Method to Express, Purify, and Biotinylate Eukaryotic Cell-Derived Major Histocompatibility Complexes

Information

  • Patent Application
  • 20210380661
  • Publication Number
    20210380661
  • Date Filed
    October 15, 2019
    4 years ago
  • Date Published
    December 09, 2021
    2 years ago
  • Inventors
    • Lowe; Devin B. (Abilene, TX, US)
    • Wooster; Amanda L. (Abilene, TX, US)
  • Original Assignees
Abstract
The present invention includes compositions and methods of making and using a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag.
Description
TECHNICAL FIELD OF THE INVENTION

The present invention relates in general to the field of immunology, and more particularly to novel methods for expressing, purifying, and post-translationally modifying eukaryotic cell-derived major histocompatibility complexes.


INCORPORATION-BY-REFERENCE OF MATERIALS FILED ON COMPACT DISC

The present application includes a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 14, 2019, is named TECH2131WO_SeqList.txt and is 114, kilo bytes in size.


BACKGROUND OF THE INVENTION

Without limiting the scope of the invention, its background is described in connection with methods of making eukaryotic cell-derived major histocompatibility complexes (MHC).


The major histocompatibility complex (MHC) class I and II molecules play an integral role in T cell development and peripheral effector responses (Alcover et al., 2018). MHC class I is retained on the plasma membrane of nucleated cells and consists of a multi-unit heavy chain whose tertiary structure is stabilized by β2 microglobulin through non-covalent forces (Wieczorek et al., 2017). To provide specific binding to antigen specific CD8+ T cells, MHC class I usually retains a short 8-10 amino acid peptide within the MHC peptide binding groove that is derived from degraded intracellular proteins (hereafter referred to as peptide/MHC).


The present understanding of basic T cell properties and dynamics under a variety of normal and diseased settings has been greatly advanced by the ability to produce and purify peptide/MHC for use in assays to specifically engage the T cell receptor (TCR). Arguably the most widespread approach incorporates fluorochrome-conjugated peptide/MHC multimers (e.g., tetramers) for analyzing or isolating antigen-specific CD8+ T cells from biological samples (Khaimar et al., 2018; Soen et al., 2003). Peptide/MHC generation has continued similarly to the process outlined in the landmark work by Altman and colleagues (Altman et al., 1996). Briefly, 02 microglobulin and MHC class I heavy chain (containing a BirA tail) are individually expressed in E. coli and later purified from inclusion bodies through a laborious lysis/solubilization process. A defined MHC class I peptide is then added alongside β2 microglobulin and heavy chain in a precise folding reaction mixture that requires several days to complete prior to affinity chromatography (AC) purification of properly folded peptide/MHC and later biotinylation steps. Although this standard production process works to eventually yield excellent reagents for immunologic assays, there exist a number of major disadvantages. Namely, the standard method is [i] time consuming, [ii] requires substantial levels of raw ingredients (particularly purified MHC class I peptide), and [iii] cannot guarantee large-scale production of properly folded peptide/MHC molecules based on predicted peptide binders. For example, it is extremely difficult to stably produce MHC molecules bearing peptides with low-to-moderate affinity to the MHC peptide-binding groove.


Prior attempts to make peptide/MHC complexes include those of White and colleagues, which designed a soluble HIV-reactive MHC class I molecule (consisting of free heavy chain+linked peptide-β2 microglobulin) for expression in baculovirus, which was capable of biotinylation/multimerization and identifying a particular T cell hybridoma by flow cytometry (White et al., 1999). An additional approach was by Greten and colleagues performed standard plasmid DNA transfection to produce a peptide-β2 microglobulin-heavy chain linked protein in J588L cells that was only capable of dimerization due to mouse IgG fusion (Greten et al., 2002).


Thus a need remains for novel compositions, methods, vectors, cells, etc., that include novel constructs that allow for the production of peptide-MHC complexes in eukaryotic cells.


