhesion are contemplated to improve the efficacy of the present embodiments. Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with certain aspects of the present embodiments to improve the treatment efficacy.
An article of manufacture or a kit is provided comprising antigen-specific immune cells, TCRs, or antigen peptides (e.g., EGFR peptide) is also provided herein. The article of manufacture or kit can further comprise a package insert comprising instructions for using the antigen-specific immune cells to treat or delay progression of cancer in an individual or to enhance immune function of an individual having cancer. Any of the antigen-specific immune cells described herein may be included in the article of manufacture or kits. Suitable containers include, for example, bottles, vials, bags and syringes. The container may be formed from a variety of materials such as glass, plastic (such as polyvinyl chloride or polyolefin), or metal alloy (such as stainless steel or hastelloy). In some embodiments, the container holds the formulation and the label on, or associated with, the container may indicate directions for use. The article of manufacture or kit may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use. In some embodiments, the article of manufacture further includes one or more of another agent (e.g., a chemotherapeutic agent, and anti-neoplastic agent). Suitable containers for the one or more agent include, for example, bottles, vials, bags and syringes.
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
Patient characteristics, PPV administration, and response assessment. Previously reported was a stage IV NSCLC patient who experienced a remarkable regression of multiple lung tumors following PPV that was associated with CD8+ T-cell responses against the widely shared EGFR-L858R mutation (Li et al., 2016). Based on this case study, a phase Ib clinical trial of PPV for stage III/IV NSCLC patients was initiated to determine the safety and feasibility of PPV, with secondary endpoints being to assess potential clinical survival benefit in addition to the immunogenicity of personalized and shared NeoAgs (
All 24 NSCLC patients had previously failed multiple lines of conventional therapy, including surgery, radiation therapy, and/or chemotherapy. Sixteen of the patients bearing EGFR-mutated tumors had also previously progressed on EGFRi therapy, with 9 of these patients failing 2 or more different EGFRi drugs. These 16 patients were given the option of either stopping or continuing EGFRi therapy concurrent with PPV immunization; 9 patients chose to continue receiving EGFRi and 7 patients opted to stop EGFRi therapy. Aside from these 9 patients, none of other 15 patients on the PPV trial received any other treatment during the follow-up period. Although patients were not initially randomized into separate cohorts, as shown below retrospective analyses revealed distinct response and survival profiles when the 24 patients were divided into the following 3 groups: EGFR wild-type (WT) patients receiving PPV only (Group 1), EGFR-mutated patients receiving PPV only (Group 2); and EGFR-mutated patients receiving PPV with concurrent EGFRi (Group 3) (
Personalized neoantigen vaccine design. Large-scale whole exome sequencing studies have demonstrated that NSCLC has one of the highest mutational burdens of all cancer types, with individual patient tumors often expressing >100 or significantly more nonsynonymous somatic mutations (Rizva et al., 2015; Lawrence et al., 2013). Based on such profiles, current HLA class I peptide-binding prediction algorithms typically generate hundreds of potential NeoAg peptide candidates, many more than can be incorporated into a single multiepitope peptide vaccine.
However, most of these mutations are considered “branch” mutations expressed by tumor sub-clones but not by all tumor cells; these mutations are also less likely to constitute driver mutations essential for maintaining tumor survival (Hao et al., 2016). In order to focus on targeting shared driver mutations, we chose to perform mutational profiling on a panel of 508 known cancer-associated genes using DNA from needle-biopsied fresh tumor tissue (Table 4). Vaccine peptides were chosen primarily based on the highest predicted binding affinity of mutation-encoding NeoAgs to each patient's individual HLA class I and class II allotypes (Table 5, Methods). Each patient was immunized with a unique, personalized mixture of short and long NeoAg peptides dissolved in saline, divided into 2 pools and administered subcutaneously into opposite extremities. Imiquimod was applied topically after each immunization to provide co-stimulatory signals through Toll-like receptor (TLR)7 (
Among the 24 enrolled patients, a mean of 6.1 coding mutations were detected per tumor (range, 1 to 20). Of the 16 patients with EGFR-mutated tumors, 14 harbored common EGFR driver mutations (7 with L858R point mutations and 7 with Exon 19 deletions). 2 of which were accompanied by T790M mutations known to confer resistance to 1st generation EGFRi. The other 2 additional patients harbored the comparatively rare H773L mutation. The number of vaccine peptides administered ranged from 5 to 14 per patient (mean, 9.4), which was primarily determined by the number of NeoAgs predicted to bind to patient HLA class I (mean, 6.5 peptides) or HLA class II (mean=2.9 peptides). Patients in Groups 2 and 3 received a mean of 4 mutated EGFR peptides each (2.8 short and 1.2 long). The number of immunizing peptides or mean predicted peptide binding affinity did not differ significantly between groups; however, patients in Groups 2 and 3 received vaccines targeting less somatic mutations overall (
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PPV induced clinical responses in multiple patients with EGFR-mutated tumors. Clinical outcomes for all 24 patients are shown in Table 6, with Group outcomes summarized in
+Pt. 17 is a complete responder.
++patients expressed each listed HLA class II allotype.
