Methods of selecting t cell lines and their donors for adoptive cell therapy

Abstract

Disclosed herein are methods of selecting an allogeneic T cell line for therapeutic administration to a patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer. Also disclosed are methods of selecting a donor from which an allogeneic T cell line is obtained for therapeutic administration to a patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer.

Description

[0001] Related Applications

[0002] This application is a divisional application of the Chinese invention patent application filed on November 4, 2015, with the invention name “Method for selecting T cell lines and their donors for adoptive cell therapy” and application number 202111030031.8.

[0003] CROSS-REFERENCE TO RELATED APPLICATIONS

[0004] This application claims the benefit of Provisional Application No. 62 / 075,856, filed November 5, 2014, which is incorporated herein by reference in its entirety.

[0005] Government Rights Statement

[0006] This invention was made with government support under Grants NCI Ca23766, SR21 CA 162002, SP30-Ca08748-40, P01 Ca 106450, P01 Ca 52477-13, P01Ca54350 awarded by the National Institutes of Health. The government has certain rights in this invention. 1. Field of the Invention

[0007] Disclosed herein are methods for selecting allogeneic T cell lines for therapeutic administration to patients carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer. Also disclosed are methods for selecting donors from whom allogeneic T cell lines for therapeutic administration to patients carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer are derived. 2. Background of the invention

[0009] Antiviral CD8+ T cells respond to a small set of potential peptide determinants encoded by the viral genome. Cytotoxic T cells recognize infected cells through the interaction of the T cell receptor (TCR) with 8-11 amino acid antigenic peptides complexed with major histocompatibility (MHC) class I molecules. These MHC-peptide complexes arise from the intracellular processing of endogenously synthesized viral proteins (Saveanu, L. et al., Immunol Rev, 2005. 207: 42-59; Strehl, B. et al., Immunol Rev, 2005. 207: 19-30).

[0010] Peptide determinants bind to predicted binding motifs within specific HLA molecules. Although multiple peptide epitopes can be produced, T cell responses are concentrated on multiple selected epitopes, a phenomenon known as immunodominance (Sercarz, EE et al., Annu Rev Immunol, 1993.11:729-66; Yewdell, JW and JR Bennink, Annu Rev Immunol, 1999.17:51-88). The highly focused nature of CD8-T cell responses to pathogens indicates that each epitope is different in its ability to induce T cell responses (Yewdell, JW and JR Bennink, Annu Rev Immunol, 1999.17:51-88).

[0011] The peptide epitopes that induce the most significant T cell response in any given individual can be further classified according to the proportional contribution of the epitope to the overall T cell response to any particular viral peptide. "Immunodominant" epitopes are recognized by the most abundant associated T cell population, while "subdominant" epitopes are recognized by less abundant T cell populations. Therefore, each epitope can be classified as dominant, co-dominant, or subdominant according to its relative contribution to the overall T cell response, thereby establishing an immunodominant stratification.

[0012] In the case of influenza virus infection in mice, CD8 T cell responses are usually directed against only a few specific epitopes (LaGruta, NL et al., Proc Natl Acad Sci USA, 2006. 103: 994-999). In a particularly extreme example, the entire CD8-T cell response to mouse parainfluenza virus (Sendai virus) is directed against a single epitope (Cole, GA et al., Int Immunol, 1994. 6: 1767-1775; Kast, WM et al., Proc Natl Acad Sci USA, 1991. 88: 2283-2287).

[0013] Characterized for several viral infections of human T cell response. Research for human immunodeficiency virus (HIV) T cell response leads to the identification of several epitopes in the different proteins of the virus, and these studies also show that immunodominant epitopes can be presented by human leukocyte antigen (HLA) alleles such as HLA A0301, B0702 or A0201 that are prevalent in individuals who inherit these HLA alleles (Day, CL et al., J Virol, 2001.75:6279-6291). In addition, at different stages of infection, multiple epitopes can be presented by these same HLA alleles (Yu, XG et al., J Virol, 2002.76:8690-8701). Evaluation of T cell responses for human cytomegalovirus (CMV) leads to the identification of several immunodominant epitopes in the most immunogenic proteins (i.e. CMVpp65 and IE1) of the virus, and presenting (presenting) HLA alleles. This is then recognized in individuals who inherit specific HLA alleles (e.g. HLA B0702 and HLA A0201), the epitopes presented by these alleles constitute the immunodominant epitopes. When these alleles are co-inherited, the epitopes presented by HLA B0702 constitute the immunodominant T cell response, while the epitopes presented by HLA A0201 are subdominant (Lacey, SF et al., Hum Immunol, 2003. 64: 440-452).

[0014] Immunodominance reflects the end product of multiple positive and negative factors that control antigen processing and presentation, as well as T cell activation and T cell receptor avidity (Yewdell, JW and JRBennink, Annu Rev Immunol, 1999. 17: 51-88). Among these, the major factors evaluated in most studies to date include the genetic HLA class I background of the infected individual, the sequence of the viral proteins and the kinetics of viral infection, as well as the binding affinity in the HLA groove and the TCR affinity of the peptide-MHC complex.

[0015] After allogeneic hematopoietic stem cell transplantation (HSCT), adoptive immunotherapy using donor-derived virus-specific T cells may be effective in clearing viral infections such as Epstein-Barr virus (EBV) and CMV. The lack of timely availability of donor-derived virus-specific T cells is a major limitation to the successful application of this treatment method. In addition, such cells cannot be produced from seronegative donors and cord blood donors. In such cases, for the treatment of severe viral infections in such patients, pre-generated third-party donor-derived virus-specific T cells can be easily obtained. Several groups have demonstrated the safety and potential efficacy of third-party donor-derived virus-specific cytotoxic T lymphocyte (CTL) lines for the treatment of EBV, CMV, and adenovirus (ADV) infections using CTL lines selected empirically based on 2 or more HLA alleles (Haque, T et al., Lancet, 2002. 360: 436-442; Barker, JN et al., Blood, 2010. 116: 5045-5049; Doubrovina, E. et al., Blood, 2012. 119: 2644-2656; Uhlin, M. et al., Clinical Infectious Diseases, 2012. 55: 1064-1073; Leen, AM et al., Blood, 2013. 121: 5113-5123). Methods for selecting CTL lines to ensure high and consistent efficacy of CTL therapy are needed.

[0016] Citation of a reference herein shall not be construed as an admission that the reference is prior art to the present disclosure. 3. Summary of the Invention

[0018] The present invention provides methods for selecting allogeneic T cell lines for therapeutic administration to human patients carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, and methods for selecting the allogeneic T cell donor from which the allogeneic T cell lines are derived.

[0019] In various aspects, methods of selecting an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer include: using (i) identifying a plurality of HLA alleles and optionally combinations of HLA alleles, and (ii) revealing a graph (hereinafter “Representation of Activity Graph”) of an indicator of the relative activity of each T cell line that recognizes at least one epitope of an antigen of the pathogen or cancer and is restricted to different HLA alleles or combinations of HLA alleles of the plurality of HLA alleles or combinations of HLA alleles. wherein each HLA allele or combination of HLA alleles identified in the graph is correlated with a corresponding index of relative activity of the T cell line restricted to that HLA allele or combination of HLA alleles, said relative activity being a relative measure of a known activity exhibited by the T cell line against a pathogen or against a cancer; wherein (A) the selected T cell line has an HLA allele or combination of HLA alleles identified in the graph to which recognition of the T cell line is restricted that is the same as the patient or a diseased cell of the patient (e.g., a cancer or a diseased cell associated with the presence of a pathogen); and (B) the HLA allele or combination of HLA alleles to which the selected T cell line is restricted is correlated in the graph with an index of highest relative activity among the HLA alleles and combinations of HLA alleles in the graph that are known to be the same as the patient or the patient's diseased cells (based on HLA matching of the patient or the patient's diseased cells) and are not otherwise disqualified.

[0020] In certain embodiments, the method of selecting an allogeneic T cell line further comprises the step of making an activity profile prior to the selection step. In certain embodiments, the method of selecting an allogeneic T cell line further comprises the step of measuring relative activity prior to the making step. In certain embodiments, the method of selecting an allogeneic T cell line further comprises the step of determining the HLA type of the patient or the patient's diseased cells prior to the selection step. In a specific embodiment, the step of determining comprises typing at least 4 HLA loci.

[0021] In various aspects, a method for selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer comprises: selecting a T cell donor that is allogeneic to the patient using an activity profile that (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of T cell lines that each recognize at least one epitope of an antigen of the pathogen or cancer and are restricted to different HLA alleles or combinations of HLA alleles of a plurality of HLA alleles or combinations of HLA alleles; wherein each identified HLA allele or combination of HLA alleles in the profile is relative to the activity of the T cell lines that are restricted to the plurality of HLA alleles or combinations of HLA alleles. The invention relates to a method for preparing a T cell line comprising: selecting a donor of T cells for use with the patient or a combination of HLA alleles selected from the donor of T cells, wherein the relative activity is a relative measure of a known activity exhibited by the T cell line against a pathogen or against a cancer; wherein (A) the selected T cell donor has at least one HLA allele or combination of HLA alleles in common with the patient or a diseased cell of the patient (e.g., a cancer or a diseased cell associated with the presence of a pathogen); and (B) one of the at least one HLA allele or combination of HLA alleles in common with the patient or the patient's diseased cells is associated in the graph with an indicator of the highest relative activity among the HLA alleles and combinations of HLA alleles known to be in common with the patient or the patient's diseased cells and not otherwise disqualified in the activity graph.

[0022] In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of making an activity diagram before the selection step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of measuring relative activity before the making step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of determining the HLA matching of the patient or the patient's diseased cells before the selection step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of determining the HLA matching of the T cell donor before the selection step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of determining the HLA matching of the patient or the patient's diseased cells and the HLA matching of the T cell donor before the selection step. In a specific embodiment, the step of determining includes typing at least 4 HLA loci.

[0023] In some embodiments, the activity diagram is a list of multiple HLA alleles and optional HLA allele combinations sorted by relative activity. In some embodiments, the activity diagram is a database overview of multiple HLA alleles and optional HLA allele combinations, each of which is related to a score indicating relative activity. In some embodiments, the activity diagram is a scatter plot. In a specific aspect of this type of embodiment, the first axis of the scatter plot represents a large number of HLA alleles and optional HLA allele combinations in different HLA alleles and optional HLA allele combinations, and the second axis of the scatter plot represents when the antigen presenting cells of one or more peptides that are autologous and load the antigenicity of pathogens or cancers are used to stimulate each T cell line, and the percentage of interferon-γ-secreting CD3+ cells derived from each T cell line for which the index of relative activity is revealed in the diagram is used as an index of the relative activity. In a preferred embodiment, relative activity is the in vivo clinical efficacy of T cell lines in the treatment of patients carrying / suffering from pathogens or cancer. In some embodiments, the activity diagram is stored in a database.

[0024] In various aspects, a method for selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer comprises: selecting a T cell donor who is allogeneic to the patient having one or more HLA alleles in common with the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of a pathogen) using a representation (hereinafter referred to as a "Representation of Frequency"), wherein the representation (i) identifies a plurality of HLA alleles, and (ii) reveals an index of the relative frequency produced by each T cell line that recognizes at least one epitope of an antigen of the pathogen or cancer and is restricted to a different HLA allele of the plurality of said HLA alleles; wherein each identified HLA allele in the representation is associated with a corresponding index of the relative frequency produced by the T cell line restricted to the HLA allele, wherein: the selected T cell donor has at least one HLA allele in common with the patient or the patient's diseased cells that is associated with an index of higher frequency produced than the HLA allele of a donor that is not the patient or the patient's diseased cells in the representation.

[0025] In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of making a frequency graph before the selection step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of measuring relative frequencies before the making step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of determining the HLA matching of the patient or the patient's diseased cells before the selection step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of determining the HLA matching of the T cell donor before the selection step. In certain embodiments, the method for selecting an allogeneic T cell donor further includes the step of determining the HLA matching of the patient or the patient's diseased cells and the HLA matching of the T cell donor before the selection step. In a specific embodiment, the step of determining includes typing at least 4 HLA loci.

[0026] In some embodiments, the frequency graph is a list of multiple HLA alleles sorted by relative frequency. In some embodiments, the frequency graph is a database overview of multiple HLA alleles, each associated with a score representing relative frequency. In some embodiments, the frequency graph is stored in a database.

[0027] Also provided herein is a method for treating a human patient who carries / suffers from or is suspected of carrying / suffering from a pathogen or cancer, the method comprising: (a) selecting an allogeneic T cell line for therapeutic administration to the patient according to the methods described in the present disclosure; and (b) administering a T cell population derived from the selected allogeneic T cell line to the patient.