SUMMARY OF THE INVENTION

In one embodiment, the present invention includes a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag. In one aspect, the peptide is an immunogenic peptide epitope. In another aspect, the MHC is a human, mouse, rat, hamster, horse, pig, cow, simian, avian, or chimeric MHC. In another aspect, the MHC is Class I MHC. In another aspect, the does not include a transmembrane sequence. In another aspect, the peptide tag is selected from wherein the peptide tag is selected from at least one of: a BirA tail, a myc, a FLAG, a glutathione-S-transferase, a His tag, a maltose binding protein, hemagglutinin (HA)-tag, a V5 tag, a T7 tag, a V9 tag, a NusA-tag, a thioredoxin-tag, or a fluorescent protein-tag, a Her2/neu-tag, a CD20-tag, or a GFP-tag. In another aspect, the first, the second, or both the first and second flexible linkers comprise glycine, serine or both glycine and serine and comprise 5 to 40 residues, but may be 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39. In another aspect, the peptide is 8 to 16 residues long. In another aspect, the peptide is selected from at least one of: ABL1; ACPP; Ad5 ElA; AdV 5 Hexon; AdV Hexon; Ag85A; alfa fetoprotein; ASP-2; BA46; BALF4; BAP31; BCL-2; BCL-2A1; BCL-2L1; BCL-X; BCR-ABL; bcr-abl 210 kD fusion protein; Beta-gal; BGLAP; BMI1; BMLF1; BMRF1; BNP; BRAF 27; BRLF1; bZIP factor; BZLF1; C1orf59; CAMEL; Carbonic anhydrase; CB9L2; CD105; CD33; CD59; CEA; CEACAM; Chondromodulin; circadian clock protein PASD1; CP; CPS; cyclin-dependent kinase 4; CYP190; Cytochrome p450; DEP DC1; DLK1; Dutpase; E6; E7; EBNA 1; EBNA 3A; EBNA 3B; EBNA 6; EBV BRLF1; EBV EBNA3A; EBV LMP2; EDDR1; EGFR; EMNA 3A; EMV-1; Enhanced Green Fluorescent Protein; Env; EphA2; Erkl; ESAT-6; EZH2; FAPa; FLT1; FOLR1; FOXM1; G250; GAD65; Gag; Gag-pol; Glypican 3; gp; gp100; gp33 (C9M); GPC3; H250; HA-1; HA-2; HA-8; HBB; HBsAg; HBV core; HBV polymerase; HBV surface antigen; HCMV IE1; HCMV pp65; HCV core; HCV E; HCV NS3; HCV NS4b; HCV NS5a; HCV NS5B; Heparanase; HER2; HER-2/neu; Histocompatibility antigen 60; HIV gag p24; HIV nef; HIV pol; HIV-1 env gp120; HIV-1 IIIB gp120; HIV-1 nef, HIV-1 p17; HIV-1 RT; HIV-1 US4 gp120; HJURP; HLA-A leader sequence peptide; HLA-A2; HLA-Cw3; Chlamydia trachomatis MOMP; HM1.24; HMMR; HMOX1; HO-1; hPSA; HPV 16 E6; HSP105; HSP90 alpha; hTERT; hTOM34p; hTRT; H-Y; IA-2; IAPP; IDO; IE-1; IE62; IGF; IGRP; IL13r; IL13Ra; Ilr1; Influenza A (PR8) NP; Influenza A MP; Influenza A MP1; Influenza A MP2; Influenza A NP; Influenza A PB1; INFγR; Insulin; Interferon gamma inducible protein (GILT) 30; IRS-2; ITGB8; K8.1; KIF20A; KLK; KLK3; L1; LANA; Large T antigen; Lengsin; Listeria monocytogenes Listeriolysin; LTVIN; LMP-1; LMP-2; LMP-2A; LMP-2A; LY6K; m139; m141; m145; M164; M2-1; M38; M45; M57; MAGE-1; MAGE-10; MAGE-3; MAGE-4; MAGE-A1; MAGEA2; MAGEA3; MAGE-A5; MAGE-C1; MAGE-C2; MART-1; MC38 adpgk neoantigen; MC-38; MCL-1; MCMV IE1; MELK; Mena; Middle T antigen; Midkine; miHAg SMCY; MOG precursor; MP; MPP11; MS4A1; MSLN; Mtb 16 kDa; Mtb 19 kDa; Mtb85A; mTERT; Mucin; muFAPα; MuLV env; Murine Survivin; MYBPC-2; Mycobacterium bovis antigen 85-A; Mycobacterium tuberculosis ESAT-6; Mycobacterium tuberculosis TB10.4; Myelin basic protein; ND; NEF; NEF; Neu/Her-2/Erbb2 proto-oncoprotein; NG2; Non muscle Myosin-9; Non-muscle Myosin; NP; NP396; NP52; NPM1; NRP-1; NRP-2; NRP-V7 superagonist peptide 8.3 Tg NOD mouse; NS3; Nucleocapsid; Nuf2; NY-ESO-1; OVA; Ovalbumin (subdominant); P1A; β2X5a; p53; p56; P79; PAP-3; PASD1; PAX-5; p-Cadherin; PDGFRbeta; PLAC1; PLAM csp; Plasmodium berghei ANKA acid phosphatase; Plasmodium berghei CSP; Plasmodium CSP; Plasmodium falciparum CSP; Plasmodium falciparum Liver stage antigen; PolA; Polymerase; Polyprotein; pp65; PPE; Pr1; PRAME; Prominin1; PSA; PSCA; PSM β2; PSMA; RGS5; RhoC; RNF43; RSV A strain F protein; RSV NP; RT; S protein; SAA; SART3; Sialidases; SIV gag; SMCY; Spike GP; STEAPI; Surface IgG (sA20-Ig) of A20; Survivin; Survivin-3a; SV40 T antigen; TACE; TARP; TARP 2M; Tax; TB10.3-4; Telomerase; TEM1; tgd057; TGFβ; TNPO3; topII; TPBG; TPR-protein; TRAG; TRP2; Trypanosoma cruzi ASP-2; Trypanosoma cruzi SP; TTK; Tyrosinase; Tyrosine-3-hydroxylase; Ubiquitin; UL105; UL138; UL44; USP9Y; V131; Vaccinia virus Copenhagen Protein G5; Vaccinia virus Host range protein 2; VACCL3_100; VEGFR1; VEGFR2; VEGFR2/KDR fragment 1; Vif; Vinculin; VP1; Vpu; VSV N; West Nile virus NY-99 polyprotein precursor; West Nile Virus polyprotein; WT1; Yellow Fever Virus 17D polyprotein; or ZnT-8. In another aspect, the MHC is selected from at least one of H-2 Db, H-2 Dd; H-2 Dk; H-2 Kb; H-2 Kd; H-2 Kk; H-2 Ld; HLA-A*0101; HLA-A*0201; HLA-A*0301; HLA-A*1101; HLA-A*2301; HLA-A*2402; HLA-A*2902; HLA-A*6801; HLA-B*0702; HLA-B*0801; HLA-B*1501; HLA-B*2705; HLA-B*3501; HLA-B*4001; HLA-B*5101; or HLA-E*0101. In another aspect, the peptide is at least one of SEQ ID NO:1-599.