Notably, none of the patients in Group 3 had a break or “drug holiday” from EGFRi treatment prior to treatment on the trial, supporting that the NeoAg vaccination played a key role in these clinical responses. Notably, Group 3 patients experienced longer median OS compared with Group 2 patients (13.8 vs. 7.6 months, P=0.038,
PPV induced NeoAg-specific T-cell responses against shared EGFR mutations. To better understand the nature of the antitumor responses, sequential immune monitoring was performed on samples of patient peripheral blood mononuclear cells (PBMC) collected pre- or post-PPV (see Methods). Vaccine-induced immune responses were initially screened by stimulating individual patient PBMC with pools of their immunizing peptides and measuring specific interferon-gamma (IFN-γ) secretion by ELISA (
ELISPOT-based immune monitoring revealed that EGFR mutations constituted the dominant targets of NeoAg-specific T-cell responses in 5 out of the 6 responding patients for which vaccine-induced responses were observed. While Pt. 11 generated a moderate IFN-γ response to a mutated AQP12A(L28R) NeoAg peptide restricted to HLA-A *0301, they did not generate any detectable response against an HLA-A*0201-restricted EGFR(H773L) NeoAg vaccine peptide (
Patient 22 (PR), in addition to generating a robust response against an A*0201-restricted FGFR1(R734W) NeoAg peptide, also generated vaccine-induced reactivity against a long DRB1 *0901-restricted NeoAg peptide (MASVDNPLMCRLLGICL) (SEQ ID NO: 958) containing the compound EGFR mutation H773L/V774M. Pts. 8 and 16 both generated immune responses against a long HLA class II-restricted EGFR NeoAg peptide (HVKITDFGRAKLLGAEE) (SEQ ID NO: 826) containing the L858R mutation (
Surprisingly, the KITDFGRAK NeoAg peptide (SEQ ID NO: 4) is predicted to bind HLA-A*1101 with lower affinity (163 nM) than the corresponding WT peptide (20 nM), though it still falls well within typical range for moderate-affinity HLA binders (
PPV drove proliferation and tumor infiltration of EGFR NeoAg-specific T cells. TCRVβ-CDR3 sequencing was performed on DNA isolated from pre- and post-vaccine PBMC collected from 17 PPV patients. Clonality scores were calculated for each time point, demonstrating increased T-cell clonality in 10 patients after PPV, with 5 patients showing decreases in clonality and 2 patients remaining unchanged (mean change, +13.2%,
Patient 5 experienced a post-PPV objective clinical response with no disease progression at >20 months, which provided a unique opportunity to analyze the longer-term dynamics of the NeoAg-specific immune response in this patient. An A*1101/KITDFGRAK (SEQ ID NO: 4) tetramer was used to sort EGFR(L858R)-specific CD8+ T cells from PBMC drawn 12 months following the initiation of PPV (
One striking feature revealed by this analysis was that 40 of the 52 Tetr clones sorted post-PPV were already present at elevated frequencies in pre-PPV PBMC and TIL samples, suggesting that spontaneous priming of EGFR NeoAg-specific cells had occurred prior to immunization. However, most of these Tet+ CDR3 clones showed significant increases in PBMC frequency over the 12-week PPV course that were associated with the patients clinical response, consistent with the IFN-γ immune monitoring results (
EGFRi promotes immune cell infiltration, antigen presentation, and T-cell activation. Although Group 2 and Group 3 patients showed similar clinical objective response rates following PPV, Group 3 patients showed significantly extended OS and PFS (
To determine if tumor samples from Group 3 patients demonstrated similar gene signatures, RNAseq analysis was performed on tumor biopsies from a small subset of PPV patients. Two tumor specimens analyzed were from patients not on EGFRi therapy (Group 2 Pts. 16 and 24), and two specimens were from patients on EGFRi therapy (Group 3 Pts. 12 and 23). Biopsies were taken during PPV immunization with the exception of the Pt. 24 specimen, which was obtained pre-PPV. Gene expression signatures for cell cycle, cell division, and cell survival in EGFRi-treated Pts. 12 and 23 correlated well with those of EGFRi-treated H1975 cells, as did gene signatures for EGFR signaling and proliferation rate (
Collectively, our study supports the following model to explain the therapeutic synergy of peptide vaccination and EGFRi therapy (
Discussion. This may be the first report demonstrating that peptide vaccination against shared NeoAgs can induce objective clinical regressions in multiple cancer patients. Owing to HLA diversity and the overwhelming prevalence of private mutations, no previous vaccine study has reported immunizing more than a single patient with potentially shared NeoAg peptides. However, the relatively high prevalence of both HLA-A* 1101 and EGFR(L858R) mutations in Asian NSCLC patients predicted that −15% of our EGFR-mutated patients would share this combined phenotype (Kobayashi et al., 2016; Gonzalez-Galarza et al., 2015). This provided a unique opportunity to immunize 5 such patients (4 in this study) with vaccines containing EGFR NeoAg peptides in common, including the A*1101-restricted KITDFGRAK peptide (SEQ ID NO: 4) (Li et al., 2016). Remarkably, 4 of the 5 patients experienced tumor regressions within 12 weeks of NeoAg vaccination, with all 4 patients demonstrating significantly increased or dominant KITDFGRAK (SEQ ID NO: 4)-specific CD8+ T-cell reactivity during the time of the clinical responses (Li et al., 2016). By showing that multiple A*101/EGFR(L858R) patients responded clinically to immunization with shared NeoAg peptides, this study provides an important first proof-of-concept in cancer vaccine studies.