[0028] Also described herein is a method for obtaining an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising: (a) selecting an allogeneic T cell donor according to the method for selecting an allogeneic T cell donor described in the present disclosure; and (b) obtaining an allogeneic T cell line from the selected allogeneic T cell donor, wherein the allogeneic T cell line recognizes at least one epitope of an antigen of the pathogen or cancer.

[0029] In different aspects, the patient carries or is suspected of carrying a pathogen, wherein the T cell line recognizes at least one epitope of an antigen of the pathogen. In different embodiments, the pathogen is a virus, bacteria, fungus, parasite or protist. In certain embodiments, the pathogen is a virus.

[0030] In some embodiments, the virus is cytomegalovirus (CMV). In a specific embodiment, the patient carries or is suspected of carrying CMV infection after the patient undergoes HSCT. In a specific embodiment, the antigen is CMV pp65. In a specific embodiment, the antigen is CMV IE1.

[0031] In some embodiments, the virus is Epstein-Barr virus (EBV).In specific embodiments, the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B, EBNA3C, LMP1 or LMP2.

[0032] In some embodiments, the virus is BKV, JCV, herpes virus, adenovirus, human immunodeficiency virus, influenza virus, Ebola virus, poxvirus, rhabdovirus, or paramyxovirus.

[0033] In some embodiments, the virus is human herpesvirus-6 (HHV-6) or human herpesvirus-8 (HHV-8).

[0034] In various aspects, the patient has or is suspected of having a cancer wherein the T cell line recognizes at least one epitope of an antigen of the cancer. In some embodiments, the cancer is a cancer of the breast, lung, ovary, stomach, pancreas, larynx, esophagus, testis, liver, parotid gland, bile duct, colon, rectum, cervix, uterus, endometrium, kidney, bladder, prostate, thyroid, brain, or skin. In some embodiments, the cancer is a blood cancer. In specific embodiments, the cancer is a lymphoproliferative disorder.

[0035] In some embodiments, the cancer is a WT1 positive cancer. In some embodiments, the antigen is WT1.

[0036] In some embodiments, the cancer is EBV-positive post-transplant lymphoproliferative disorder (EBV-PTLD). In specific embodiments, the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B, or EBNA3C. In specific embodiments, the antigen is LMP1 or LMP2.

[0037] In some embodiments, the cancer is EBV-positive nasopharyngeal carcinoma.In specific embodiments, the antigen is EBNA1, LMP1, or LMP2.

[0038] In various embodiments, the methods of selecting an allogeneic T cell line according to the present disclosure are computer-implemented. In various embodiments, the methods of selecting an allogeneic T cell donor according to the present disclosure are computer-implemented.

[0039] Also provided herein is a computer system for selecting an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, comprising: a central processing unit; and a memory connected to the central processing unit, the memory storing instructions for executing the steps of any method for selecting an allogeneic T cell line or any method for selecting an allogeneic T cell donor as described in the present disclosure.

[0040] Also provided herein are computer-readable media having computer-executable instructions for performing steps of any of the methods of selecting an allogeneic T cell line or any of the methods of selecting an allogeneic T cell donor as described in the present disclosure.

[0041] In various embodiments, the patient has been a recipient of a hematopoietic stem cell transplant (HSCT). In specific embodiments, the HSCT is a bone marrow transplant, a peripheral blood stem cell transplant, or a cord blood transplant. In various embodiments, the patient has been a recipient of a solid organ transplant (SOT).

[0042] References to patients in this disclosure are to human patients. 4. Brief description of the accompanying drawings

[0044] Figure 1 is a graph showing the percentage of interferon-γ-secreting CD3+ cells for each T cell line in a library of 119 CMV-specific CTL lines restricted by HLA alleles or HLA allele combinations presenting immunodominant epitopes clustered by their respective HLA alleles or HLA allele combinations as described in the Examples in Section 6.2.3. 5. Detailed description of the invention

[0046] The present invention provides methods for selecting allogeneic T cell lines for therapeutic administration to human patients carrying / suffering from or suspected of carrying / suffering from pathogens or cancers, and methods for selecting allogeneic T cell donors from which said allogeneic T cell lines are derived. According to the present invention, there is a stratification of HLA alleles presenting immunodominant epitopes that result in preferential amplification of epitope-specific T cells restricted to a particular HLA allele relative to other cells that inherit and express it. The present invention utilizes a graph reflecting this amplification stratification (reflected by anti-pathogen or anti-cancer activity) to select allogeneic T cell lines for therapy and to select donors from which the allogeneic T cell lines are derived.

[0047] There are also stratifications of HLA alleles presenting immunodominant epitopes that result in preferential production of epitope-specific T cells restricted to a particular HLA allele over other cells that inherit and express it. The present invention utilizes a graph reflecting this production stratification (reflected by the frequency of production) to select donors from which T cell lines are derived.

[0048] 5.1. Selection of T cell lines for adoptive cell therapy

[0049] Provided herein are methods for selecting allogeneic T cell lines for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer.

[0050] In various aspects, a method for selecting an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer comprises: selecting a T cell line that is allogeneic to the patient that recognizes at least one epitope of an antigen of the pathogen or cancer using a profile (hereinafter referred to as an "activity profile"), wherein the profile (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of each T cell line that recognizes at least one epitope of an antigen of the pathogen or cancer and is restricted to different HLA alleles or combinations of HLA alleles of a plurality of HLA alleles or combinations of HLA alleles; wherein each identified HLA allele or combination of HLA alleles in the profile is relative to the T cell line restricted to the HLA alleles or combinations of HLA alleles. The invention relates to a T cell line selected by the present invention for a therapeutic agent that is a relative measure of a known activity exhibited by the T cell line against a pathogen or against a cancer; wherein (A) the selected T cell line has an HLA allele or combination of HLA alleles to which recognition of the T cell line identified by the graph is restricted that is common to the patient or a diseased cell of the patient (e.g., a cancer or a diseased cell associated with the presence of a pathogen); and (B) the HLA allele or combination of HLA alleles to which the selected T cell line is restricted is associated in the graph with the highest relative activity among the HLA alleles and combinations of HLA alleles in the graph that are known to be common to the patient or the patient's diseased cells (based on the HLA matching of the patient or the patient's diseased cells) and are not otherwise disqualified. An HLA allele or combination of HLA alleles is deemed "otherwise disqualified" if, for whatever reason, a T cell line restricted by that HLA allele or combination of HLA alleles is known to be unsuitable for therapeutic administration. For example, if an experimentally selected T cell line is observed to have no or too few viable cells in a cell line sample, then the HLA allele or HLA allele combination to which such T cell line is restricted may be considered disqualified. As another example, if the relative activities in an activity profile are based on an in vitro or ex vivo assay of activity, and the relative in vivo activity of a T cell line known to be restricted to a particular HLA allele or HLA allele combination is not related to the relative in vitro or ex vivo assay used to generate the activity profile, such that the highest relative activity in the activity profile is not the highest relative in vivo activity, then the particular HLA allele or HLA allele combination to which such T cell line is restricted may be considered disqualified.For example, it was observed that for T cell lines restricted to HLA-B35, in vivo activity against CMV infection in human patients was clinically ineffective (thus negligible relative in vivo activity), although the percentage of interferon-γ secreting CD3+ T cells derived from T cell lines restricted to HLA-B35 indicated a much higher relative activity; therefore, in the case of treatment of CMV infection, if a T cell line restricted to HLA-B35 is experimentally selected, it is preferred that HLA-B35 may be "otherwise disqualified". By using the claimed method, the T cell line to be selected is specific for an epitope of a pathogen or cancer that is presented by an HLA allele or HLA allele combination shared by the patient that is associated with the highest activity in the patient's HLA allele or HLA allele combination. In a relatively specific embodiment, an HLA allele or HLA allele combination is considered disqualified if a T cell line restricted to an HLA allele or HLA allele combination is known to be clinically ineffective in the treatment of patients carrying / suffering from a pathogen or cancer.

[0051] In another embodiment, the present invention provides a method for selecting a candidate allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising: selecting a T cell line that is allogeneic to the patient that recognizes at least one epitope of an antigen of the pathogen or cancer using an activity profile, the activity profile (i) identifying a plurality of HLA alleles and optionally HLA allele combinations, and (ii) revealing an indicator of the relative activity of each T cell line that recognizes at least one epitope of an antigen of the pathogen or cancer and is restricted to different HLA alleles or HLA allele combinations of a plurality of HLA alleles or HLA allele combinations; wherein each identified HLA allele or HLA allele combination in the profile is relative to the T cell line that is restricted to the HLA alleles or HLA allele combinations of the patient. The invention relates to a method for treating a T cell line having an HLA allele or HLA allele combination identified by the graph that is the same as the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of a pathogen) and a corresponding index of the relative activity of a T cell line that has an HLA allele or HLA allele combination identified by the graph that is limited to recognition of the T cell line; wherein (A) the selected T cell line has an HLA allele or HLA allele combination identified by the graph that is the same as the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of a pathogen) and is related to a corresponding index of the relative activity of a T cell line that has an HLA allele or HLA allele combination identified by the graph that is the same as the patient or the patient's diseased cells (based on the HLA matching of the patient or the patient's diseased cells) in the graph.

[0052] In certain embodiments, the method further comprises the step of making an activity profile prior to the selecting step. Methods that can be used to make an activity profile are described below. In certain embodiments, the method further comprises the step of measuring relative activity prior to the making step. In certain embodiments, the method further comprises the step of determining the HLA type of the patient or the patient's diseased cells prior to the selecting step.

[0053] In a specific embodiment, the selected T cell line recognizes at least one epitope of an antigen of a pathogen or cancer that is presented by the same HLA allele or combination of HLA alleles as the patient or a diseased cell in the patient, wherein the HLA allele or combination of HLA alleles is associated with an indicator of the highest relative activity among the HLA alleles and combination of HLA alleles in the patient or the patient's diseased cells (and not otherwise disqualified as described above). In a preferred aspect of such embodiments, the relative activity is the in vivo clinical efficacy of the T cell line in the treatment of patients carrying / suffering from the pathogen or cancer.

[0054] In specific embodiments of the methods described herein, the at least one epitope is at least one immunodominant epitope.

[0055] In certain embodiments of the methods of the present invention, the selected T cell line has the same HLA allele or HLA allele combination as the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of pathogens) that the recognition of the T cell line identified by the activity diagram is restricted by it. In some embodiments, the patient is a transplant recipient. In a specific embodiment in which the patient is a transplant recipient, the same HLA allele or HLA allele combination as the patient or the patient's diseased cells (e.g., cancerous or pathogen-infected cells) refers to the same HLA allele or HLA allele combination as the patient before and / or after transplantation. In some embodiments, the patient's diseased cells are derived from a transplant given to the patient, and thus express the HLA alleles of the transplant; in such embodiments, the HLA matching of the patient's diseased cells can be determined by typing the HLA alleles in the transplant given to the patient. In other embodiments, the patient's diseased cells do not originate from a transplant given to the patient, and therefore have the HLA matching of the patient before transplantation. In a specific embodiment, the transplant is HSCT or a solid organ transplant.

[0056] 5.1.1. Generation of T cell lines

[0057] T cell lines selected therefrom for therapeutic administration and / or use to obtain mapping information can be prepared as described herein.T cell lines that recognize at least one epitope of an antigen of a pathogen or cancer can be generated by any method known in the art or described herein. Non-limiting exemplary methods of producing T cell lines that produce at least one epitope of an antigen of a pathogen or cancer can be found in Trivedi, D. et al., Blood, 2005. 105:2793-2801; Koehne, G. et al., Blood, 2000. 96:109-117; Koehne, G. et al., Blood, 2002. 99:1730-1740; Doubrovina, E. et al., Blood, 2012. 119:2644-2656; Barker, JN et al., Blood, 2010. 116:5045-5049; O'Reilly, RJ et al., Immunol Res, 2007. 38:237-250; and O'Reilly, RJ et al., Best Practice & Research Clinical Haematology, 2011. 24:381-391.