In another embodiment, the present invention includes a nucleic acid that expresses a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag. In one aspect, the peptide is an immunogenic peptide epitope. In another aspect, the MHC is a human, mouse, rat, hamster, horse, pig, cow, simian, avian, or chimeric MHC. In another aspect, the MHC is Class I MHC. In another aspect, the MHC does not include a transmembrane sequence. In another aspect, the peptide tag is selected from at least one of: a BirA tail, a myc, a FLAG, a glutathione-S-transferase, a His tag, a maltose binding protein, hemagglutinin (HA)-tag, a V5 tag, a T7 tag, a V9 tag, a NusA-tag, a thioredoxin-tag, or a fluorescent protein-tag, a Her2/neu-tag, a CD20-tag, or a GFP-tag. In another aspect, the first, the second, or both the first and second flexible linkers comprise glycine, serine or both glycine and serine and comprise 5 to 40 residues. In another aspect, the peptide is 8 to 16 residues long. In another aspect, the peptide is selected from at least one of: ABL1; ACPP; Ad5 ElA; AdV 5 Hexon; AdV Hexon; Ag85A; alfa fetoprotein; ASP-2; BA46; BALF4; BAP31; BCL-2; BCL-2A1; BCL-2L1; BCL-X; BCR-ABL; bcr-abl 210 kD fusion protein; Beta-gal; BGLAP; BMI1; BMLF1; BMRF1; BNP; BRAF 27; BRLF1; bZIP factor; BZLF1; C1orf59; CAMEL; Carbonic anhydrase; CB9L2; CD105; CD33; CD59; CEA; CEACAM; Chondromodulin; circadian clock protein PASD1; CP; CPS; cyclin-dependent kinase 4; CYP190; Cytochrome p450; DEP DC1; DLK1; Dutpase; E6; E7; EBNA 1; EBNA 3A; EBNA 3B; EBNA 6; EBV BRLF1; EBV EBNA3A; EBV LMP2; EDDR1; EGFR; EMNA 3A; EMV-1; Enhanced Green Fluorescent Protein; Env; EphA2; Erkl; ESAT-6; EZH2; FAPa; FLT1; FOLR1; FOXM1; G250; GAD65; Gag; Gag-pol; Glypican 3; gp; gp100; gp33 (C9M); GPC3; H250; HA-1; HA-2; HA-8; HBB; HBsAg; HBV core; HBV polymerase; HBV surface antigen; HCMV IE1; HCMV pp65; HCV core; HCV E; HCV NS3; HCV NS4b; HCV NS5a; HCV NS5B; Heparanase; HER2; HER-2/neu; Histocompatibility antigen 60; HIV gag p24; HIV nef; HIV pol; HIV-1 env gp120; HIV-1 IIIB gp120; HIV-1 nef; HIV-1 p17; HIV-1 RT; HIV-1 US4 gp120; HJURP; HLA-A leader sequence peptide; HLA-A2; HLA-Cw3; Chlamydia trachomatis MOMP; HM1.24; HMMR; HMOX1; HO-1; hPSA; HPV 16 E6; HSP105; HSP90 alpha; hTERT; hTOM34p; hTRT; H-Y; IA-2; IAPP; IDO; IE-1; IE62; IGF; IGRP; IL13r; IL13Ra; Ilr1; Influenza A (PR8) NP; Influenza A MP; Influenza A MP1; Influenza A MP2; Influenza A NP; Influenza A PB1; INFyR; Insulin; Interferon gamma inducible protein (GILT) 30; IRS-2; ITGB8; K8.1; KIF20A; KLK; KLK3; L1; LANA; Large T antigen; Lengsin; Listeria monocytogenes Listeriolysin; LIVIN; LMP-1; LMP-2; LMP-2A; LMP-2A; LY6K; m139; m141; m145; M164; M2-1; M38; M45; M57; MAGE-1; MAGE-10; MAGE-3; MAGE-4; MAGE-A1; MAGEA2; MAGEA3; MAGE-A5; MAGE-C1; MAGE-C2; MART-1; MC38 adpgk neoantigen; MC-38; MCL-1; MCMV IE1; MELK; Mena; Middle T antigen; Midkine; miHAg SMCY; MOG precursor; MP; MPP11; MS4A1; MSLN; Mtb 16 kDa; Mtb 19 kDa: Mtb85A; mTERT; Mucin; muFAPα; MuLV env; Murine Survivin; MYBPC-2; Mycobacterium bovis antigen 85-A; Mycobacterium tuberculosis ESAT-6; Mycobacterium tuberculosis TB10.4; Myelin basic protein; ND; NEF; NEF; Neu/Her-2/Erbb2 proto-oncoprotein; NG2; Non muscle Myosin-9; Non-muscle Myosin; NP; NP396; NP52; NPM1; NRP-1; NRP-2; NRP-V7 superagonist peptide 8.3 Tg NOD mouse; NS3; Nucleocapsid; Nuf2; NY-ESO-1; OVA; Ovalbumin (subdominant); P1A; β2X5a; p53; p56; P79; PAP-3; PASD1; PAX-5; p-Cadherin; PDGFRbeta; PLAC1; PLAM csp; Plasmodium berghei ANKA acid phosphatase; Plasmodium berghei CSP; Plasmodium CSP; Plasmodium falciparum CSP; Plasmodium falciparum Liver stage antigen; PolA; Polymerase; Polyprotein; pp65; PPE; Pr1; PRAME; Prominin1; PSA; PSCA; PSM β2; PSMA; RGS5; RhoC; RNF43; RSV A strain F protein; RSV NP; RT; S protein; SAA; SART3; Sialidases; SIV gag; SMCY; Spike GP; STEAPI; Surface IgG (sA20-Ig) of A20; Survivin; Survivin-3a; SV40 T antigen; TACE; TARP; TARP 2M; Tax; TB10.3-4; Telomerase; TEM1; tgd057; TGFβ; TNP03; topII; TPBG; TPR-protein; TRAG; TRP2; Trypanosoma cruzi ASP-2; Trypanosoma cruzi SP; TTK; Tyrosinase; Tyrosine-3-hydroxylase; Ubiquitin; UL105; UL138; UL44; USP9Y; V131; Vaccinia virus Copenhagen Protein G5; Vaccinia virus Host range protein 2; VACCL3_100; VEGFR1; VEGFR2; VEGFR2/KDR fragment 1; Vif, Vinculin; VP1; Vpu; VSV N; West Nile virus NY-99 polyprotein precursor; West Nile Virus polyprotein; WT1; Yellow Fever Virus 17D polyprotein; or ZnT-8. In another aspect, the MHC is selected from at least one of H-2 Db, H-2 Dd; H-2 Dk; H-2 Kb; H-2 Kd; H-2 Kk; H-2 Ld; HLA-A*0101; HLA-A*0201; HLA-A*0301; HLA-A*1101; HLA-A*2301; HLA-A*2402; HLA-A*2902; HLA-A*6801; HLA-B*0702; HLA-B*0801; HLA-B*1501; HLA-B*2705; HLA-B*3501; HLA-B*4001; 1HLA-B*5101; or HLA-E*0101. In another aspect, the peptide is at least one of SEQ ID NO:1-599.