Our study also found evidence that at least 2 other EGFR mutations can be immunogenic in NSCLC patients, with 2 additional clinical responses being associated with dominant vaccine-induced co4+ or cos+ T-cell responses against the H773L/V774M or T790M mutations, respectively (
Since peptide-based cancer vaccine studies have only rarely reported clinical responses following immunization, it is worth discussing the unique features of our vaccination approach. To activate both CD4+ and CD8+ T cell-mediated immunity, we chose to immunize patients with mixtures of long and short NeoAg peptides, often including multiple peptides (up to six) against the same targeted NeoAg (Table 5). Peptides were solubilized and administered in saline to avoid any inhibitory long-term antigen depot effects; in order to compensate for the typically short half-life of saline-solubilized peptides, vaccinations were administered weekly (Li et al., 2016; Overwijk et al., 2015). Focusing the mutation calling on a panel of 508 cancer-associated, potential driver genes greatly simplified PPV design, but also restricted the number of potential NeoAg targets identified per patient, a significant limitation of our study. However, this more focused approach did allow for EGFR mutations to be identified as shared NeoAgs with promising therapeutic potential. For a vaccine adjuvant, we employed topically-applied Imiquimod cream, a TLR7 agonist known to be moderately effective at activating local antigen-presenting cells. Based on the breadth, magnitude, and timing of the NeoAg-specific T-cell responses observed, we interpret that our immunization approach was likely most effective at boosting T-cell responses that had previously been spontaneously primed in patients, while demonstrating limited efficacy for priming new T-cell responses. Incorporating more potent and promising vaccine adjuvants such as polyl:C, anti-CD40, or STING agonists into future peptide vaccine formulations may help to address lack of de novo T-cell priming. Nevertheless, PPV-mediated activation of pre-existing immune responses was effective at inducing multiple clinical responses in our study, a finding that strongly supports NeoAg immunoreactivity pre-screening to guide future vaccine design for NSCLC patients (Malekzadeh et al., 2019).
EGFRi therapy, while not impacting the clinical response rate to PPV nor the magnitude of PPV-induced immune responses, did have a surprisingly positive impact on patient OS and PFS in spite of prior failure as a monotherapy (
Although many significant challenges to personalized NeoAg identification remain to be addressed, these results provide the first evidence that shared NeoAgs can constitute therapeutic vaccine targets capable of inducing immune and clinical responses in multiple cancer patients. Based on the prevalence of HLA-A*1101 and L858R mutations, the KITDFGRAK NeoAg peptide (SEQ ID NO: 4) is estimated to be presented by up to 8.4% of Asian and 1.2% of North American NSCLC patients, making it one of the most widely shared NeoAgs in cancer (Kobayashi et al., 2016; Gonzalez-Galarza et al., 2015; Wirth and Kuhnel, 2017; Lu and Robbins, 2016). It is demonstrated that multiple other EGFR mutations can also be immunogenic for patients expressing specific HLA haplotypes, and that there is a natural antigen presentation ‘synergy’ between the most prevalent EGFR mutations and the HLA-A3 superfamily of class I allotypes, findings that have important practical implications for future vaccine development and patient selection. It is also important to note that since tumor burden and pleural effusion were both associated with worse overall survival of PPV patients (
Data reporting. No statistical methods were employed to predetermine patient sample numbers. The study was not randomized and some investigators were not blinded during experiments and outcome assessments.
Clinical Trial Design and Treatment.
Between November 2016 and December 2018, a single-arm trial was conducted at Tianjin Beichen Hospital in China. The study protocol conformed to the ethical guidelines of the 1975 Declaration of Helsinki and was approved by the internationally-recognized ChiCTR and the Ethics Committee of Tianjin Beichen Hospital (Chinese Clinical Trial Registry (ChiCTR) No.: ChiCTR-IIR-16009867. Primary endpoints of the trial were safety and tolerability, feasibility of the personalized approach, and secondary endpoints were anti-tumor immune reactivity, clinical response and potential survival benefit. All patients provided written informed consent before enrolling in the study.
Patient eligibility. Twenty-four patients with stage III-IV NSCLC (18 adenocarcinoma and 6 squamous cell carcinoma) were enrolled in this clinical study of personalized neoantigen peptide vaccine (PPV) and were successfully immunized. The 24 study patients were selected according to the following inclusion criteria: adult patients aged 18 or more; clinical assessments classified all patients with NSCLC stage III/IV according to NCCN Clinical Practice Guidelines in Oncology, Version 3.2016, Non-Small Cell Lung Cancer and the Eighth Edition Lung Cancer Stage Classification; NSCLC diagnosis was confirmed by biopsy and pathological assessment; patients experienced disease recurrence after failing conventional treatments including surgery, chemotherapy, radiotherapy and/or EGFR inhibitor (EGFRi) therapy, and had no active treatments; patients showed good or moderate Eastern Cooperative Oncology Group (ECOG) performance status (PS≤3); patients were undergoing no other concurrent immunotherapies; pretreatment biopsy samples were available, and showed at least one genetic mutation; patients had a life expectancy of >3 months. Patients were excluded if they: were pregnant or lactating; had known or suspected autoimmune disease, or other immune system disease; had systemic cytotoxic chemotherapy or experimental drugs for treatment of metastatic NSCLC within 4 weeks prior to first dose of personalized vaccine (not including EGFRi); had participated in any other clinical trial involving another investigational agent within 4 weeks prior to first dose of personalized vaccine; had liver or kidney dysfunction, severe heart disease, coagulation dysfunction or hematopoietic impairment; had any active infection requiring systemic treatment; suffered from other current malignancies either in progress or treated within the past five years. Pre-treatment tumor biopsies were required for the trial, and post-treatment biopsies were optional and required additional patient consent. The clinical characteristics of study patients are shown in
Generation of Personalised Neoantigen Vaccines.