[0058] In certain embodiments, the T cell line is produced by stimulating T cells from seropositive donors with antigen presenting cells presenting one or more peptides of antigens showing the antigenicity of (patients) pathogens or cancers. Preferably, antigen presenting cells are autologous to T cells (thus derived from T cell donors). In specific embodiments, T cells are stimulated with dendritic cells loaded with peptide libraries of one or more antigens of pathogens or cancers. In some embodiments, dendritic cells are derived from T cell donors. In specific embodiments, T cells are stimulated with cytokine-activated monocytes (CAMS) loaded with peptide libraries of one or more antigens of pathogens or cancers. In some embodiments, CAMS are derived from T cell donors. In specific embodiments, T cells are stimulated with peripheral blood mononuclear cells (PBMC) loaded with peptide libraries of one or more antigens of pathogens or cancers. In some embodiments, PBMC are derived from T cell donors. In certain embodiments, T cell lines are produced by stimulating T cells with B lymphocyte cell lines (BLCL) loaded with peptide libraries of one or more antigens of pathogens or cancers. In some embodiments, BLCL is derived from T cell donors. In specific embodiments, the BLCL is an EBV-transformed BLCL derived from a donor of T cells.In certain embodiments, the T cell line is generated by stimulating T cells with artificial antigen presenting cells (AAPCs) loaded with a peptide library of one or more antigens of a pathogen or cancer.

[0059] In various embodiments, the peptide library is an overlapping peptide library spanning antigens of pathogens or cancers. In various embodiments, the peptide library is an overlapping peptide library spanning more than one antigen of a pathogen or cancer. In a specific embodiment, the overlapping peptide library is an overlapping 15-peptide library.

[0060] In certain embodiments, the T cell line is generated by stimulating T cells with AAPCs that are genetically engineered to express at least one immunogenic peptide or protein of a pathogen. In certain embodiments, the T cell line is generated by stimulating T cells with BLCLs transformed by a virus, wherein the virus is a pathogen.

[0061] In some embodiments, T cells are stimulated in culture for a period of 28-40 days. In specific embodiments, T cells are stimulated in the presence of IL-2. In various embodiments, after stimulation, the T cell line is stored refrigerated. In a specific embodiment, where the T cell line is selected according to the claimed method and stored refrigerated, the T cell line is thawed prior to therapeutic administration. In yet another specific embodiment, the thawed T cell line is optionally expanded in culture prior to therapeutic administration.

[0062] In various embodiments, T cells used to generate T cell lines are purified by methods known in the art. In certain embodiments, T cells are enriched from peripheral blood lymphocytes isolated from PBMCs. In some embodiments, T cells are enriched from peripheral blood lymphocytes isolated from PBMCs by consuming adherent monocytes followed by consuming natural killer cells.

[0063] Dendritic cells of T cell lines that can be used to stimulate T cells to produce at least one epitope of an antigen that recognizes a pathogen or cancer can be derived from cytokine-activated monocytes (CAMS). In some embodiments, CAMS are produced by incubating PBMCs with cytokines such as GM-CSF, IL-4, TNF-α, IL-1β, IL-6, and / or prostaglandin-E2.

[0064] BLCLs of T cell lines that can be used to stimulate T cells to produce T cells that recognize at least one epitope of an antigen of a pathogen or cancer can be generated from PBMCs using any method known in the art, such as described in Koehne, G. et al., Blood, 2000. 96: 109-117 or Koehne, G. et al., Blood, 2002. 99: 1730-1740.

[0065] Each HLA allele or combination of HLA alleles restricted by a generated T cell line that recognizes at least one epitope of an antigen of a pathogen or cancer can be determined by any method known in the art, such as described in Trivedi, D. et al., Blood, 2005. 105: 2793-2801; Barker, JN et al., Blood, 2010. 116: 5045-5049; Hasan, AN et al., J Immunol, 2009. 183: 2837-2850 or Doubrovina, E. et al., Blood, 2012. 120: 1633-1646.

[0066] 5.1.2. Determine HLA matching

[0067] The step of determining HLA matching (i.e., typing the HLA loci) can be performed by any method known in the art. Non-limiting exemplary methods for determining HLA matching can be found in Lange, V. et al., BMC Genomics, 2014.15:63; Erlich, H., Tissue Antigens, 2012.80:1-11; Bontadini, A., Methods, 2012.56:471-476; Dunn, PP, Int J Immunogenet, 2011 38:463-473; and Hurley, CK, "DNA-based typing of HLA for transplantation." In Leffell, MS et al., Handbook of Human Immunology, 1997. Boca Raton: CRC Press. In some embodiments, the step of determining HLA matching includes typing at least 4 HLA loci, preferably HLA-A, HLA-B, HLA-C, and HLA-DRB1. In some embodiments, the step of determining HLA typing comprises typing 4 HLA loci, preferably HLA-A, HLA-B, HLA-C and HLA-DRB1. In some embodiments, the step of determining HLA typing comprises typing at least 6 HLA loci. In some embodiments, the step of determining HLA typing comprises typing 6 HLA loci. In some embodiments, the step of determining HLA typing comprises typing at least 8 HLA loci. In some embodiments, the step of determining HLA typing comprises typing 8 HLA loci. In some embodiments, the step of determining HLA typing comprises typing all known HLA loci. In some embodiments, the step of determining HLA typing comprises typing less than all known HLA loci.

[0068] In general, typing of more HLA loci is preferred in practicing the present invention because the more HLA loci that are typed, the more likely it is that the selected allogeneic T cell line will have the highest activity relative to other allogeneic T cell lines that have the same HLA alleles or HLA allele combinations as the patient or the patient's diseased cells.

[0069] 5.1.3. Production of activity graphs for selecting T cell lines

[0070] The activity graph identifies a plurality of HLA alleles and optionally HLA allele combinations and reveals (i) at least one epitope of an antigen of a pathogen or cancer (of the patient) that each recognizes, and (ii) an indicator of the relative activity of T cell lines restricted to different HLA alleles or HLA allele groups of the plurality of HLA alleles or HLA allele combinations. In the activity graph, each identified HLA allele or HLA allele combination is associated with a corresponding indicator of the relative activity of the T cell line restricted to the HLA allele or HLA allele combination, the relative activity being a relative measure of the known activity exhibited by the T cell line against the pathogen or against the cancer.

[0071] The relative activity of T cell lines can be determined by any in vitro, ex vivo or in vivo method known in the art.

[0072] In a preferred embodiment, relative activity is measured with the in vivo clinical efficacy of T cell lines in the treatment of patients carrying / suffering from pathogens or cancers. In a specific aspect of such embodiments, relative activity can be measured with the percentage of patients carrying / suffering from or suspected of carrying / suffering from pathogens or cancers who achieve complete remission (CR) after treatment with T cell lines. In a specific embodiment, relative activity is measured with the percentage of patients carrying / suffering from or suspected of carrying / suffering from pathogens or cancers who achieve CR or partial remission (PR) after treatment with T cell lines.

[0073] In some embodiments, relative activity is measured as the percentage of interferon-γ-producing CD3+ cells derived from each T cell line when stimulated with antigen presenting cells presenting one or more peptides showing antigenicity of a pathogen or cancer. In specific embodiments, where the antigen is CMV or EBV, relative activity is measured by a method modified and described from Koehne, G. et al., Blood, 2002.99:1730-1740 or Waldrop, SL et al., J Clin Invest, 1997.99:1739-1750.

[0074] In some embodiments, relative activity is measured as the percentage of cells expressing an antigen of a pathogen or cancer that are lysed when exposed to each T cell line in a cytotoxicity assay performed according to methods known in the art.

[0075] According to the present invention, the relative activity is not measured as the binding affinity of the epitope recognized by each T cell line to the HLA allele presenting the epitope.

[0076] In some aspects, the activity profile is a list of a plurality of HLA alleles and optional HLA allele combinations ranked by relative activity. In some embodiments, the step of selecting an allogeneic T cell line is performed by examining a list of a plurality of HLA alleles and optional HLA allele combinations ranked by relative activity, wherein the highest stratum in the list is an indicator of the highest relative activity; determining the highest ranked HLA allele or HLA allele combination known to be the same as the patient or the patient's diseased cells; and selecting an allogeneic T cell line that is restricted to the HLA allele or HLA allele combination. For example, in a specific embodiment, the activity profile is a list as shown in Table 6.

[0077] In some aspects, the activity profile is a database (e.g., table) listing a plurality of HLA alleles and optional HLA allele combinations, each associated with a score indicating relative activity. In some embodiments, the step of selecting an allogeneic T cell line is performed by examining a database listing a plurality of HLA alleles and optional HLA allele combinations, each associated with a score indicating relative activity, with the highest score in the database being an indicator of the highest relative activity; determining the highest scoring HLA allele or HLA allele combination known to be the same as the patient or the patient's diseased cells; and selecting an allogeneic T cell line that is restricted to the HLA allele or HLA allele combination. In a specific embodiment, the step of selecting an allogeneic T cell line using an activity profile (i.e., such a database) can be performed by first filtering out (excluding) all HLA alleles and HLA allele combinations in the database that are different from the patient or the patient's diseased cells, and then determining the HLA allele or HLA allele combination associated with the highest relative activity index among the remaining ones, and then selecting an allogeneic T cell line restricted to that HLA allele or HLA allele combination.

[0078] In some aspects, the activity graph is a scatter plot. In certain embodiments, the first axis of the scatter plot represents different HLA alleles and optional HLA allele combinations of HLA alleles and optional HLA allele combinations in a large number of HLA alleles and optional HLA allele combinations. In certain embodiments, the second axis of the scatter plot represents relative activity. In a specific embodiment, the second axis of the scatter plot represents the percentage of interferon-γ-secreting CD3+ cells derived from each T cell line that reveals an indicator of relative activity against it in the activity graph when stimulated with antigen presenting cells presenting one or more peptides of one or more antigens showing the antigenicity of a pathogen or cancer. In a specific embodiment, the stimulation is with antigen presenting cells that are autologous to each T cell line and loaded with one or more peptides showing the antigenicity of a pathogen or cancer, as an indicator of the relative activity. For example, in a specific embodiment, the activity graph is Figure 1 The scatter plot shown.

[0079] In some embodiments, the activity profile is stored in a database.

[0080] In various embodiments, the method of selecting an allogeneic T cell line is computer-implemented. In some embodiments, the method of selecting an allogeneic T cell line is computer-implemented using a computer system as described in Section 5.6. In some embodiments, the method of selecting an allogeneic T cell line is computer-implemented using a readable medium as described in Section 5.6.

[0081] Once the additional data is available, the activity map can be updated with the additional data.

[0082] 5.2. Therapeutic applications of selected T cell lines

[0083] Also provided herein is a method for treating a human patient who carries / suspected of carrying / suffering from a pathogen or cancer, the method comprising: (a) selecting an allogeneic T cell line for therapeutic administration to a patient according to any of the methods for selecting an allogeneic T cell line described in Section 5.1; and (b) administering a population of T cells derived from the selected allogeneic T cell line to the patient. Thus, in patients with cancer, the present invention provides a method for treating cancer; in patients carrying a pathogen, the present invention provides a method for treating a disease, disorder or condition associated with the presence of the pathogen.

[0084] In certain embodiments, administration is by infusion of a T cell population derived from a selected allogeneic T cell line. In some embodiments, administration is by intravenous push of a T cell population derived from a selected allogeneic T cell line. The amount to be administered can be determined based on the patient's condition and the physician's knowledge. In certain embodiments, administration comprises administering at least about 1 x 10 5T cells / kg / dose / week are administered to a patient, wherein the T cell population is derived from a selected allogeneic T cell line. In some embodiments, administration comprises administering about 1 x 10 6 -2x 10 6 T cells / kg / dose / week are administered to a patient, wherein the T cell population is derived from a selected allogeneic T cell line. In some embodiments, administration comprises administering about 1 x 10 6 cells / kg / dose / week to a patient, wherein the T cell population is derived from a selected allogeneic T cell line. In some embodiments, administration comprises administering about 2x10 6 In some embodiments, the dosage regimen is carried out for at least 3 weeks, so that at least 3 doses are given. In some embodiments, the dosage regimen is carried out for 3 weeks, so that at least 3 doses are given. In some embodiments, the dosage regimen is carried out for 6 weeks, so that 6 doses are given. In some embodiments, the dosage regimen is carried out for 3 weeks, so that at least 3 doses are given, and the T cell population derived from the selected allogeneic T cell line is given for at least one week by another dosage regimen, wherein the second dosage regimen is about 1 x 10 7 In certain embodiments, the above dosage regimen is carried out for 3 weeks, so that at least 3 doses are given, and the T cell population derived from the selected allogeneic T cell line is given for 3 weeks by another dosage regimen, wherein the second dosage regimen is about 1 x 10 7 T cells / kg / dose / week. In certain embodiments, wherein the patient has cancer, administration of about 1 x 10 8- 1x 10 9 5 repeated infusion doses of 1 T cell / kg / dose / week.