In another embodiment, the present invention includes a method of making a soluble eukaryotic-derived peptide/MHC complex comprising: expressing in a cell a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag. In another aspect, the method further comprises isolating the fusion protein from a supernatant. In another aspect, the method further comprises forming dimers, trimers, tetramers, or multimers of the fusion protein by mixing the fusion protein with one or more agents that bind to two or more fusion proteins. In another aspect, the agent is selected from an antibody, a cross-linking agent, a ligase, an avidin, a streptavidin, a Protein A, or a J-chain. In another aspect, the peptide is an immunogenic peptide epitope. In another aspect, the MHC is a human, mouse, rat, hamster, horse, pig, cow, simian, avian or chimeric MHC. In another aspect, the MHC is Class I MHC. In another aspect, the MHC does not include a transmembrane sequence. In another aspect, the peptide tag is selected from at least one of a BirA tail, a myc, a FLAG, a glutathione-S-transferase, a His tag, a maltose binding protein, hemagglutinin (HA)-tag, a V5 tag, a T7 tag, a V9 tag, a NusA-tag, a thioredoxin-tag, or a fluorescent protein-tag, a Her2/neu-tag, a CD20-tag, or a GFP-tag. In another aspect, the irst, the second, or both the first and second flexible linkers comprise glycine, serine or both glycine and serine and comprise 5 to 40 residues. In another aspect, the peptide is 8 to 16 residues long.


In another embodiment, the present invention includes a cell line expressing a fusion protein comprising a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag. In one aspect, the fusion protein is integrated into the genome by co-transfecting a fusion protein expressing vector with a transposase vector that expresses a transposase and wherein the fusion protein expressing vector, the transposase vector, or both further comprise a selectable marker. In one aspect, the peptide is an immunogenic peptide epitope. In another aspect, the MHC is a human, mouse, rat, hamster, horse, pig, cow, simian, avian, or chimeric MHC. In another aspect, the MHC is Class I MHC. In another aspect, the MHC does not include a transmembrane sequence. In another aspect, the peptide tag is selected from at least one of: a BirA tail, a myc, a FLAG, a glutathione-S-transferase, a His tag, a maltose binding protein, hemagglutinin (HA)-tag, a V5 tag, a T7 tag, a V9 tag, a NusA-tag, a thioredoxin-tag, or a fluorescent protein-tag, a Her2/neu-tag, a CD20-tag, or a GFP-tag. In another aspect, the first, the second, or both the first and second flexible linkers comprise glycine, serine or both glycine and serine and comprise 5 to 40 residues. In another aspect, the peptide is 8 to 16 residues long.





BRIEF DESCRIPTION OF THE DRAWINGS

For a more complete understanding of the features and advantages of the present invention, reference is now made to the detailed description of the invention along with the accompanying figures and in which:



FIG. 1A shows a representative DNA schematic of the synthetic peptide/MHC complex. The designed peptide/MHC molecule contains distinct peptide, beta-2-microglobulin, and MHC heavy chain regions that are linked via explicit glycine/serine amino acids. The MHC heavy chain lacks a transmembrane domain (designated sHeavy chain), ensuring that properly folded peptide/MHC protein is secreted from cells into the culture medium. The peptide/MHC construct also contains a terminal BirA tail for enzymatic conjugation of biotin. FIG. 1B shows a standard workflow for expressing, purifying, and biotinylating eukaryotic-derived peptide/MHC molecules. [1] A suitable eukaryotic host cell line (such as CHO cells) is transiently transfected with two vectors that allow for transposon-directed integration of genes of interest. Vector 1 encodes the SB transposase (SB100X) while vector 2 is a transposon-compatible plasmid that encodes the synthetic peptide/MHC complex and puromycin resistance transgenes. [2] A stable cell line secreting peptide/MHC complexes is generated in as little as 2 weeks following antibiotic selection and expansion. [3] Spent culture media is processed through AC (against the sHeavy chain) to selectively purify peptide/MHC complexes. [4] A biotin ligase may then be employed to enzymatically conjugate biotin to the BirA tail of the synthetic peptide/MHC protein. [5] Following an additional polishing step such as size exclusion chromatography and [6] multimerization steps, the peptide/MHC reagent can be incorporated into immunologically-relevant assays that, for example, detect antigen-specific T cells. Abbreviation used: secretory MHC class I heavy chain (sHeavy chain), major histocompatibility complex (MHC)



FIGS. 2A and 2B show that stable CHO cells lines were established by a SB transposon system to secrete peptide/MHC molecules into culture media. (FIG. 2A) Evidence of extracellular peptide/MHC protein was first determined from cell-free supernatants by SDS-PAGE and coomassie blue staining. (FIG. 2B) Representative chromatogram of small scale AC purification of peptide/MHC-containing media. Cell-free supernatant was passed through an equilibrated agarose bead column containing the MHC class I-reactive antibody M1/42. After washing away unbound material, peptide/MHC protein was eluted, buffer-exchanged, and concentrated. Protein purity was then assessed using SDS-PAGE and coomassie blue staining. Arrow inset indicating peptide/MHC around the predicted molecular weight. Abbreviation used: protein ladder (L), affinity chromatography (AC), preparation (prep)



FIG. 3A shows Purified peptide/MHC (i.e., SIINFEKL/H-2 Kb) identify was confirmed by western blot using monoclonal antibodies reactive to the β2 microglobulin and BirA tail regions of the design molecule as depicted in FIG. 1A. FIG. 3B shows that peptide/MHC ligand binding was determined through immunoprecipitation and western blot following incubation of SIINFEKL/H-2 Kb and a TCR-like antibody specific to this particular peptide/MHC class I complex. AC-purified peptide/MHC was also incorporated as a positive control. Abbreviations used: protein ladder (L), SIINFEKL epitope+MHC class I (SIINFEKL/H-2 Kb), isotype (Iso), positive (Pos), control (ctrl)



FIGS. 4A to 4C show that the peptide/MHC was biotinylated as detailed in the Materials and Methods and specific streptavidin binding initially confirmed through (FIG. 4A) western blot and (FIG. 4B) ELISA using wells coated with streptavidin. (FIG. 4C) Biotinylated peptide/MHC was also incubated with streptavidin-conjugated 5 μm beads and washed extensively. Beads were then exposed to isotype, anti-SIINFEKL/H-2 Kb, or anti-MHC monoclonal antibodies followed by washing steps and incubation with relevant secondary PE-conjugated antibodies. Specific ligand reactivity was subsequently determined by flow cytometry. Abbreviations used: protein ladder (L), SIINFEKL epitope+MHC class I (SIINFEKL/H-2 Kb), biotinylated SIINFEKL/H-2 Kb (b-SIINFEKL/H-2 Kb), positive (Pos), isotype (Iso), control (ctrl), major histocompatibility complex (MHC), horseradish peroxidase (HRP), streptavidin (SA), primary antibody (1° Ab)