Somatic mutation analysis. Patient tumor specimens were obtained by fine-needle biopsy of tumor sites in the lung or lymph node (Table 7). Tumor biopsies from individual patients underwent DNA sequencing using a 508 gene panel, in conjunction with standard clinical and pathology laboratory test procedures at Tianjin Beichen Hospital (Tianjin. China). This genotyping panel was designed to detect shared, tumor-associated driver mutations within 508 cancer-associated genes (Table 4). Tumor DNA was extracted from biopsy samples according to the instructions of the TIANamp Genomic DNA Kit (Tiangen, China), and detected by Hiseq X-10 (Illumina, USA) which profiled using exon capture by hybridization followed by next-generation DNA sequencing (HengJia Medical Laboratory, Tianjin, China). For somatic mutation calling, analyses of next generation sequencing data of tumor and matched PBMCs (as source of normal germline DNA) from the patients were used to identify the specific coding-sequence mutations, including single-, di- or tri-nucleotide variants that lead to single amino acid missense mutations and small insertions/deletions (indels). Output from Illumina software was processed by the Broad Picard Pipeline to yield BAM files, which contained aligned reads (bwa version 0.7.8, aligned to the NCBI Human Reference Genome Build hg19) with well-calibrated quality scores. Somatic single nucleotide variations (sSNVs), somatic small insertions and deletions were all detected using Varscan2 (version 2.4.3). All indels were manually reviewed using the Integrative Genomics Viewer (version 2.4.1). All somatic mutations, insertions and deletions were annotated using Annovar (version 2013-07-28 11:32:41). Neoantigen peptides were chosen based on nonsynonymous somatic mutations detected at a mutated variant allele frequency of 0.04 or higher.
HLA typing. Peripheral blood was drawn for high resolution HLA typing at the time of enrollment. Human leukocyte antigen (HLA) loci were typed via polymerase chain reaction-sequence-based typing (PCR-SBT) method employing a DNA amplification step (CapitalBio, China). Briefly, DNA was extracted from peripheral blood of patients according to the instructions of the Magic Beads DNA Extraction Kit (TANBead, China). Exons 2 and 3 of HLA class I genes (HLA-A, B, and C) and exon 2 of HLA class II a and P genes (HLA-DQ and DR) were amplified and purified, and PCR products were sequenced on ABI 3730XL DNA Analyzer (Applied Biosystems, USA). Sequence chromatograms were analyzed using ATF1.5 software (Conexio Genomics, Australia).
Vaccine peptide selection. Due to the high number of somatic mutations typically found in lung cancers and the fact that the majority constitute private ‘passenger’ mutations, we chose to target somatic mutations detected from a focused panel of 508 tumor-associated genes. The rationale for this approach was two-fold: (1) It would enable targeting of mutations more likely to be essential for the tumor phenotype and thus less likely to be lost through immune editing, and (2) It would increase the chances of identifying shared neoantigen targets that could potentially be beneficial to multiple NSCLC patients. Non-synonymous coding mutations detected by the 508-gene panel were translated in silico and the resulting neoantigen sequences were assessed for predicted binding affinity to patient HLA class I and class II molecules according to the HLA-peptide prediction algorithms NetMHC4.0, NetMHCpan3.0, NetMHCpan4.0, NetMHCII2.2 and NetMHCII2.3 (Andretta et al., 2015; Jensen et al., 2018). Immunizing neoantigen peptides were chosen primarily based on highest predicted binding affinity to the patient's HLA class I and class II molecules. However, vaccines were also designed to maximize the number of different HLA molecules engaged and minimize intra-HLA peptide competition when possible. Certain biochemical properties (such as elevated hydrophobicity or the presence of multiple cysteines) which can negatively impact the synthesizability or solubility of the immunizing peptides were also considered. In addition, we aimed to design individual patient vaccines to contain an approximately 2:1 ratio of short to long vaccine peptides, or as close as the somatic mutation profiling and HLA/peptide binding predictions would allow. For each patient, up to 14 peptides of 9 to 17 amino acids in length arising from up to 12 independent mutations were selected and prioritized. A mean of 9.4 neoantigen peptides per patient were chosen for peptide synthesis, which included on average 6.5 short, HLA class I-restricted peptides and 2.9 long, HLA class II-restricted peptides (Table 5).
Patient immunizations. Immunizing peptides were synthesized using standard solid-phase synthetic peptide chemistry, purified to >98% using reverse phase high performance liquid chromatography and tested for sterility and the presence of endotoxin to ensure safety and tolerability using methodologies consistent with Good Manufacturing Practice (HengJia Neoantigen Biotechnology (Tianjin) Co., Ltd.). As shown in Table 5, 5 to 14 peptides per patient were synthesized, solubilized individually in sterile phosphate-buffered saline (PBS), and mixed into 2 separate peptide cocktails, each with 2-7 short peptides and 1-3 long peptides in 1 ml total volume. Peptides binding to the same HLA allotypes were separated into different cocktails to reduce potential antigen competition. Patients received 200 μg of each peptide per immunization, injected subcutaneously into the left and right extremities, and administered weekly for a minimum of 12 weeks. In order to provide concurrent Toll-like receptor (TLR)-7 stimulation of pAPCs, Aldara cream with 5% imiquimod was applied topically as a vaccine adjuvant over the vaccine site immediately after peptide cocktail administration. Patients were permitted to continue immunizations after 12 weeks if desired and in the patient's best interest. 11 of the 24 patients continued to receive vaccinations beyond 12 weeks, as shown in
Sample collection. Serial peripheral blood mononuclear cells (PBMC) samples were collected at pre-treatment, as well as at 4, 8, and 12 weeks post-vaccination. A maximum of 15 ml of blood was drawn per month, according to Tianjin Beichen Hospital regulations for advanced-stage cancer patients. Collection of additional blood samples beyond the 12 weeks of the trial period were optional and required additional patient consent. Extra blood samples were collected from Patients 5, 8, and 17, who had all experienced clinical objective responses. Viable PBMCs were collected and stored at −80° C. Collection of post-vaccine tumor biopsies was optional but not required in this trial due to the invasive nature of the procedure, uncertain feasibility, and the general reluctance of most patients. Tumor tissues obtained for further RNA sequencing and/or bulk T cell receptor VB CDR3 sequencing analysis were collected from PPV trial Patients 5, 12, 16, 23 and 24 after providing written informed consent.