[0085] 5.3. Selection of T cell donors for adoptive cell therapy

[0086] Also provided herein are methods of selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer.

[0087] 5.3.1. Selection of T cell donors based on activity profiles

[0088] In various aspects, a method for selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer comprises: selecting a T cell donor that is allogeneic to the patient using an activity profile that (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of T cell lines that each recognize at least one epitope of an antigen of the pathogen or cancer and are restricted to different HLA alleles or combinations of HLA alleles of a plurality of HLA alleles or combinations of HLA alleles; wherein each identified HLA allele or combination of HLA alleles in the profile is relative to the activity of the T cell lines that are restricted to the plurality of HLA alleles or combinations of HLA alleles. or HLA allele combination, the relative activity being a relative measure of a known activity exhibited by the T cell line against a pathogen or against a cancer; wherein (A) the selected T cell donor has at least one HLA allele or HLA allele combination in common with the patient or a diseased cell of the patient (e.g., a cancer or a diseased cell associated with the presence of a pathogen); and (B) one of the at least one HLA allele or HLA allele combination in common with the patient or the patient's diseased cells is associated in the graph with the highest relative activity among the HLA alleles and HLA allele combinations in the activity graph that are known to be in common with the patient or the patient's diseased cells and are not otherwise disqualified. An HLA allele or HLA allele combination is considered "otherwise disqualified" if, for whatever reason, a T cell line restricted by that HLA allele or HLA allele combination is known to be unsuitable for therapeutic administration. For example, if the relative activity in an activity profile is based on an in vitro or ex vivo assay of activity, and the relative in vivo activity of a T cell line restricted to a particular HLA allele or combination of HLA alleles is known to be independent of the relative in vitro or ex vivo assay used to generate the activity profile, such that the highest relative activity in the activity profile is not the highest relative in vivo activity, then the particular HLA allele or combination of HLA alleles (to which such T cell line is restricted) may be considered disqualified. For example, it was observed that in vivo activity against CMV infection in human patients for a T cell line restricted to HLA-B35 was clinically ineffective (and therefore negligible relative in vivo activity), even though the percentage of interferon-γ secreting CD3+ T cells derived from the T cell line restricted to HLA-B35 indicated a much higher relative activity; therefore, in the case of treating CMV infection, if a T cell donor with HLA-B35 is experimentally selected, then HLA-B35 may be "otherwise disqualified".In a relatively specific embodiment, an HLA allele or HLA allele combination is considered ineligible if a T cell line restricted to that HLA allele or HLA allele combination is known to be clinically ineffective in the treatment of patients carrying / suffering from a pathogen or cancer.

[0089] In another embodiment, the present invention provides a method for selecting a candidate allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising: selecting a T cell donor that is allogeneic to the patient using an activity profile that (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of T cell lines that each recognize at least one epitope of an antigen of the pathogen or cancer and are restricted to different HLA alleles or combinations of HLA alleles of a plurality of HLA alleles or combinations of HLA alleles; wherein each identified HLA allele or HLA allele in the profile is selected as an allogeneic T cell donor to the patient. The HLA allele combination is associated with a corresponding index of the relative activity of a T cell line restricted by the HLA allele or HLA allele combination, wherein the relative activity is a relative measure of a known activity displayed by the T cell line against a pathogen or against a cancer; wherein (A) the selected T cell donor has at least one HLA allele or HLA allele combination in common with the patient or the patient's diseased cells (e.g., a cancer or a diseased cell associated with the presence of a pathogen); and (B) one of the at least one HLA allele or HLA allele combination in common with the patient or the patient's diseased cells is associated in the graph with the index of the highest relative activity among the HLA alleles and HLA allele combinations known to be in common with the patient or the patient's diseased cells in the activity graph.

[0090] In certain embodiments, the method further comprises the step of making an activity graph before the selection step. Methods that can be used to make activity graphs are described in Section 5.1.3. In certain embodiments, the method further comprises the step of measuring relative activity before the making step. In certain embodiments, the method further comprises the step of determining the HLA matching of the patient or the patient's diseased cells before the selection step. In certain embodiments, the method further comprises the step of determining the HLA matching of the T cell donor before the selection step. In certain embodiments, the method further comprises the step of determining the HLA matching of the patient or the patient's diseased cells and the HLA matching of the T cell donor before the selection step.

[0091] In a specific embodiment, the selected T cell donor has at least one HLA allele or HLA allele combination in common with the patient or the patient's diseased cells, wherein one of the at least one HLA allele or HLA allele combination is associated with an indicator of the highest relative activity among the patient's HLA alleles and HLA allele combinations (and not otherwise disqualified as described above). In a preferred aspect of such embodiments, the relative activity is the in vivo clinical efficacy of the T cell line in the treatment of patients carrying / suffering from a pathogen or cancer.

[0092] In specific embodiments of the methods described herein, the at least one epitope is at least one immunodominant epitope.

[0093] In certain embodiments of the methods of the present invention, the selected T cell donor has at least one HLA allele or HLA allele combination that is the same as the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of pathogens). In some embodiments, the patient is a transplant recipient. In a specific embodiment in which the patient is a transplant recipient, the HLA allele or HLA allele combination that is the same as the patient or the patient's diseased cells (e.g., cancerous or pathogen-infected cells) refers to the same HLA allele or HLA allele combination as the patient before and / or after transplantation. In some embodiments, the patient's diseased cells are derived from a transplant given to the patient, and thus express the HLA alleles of the transplant; in such embodiments, the HLA typing of the patient's diseased cells can be performed by typing the HLA alleles in the transplant given to the patient. In other embodiments, the patient's diseased cells do not originate from a transplant given to the patient, and therefore have the HLA typing of the patient before transplantation. In a specific embodiment, the transplant is HSCT or a solid organ transplant.

[0094] T cell lines for activity profiling can be prepared as described in Section 5.1.1.

[0095] The step of determining HLA matching can be performed as described in Section 5.1.2. In general, for practicing the present invention, it is preferred to type more HLA loci because the more HLA loci that are typed, the more likely it is that the selected T cell donor can obtain an allogeneic T cell line with the highest activity relative to other allogeneic T cell lines derived from other T cell donors that have at least one HLA allele or HLA allele combination in common with the patient or the patient's diseased cells.

[0096] 5.3.1.1. Generation of activity profiles for donor selection

[0097] Activity diagrams may be prepared consistent with that discussed in Section 5.1.3 and as described herein.

[0098] In some aspects, the activity graph is a list of a plurality of HLA alleles and optional HLA allele combinations ranked by relative activity. In some embodiments, the step of selecting an allogeneic T cell donor is performed by examining a list of a plurality of HLA alleles and optional HLA allele combinations ranked by relative activity, wherein the highest stratum in the list is indicative of the highest relative activity; determining the highest ranked HLA allele or HLA allele combination known to be the same as the patient or the patient's diseased cells; and selecting an allogeneic T cell donor having the HLA allele or HLA allele combination. For example, in a specific embodiment, the activity graph is a list as shown in Table 6.

[0099] In some aspects, the activity profile is a database (e.g., table) listing a plurality of HLA alleles and optional HLA allele combinations, each associated with a score indicating relative activity. In some embodiments, the step of selecting an allogeneic T cell donor is performed by examining a database listing a plurality of HLA alleles and optional HLA allele combinations, each associated with a score indicating relative activity, wherein the highest score in the database is an indicator of the highest relative activity; determining the highest scoring HLA allele or HLA allele combination known to be the same as the patient or the patient's diseased cells; and selecting an allogeneic T cell donor having the HLA allele or HLA allele combination. In a specific embodiment, the step of selecting an allogeneic T cell donor using an activity profile (i.e., such a database) can be performed as follows: first filter out (exclude) all HLA alleles and HLA allele combinations in the database that are different from the patient or the patient's diseased cells, and then determine the HLA allele or HLA allele combination associated with the highest relative activity index among the remaining ones, and then select the allogeneic T cell donor having the HLA allele or HLA allele combination.

[0100] In some aspects, the activity diagram is a scatter plot. In certain embodiments, the first axis of the scatter plot represents different HLA alleles and optional HLA allele combinations of HLA alleles and optional HLA allele combinations in a large number of HLA alleles and optional HLA allele combinations. In certain embodiments, the second axis of the scatter plot represents relative activity. In a specific embodiment, the second axis of the scatter plot represents the percentage of interferon-γ-secreting CD3+ cells derived from each T cell line that reveals an indicator of relative activity against it in the activity diagram when stimulated with antigen presenting cells presenting one or more peptides of one or more antigens showing the antigenicity of a pathogen or cancer. In a specific embodiment, the stimulation is with antigen presenting cells that are autologous to each T cell line and loaded with one or more peptides showing the antigenicity of a pathogen or cancer, as an indicator of the relative activity. For example, in a specific embodiment, the activity diagram is Figure 1 The scatter plot shown.

[0101] In some embodiments, the activity profile is stored in a database.

[0102] In various embodiments, the methods for selecting an allogeneic T cell donor described herein are computer-implemented. In some embodiments, the methods for selecting an allogeneic T cell donor described herein are computer-implemented using a computer system as described in Section 5.6. In some embodiments, the methods for selecting an allogeneic T cell donor as described in Section 5.3.1 are computer-implemented using a readable medium as described in Section 5.6.

[0103] Once additional data is available, the additional data can be used to create activity maps.

[0104] 5.3.2. Selection of T cell donors based on frequency profiles

[0105] In various aspects, a method for selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer comprises: selecting a T cell donor who is allogeneic to the patient who has one or more HLA alleles in common with the patient or diseased cells of the patient (e.g., cancer or diseased cells associated with the presence of a pathogen) using a graph (hereinafter referred to as a "frequency graph"), wherein the graph (i) identifies a plurality of HLA alleles, and (ii) reveals an index of the relative frequency produced by each T cell line that recognizes at least one epitope of an antigen of the pathogen or cancer and is restricted to a different HLA allele of the plurality of said HLA alleles; wherein each identified HLA allele in the graph is associated with a corresponding index of the relative frequency produced by the T cell line restricted to the HLA allele, wherein: the selected T cell donor has at least one HLA allele in common with the patient or diseased cells of the patient that is associated with an index of higher frequency produced than the HLA allele of a donor that is not the same as the patient or diseased cells of the patient in the graph.

[0106] In another embodiment, the present invention provides a method for selecting a candidate allogeneic T cell donor from which to obtain an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising: selecting a T cell donor who is allogeneic to the patient having one or more HLA alleles in common with the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of a pathogen) using a frequency profile, the frequency profile (i) identifying a plurality of HLA alleles, and (ii) revealing an index of the relative frequency produced by each T cell line that recognizes at least one epitope of an antigen of the pathogen or cancer and is restricted to a different HLA allele of the plurality of said HLA alleles; wherein each identified HLA allele in the profile is associated with a corresponding index of the relative frequency produced by the T cell line restricted to the HLA allele, wherein: the selected T cell donor has at least one HLA allele in common with the patient or the patient's diseased cells that is associated with an index of higher frequency produced than an HLA allele in the profile from a donor that is not the same as the patient or the patient's diseased cells.

[0107] In certain embodiments, the method further includes the step of making a frequency graph before the selection step. Methods that can be used to make a frequency graph are described below. In certain embodiments, the method further includes the step of measuring relative frequencies before the making step. In certain embodiments, the method further includes the step of determining the HLA matching of the patient or the patient's diseased cells before the selection step. In certain embodiments, the method further includes the step of determining the HLA matching of the T cell donor before the selection step. In certain embodiments, the method further includes the step of determining the HLA matching of the patient or the patient's diseased cells and the HLA matching of the T cell donor before the selection step.

[0108] In specific embodiments of the methods described herein, the at least one epitope is at least one immunodominant epitope.

[0109] In certain embodiments of the methods of the present invention, the selected T cell donor has at least one HLA allele that is the same as the patient or the patient's diseased cells (e.g., cancer or diseased cells associated with the presence of a pathogen) associated with an indicator of a higher frequency in the frequency diagram compared to the HLA alleles of a donor that is different from the patient or the patient's diseased cells. In some embodiments, the patient is a transplant recipient. In a specific embodiment in which the patient is a transplant recipient, the HLA alleles that are the same as the patient or the patient's diseased cells (e.g., cancerous or pathogen-infected cells) refer to the HLA alleles that are the same as the patient before and / or after the transplant. In some embodiments, the patient's diseased cells are derived from a transplant given to the patient, and therefore express the HLA alleles of the transplant; in such embodiments, the HLA matching of the patient's diseased cells can be determined by typing the HLA alleles in the transplant given to the patient. In other embodiments, the patient's diseased cells do not originate from a transplant given to the patient, and therefore have the HLA matching of the patient before the transplant. In a specific embodiment, the transplant is HSCT or a solid organ transplant.