FIG. 5 shows that the biotinylated peptide/MHC was incubated with PE-conjugated streptavidin to produce “small-scale” batches of SIINFEKL-reactive tetramers. Purified CD8+ T cells harvested from either wild-type or OT-1 mice were incubated with tetramers, washed, and stained with an anti-CD8 FITC antibody. Cells were again washed, fixed, and analyzed by flow cytometry for ligand binding. Abbreviations used: wild-type (WT), streptavidin (SA)



FIG. 6 shows the determination of the ability to construct and express a membrane-bound OVA-specific peptide/MHC molecule (i.e., SIINFEKL/H-2 Kb). 4T1 cells were transiently transfected with two plasmids that allow transposon-directed genomic integration and cultured over a period of two weeks in puromycin-containing culture media (as outlined in FIG. 1B). The remaining “stably engineered” cells were then incubated with either an isotype control antibody or antibody that binds the OVA-specific epitope SIINFEKL within the constraints of MHC class I and assessed for reactivity by flow cytometry. Abbreviations used: SIINFEKL epitope+MHC class I (SIINFEKL/H-1-2 Kb), major histocompatibility complex (MHC)



FIG. 7 is a DNA coding sequence of the synthetic SIINFEKL/H-2 Kb molecule (SEQ ID NO: 600).





DETAILED DESCRIPTION OF THE INVENTION

While the making and using of various embodiments of the present invention are discussed in detail below, it should be appreciated that the present invention provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific embodiments discussed herein are merely illustrative of specific ways to make and use the invention and do not delimit the scope of the invention.


To facilitate the understanding of this invention, a number of terms are defined below. Terms defined herein have meanings as commonly understood by a person of ordinary skill in the areas relevant to the present invention. Terms such as “a”, “an” and “the” are not intended to refer to only a singular entity, but include the general class of which a specific example may be used for illustration. The terminology herein is used to describe specific embodiments of the invention, but their usage does not limit the invention, except as outlined in the claims.


The present invention includes compositions, vectors, cells, and methods of making MHC class I-specific reagents such as fluorescently-labeled multimers (e.g., tetramers) that can be used to study CD8+ T cells under normal and diseased states. However, recombinant MHC class I components (comprising MHC class I heavy chain and p2 microglobulin) are usually produced in bacteria following a lengthy purification protocol that requires additional non-covalent folding steps with exogenous peptide for complete molecular assembly. The present inventors have developed an alternative and rapid approach to generating soluble and fully-folded MHC class I molecules in eukaryotic cell lines (such as CHO cells) using, e.g., a Sleeping Beauty transposon system. Importantly, this method generates stable cell lines that reliably secrete epitope-defined MHC class I molecules into the tissue media for convenient purification and eventual biotinylation/multimerization. Additionally, MHC class I components are covalently linked, providing the opportunity to produce a diverse set of CD8+ T cell-specific reagents bearing peptides with various affinities to MHC class I.


As used herein, the term “gene” refers to a functional protein, polypeptide or peptide-encoding unit. As will be understood by those in the art, this functional term includes both genomic sequences, cDNA sequences, or fragments or combinations thereof, as well as gene products, including those that may have been altered by the hand of man. Purified genes, nucleic acids, protein and the like are used to refer to these entities when identified and separated from at least one contaminating nucleic acid or protein with which it is ordinarily associated.


As used herein, the term “vector” is used in reference to nucleic acid molecules that transfer DNA segment(s) from one cell to another. The vector may be further defined as one designed to propagate specific sequences, or as an expression vector that includes a promoter operatively linked to the specific sequence, or one designed to cause such a promoter to be introduced. The vector may exist in a state independent of the host cell chromosome, or may be integrated into the host cell chromosome


As used herein, the term “host cell” refers to cells that have been engineered to contain nucleic acid segments or altered segments, whether archeal, prokaryotic, or eukaryotic. Thus, engineered, or recombinant cells, are distinguishable from naturally occurring cells that do not contain recombinantly introduced genes through the hand of man.


A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it effects the transcription of the sequence; or a ribosome binding site is operably linked to e coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” refers to a DNA sequences being linked are contiguous and, in the case of a secretory leader, contiguous and in same reading frame. Enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, then synthetic oligonucleotide adaptors or linkers are used in accord with conventional practice.


As used herein, the terms “cell” and “cell culture” are used interchangeably end all such designations include progeny. Thus, the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Different designations are will be clear from the contextually clear.


As used herein, the term “plasmid” are designated by a lower case p preceded and/or followed by capital letters and/or numbers and refer to self-replicating circular DNA that include an origin of replication, and typically one or more selectable markers. The starting plasmids herein are commercially available, are publicly available on an unrestricted basis, or can be constructed from such available plasmids in accord with published procedures. In addition, other equivalent plasmids are known in the art and will be apparent to the ordinary artisan.


As used herein, the term “selectable marker” refers to the use of a gene that encodes an enzymatic activity and which confers the ability to grow in medium lacking what would otherwise be an essential nutrient (e.g., the HIS3 gene in yeast cells); in addition, a selectable marker may confer resistance to an antibiotic or drug upon the cell in which the selectable marker is expressed. A review of the use of selectable markers in mammalian cell lines is provided in Sambrook, J., et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd ed., Cold Spring Harbor Laboratory Press, New York (1989) pp. 160.9-160.15.


As used herein the terms “protein”, “polypeptide” or “peptide” refer to compounds comprising amino acids joined via peptide bonds and are used interchangeably.


As used herein, the terms “fusion protein” or “chimeric protein” refer to a hybrid protein, that includes portions of two or more different polypeptides, or fragments thereof, resulting from the expression of a polynucleotide that encodes at least a portion of each of the two polypeptides.


As used herein, the term “transformation,” refers to a process by which exogenous DNA enters and changes a recipient cell. It may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed and may include, but is not limited to, viral infection, electroporation, lipofection, and particle bombardment. Such “transformed” cells include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome.