Tumor response evaluation criteria. Objective tumor response assessments were made according to the Response Evaluation Criteria in Solid Tumors (RECIST version 1.1) guidelines. We utilized computerized tomography (CT) and/or magnetic resonance imaging (MRI) scans to measure selected target lesions. Patients were required to perform at least one pre-treatment scan for baseline measurements and another scan at 3 to 4 months post-vaccine for response assessment. Additional patient scans were taken monthly during the first 12 weeks of vaccination if feasible. Target lesions with a minimum size of 10 mm (15 mm for malignant lymph nodes) were measured in the longest diameter by three different radiologists, with the mean of the three independent measurements used for clinical assessments. A maximum of two target lesions per organ were measured, with the two largest lesions selected, up to a maximum of five lesions in total. Tumor burden was calculated as the sum of the diameters of all target lesions (
Clinical trial statistical plan. Statistical analysis was primarily descriptive, including enumeration of patients who experienced any adverse events. All statistical tests were 2-sided with an alpha level of 0.05. Confidence intervals to be evaluated were constructed with a significance level of 0.05. Additional exploratory analyses of the data were conducted as deemed appropriate.
Analysis of Primary Endpoints. Treatment-associated adverse events were analyzed based on those categorized and graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events (version 4.0). During the first 12 weeks of vaccine treatment and continued vaccination beyond 12 weeks, safety assessments were performed starting on the day of each vaccination for up to 48 hours afterwards. Safety assessments were performed every 2 months for patients with extended follow-up time. Disease-associated symptoms that were present at baseline (pre-treatment) were not reported unless they worsened after vaccination.
Analysis of Secondary Endpoints. Secondary endpoints including progression-free survival (PFS) and overall survival (OS) were summarized using the Kaplan-Meier method. Measurements of the immune responses via ELISA, ELISPOT and tetramer analysis prior to the first vaccination and every 4 weeks after each vaccination were summarized descriptively. Determinations of PFS and OS for enrolled subjects were calculated from the date of enrollment to disease progression and/or death, or 31Dec. 2018, respectively. Sub-Group Analyses. Based on differing response and survival profiles, we analyzed the enrolled patients according to subgroup based on wild-type (WT) or mutated (Mut) EGFR mutation status, and if EGFR inhibitor use was continued or stopped prior to the start of immunization. These groups were defined as EGER WT-PPV only (Group 1), EGFR Mut-PPV only (Group 2) and EGFR Mut-PPV+EGFRi (Group 3).
Enzyme-linked immunosorbent (ELISA) and Enzyme-linked Immunospot (ELISPOT) assays. Peripheral blood mononuclear cells (PBMCs) collected prior to the start of immunization and at different time points following PPV were isolated by Ficoll density gradient centrifugation and counted in the presence of trypan blue dye to evaluate viability prior to cryopreservation. For ELISA analysis, 5×105 PBMCs in RPMI-1640 containing 10% FBS were added to each well of 96-well plate with a total volume of 250 ul. PBMC were cultured in the presence of vaccine peptide pools, individual vaccine peptides, or irrelevant control peptides (7.5 ug/ml) along with 300 IU/ml interleukin (IL-2) in a 37° C. humidified incubator with 5% CO2 for 5 days. Following 24 hours of peptide re-stimulation, the IFN-γ concentration of cell supernatants was measured using a human IFN-γ ELISA kit (Dakewe, China), according to the manufacturer's instructions. A level of IFN-γ secretion 1.5-fold or greater over background signal with no peptide control was considered to be a positive immune response. Immune Response ComboScores (IRC) that considered breadth, intensity, and persistence of vaccine-induced immune responses were calculated for each patient as follows: ComboScore=sum of fold changes >1.5 for all vaccine peptides at all time points (pre-treatment, 4, 8, and 12 weeks). For ELISPOT assays, 2.5×10 PBMCs were prepared in RPMI-1640 containing 0.5% FBS with a total volume of 150 μL for each well in a 96-well plate. Ex vivo PBMC were stimulated in triplicate with individual vaccine peptides at a final concentration of 10 ug/ml and plates were incubated at 37° C. in humidified incubator with 5% CO2 for 36 hours. Spot detection was performed using a Human IFN-γ ELISpotPRO kit (MABTECH Inc., USA), and normalized to the number of IFN-γ spots detected per 106 PBMC.