[0110] T cell lines for frequency profiling can be prepared as described in Section 5.1.1.

[0111] The step of determining HLA matching can be performed as described in Section 5.1.2. Generally speaking, typing more HLA loci is preferred for practicing the present invention.

[0112] The steps for determining HLA matching can be performed as described in Section 5.1.2.

[0113] 5.3.2.1. Generation of frequency plots for donor selection

[0114] The frequency plot identifies multiple HLA alleles and reveals an indicator of the relative frequency of production of T cell lines that (i) each recognize at least one epitope of an antigen of a (patient's) pathogen or cancer, and (ii) are restricted to different HLA alleles of the HLA allele. In the frequency plot, each identified HLA allele is associated with a corresponding indicator of the relative frequency of production of the T cell line restricted to the HLA allele.

[0115] In some aspects, the frequency plot is a list of a plurality of HLA alleles ranked by relative frequency. In some embodiments, the step of selecting an allogeneic T cell donor is performed by examining the list of a plurality of HLA alleles ranked by relative frequency, the highest stratum in the list being an indicator of the highest relative frequency; and selecting an allogeneic T cell donor that shares at least one HLA allele with the patient or the patient's diseased cells that is associated with a higher rank in the list compared to an HLA allele of a donor that is not the same as the patient or the patient's diseased cells.

[0116] In some aspects, the frequency plot is a database (e.g., a table) listing a plurality of HLA alleles, each associated with a score representing a relative frequency. In some embodiments, the step of selecting an allogeneic T cell donor is performed by examining a database listing HLA alleles, each associated with a score representing a relative frequency, with the highest score in the database being an indicator of the highest relative frequency; and selecting an allogeneic T cell donor that shares at least one HLA allele in common with the patient or the patient's diseased cells in the database that is associated with a higher score compared to an HLA allele of a donor that is not the same as the patient or the patient's diseased cells.

[0117] In some embodiments, the frequency profile is stored in a database.

[0118] In various embodiments, the method of selecting an allogeneic T cell donor described in the present disclosure is computer-implemented. In some embodiments, the method of selecting an allogeneic T cell donor described in the present disclosure is computer-implemented using a computer system as described in Section 5.6. In some embodiments, the method of selecting an allogeneic T cell donor described in the present disclosure is computer-implemented using a readable medium as described in Section 5.6.

[0119] The frequency graph may be updated with the additional data once it becomes available.

[0120] 5.4. Obtaining T cell lines

[0121] Also described herein is a method for obtaining an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising: (a) selecting an allogeneic T cell donor according to the method described in Section 5.3; and (b) obtaining an allogeneic T cell line from the selected allogeneic T cell donor, wherein the allogeneic T cell line recognizes at least one epitope of an antigen of the pathogen or cancer.

[0122] 5.5. Patients

[0123] References to patients in this disclosure are to human patients.

[0124] In different embodiments, the patient was a recipient of a transplant. In a specific embodiment, the transplant is a HSCT. In certain embodiments, the HSCT is a bone marrow transplant (BMT). In certain embodiments, the HSCT is a peripheral blood stem cell transplant (PBSCT). In certain embodiments, the HSCT is a cord blood transplant (CBT). In a specific embodiment, the transplant is a solid organ transplant.

[0125] In various embodiments, the patient is not a recipient of a transplant. In a specific embodiment, the patient is not a recipient of a HSCT. In a specific embodiment, the patient is not a recipient of a solid organ transplant.

[0126] In various aspects, the patient carries or is suspected of carrying a pathogen. In a specific embodiment, the patient carries a pathogen. In a specific embodiment, the patient is seropositive for the pathogen and has symptoms of infection by the pathogen. The pathogen can be a virus, bacteria, fungus, parasite, or protist. In certain embodiments, the pathogen is a virus.

[0127] In some embodiments, the virus is cytomegalovirus (CMV). In a specific embodiment, the patient carries or is suspected of carrying CMV infection after the patient undergoes HSCT. In a specific embodiment, the antigen of CMV is CMV pp65. In a specific embodiment, the antigen of CMV is CMV IE1.

[0128] In some embodiments, the virus is Epstein-Barr virus (EBV).In specific embodiments, the antigen of EBV is EBNA1, EBNA2, EBNA3A, EBNA3B, EBNA3C, LMP1 or LMP2.

[0129] In some embodiments, the virus is polyoma BK virus (BKV), John Cunningham virus (JCV), herpes virus, adenovirus (ADV), human immunodeficiency virus (HIV), influenza virus, Ebola virus, poxvirus, rhabdovirus or paramyxovirus. In specific embodiments, the virus is BKV. In specific embodiments, the virus is JCV. In specific embodiments, the virus is ADV. In specific embodiments, the virus is human herpes virus-6 (HHV-6) or human herpes virus-8 (HHV-8).

[0130] In one embodiment, the patient has a viral infection that is unresponsive to antiviral (small molecule) drug therapy.

[0131] In various aspects, the patient has or is suspected of having cancer. In a specific embodiment, the patient has cancer. Cancer can include cancer of the blood, breast, lung, ovary, stomach, pancreas, larynx, esophagus, testicles, liver, parotid gland, bile duct, colon, rectum, cervix, uterus, endometrium, kidney, bladder, prostate, thyroid, brain, or skin. In some embodiments, the cancer is a blood cancer. In specific embodiments, the cancer is a lymphoproliferative disorder. In other embodiments, the cancer is a brain cancer.

[0132] In some embodiments, the cancer is a WT1 positive cancer. In specific embodiments, the antigen of the cancer is WT1.

[0133] In some embodiments, the cancer is EBV-positive post-transplant lymphoproliferative disorder (EBV-PTLD). In specific embodiments, the antigen of EBV-PTLD is EBNA1, EBNA2, EBNA3A, EBNA3B or EBNA3C. In other specific embodiments, the antigen is LMP1 or LMP2.

[0134] In some embodiments, the cancer is EBV-positive nasopharyngeal carcinoma. In specific embodiments, the antigen of EBV-positive nasopharyngeal carcinoma is EBNA1, LMP1 or LMP2.

[0135] As described herein, the cancer antigen may be a cancer-specific or cancer-associated antigen, and thus may be a peptide or protein that is expressed more in cancer tissue or cancer cells than in non-cancerous tissue or non-cancer cells, or a peptide or protein that is expressed only in cancer tissue or cancer cells relative to non-cancerous tissue or non-cancer cells.

[0136] 5.6. Computer system and computer readable medium

[0137] In various embodiments, a computer system or computer readable medium is configured to perform any of the methods of selecting an allogeneic T cell line and any of the methods of selecting an allogeneic T cell donor as described in the present disclosure.

[0138] Also provided herein is a computer system for selecting an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer. In a specific embodiment, such a computer system comprises: a central processing unit; a memory connected to the central processing unit, the memory storing instructions for performing any of the steps of the method for selecting an allogeneic T cell line or any of the methods for selecting an allogeneic T cell donor as described in the present disclosure. In some embodiments, the computer system further comprises a display device in effective communication with the central processing unit.

[0139] Also provided herein is a computer-readable medium having computer-executable instructions for performing the steps of any of the methods of selecting an allogeneic T cell line or any of the methods of selecting an allogeneic T cell donor as described in the present disclosure.

[0140] In some embodiments, the computer system or computer readable medium is loaded with software components that are standard in the art. The software components together enable the computer to function according to the method for selecting an allogeneic T cell line or the method for selecting an allogeneic T cell donor as described in the present disclosure. In some embodiments, the computer system or computer readable medium is loaded with software components that are standard in the art and one or more computer program products that are unique to the present invention. In specific embodiments, one or more computer program products enable the computer system to function according to the method for selecting an allogeneic T cell line or the method for selecting an allogeneic T cell donor as described in the present disclosure. In specific embodiments, one or more computer program products that are unique to the present invention and software components that are standard in the art together enable the computer system to function according to the method for selecting an allogeneic T cell line or the method for selecting an allogeneic T cell donor as described herein.

[0141] In certain embodiments, the computer system or computer readable medium is configured to select an allogeneic T cell line for therapeutic administration to a patient with high and consistent efficacy. In certain embodiments, the computer system or computer readable medium is configured to select an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a patient with high and consistent efficacy. 6. Examples

[0142] Certain embodiments provided herein are illustrated by the following non-limiting examples, which demonstrate techniques that allow for optimized selection of therapeutically active CMVpp65-specific T cells for the treatment of CMV infection from a bank of HLA partially matched third-party donor-derived T cell lines based on stratification by HLA alleles shared by donors and recipients presenting immunodominant viral peptides.

[0143] 6.1. Methods:

[0144] 6.1.1. Establishment of CMV CTL library:

[0145] All cell production was performed in the GMP facility of Memorial Sloan Kettering Cancer Center (MSKCC) according to standard operating procedures (SOPs) and FDA-compliant protocols.

[0146] 6.1.1.1. Production of autologous cytokine-activated monocytes (CAMS):

[0147] Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of seropositive donors by density gradient centrifugation using ficoll hypaque.

[0148] PBMCs were allowed to grow at 10% in RPM-1640 medium containing 1% autologous serum. 7 / ml concentration at 37 ° C in 6-well tissue culture plates for 2 hours, after which non-adherent monocytes were gently removed. Adherent monocytes were cultured with 2 ml serum-free IMDM / well, supplemented with GM-CSF 2000IU (50μl) and IL-4 1000U (25μl) of IL-4 every other day until the 5th day. On the 5th day, tumor necrosis factor-α (SIGMA, St. Louis) was added to reach a final concentration of 10ng / ml, interleukin-1β to 400IU / ml, interleukin-6 (R&D systems, Inc, Minneapolis, MN USA) to 1000IU / ml and prostaglandin-E2 (Calbiochem, La Jolla, CA USA) to 25mM / ml to induce the final maturation of CAMS. On day 7, mature CAMS were harvested as described below, characterized for their expression of HLA class II, counted for CD14 and co-stimulatory molecules by FACS, aliquoted and used for sensitization of T cell lines.

[0149] 6.1.1.2. Generation of Autologous Transformed B Lymphocyte Cell Lines (BLCL):

[0150] EBV-BLCL from each donor was generated by infecting PBMC with EBV strain B95.8 as described previously (Koehne, G. et al., Blood, 2000. 96: 109-117; Koehne, G. et al., Blood, 2002. 99: 1730-1740). Cells were maintained in RPMI 1640 (Invitrogen, Inc, Carlsbad, CA USA) supplemented with 10% fetal calf serum (FCS) and acyclovir.

[0151] 6.1.1.3. Generation of CMVpp65-specific T cells:

[0152] By using microbeads (Miltenyi Biotech Inc.) pre-coated with immunomagnetic CD56 to perform immunomagnetic separation of CD56+ cells, T cells were enriched from peripheral blood lymphocytes isolated from PBMC by consuming adherent monocytes followed by consuming natural killer cells. As previously described, purified T cells were co-cultured with irradiated autologous CAMS loaded with a GMP-grade overlapping 15-peptide (PL CAM) library (Trivedi, D. et al., Blood, 2005.105:2793-2801). As previously described, T cells were cultured in the presence of IL-2 (5-40U / ml) at a ratio of 20:1 for effectors to stimulators for 28-40 days, and re-stimulated with CAMS loaded with irradiated autologous peptides every week (Trivedi, D. et al., Blood, 2005.105:2793-2801).

[0153] 6.1.2. Characterization of CMVpp65-specific T cells:

[0154] 6.1.2.1. Tetramer analysis:

[0155] The proportion of CMVpp65 epitope-specific T cells was quantitatively determined using HLA-peptide tetramers (Beckman Coulter, Inc Fullerton, CA) using commercially available CMVpp65 MHC-peptide tetramers for HLA A0201, A2402, and B0702 carrying the peptide sequences NLVPMVATV, QYDPVAALF, and TPRVTGGGAM, respectively. T cells were incubated on ice for 20 minutes with tetramer complexes conjugated with CD3FITC, CD8 PE, CD4 PerCP (BD Bioscience, San Jose, CA), and APC, washed, and then analyzed by FACS (BD LSR II). Data were analyzed using Flowjo software (Tree Star Inc, Ashland, OR). The proportion of CD4 and CD8+T cells in the culture and the proportion of CD3+ and CD8+T cells bound to HLA-peptide tetramers were determined.