As used herein, the term “transfection” refers to the introduction of foreign DNA into eukaryotic cells. Transfection may be accomplished by a variety of methods known to the art including, e.g., calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, protoplast fusion, retroviral infection, and biolistics. Thus, the term “stable transfection” or “stably transfected” refers to the introduction and integration of foreign DNA into the genome of the transfected cell. The term “stable transfectant” refers to a cell that has stably integrated foreign DNA into the genomic DNA. The term also encompasses cells that transiently express the inserted DNA or RNA for limited periods of time. Thus, the term “transient transfection” or “transiently transfected” refers to the introduction of foreign DNA into a cell where the foreign DNA fails to integrate into the genome of the transfected cell. The foreign DNA persists in the nucleus of the transfected cell for several days. During this time the foreign DNA is subject to the regulatory controls that govern the expression of endogenous genes in the chromosomes. As used herein, the term “transient transfectant” refers to cells that have taken up foreign DNA but have failed to integrate this DNA.


The present invention can be used to circumvent drawbacks in the prior art, in particular, stabilizing peptide binding to the MHC peptide binding groove. Previous efforts have revealed the ability to engineer and produce peptide/MHC molecules in bacteria by covalently joining the MHC class I peptide, β2 microglobulin, and heavy chain with discrete amino acid linkers (designated single-chain trimers [SCTs]) (Yu et al., 2002). For most SCTs reported, these engineered proteins fold correctly and specifically engage CD8+ T cells as tetramers (Mitaksov et al., 2007), irrespective of the artificial linker design (Hansen et al., 2009). However, this particular SCT method still utilizes a bacterial expression system and requires substantial purification and refolding efforts.


The present inventors have developed an alternative method to potentially improve the production of peptide/MHC based on the SCT approach. The present invention has the ability to rapidly generate eukaryotic cell lines that stably express and secrete peptide/MHC into the tissue media for purification and biotinylation. This novel protocol provides a much faster/convenient route to generating properly folded peptide/MHC with minimal user intervention, especially for MHC class I targets with high demand (such as the model OVA epitope SIINFEKL). By using a SCT strategy, it was possible to generate MHC molecules presenting a range of class I peptides (i.e., low-to-high binding affinity), which can be reliably generated. Additionally, these eukaryotic-derived peptide/MHC molecules can be used to recapitulate binding dynamics with TCRs in downstream assays (Schmidt and Lill 2018).


Mice. Female 6-8-week-old C57BL/6J (stock #000664) and OT-1 (stock #003831) mice were purchased from The Jackson Laboratory (Bar Harbor, Me., USA) and maintained in micro-isolator cages under sterile conditions. Animals were humanely euthanized and spleens/lymph nodes harvested and combined for Ficoll gradient centrifugation (GE HealthCare, Piscataway, N.J.). The lymphocyte interphase was then subjected to ACK lysis and eventual CD8+ T cell purification using MACS bead positive selection as instructed by the manufacturer (Miltenyi Biotec, Cambridge, Mass.). Purified CD8+ T cells were aliquoted in 90% FBS/10% DMSO and stored in liquid nitrogen until use. All mouse procedures were followed in accordance with TTUHSC IACUC-approved protocols.


Cell lines and culture. FreeStyle™ Chinese Hamster Ovary (CHO-S) (Thermo Fisher Scientific, Waltham, Mass.) and 4T1 (ATCC, Manassas, Va.) cells were utilized for in vitro studies. CHO-S cells were passaged in FreeStyle™ CHO Expression Medium (Thermo Fisher Scientific) according to the manufacturer's recommendations. 4T1 cells are naturally deficient in H-2 Kb expression and were grown in RPMI 1640 supplemented with 10% heat-inactivated FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, and 10 mmol/l L-glutamine (all from Thermo Fisher Scientific). All cell lines were maintained in vented flasks at 37° C. with 5% CO2.


Cloning strategy and construction of transposon expression vectors. Full-length mouse p2 microglobulin (NCBI Reference Sequence: NM 009735.3) and MHC class I heavy chain (H-2 Kb) (NCBI Reference Sequence: NM_001001892.2), relevant sequences incorporated herein by reference, cDNA were synthesized from C57BL/6J splenocytes following TRIzol lysis (Thermo Fisher Scientific) and RT-PCR using oligo(dT) primers (SuperScript IV First-Strand Synthesis Kit; Thermo Fisher Scientific). Secretory MHC class I heavy chain was designed to not include the transmembrane domain. The leader signal, SIINFEKL epitope, and Gly/Ser amino acid linkers were ultimately added by overhang PCR as previously reported (Hansen et al., 2009) using the Phusion High-Fidelity DNA Polymerase (Thermo Scientific Fisher). PCR fragments were gel excised/purified and ligated (LigaFast™ Rapid DNA Ligation System; Promega, Madison, Wis.) into puc19 (NEB, Ipswich, Mass.) via SacI/HindIII restriction enzyme sites and fragments pieced together using the unique NheI/BamHI sites of the synthetic peptide/MHC sequence. The BirA AviTag™ amino acid sequence (GLNDIFEAQKIEWHE SEQ ID NO: 600) was subsequently added to the construct's terminus by overlap-extension PCR and cloned into a separate puc19 holding vector. Full-length peptide/MHC was then amplified and cloned into the pSBbi-pur transposon vector (kindly provided by Dr. Eric Kowarz [Addgene plasmid #60523]) using the SfI restriction enzyme sites (Kowarz et al., 2015). Plasmid transformations were carried out in chemically-competent NEB-5 alpha E. coli (NEB) using ampicillin selection. All vector constructs were confirmed by restriction enzyme digestion and DNA sequencing.


Sleeping Beauty (SB) transposon system. Parental cell lines were transiently transfected with transposon-related vectors using Lipofectamine reagent (Thermo Fisher Scientific) as directed by the manufacturer. A plasmid encoding the SB 100× transposase (pCMV[CAT]T7-SB100; designated Vector 1), a gift from Dr. Zsuzsanna Izsvak (Addgene plasmid #34879), and a transposon plasmid containing the necessary inverted terminal repeats (pSBbi-pur; designated Vector 2) were used. Both vectors were provided concurrently to stably integrate peptide/MHC transgenes into cells. Briefly, 1×105 cells were plated in 24-well plates (Corning, Corning N.Y.) and exposed to Vector 1 (12.5 ng)/Vector 2 (488 ng) in a total volume of 500 μl media as similarly described (Kowarz et al., 2015). Culture media was replenished with 2 ml fresh media after 24 hrs and 48 hrs, whereupon cells were exposed to lethal doses of puromycin (CHO-S—10 μg/ml; 4T1—5 μg/ml) (Invivogen, San Diego, Calif.). Fresh media containing puromycin was provided every 2-3 days as needed. Generally, actively dividing cells were ready for expansion by 2 weeks, with virtually all cell clones expressing peptide/MHC molecules.