Tetramer staining and flow cytometric analyses. Selected custom phycoerythrin (PE) or APC-conjugated HLA-peptide tetramers (Baylor College of Medicine, USA; MBL, Japan) were successfully generated (
Tumor RNA sequencing and bulk T cell receptor Vβ CDR3 sequencing analysis. Post-vaccination tumor samples were collected from Patients 12, 16, 23 and 24 after obtaining patient consent. RNA was isolated from patient tumor tissues using an RNA Extraction Kit (Qiagen, USA). Libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit (Illumina, USA) following manufacturer's instructions. Libraries were purified with AMPure XP system (Beckman Coulter, Germany) and samples were sequenced using an Illumina NovaSeq platform (Illumina, USA). For T cell receptor (TCR) diversity analysis, DNA samples were extracted from patient PBMC or pre- and post-treatment tumor biopsies from Patient 5 using a DNA extraction kit (Qiagen, USA), followed by library construction with two rounds of PCR-based amplification. CDR3 fragments were first amplified using specific primers for each V and J gene, and target fragments of multiplex-PCR products were purified using magnetic beads (A63882, Beckman, Germany). Next, PCR was performed using universal primers, and target fragments 200-350 bp were retrieved and purified by QIAquick Gel Purification Kit (Qiagen, USA). PCR products were then sequenced using the Illumina X10 platform. Single-read CDR3 sequences eliminated and the remaining sequences were analyzed to evaluate TCRVβ IMGT clonality of patients before and after treatment, as previously described (Tumeh et al., 2014).
Single-cell T cell receptor sequencing. HLA-A*1101/KITDFGRAK (SEQ ID NO: 4) Tetramer+ CD8 T cells from post-PPV PBMCs of Patient 5 were sorted using a flow-based cell sorter (BD FACSAria HI, USA) and imaged by confocal microscope (Leica SP8, Germany). Sorted Tet+ cells were adjusted to 1×106 cells per ml in PBS, and loaded on a Chromium Single Cell Controller (10X Genomics, USA) to generate single-cell gel beads in emulsion (GEMs) using a Single Cell 5+ Library and Gel Bead Kit (10× Genomics, USA). Captured cells were lysed and released RNA was barcoded through reverse transcription to produce barcode-containing cDNA in individual GEMs as per the manufacturer's introductions. V(D)J sequences were enriched by nested PCR amplification with specific primers targeting conserved TCR sequences. Sequencing was performed on an Illumina NovaSeq platform with 150 bp (PE150) paired ends. Cellranger VDJ was used for analyzing V(D)J recombination, T cell diversity, and pairing of appropriate TCR a and R chain sequences for each individual T cell. Single-cell sequencing of Tet+ cells resulted in the identification of 639 distinct TCRα/β pairs. However, since tetramer-based cell sorting can result in contamination with non-antigen specific T cells, we chose to select TCR clones for which a minimum of 10 VβCDR3 reads were detected, resulting in 51 unique TCR clones. Four clones with Vβ-CDR3 sequences that showed little or no presence in any PBMC or TIL samples were eliminated from the analysis, and 5 additional TCR clones with 7 or 8 CDR3 reads were included based on their increasing frequencies in PBMC and/or TIL during PPV, as would be expected for a neoantigen-specific T cell clone.
TCR cloning and validation. The variable region sequences of TCR Vα-N1 and Vβ-N1 chains obtained by single cell sequencing were fused to an engineered human constant region to enhance α and β chain pairing (Cohen et al., 2007). These modified Vα and Vβ chain sequences were synthesized and inserted into an EF1a promoter based lentiviral expression vector pCDH to create lentivirus lenti-EF1a-TCR-N1. Healthy donor PBMC were prepared using lymphocyte separation medium (Stem Cell, Canada). T cells were isolated using the Dynabeads® Human T-Expander CD3/CD28 Kit (Thermofisher, USA), mixed with 3 ml X-Vivo15 serum-free medium (Lonza, Switzerland) and cultured at 37° C. in 5% CO2 for 48 hours. Cell density was adjusted to 1×106/mL and co-cultured with packaged lentivirus lenti-EF1a-TCR-N1 for 4 days at 37° C. in 5% CO2. TCR-N1 expression and antigen specificity was confirmed by staining with the HLA-A*1101/KITDFGRAK (SEQ ID NO: 4)tetramer. A minigene encoding the KITDFGRAK peptide (SEQ ID NO: 4) linked to the HLA-A*l101 cDNA through an IRES sequence was synthesized and inserted into lentiviral vector pCDH with EF1a promoter to create lentivirus lenti-EF1a-KIT-A11. Control lentiviral constructs included vectors that expressed either the KITDFGRAK (SEQ ID NO: 4) minigene or HLA-A*1101 individually. Lentiviral-transduced A549 lung cancer cells stably expressing the gene(s) of interest were selected through purinomycin-based selection. HLA-A*1101 surface expression was confirmed by staining with an A*1101-specific mAb followed by flow cytometric analysis. Engineered TCR-N1-T cells were co-cultured with parental A549, A549-A11, A549-KIT, or A549-A11.KIT cells (20,000 target cells per well) at 37° C. in 5% CO2 with effector-to-target ratios of 1:1, 2.5:1, 5:1 and 10:1. Non-transduced, expanded T cells from the same PBMC donor were used for a control. Supernatants were collected after 24 hours of co-culture to assess levels of IFN-γ secretion by ELISA.