[0156] 6.1.2.2.TCR Vβ Repertoire

[0157] A commercially available kit (1000) containing antibodies of 24 subfamilies of human TCR Vβ regions was used according to the procedure provided by the manufacturer (Wei, S. et al., Immunogenetics, 1994. 40: 27-36). Beta Mark, Beckman Coulter, Inc, France), and CMV peptide-HLA tetramer+ T cells were analyzed by flow cytometry against the TCRVβ repertoire.

[0158] 6.1.2.3. Quantification of CMV-specific and alloreactive IFN-γ-producing T cells

[0159] Initially and at several points during the development of each CMV-specific T cell line, 1 × 10 6 Donor T lymphocytes at a concentration of 1 μg / mL were mixed with autologous CAMS loaded with CMVpp65 peptide pool (20 ug / ml) at an effector-stimulator cell ratio of 5:1. Control tubes containing effector cells and PBMCs without any peptide were set in parallel. Brefeldin A was added to the unstimulated and peptide-stimulated samples at a concentration of 10 μg / mL cells. The tubes were incubated overnight at 37°C for 16 hours in a humidified 5% CO2 incubator.

[0160] Aliquots of the entire batch of unstimulated and stimulated cultures were transferred to tubes for staining with monoclonal antibodies. The cells were stained with 5 μL of monoclonal anti-CD3 or anti-CD4 PerCP (BD Biosciences, San Jose, CA) labeled with allophycocyanin (APC) and 10 μL of anti-CD8 peridinin chlorophyll protein (PerCP) and incubated at room temperature in the dark for 20 minutes. The cells were washed with 2 mL of phosphate buffered saline (PBS)-bovine serum albumin (BSA)-azide (AZ) (PBS+0.5% BSA+0.1% AZ). The cells were centrifuged, the supernatant was discarded, and 100 μL of reagent A (Fix&Perm Cell PermeabilizationReagents A&B; Caltag Laboratories, Burlingame, CA) was added to each tube to fix the cells. The cells were then incubated for 15 minutes. The cells were washed with PBS+BSA+AZ and 100 μL of reagent B (Caltag Laboratories) was added for permeabilization. Intracellular staining was performed by adding 10 μL of mouse IgG1 isotype control fluorescein isothiocyanate (FITC) or IFN-γFITC (BD PharMingen, San Diego, CA) monoclonal antibody. Cells were incubated at room temperature in the dark for 20 minutes, washed twice, and further fixed in 1% formalin.

[0161] The stained and fixed cells were then acquired using a LSR II flow cytometer (BD Biosciences) with a three-laser 10-color capability and analyzed using flowjo software. Cells were first identified by forward scatter and side scatter and then by gating CD3+ cells in the CD3 APC vs. side scatter dot plot. 20,000-50,000 events were acquired in the integrated gate. For further identification of the cells, gating on CD3+CD8+ or CD3+CD4+ cells was performed. Quadrant markers were established based on the analysis of unstimulated control and isotype control tubes.

[0162] 6.1.3. Establishing stratification: quantification of antiviral CD8+ T cell responses to different CMVpp65 epitopes

[0163] 6.1.3.1. Epitope mapping using a library of overlapping 15aa peptides

[0164] By following the technique of Waldrop et al. (Waldrop, SL et al., J Clin Invest, 1997. 99: 1739-1750) modified by Koehne et al. (Koehne, G. et al., Blood, 2002. 99: 1730-1740), the T cell response to a specific peptide within CMV pp65 was identified and quantified by measuring the number of IFNγ-positive T cells produced when stimulated with autologous APCs loaded with the target peptide or peptide pool (PL). A series of overlapping peptide pools allow identification of specific epitopes that induce T cell responses. Peptide-loaded PBMCs that are autologous to the T cell donor, CAMS that are autologous to the T cell donor, or BLCL that are autologous to the T cell donor are used as APCs to stimulate responsive T cells for epitope mapping.

[0165] 6.1.3.2. In vitro cytotoxic activity

[0166] As mentioned above, the standard 51Chromium release assay All T cell lines were evaluated for their ability to lyse CMVpp65-loaded targets (Koehne, G. et al., Blood, 2002. 99: 1730-1740; Trivedi, D. et al., Blood, 2005. 105: 2793-2801). The targets used for all experiments consisted of a panel of EBV-BLCLs, each of which shared a single HLA allele with the T cells of the indicated donor. As specified in the given experiment, these cells were loaded with the complete CMV pp65 peptide library or a specific subset thereof, a single 15-peptide, or a CMV pp65 nonamer known to be presented by that allele (e.g., NLVPMVATV for HLA A0201, QYDPVAALF and TPRVTGGGAM for HLA A2402, and RPHERNGFTV for HLA B0702) (Trivedi, D. et al., Blood, 2005. 105: 2793-2801; Hasan, AN et al., J Immunol, 2009. 183: 2837-2850). Targets loaded with peptides presented by non-shared HLA alleles were used as controls. HLA restriction was identified by the reactivity of targets pulsed with identified peptide epitopes presented by specific shared HLA alleles and the lack of reactivity of peptides loaded on EBV BLCL carrying other shared alleles or completely mismatched EBV BLCL.

[0167] 6.2. Data:

[0168] 6.2.1. GMP-grade CMV CTL libraries generated from a genetically heterogeneous donor population with a range of different HLA alleles

[0169] Since the initiation of clinical trials using donor-derived CMVpp65-specific T cells for the treatment of CMV viremia in allogeneic HSCT recipients, a total of 119 CMVpp65-specific CTL lines have been generated over a period of 7 years.

[0170] The donor pool used to generate the CTL lines inherited 180 different HLA alleles, which represent the common HLA alleles prevalent in the multi-ethnic population of New York. The distribution of HLA alleles in the donor CTL pool was closely related to the HLA allele frequencies that occur in various ethnic groups, including Caucasians, Asians, and blacks, with the exception of HLA A0201 and B0702, which were overrepresented; 33% vs. 25% and 21% vs. 8.7%, respectively (Table 1). The order of frequency of inherited HLA class I alleles in the 119 donors was as follows: A0201 (n=39), A0301 (n=28), B0702 (n=25), B 44 (n=24), HLA B0801 (n=22), B 3501-11 (n=19), A1101 (n=16), A2402 (n=14), B 1501-17 (n=14), B1801-07 (n=12), 3201-03 (n=11), A3301-04 (n=10), B 4001-06 (n=9), and A2601 (n=9), B5701 (n=9). Other HLA class I alleles occur at lower frequencies, such as HLA B 5201 (n=8), B 3801 (n=6), A6801-09 (n=5), B 5801 (n=5). For HLA class II alleles, there are 6 highly occurring HLA DRB1 alleles, as expected from their higher frequencies in the general population (Table 1). In order of frequency, these include DRB11501-08, 0401-32, 0301-13, 0701-04, 1101-20, 1301-34.

[0171] Table 1. HLA allele frequencies in the general population and characterization of 119 CMVpp65-specific CTL lines.

[0172]

[0173]

[0174] 6.2.2. CMVpp65-specific T cell responses are dominant based on epitopes presented by a minority of HLA class I and class II alleles

[0175] In 103 of 119 (87%) CTL lines, the immunodominant T cell response was restricted by HLA class I alleles, and in 16 CTL lines, it was restricted by HLA class II alleles. In 54% of the CTL lines, the immunodominant T cell response was restricted by 3 HLA class I alleles: A0201 (25%), B 0702 (21%), and B3501-11 (8%). Other alleles presenting immunodominant epitopes included HLA A 2402, B 4001, B4006, B 4202, B 4204, B 4402, B 4403, DRB10401 and 0404, DRB1 1101, and DRB1 1202. Thus, despite the broad repertoire of class I and class II HLA alleles provided in the library, only 19 of these alleles presented epitopes that induced immunodominant T cell responses. Furthermore, any detectable level of T cell response was specific for epitopes presented by only 49 of the 180 HLA alleles inherited by the donors in the library.

[0176] 6.2.3. HLA alleles presenting immunodominant epitopes exist in a stratified order within individuals who co-inherit a particular haplotype

[0177] Evaluation of T cell lines in the library also showed that epitopes presented by specific HLA alleles were always dominant, as measured by quantification of epitope-specific IFNγ+ T cells and determination of their HLA restriction. Previous studies provided evidence that the epitope of CMVpp65 presented by HLA B0702 was dominant in patients who co-inherited HLA A0201 and B0702 (Lacey, SF et al., Hum Immunol, 2003. 64: 440-452). In the series of this example, HLA B0702 was consistently the allele (100%) that restricted the immunodominant T cell response in all 25 donors in the library that inherited this allele, including 9 that co-inherited HLA A0201. Therefore, responses restricted by HLA B0702 are dominant regardless of the other HLA class I and class II alleles inherited.

[0178] On the other hand, in 30 of the 39 donors that inherited HLA A0201 (77%), the immunodominant T cell response was restricted by HLA A0201. The remaining 9 donors were donors that co-inherited HLA A0201 and B0702, and in each of these 9 donors, the immunodominant T cell response was restricted by HLA B 0702. Thus HLA A0201 is an allele that restricts immunodominant T cell responses when co-inherited with any other HLA class I or class II allele (except when co-inherited with HLA B0702). For example, of the 22 donors that inherited the HLA B44 allele, only 4 induced a dominant response that was restricted by this allele. When these alleles (B4401, B4402, B4403) were co-inherited with HLA A0201, the immunodominant CTL responses were restricted to HLA A0201 in 11 of the 12 donors (91.6%); the other donors also co-inherited HLA B0702 and induced HLA B0702-restricted responses.

[0179] Another striking feature of the T cell responses in donors inheriting HLA B 0702 or A0201 is the fact that the observed responses are specific to epitopes presented by these alleles. In contrast, in T cell lines in which the response to an immunodominant epitope is restricted by other HLA alleles, subdominant T cell populations specific for other epitopes and restricted by other HLA alleles are often observed. This analysis allows the presentation of Figure 1 Identification of hierarchical clustering of HLA alleles of immunodominant epitopes is shown.

[0180] HLA alleles presenting immunodominant epitopes were stratified only according to their level of functional activity in response to peptide stimulation. There was no correlation between the affinity of the peptides for HLA binding and their ability to induce immunodominant T cell responses (Table 2).

[0181] Table 2. Characterization of HLA alleles presenting immunodominant epitopes.

[0182]

[0183]

[0184]

[0185] 6.2.4. Epitope repertoires and HLA alleles that make up the CMV CTL pool can be used to treat different patient groups

[0186] A very limited repertoire of immunodominant CMVpp65 epitopes that induce T cell responses was found within the 119 CTL lines that make up the GMP library, which are presented by a limited number of HLA loci. Given that T cell responses are defined by such fine specificity, for antigen-specific T cells to be clinically effective in a third-party setting, the selected T cells should need to react to epitopes presented by HLA loci shared by the patient. Among these parameters, patients of different ethnicities that could potentially be treated with CTL from this library were analyzed.

[0187] A series of consecutive T cell depleted transplants from related or unrelated donors and cord blood donors that were HLA matched or HLA mismatched performed at Memorial Sloan-Kattering Cancer Center over the past 3-5 years was reviewed. At this center, in a series of 239 HLA matched related or unrelated transplants, in 86% of the cases, it was possible to identify CTL lines with a CMV T cell response restricted by the HLA alleles shared by the patients and matched in 1-2 other HLA alleles. Similarly, in a series of 137 HLA mismatched transplants and 70 cord blood transplants, appropriately restricted CTL lines could be identified in 93% and 81% of the cases, respectively. Thus, despite the broad presentation of HLA alleles in the CTL pool, T cells restricted by a limited HLA allele pool can be identified and used to treat the majority of patients in this ethnically diverse population.

[0188] 6.2.5. Clinical activity of therapeutic CMV CTLs selected from transplant donors or third-party donors using newly defined epitopes and HLA restriction criteria

[0189] A total of 54 evaluable patients received CMV CTL as a treatment for clinical infection or persistent viremia that could not respond to antiviral drugs. Of these people, 19 received CMVpp65-specific T cells from their HCT donor (NCTO1646645), and 35 received T cells from third-party donors with >2HLA allele matches. The results are summarized in Tables 3 and 4. In this analysis, CR is defined as the clearance of clinical infection and / or the clearance of detectable CMV from the blood. PR is defined as a reduction of CMV in the blood>2log10. SD is defined as a patient with a stable clinical condition and CMV reduction<2log10. POD is defined as viremia and continued progression of clinical disease.

[0190] Table 2. HLA-restricted responses of administered CMVpp65-specific T cells.