SDS-PAGE and western blot. To remove extraneous tissue media components such as surfactants, CHO cell supernatants were passed onto PD10 columns (GE Healthcare) and concentrated/washed in PBS using a 30 MWCO Amicon centrifugal unit (MilliporeSigma, Burlington, Mass.). Protein concentration was determined using a BCA protein assay kit (Thermo Scientific Fisher) and sample aliquots stored at −80° C. until use. Protein purity was assessed with SDS-PAGE and coomassie blue staining while protein identity was confirmed through western blotting. Briefly, proteins were resolved on a 4%/12% polyacrylamide gel, transferred to a PVDF membrane (Amersham Hybond, 0.2 μm; GE Healthcare), and blocked with 5% milk in PBST (0.1% Tween 20 in PBS) for 1 hr at RT. Membranes were then incubated with various primary antibodies (1 μg/ml) in block solution with rocking at 4° C. overnight. Specific primary reagents included anti-mouse β2 microglobulin (clone 893803; R&D Systems, Minneapolis, Minn.) or anti-BirA tail (clone Abc; Avidity, Aurora, Colo.) antibodies. Blots were then washed extensively with PBST and incubated in block with secondary HRP-conjugated goat antibodies specific to rat IgG (H+L) or mouse IgG (H+L) (Thermo Scientific Fisher) for 1 hr at RT. Washed blots were finally developed with a SignalFire ECL reagent (Cell Signaling, Danvers, Mass.) and exposed/imaged on a ChemiDoc™ Touch Imaging System (Bio-Rad, Hercules, Calif.). In separate experiments, blots containing biotinylated protein were probed with a Streptavidin-HRP reagent (Thermo Scientific Fisher) for 1 hr at RT to confirm streptavidin binding potential.


Immunoprecipitation. A Pierce Classic IP kit (Thermo Scientific Fisher) was used to investigate ligand binding of soluble peptide/MHC protein. Peptide/MHC protein was incubated overnight at 4° C. with 2 μg of the anti-SIINFEKL (clone eBio25-D1.16; Thermo Scientific Fisher) or mouse IgG isotype (clone MOPC-21; MP Biomedicals, Santa Ana, Calif.) antibodies. The anti-SIINFEKL antibody functions as a TCR-like antibody (Lowe et al., 2017), and binds SIINFEKL/H-2 Kb much like SIINFEKL-reactive T cells such as OT-1 CD8+ T cells. Following purification of IgG containing complexes, samples were boiled and analyzed by western blot as described above.


Affinity chromatography (AC). The MHC class I-reactive M1/42 antibody (Bio X Cell, West Lebanon, N.H.) was covalently bound to an NHS-activated agarose bead column (HiTrap™ NHS-activated HP; GE Healthcare) manually as directed by the manufacturer. The column was attached to an ÄKTA™ start chromatography system (GE Healthcare) for automatic operation and equilibrated with 20 mM sodium phosphate, pH 7.0 (binding buffer). Cell-free supernatants were first desalted in PBS using PD-10 columns and diluted 1:2 in binding buffer prior to AC. Samples were then applied to the M1/42 column, unbound material washed away with binding buffer, and peptide/MHC molecules eluted using 0.1 M glycine, pH 2.7. Eluates were dispensed in tubes containing 1 M Tris, pH 9 and relevant fractions combined and concentrated/washed in PBS as explained above.


Biotinylation and tetramerization. Peptide/MHC was biotinylated using 2.5 μg BirA ligase (Avidity) overnight at 4° C. according to the manufacturer's guidelines. Reaction components were removed by successive washes in PBS using a 30 MWCO centrifugal filter (MilliporeSigma). Alternatively, larger reaction mixtures could be exclusively polished through size exclusion chromatography (Altman and Davis 2016) using a HiPrep™ 16/60 Sephacryl™ S-200 HR column (GE Healthcare) as indicated in FIG. 1B. In order to produce small-scale tetramer batches, biotinylated peptide/MHC was incubated with PE-conjugated streptavidin (BD Biosciences, San Jose, Calif.) at a 4:1 molar ratio in the dark for 30 min at RT. Tetramers were then stored at 4° C. shielded from light.


Enzyme-Linked Immunosorbent Assay (ELISA). To investigate the success of peptide/MHC biotinylation, a 96-well high protein binding plate (Corning) was first coated overnight at 4° C. with 4 μg/ml streptavidin (Promega) in 0.1 M sodium carbonate and then blocked (3% BSA/PBS) for 1 hr at RT. Biotinylated protein samples were diluted in block and added to wells at various dilutions and incubated at RT for 1 hr. Wells were washed extensively with PBST and then exposed to 4 μg/ml of either a MHC class I-reactive (clone M1/42; Biolegend) or rat isotype control IgG (Biolegend) antibody in block. In separate wells, a positive control biotinylated irrelevant rat antibody (Biolegend) was incorporated to validate the extent of streptavidin binding. The plate was again washed with PBST and relevant wells provided a goat anti-rat HRP (Thermo Scientific Fisher) or goat anti-mouse FcγR-specific HRP (Jackson ImmunoResearch, West Grove, Pa.) antibody in block for 1 hr at RT. Wells were washed with PBST and developed for 5 min after the addition of 200 μl 1-Step Ultra TMB (Thermo Scientific Fisher). Reactions were terminated with 100 μl TMB stop solution (KPL), and the absorbance immediately read at 450 nm using a Cytation 5 Imaging Reader (Biotek, Winooski, Vt.).