Immunoprecipitation and Western Blot. H1975 (EGFR-L85R/T790M) and H1299 (EGFR-WT) lung cancer cell lines (ATCC, USA) were treated with different concentrations (0.1, 1, 2, and 5 μM) of EGFRi Osimertinib (LC Laboratories, USA) for different time periods to optimize EGFRi treatment conditions. Cells were washed with cold PBS and lysed using lysis buffer (1% Triton X-100, Sigma, USA) and Halt Protease Inhibitor Cocktail 100X and 0.5 μM EDTA 100X (Thermo Scientific, USA). Lysates were collected and centrifuged at high speed for 30 minutes at 4° C. prior to measuring protein concentration with a Bradford assay kit (BioRad, USA). Preclearing was performed using 10 μL Pierce Protein A/G Ultra Link resin (Thermo Scientific) per sample and incubating for 2 hours at 4° C. Immunoprecipitations were performed using the same amount of total protein and by incubating cell lysates for 18 hours at 4° C. with the following antibodies at a 500:1 dilution: anti-phospho-EGFR (EMD Millipore), anti-EGFR, Anti-p44/42 MAPK ERK1/2, anti-phospho-p44/42 MAPK ERK1/2, and anti-GAPDH (Cell Signaling Technology). Protein A/G crosslinking beads were added and incubated for 4 hours prior to washing with cold PBS. Samples were run using an SDS-PAGE gradient (8-16%) gel (Invitrogen, USA). Proteins were transferred to a PVDF membrane (Thermo Scientific, USA) and blots were blocked with 5% milk prior to incubation with specific antibodies overnight at a concentration of 1:1000. Blots were washed and incubated with peroxidase-conjugated anti-rabbit secondary antibody (1:10,000) (Jackson Immuno Research, USA). Blots were developed using the Super Signal West Pico PLUS Chemiluminescent enhanced horseradish peroxidase substrate (Thermo Scientific, USA) and visualized with X-ray film.
RNA sequencing of lung tumor cell lines. H1975 and H1299 lung cancer cells were treated with 1 μM of EGFRi Osimertinib (LC Laboratories, USA) for 0 h, 12 h, or 24 h; or 24 h with 1 μM of EGFRi Osimertinib (LC Laboratories, USA)+500 U/mL recombinant human IFNγ (R&D Systems, USA) added for the last 12 hours of culture. Cells were lysed and total RNA prepared using an RNeasy Mini Kit (Qiagen, USA) according to the manufacturer's protocol. RNAseq was performed by the Avera Institute for Human Genetics (South Dakota, USA) as follows: Total RNA was assessed for degradation on an RNA 6000 Nano chip ran on a 2100 Bioanalyzer (Agilent, USA) where the average RNA integrity score for the sample set was 9.7. Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, Inc, USA) following the low sample procedure. Briefly, ribosomal RNA (rRNA) was depleted from total RNA and the remaining RNA was purified, fragmented appropriately, and primed for cDNA synthesis. Blunt-ended cDNA was generated after first and second strand synthesis. Adenylation of the 3′ blunt-ends was followed by adapter ligation prior to the enrichment of the cDNA fragments. Final library quality control was carried out by evaluating the fragment size on a DNA1000 chip ran on a 2100 BioAnalyzer (Agilent, USA). The average library yielded an insert bp size of 326. The concentration of each library was determined by quantitative PCR (qPCR) by the KAPA Library Quantification Kit for Next Generation Sequencing (KAPA Biosystems, USA) prior to sequencing. Libraries were normalized to 2 nM in 10 mM Tris-Cl, pH 8.5 with 0.1% Tween 20 then pooled evenly. The pooled libraries were denatured with 0.05 M NaOH and diluted to 20 μM. Cluster generation of the denatured libraries was performed according to the manufacturer's specifications (Illumina, Inc, USA) utilizing the HiSeq PE Cluster Kit v2 chemistry and flow cells. Libraries were clustered appropriately with a 1% PhiX spike-in. Sequencing-by-synthesis (SBS) was performed on a HiSeq2500 utilizing v2 chemistry with paired-end 101 bp reads resulting in an average of 52.4 million paired-end reads per sample. Sequence read data were processed and converted to FASTQ format for downstream analysis by Illumina BaseSpace analysis software, FASTQ Generation v1.0.0.
RNA sequencing data analysis. Quality control of patient and cell line RNAseq data was performed using FastQC v0.11.5, FastQ Screen v0.11.1, RSeQC v3.0.0, MultiQC v1.6 and proprietary algorithms of the BostonGene platform (Wingett et al., 2018). Four patient samples with the acceptable quality (good phred scores, good per base sequencing content along the read length, coding reads >50 M, adapter content <15%, <5% microbiome/mouse unique genomes contamination) were chosen for further analysis. RNAseq reads were pseudo-aligned using Kalisto v0.42.4 to GENCODE v23 transcripts (Bray et al., 2016). Transcripts with transcript type in [protein_coding, IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, TR_C_gene, TR_V_gene, TR_D_gene, TR_J_gene] were selected, then non-coding RNA transcripts and histones and mitochondrial transcripts were removed resulting in 20,062 protein coding genes. Gene expressions were quantified as transcripts per million (TPM) and log 2 transformed (Conesa et al., 2016). Gene expression changes in cell lines treated with EGFRi were shown as relative (log) expression normalized to untreated control cells. Patients' tumor gene expression was median-centered within the 4 patient samples, with gene expression relative to the control median value shown on the heatmaps. PROGENy v1.4.1 was used to calculate 7 pathways activity scores (EGFR, MAPK, PI3K, TRAIL, TNFa, NFkB, JAK-STAT; Schubert et al., 2018). Other pathway signature scores were calculated using ssGSEA using in-house python implementation. The pathways activity were represented as gene signatures, downloaded from mSiGdB v6.2 (Subramanian et al., 2005), unless other specified: “Cell cycle signature”—HALLMARK_G2M_CHECKPOINT, “Apoptosis signature”—HALLMARK_APOPTOSIS, MYC HALLMARK_MYC_TARGETS_V2, “EMT signature” 788-HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION, “iFN-0 signature” HALLMARK_INTERFERON_GAMMA_RESPONSE, “HLA expression”—gene set (HILA-A, HLA-B, HLA-C). Pathway score differences relative to the control were normalized to the maximum values in each pathway separately and displayed on the line plots. For schematic representation, the maximum absolute deviation of the pathway activity score change from the control point (0 h) to the 24 h time point was calculated within each pathway. Pathway colors on the schema corresponds to the percent of the maximum absolute deviation. Cell deconvolution was performed from RNAseq data using the quanTIseq approach (Finotello et al., 2018). Heatmaps, dot plots, line plots, bar plots were created using pandas v0.23.4, matplotlib v2.1.1 and seaborn v0.9.0 python packages (Liang et al., 2016).