[0191]

[0192]

[0193] Table 3. Immunodominant HLA alleles detected in other CMVpp65-specific T cells administered

[0194]

[0195] As can be seen, of the 19 patients who received T cells specific for the CMVpp65 epitope presented by HLA A201, 14 achieved CR or PR. Of the 9 patients treated with T cells specific for the immunodominant epitope presented by HLA B0702, 8 achieved CR. Likewise, in each of the 5 cases treated, the immunodominant T cells were restricted by HLA A2402 (N=2) and B0801 (N=3) induced CR.

[0196] In contrast, 7 / 7 recipients of CMVpp65-specific T cells specific for immunodominant epitopes presented by allelic variants of HLA B35 did not respond. Likewise, immunodominant T cells specific for epitopes of A2601 (N=3), A2407 (N=1), and B5001 (N=1) were unable to clear infection or reduce viremia.

[0197] These expected results provide evidence that immunodominant epitopes presented by specific HLA alleles induce T cells with better therapeutic activity in vivo.

[0198] A retrospective review was also performed on patients who received transplants from donors who also consented to have their CMVpp65-specific T cells included in the bank for individuals to whom they also donated HLA-compatible HCT. The reason is that T-cell-depleted transplants from such donors typically contain 2-8x10 3 T cells / kg recipient body weight, may also provide a small number of immunodominant CMV-specific T cells, since the frequency of IFNγ+CMV-specific T cells in the blood of seropositive donors ranges from 0.1-1% of circulating T cells. Table 5 provides the results of this preliminary analysis.

[0199] Table 4. Analysis of CMV reactivation, disease, and ultimate response to CMV-directed therapy in patients receiving transplants from HLA-compatible donors who also donated cells to the bank as third-party donors.

[0200]

[0201] Furthermore, as seen in patients treated with CMVpp65-specific T cells, recipients of transplants from donors who shared the HLA B0702 and A0201 alleles had a reduced risk of developing CMV disease with persistent viremia in response to treatment, whereas those who received transplants from donors lacking these alleles had a significant incidence of overt infection. This was again particularly observed in patients carrying variants of HLA B35 that lacked HLA B0702 or A0201.

[0202] Clinical data allowed us to identify a stratification of certain HLA alleles presenting immunodominant epitopes of CMVpp65 that induce peptide-specific T cell responses (see Table 6), an example of an activity profile.

[0203] Table 5. Stratification of HLA alleles presenting immunodominant epitopes of CMVpp65 that induce peptide-specific T cell responses.

[0204]

[0205]

[0206] a Higher grades correspond to better clinical efficacy of T cell lineages restricted by HLA alleles in treating patients with CMV infection or persistent viremia who are unresponsive to antiviral drugs.

[0207] Our data suggest that HLA-B35 variants should not be used (and therefore can be considered "disqualified" among the HLA alleles present).

[0208] 6.3. Data show that:

[0209] 1. A limited repertoire of CMVpp65 epitopes induced functional CMV-specific cytotoxic T cell responses, and a total of 49 HLA alleles among the 181 alleles present in the CTL repertoire presented these immunodominant CMVpp65 epitopes.

[0210] 2. The identified peptide epitopes can be used to develop effective peptide vaccines or as limited peptide libraries to generate highly functional CMV CTLs for adoptive immunotherapy in the future.

[0211] 3. Incorporation of HLA-stratified analysis into the selection of CTL lines for therapy may promote higher and more consistent efficacy of third-party CTL therapy.

[0212] 6.4. Summary of Clinical and Experimental Results

[0213] Effective adoptively transferred virus-specific T cells must be specific for viral peptide epitopes expressed by virus-infected host cells and presented by HLA alleles expressed by donor T cells that recognize the viral epitopes.

[0214] After resolution of the initial infection with CMV, the initially large pool of responding T cells shrinks so that only T cells specific for a few immunodominant epitopes remain. Thus, CMVpp65-specific T cell lines expanded from latently infected CMV seropositive normal donors are typically specific for only 1-2 immunodominant CMVpp65 peptides presented by only 1-2 HLA alleles expressed by the donor.

[0215] We found that there is a stratification of HLA alleles presenting immunodominant epitopes of CMVpp65 that induce peptide-specific T cell responses, which results in preferential expansion of CMVpp65-specific T cells presented by a particular HLA allele relative to all other cells of the same genetic and expressed allele. This stratification is not based on the binding affinity of the peptide to the presenting allele. As a result of this stratification of HLA restriction:

[0216] 1. The immunodominant epitopes that induced CMVpp65-specific T cells detected in in vitro expanded T cell lines were presented only by a few HLA alleles.

[0217] 2. Furthermore, in individuals who inherit two or more HLA alleles from this limited pool of HLA alleles presenting immunodominant peptide epitopes, certain HLA alleles (eg HLA B0702 or HLA A0201) consistently present epitopes that induce an exclusive response.

[0218] Early results from a Phase II trial further suggest that in patients with CMV infection or persistent viremia who failed antiviral drug therapy and were then treated with CMVpp65-specific T cells derived from a third-party donor that were restricted by the HLA allele expressed by the host's infected cells, those who received CMVpp65-specific T cells restricted by the same highest HLA allele in that stratum (e.g., HLA B0702 or HLAA0201) consistently responded, whereas treatment with CMVpp65-specific T cells restricted by HLA alleles lower in the stratum cleared the infection, with less consistent responses.

[0219] 7. Join by reference

[0220] Various publications are cited herein, the disclosures of which are incorporated by reference in their entireties. Specific implementation method:

[0221] 1. A method for selecting an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising:

[0222] T cell lines that are allogeneic to a patient that recognizes at least one epitope of an antigen of a pathogen or cancer are selected using a graph that (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of each T cell line that recognizes at least one epitope of an antigen of a pathogen or cancer and is restricted to a different HLA allele or combination of HLA alleles of a plurality of HLA alleles or combinations of HLA alleles; wherein each identified HLA allele or combination of HLA alleles in the graph is associated with a corresponding indicator of the relative activity of the T cell line restricted to that HLA allele or combination of HLA alleles, the relative activity being a relative measure of a known activity exhibited by the T cell line against the pathogen or against the cancer; wherein

[0223] (A) the selected T cell line has the same HLA allele or combination of HLA alleles as the patient or diseased cells in the patient, to which recognition of the T cell line identified by the diagram is restricted; and

[0224] (B) The HLA alleles or HLA allele combinations to which the selected T cell line is restricted are associated in the graph with an index of the highest relative activity among the HLA alleles and HLA allele combinations known to be consistent with the patient or the patient's diseased cells and not otherwise disqualified in the graph.

[0225] 2. The method of embodiment 1 further comprises the step of making a diagram before the selection step.

[0226] 3. The method of embodiment 2, further comprising a step of measuring relative activity before the producing step.

[0227] 4. The method of any one of embodiments 1-3, further comprising the step of determining the HLA matching of the patient or the patient's diseased cells before the selection step.

[0228] 5. The method of embodiment 4, wherein the step of determining comprises typing at least 4 HLA loci.

[0229] 6. The method of any one of embodiments 1-5, wherein the graph is a list of a large number of HLA alleles and optional HLA allele combinations ranked by relative activity.

[0230] 7. The method of any one of embodiments 1-5, wherein the representation is a database listing a large number of HLA alleles and optionally combinations of HLA alleles, each associated with a score indicating relative activity.

[0231] 8. The method of any one of embodiments 1-5, wherein the graph is a scatter plot.

[0232] 9. The method of claim 8, wherein a first axis of the scatter plot represents different HLA alleles and optional HLA allele combinations among a plurality of HLA alleles and optional HLA allele combinations; and wherein a second axis of the scatter plot represents interferon-γ-secreting CD3+ derived from each T cell line for which the relative activity is revealed in the graph when stimulated with antigen presenting cells that are autologous to the respective T cell line and loaded with one or more peptides that display antigenicity of a pathogen or cancer. + The percentage of cells was used as an indicator of the relative activity.

[0233] 10. The method of any one of embodiments 1-8, wherein the relative activity is the in vivo clinical efficacy of the T cell line in the treatment of patients carrying / suffering from a pathogen or cancer.

[0234] 11. The method of any one of embodiments 1-10, wherein the diagram is stored in a database.

[0235] 12. The method of any one of embodiments 1-11, wherein the method is computer-implemented.

[0236] 13. The method of any one of embodiments 1-12, wherein the patient carries or is suspected of carrying a pathogen, wherein the T cell line recognizes at least one epitope of an antigen of the pathogen, and wherein the relative activity is a relative measure of a known activity against the pathogen.

[0237] 14. The method of embodiment 13, wherein the pathogen is a virus, a bacterium, a fungus, a parasite or a protist.

[0238] 15. The method of embodiment 14, wherein the pathogen is a virus.

[0239] 16. The method of embodiment 15, wherein the virus is CMV.

[0240] 17. The method of embodiment 16, wherein the patient has or is suspected of having CMV infection after the patient undergoes hematopoietic stem cell transplantation (hereinafter referred to as "HSCT").

[0241] 18. The method of embodiment 16 or 17, wherein the antigen is CMV pp65.

[0242] 19. The method of embodiment 16 or 17, wherein the antigen is CMV IE1.

[0243] 20. The method of embodiment 15, wherein the virus is EBV.

[0244] 21. The method of embodiment 20, wherein the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B, EBNA3C, LMP1 or LMP2.

[0245] 22. The method of embodiment 15, wherein the virus is BKV, JCV, herpes virus, adenovirus, human immunodeficiency virus, influenza virus, Ebola virus, poxvirus, rhabdovirus or paramyxovirus.

[0246] 23. The method of embodiment 15, wherein the virus is human herpesvirus-6 (HHV-6) or human herpesvirus-8 (HHV-8).

[0247] 24. The method of any one of embodiments 1-12, wherein the patient has or is suspected of having cancer, wherein the T cell line recognizes at least one epitope of an antigen of the cancer, and wherein the relative activity is a relative measure of a known activity against the cancer.

[0248] 25. The method of embodiment 24, wherein the cancer is a blood cancer.

[0249] 26. The method of embodiment 24, wherein the cancer is cancer of the breast, lung, ovary, stomach, pancreas, larynx, esophagus, testis, liver, parotid gland, bile duct, colon, rectum, cervix, uterus, endometrium, kidney, bladder, prostate, thyroid, brain, or skin.

[0250] 27. The method according to embodiment 24, wherein the antigen is WT1.

[0251] 28. The method of embodiment 24, wherein the cancer is a lymphoproliferative disorder.

[0252] 29. The method of embodiment 28, wherein the cancer is an EBV-positive post-transplantation lymphoproliferative disorder.

[0253] 30. The method of embodiment 29, wherein the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B or EBNA3C.

[0254] 31. The method of embodiment 29, wherein the antigen is LMP1 or LMP2.

[0255] 32. The method of embodiment 24, wherein the cancer is EBV-positive nasopharyngeal carcinoma.

[0256] 33. The method of embodiment 32, wherein the antigen is EBNA1, LMP1 or LMP2.

[0257] 34. A method of selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising:

[0258] A donor of T cells that is allogeneic to the patient is selected using a graph that (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of each T cell line that recognizes at least one epitope of an antigen of a pathogen or cancer and is restricted to a different HLA allele or combination of HLA alleles of a plurality of HLA alleles or combinations of HLA alleles; wherein each identified HLA allele or combination of HLA alleles in the graph is associated with a corresponding indicator of the relative activity of the T cell line restricted to the HLA allele or combination of HLA alleles, the relative activity being a relative measure of a known activity exhibited by the T cell line against the pathogen or against the cancer; wherein

[0259] (A) the selected T cell donor has at least one HLA allele or combination of HLA alleles in common with the patient or diseased cells in the patient; and

[0260] (B) one of the at least one HLA allele or combination of HLA alleles that is common to the patient or the patient's diseased cells is associated with an indicator of the highest relative activity among the HLA alleles and combinations of HLA alleles in the graph that are known to be common to the patient or the patient's diseased cells and are not otherwise disqualified.

[0261] 35. The method of embodiment 34 further comprises the step of producing a diagram before the selecting step.

[0262] 36. The method of embodiment 35, further comprising the step of measuring the relative activity before the producing step.

[0263] 37. The method of any one of embodiments 34-36, further comprising the step of determining the HLA matching of the patient or the patient's diseased cells and the HLA matching of the T cell donor before the selection step.

[0264] 38. The method of embodiment 37, wherein the step of determining comprises typing at least 4 HLA loci.

[0265] 39. The method of any one of embodiments 34-38, wherein the graph is a list of a large number of HLA alleles and optional HLA allele combinations ranked by relative activity.

[0266] 40. The method of any one of embodiments 34-38, wherein the representation is a database listing a large number of HLA alleles and optional HLA allele combinations, each associated with a score indicating relative activity.

[0267] 41. The method of any one of embodiments 34-38, wherein the graph is a scatter plot.

[0268] 42. The method of embodiment 41, wherein a first axis of the scatter plot represents different HLA alleles and optional HLA allele combinations among a plurality of HLA alleles and optional HLA allele combinations; and wherein a second axis of the scatter plot represents interferon-γ-secreting CD3+ derived from each T cell line for which the relative activity is revealed in the graph when stimulated with antigen presenting cells that are autologous to the respective T cell line and loaded with one or more peptides that display antigenicity of a pathogen or cancer. + The percentage of cells was used as an indicator of the relative activity.

[0269] 43. The method of any one of embodiments 34-41, wherein the relative activity is the in vivo clinical efficacy of the T cell line in the treatment of patients carrying / suffering from a pathogen or cancer.

[0270] 44. The method of any one of embodiments 34-43, wherein the diagram is stored in a database.

[0271] 45. The method of any one of embodiments 34-44, wherein the method is computer-implemented.

[0272] 46. ​​The method of any one of embodiments 34-45, wherein the patient carries or is suspected of carrying a pathogen, wherein the T cell line recognizes at least one epitope of an antigen of the pathogen, and wherein the relative activity is a relative measure of a known activity against the pathogen.

[0273] 47. The method of embodiment 46, wherein the pathogen is a virus, a bacterium, a fungus, a parasite or a protist.

[0274] 48. The method of embodiment 46, wherein the pathogen is a virus.

[0275] 49. The method of embodiment 48, wherein the virus is CMV.

[0276] 50. The method of embodiment 49, wherein the patient has or is suspected of having CMV infection after the patient underwent HSCT.

[0277] 51. The method of embodiment 49 or 50, wherein the antigen is CMV pp65.

[0278] 52. The method of embodiment 49 or 50, wherein the antigen is CMV IE1.

[0279] 53. The method of embodiment 48, wherein the virus is EBV.

[0280] 54. The method of embodiment 53, wherein the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B, EBNA3C, LMP1 or LMP2.

[0281] 55. The method of embodiment 48, wherein the virus is BKV, JCV, herpes virus, adenovirus, human immunodeficiency virus, influenza virus, Ebola virus, poxvirus, rhabdovirus or paramyxovirus.

[0282] 56. The method of embodiment 48, wherein the virus is human herpesvirus-6 (HHV-6) or human herpesvirus-8 (HHV-8).

[0283] 57. The method of any one of embodiments 34-45, wherein the patient has or is suspected of having cancer, wherein the T cell line recognizes at least one epitope of an antigen of the cancer, and wherein the relative activity is a relative measure of a known activity against the cancer.

[0284] 58. The method of embodiment 57, wherein the cancer is a blood cancer.

[0285] 59. The method of embodiment 57, wherein the cancer is cancer of the breast, lung, ovary, stomach, pancreas, larynx, esophagus, testis, liver, parotid gland, bile duct, colon, rectum, cervix, uterus, endometrium, kidney, bladder, prostate, thyroid, brain, or skin.

[0286] 60. The method according to embodiment 57, wherein the antigen is WT1.

[0287] 61. The method of embodiment 57, wherein the cancer is a lymphoproliferative disorder.

[0288] 62. The method of embodiment 61, wherein the cancer is an EBV-positive post-transplantation lymphoproliferative disorder.

[0289] 63. The method of embodiment 62, wherein the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B or EBNA3C.

[0290] 64. The method of embodiment 62, wherein the antigen is LMP1 or LMP2.

[0291] 65. The method of embodiment 57, wherein the cancer is EBV-positive nasopharyngeal carcinoma.

[0292] 66. The method of embodiment 65, wherein the antigen is EBNA1, LMP1 or LMP2.

[0293] 67. A method of selecting an allogeneic T cell donor from which an allogeneic T cell line is derived for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising:

[0294] T cell donors that are allogeneic to a patient having one or more HLA alleles in common with the patient or diseased cells in the patient are selected using a graph that (i) identifies a plurality of HLA alleles, and (ii) reveals an indicator of the relative frequency of production of a T cell line that recognizes at least one epitope of an antigen of a pathogen or cancer and is restricted to a plurality of different HLA alleles of said HLA alleles; wherein each identified HLA allele in the graph is associated with a corresponding indicator of the relative frequency of production of said T cell line that is restricted to said HLA allele, wherein:

[0295] The selected T cell donor has at least one HLA allele in common with the patient or the patient's diseased cells that is associated with a higher frequency of the indicator produced in the diagram compared to HLA alleles from a donor that is not the same as the patient or the patient's diseased cells.

[0296] 68. The method of embodiment 67 further comprises the step of producing a diagram before the selection step.

[0297] 69. The method of embodiment 68, further comprising a step of measuring the relative frequency before the manufacturing step.

[0298] 70. The method of any one of embodiments 67-69, further comprising the step of determining the HLA matching of the patient or the patient's diseased cells and the HLA matching of the T cell donor before the selecting step.

[0299] 71. The method of embodiment 70, wherein the step of determining comprises typing at least 4 HLA loci.

[0300] 72. The method of any one of embodiments 67-71, wherein the graph is a list of a large number of HLA alleles sorted by the relative frequencies.

[0301] 73. The method of any one of embodiments 67-71, wherein the representation is a database listing a large number of HLA alleles, each associated with a score representing relative frequency.

[0302] 74. The method of any one of embodiments 67-73, wherein the diagram is stored in a database.

[0303] 75. The method of any one of embodiments 67-74, wherein the method is computer-implemented.

[0304] 76. The method of any one of embodiments 67-75, wherein the patient carries or is suspected of carrying a pathogen, and wherein the T cell line recognizes at least one epitope of an antigen of the pathogen.

[0305] 77. The method of embodiment 76, wherein the pathogen is a virus, a bacterium, a fungus, a parasite or a protist.

[0306] 78. The method of embodiment 76, wherein the pathogen is a virus.

[0307] 79. The method of embodiment 78, wherein the virus is CMV.

[0308] 80. The method of embodiment 79, wherein the patient has or is suspected of having CMV infection after the patient underwent HSCT.

[0309] 81. The method of embodiment 79 or 80, wherein the antigen is CMV pp65.

[0310] 82. The method of embodiment 79 or 80, wherein the antigen is CMV IE1.

[0311] 83. The method of embodiment 78, wherein the virus is EBV.

[0312] 84. The method of embodiment 83, wherein the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B, EBNA3C, LMP1 or LMP2.

[0313] 85. The method of embodiment 78, wherein the virus is BKV, JCV, herpes virus, adenovirus, human immunodeficiency virus, influenza virus, Ebola virus, poxvirus, rhabdovirus or paramyxovirus.

[0314] 86. The method of embodiment 78, wherein the virus is human herpesvirus-6 (HHV-6) or human herpesvirus-8 (HHV-8).

[0315] 87. The method of any one of embodiments 67-75, wherein the patient has or is suspected of having cancer, wherein the T cell line recognizes at least one epitope of an antigen of the cancer.

[0316] 88. The method of embodiment 87, wherein the cancer is a blood cancer.

[0317] 89. The method of embodiment 87, wherein the cancer is cancer of the breast, lung, ovary, stomach, pancreas, larynx, esophagus, testis, liver, parotid gland, bile duct, colon, rectum, cervix, uterus, endometrium, kidney, bladder, prostate, thyroid, brain, or skin.

[0318] 90. The method according to embodiment 87, wherein the antigen is WT1.

[0319] 91. The method of embodiment 87, wherein the cancer is a lymphoproliferative disorder.

[0320] 92. The method of embodiment 91, wherein the cancer is an EBV-positive post-transplantation lymphoproliferative disorder.

[0321] 93. The method of embodiment 92, wherein the antigen is EBNA1, EBNA2, EBNA3A, EBNA3B or EBNA3C.

[0322] 94. The method of embodiment 92, wherein the antigen is LMP1 or LMP2.

[0323] 95. The method of embodiment 87, wherein the cancer is EBV-positive nasopharyngeal carcinoma.

[0324] 96. The method of embodiment 95, wherein the antigen is EBNA1, LMP1 or LMP2.

[0325] 97. The method of any one of embodiments 1-96, wherein the patient is a recipient of HSCT.

[0326] 98. The method of embodiment 97, wherein HSCT is a bone marrow transplant, a peripheral blood stem cell transplant, or an umbilical cord blood transplant.

[0327] 99. The method of any one of embodiments 1-96, wherein the patient is a recipient of a solid organ transplant.

[0328] 100. A computer system for selecting an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, comprising:

[0329] CPU;

[0330] A memory connected to the central processing unit, the memory storing instructions for executing the steps of the method of any one of embodiments 1-99.

[0331] 101. A computer-readable medium having computer-executable instructions for performing the steps of the method of any one of embodiments 1-99.

[0332] 102. A method of treating a human patient who is carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising:

[0333] (a) selecting an allogeneic T cell line for therapeutic administration to a patient according to the method of any one of embodiments 1-33; and

[0334] (b) administering a T cell population derived from the selected allogeneic T cell line to the patient.

[0335] 103. The method of embodiment 102, wherein the patient is a recipient of HSCT.

[0336] 104. The method of embodiment 103, wherein HSCT is a bone marrow transplant, a peripheral blood stem cell transplant, or an umbilical cord blood transplant.

[0337] 105. The method of embodiment 102, wherein the patient is a recipient of a solid organ transplant.

[0338] 106. A method of obtaining an allogeneic T cell line for therapeutic administration to a human patient carrying / suffering from or suspected of carrying / suffering from a pathogen or cancer, the method comprising:

[0339] (a) selecting an allogeneic T cell donor according to the method of any one of embodiments 34-99; and

[0340] (b) obtaining an allogeneic T cell line from the selected allogeneic T cell donor, wherein the allogeneic T cell line recognizes at least one epitope of an antigen of a pathogen or cancer.

Claims

1. A method for selecting an allogeneic T cell line for therapeutic administration to a human patient suffering from or suspected of suffering from cancer, comprising: selecting a T cell line that is allogeneic to a patient that recognizes at least one epitope of a cancer antigen using a graph that (i) identifies a plurality of HLA alleles and optionally a combination of HLA alleles, and (ii) reveals an indicator of the relative activity of each T cell line that recognizes at least one epitope of an antigen of the cancer and is restricted to a plurality of HLA alleles or combinations of HLA alleles; wherein in the graph each identified HLA allele or combination of HLA alleles is associated with a corresponding indicator of the relative activity of the T cell line restricted to the HLA allele or combination of HLA alleles, the relative activity being a relative measure of a known activity exhibited by the T cell line against the cancer; in (A) the selected T cell line has the same HLA allele or combination of HLA alleles as the patient or diseased cells in the patient, to which recognition of the T cell line identified by the diagram is restricted; and (B) The HLA alleles or HLA allele combinations to which the selected T cell line is restricted are associated in the graph with an index of the highest relative activity among the HLA alleles and HLA allele combinations known to be consistent with the patient or the patient's diseased cells and not otherwise disqualified in the graph.

2. The method of claim 1, further comprising the step of producing a diagram before the step of selecting.

3. The method of claim 2, further comprising the step of measuring relative activity prior to the producing step.

4. The method of claim 1, further comprising the step of determining the HLA matching of the patient or the patient's diseased cells prior to the selecting step.

5. The method of claim 4, wherein the step of determining comprises typing at least four HLA loci.

6. The method of claim 1, wherein the representation is a table of a plurality of HLA alleles and optional combinations of HLA alleles ranked by relative activity.

7. The method of claim 1, wherein the representation is a database listing a large number of HLA alleles and optional HLA allele combinations, each associated with a score indicating relative activity. The method of claim 1 , wherein the graph is a scatter plot.

9. The method of claim 8, wherein a first axis of the scatter plot represents different HLA alleles and optional HLA allele combinations among a plurality of HLA alleles and optional HLA allele combinations; and a second axis of the scatter plot represents interferon-γ-secreting CD3+ derived from each T cell line for which the relative activity is revealed in the graph when stimulated with antigen presenting cells that are autologous to the respective T cell line and loaded with one or more peptides that display antigenicity of the cancer. + The percentage of cells was used as an indicator of the relative activity.

10. The method of claim 1, wherein the relative activity is the in vivo clinical efficacy of the T cell line in the treatment of a patient suffering from cancer.

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