Luminex assay. Duplicate samples of supernatants from untreated and 1 μM EGFRi-treated H1975 and H1299 cell lines were analyzed for the presence of CCL2, CXCL1, CXCL2, CXCL8, IP10, IL1RA, IL6, VEGFA, CSF2, and CSF3 proteins using a custom Luminex kit according to the manufacturer's instructions (R&D Systems. USA). Fifty microliters of test supernatant and the appropriate microparticle cocktails were added (1:10 dilution) to each well and incubated for 2 hours in a microplate shaker at room temperature. Plate was washed 3 times and 50 μl microliters of Biotin-Antibody cocktail (1:10 dilution) was added and incubated for 1 hour, followed by 3 washes. After incubating with 50 μl of Streptavidin (1:25 dilution) for 30 minutes, the plate was washed 3 times, microparticles were resuspended in buffer and the plate was read using a Luminex plate reader. EGFRi-induced changes were expressed as fold increase or fold decrease compared to measured baseline (0 h) concentrations. In cases where concentrations measured fell below the level of detection, the minimum threshold of detection according to the manufacturer was used.
T-cell functional assays. T-cell migration: EGFRi Osimertinib (LC laboratories, USA) at 1 μM concentration was used to treat H1975 cells for 24 hrs. DMSO only with media was used as a control. Cells were then washed and incubated in ImmunoCulut-XF T cell expansion medium (Stem Cell Technology, Canada) for 24 hrs, after which cell supernatants were collected and filtered using a Millex-GS filter. Healthy donor PBMC or expanded melanoma CD8+ tumor-infiltrating lymphocytes (TIL 3311 and TIL3329) were thawed ˜16 hours prior to performing the migration assay. 650 μL of H1975 cell supernatant was placed at the bottom of a transwell plate (Corning, USA) and incubated with 3×105 healthy donor PBMCs in the top well for 6 hrs. Migrated cells at the well bottom were collected and stained for CD4, CD8, or CD14 (Biolegend) for 30 mins at 4° C., washed with PBS and fixed with 4% PFA. 50 μl of counting beads were added to each sample to obtain accurate cell counts. Samples were run on a Canto II flow cytometer and analyzed using FlowJo V10.
HLA class I quantitation and T-cell antigen recognition: H1299 and H1975 cells were treated with 1 μM EGFRi Osimertinib (LC laboratories) or DMSO control for 6 hrs or 20 hrs. Cells were collected and stained for total class I (W6/32-APC, Thermo-Fisher, USA), washed, and fixed in 4% PFA. Samples were run on a Canto II flow cytometer and analyzed using FlowJo V10. H1975 cells were seeded at 50,000 cells per well in 96-well plates and EGFRi was used to treat cells at concentrations of 0, 0.1, and 0.3 μM per well for 24 hrs. H1975 cells were then pulsed with 0, 10, or 100 nM of cognate HLA-A0101-restricted VGLL1 peptide LSELETPGKY (SEQ ID NO: 978) for one hour prior to washing. VGLL1 peptide antigen-specific CD8+ T cells were then added at a 1:1 effector-to-target cell ratio and co-cultured overnight. IFN-γ in 24 hour cell supernatants was analyzed using a human IFN-7 ELISA kit (Invitrogen, USA) and plates were read using SpectraMax® M5/M5e Multimode PlateReader.
Statistical analysis. All statistical analyses were performed using the GraphPad Prism 5 (GraphPad Software Inc., La Jolla, Calif.). Survival curves and rates were calculated using the Log-rank (Mantel-Cox) Test, and overall survival was measured from the date of enrollment up to Dec. 31, 2018 or the time of death. Two-tailed Student's t test or Mann-Whitney U test was used to analyze the statistical significance between groups. A P-value less than or equal to 0.05 was the threshold used to determine statistical significance.
Data Availability. Raw data of bulk RNA sequencing of patient tumors and cell lines, single cell TCR paired as chain sequencing, TCR VβCDR3 sequencing generated and analyzed during the current study are available through NCBI Sequence Read Archive (SRA) (code SRP188005). DNA sequencing data (for finding mutations) with potential patient identification was not include in the informed consent of enrolled patients, data without identifying information can be shared upon reasonable request. All other data are available from the corresponding author upon reasonable request.
All of the methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims. The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.
This application is an international application under the Patent Cooperation Treaty which claims priority to U.S. Provisional Patent Application No. 62/906,688, filed 26 Sep. 2019, the content of which is hereby incorporated by reference is its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US20/52930 | 9/25/2020 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 62906688 | Sep 2019 | US |