Flow cytometry. To confirm gene expression, the 4T1 cell line (1×105 cells) was stained with relevant primary antibodies (anti-SIINFEKL/H-2 Kb or mouse IgG isotype antibodies at 2 μg/ml) in FACS buffer (0.5% BSA/0.1% NaN3 in PBS) for 20 min at 4° C., washed, incubated with a PE-conjugated anti-mouse secondary antibody (Jackson ImmunoResearch), washed again, and resuspended in FACS buffer for analysis (FIG. 6). To ensure proper orientation, biotinylated peptide/MHC was incubated with 5 μm PMMA beads conjugated to streptavidin (PolyAn, Berlin, Germany), washed, and incubated at 4° C. with correct pairs of primary and PE-conjugated secondary antibodies (as indicated in FIGS. 4A to 4C) prior to analysis in FACS buffer. Frozen CD8+ T cells were thawed, washed, and resuspended in FACS buffer so that each stain consisted of 2×105 viable CD8+ T cells. Cells were exposed to 50 nM dasatinib (Selleck Chemicals, Houston, Tex.) for 30 min at 37° C. and promptly incubated with peptide/MHC tetramers for 20 min at RT in the dark (Dolton et al., 2015). Cells were washed with FACS buffer and labeled with an anti-CD8-FITC antibody (clone 53-6.7; BioLegend, San Diego, Calif.) at 4° C. for 20 min shielded from light. After additional wash steps, cells were resuspended in fix solution (1% FBS, 2.5% formaldehyde in PBS) and assessed by flow cytometry using a BD LSRFortessa. Single and double color stain analysis was carried out using FlowJo software. In the case of tetramer analysis, PE/FITC compensated events were first gated based on FSC/SSC profiles and subsequently evaluated by PE and FITC fluorescence.


Cloning, expression, and purification strategy for soluble eukaryotic-derived peptide/MHC. The design of linked peptide/MHC class I molecules closely followed the previously reported generation of SCTs in bacteria (Hansen et al., 2009). Essentially, as presented in FIG. 1A, flexible glycine/serine linkers join a particular peptide epitope, β2 microglobulin, and MHC class I heavy chain. A BirA tail was also genetically encoded to the 3′ end of the molecule for enzyme-directed biotinylation of secreted protein. Yet, a notable difference of this design involved omitting the transmembrane region of MHC class I (designated sHeavychain) to allow for functional and fully-folded secreted protein. This process for eukaryotic expression centered on the use of a SB transposon system to stably integrate transgene content into relevant cell lines (FIG. 1B). Therefore, CHO cells would be transiently transfected with transposon-relevant plasmids (encoding separately a SB transposase and synthetic peptide/MHC molecule) and stable cells generated through antibiotic selection. After expanding relevant CHO cell clones, secreted peptide/MHC could be purified by AC, biotinylated, and multimerized to produce, for example, tetramers capable of binding antigen-specific T cells.


Purification of secreted and fully-folded peptide/MHC protein. The suitability of the SB transposon system to stably integrate the peptide/MHC transgene was first determined. However, this particular peptide/MHC construct differed from the aforementioned soluble design in FIG. 1A by encoding full-length MHC class I heavy chain (i.e., the murine MHC haplotype H-2 Kb), thereby, ensuring cell surface expression for relative ease of detection. Briefly, 4T1 (H-2 Kb null) cells were exposed to transposon vectors that expressed either a null or SIINFEKL/H-2 Kb construct and puromycin resistant clones selected and expanded in culture. Cells were then stained with isotype or anti-SIINFEKL/H-2 Kb antibodies and analyzed by flow cytometry using a PE-conjugated secondary antibody. In comparison to 4T1-null cells, 4T1-SIINFEKL/H-2 Kb cells expressed clear and robust levels of synthetic peptide/MHC (FIG. 7). These confirmatory results were expected, given the widespread use of the SB approach to induce expression of various protein classes in established cell lines and primary cells (Kebriaei et al., 2017).


CHO cells were next transfected with SB-related vectors as described in FIGS. 1A and 1 B to induce stable expression of soluble peptide/MHC. Parental CHO cells exhibited enhanced resistance to puromycin, requiring sustained culturing in high concentrations of puromycin at 10 μg/ml. However, the inventors were able to expand puromycin-resistant clones by 2 weeks post plasmid transfection. Cells were then grown to saturating conditions in culture for at least 4 days to generate suitable whole protein concentrations from a total volume of 20 ml media. Yet, the choice of serum-free media contained a number of proprietary agents such as surfactants that could potentially interfere with protein purification and validation assays. The inventors, therefore, took the precautionary step of desalting and concentrating cell-free supernatants in PBS prior to downstream analysis. The initial assessment of CHO-derived extracellular proteins by SDS-PAGE (under reducing conditions) and coomassie blue staining revealed distinct protein bands around a predicted 51 kDa molecular weight for synthetic peptide/MHC (FIG. 2A) that was not evident from CHO cells expressing a null construct (data not shown). This specific protein band was subsequently confirmed following AC as exhibited in FIG. 2B. That is, cell-free supernatants were passed onto an agarose bead column containing the MHC class I-reactive M1/42 antibody and bound material eluted and ultimately assessed again by SDS-PAGE. The inventors typically harvested at least 100 μg/ml AC-purified peptide/MHC from small-scale culturing efforts. However, the described protocol can be scaled-up (or down) depending on the desired peptide/MHC total yield. Although beyond the scope of this report, alternative culturing parameters and/or leader signals (Haryadi et al., 2015) may potentially enhance overall CHO secretion of peptide/MHC. The AC procedure appeared to provide substantial protein purity based on obtaining [i] one distinct chromatogram elution peak and [ii] a protein band comprising >95% of detectable protein by coomassie blue staining.


Determination of peptide/MHC identity and upstream binding potential. Next, the inventors confirmed the identity of AC purified protein by western blot separate from MHC class I reactivity. Based on the linked design of polychain peptide/MHC molecules (FIG. 1A), the inventors incorporated monoclonal antibodies specific to mouse 02 microglobulin and the BirA tail peptide GLNDIFEAQKIEWHE (SEQ ID NO: 600). Developed blots clearly verified the integrity of synthetic peptide/MHC molecule expression, indicating no observable issues in CHO cells secreting these artificial proteins (FIG. 3A). An immunoprecipitation reaction was subsequently attempted in order to demonstrate ligand binding potential of linked SIINFEKL to the MHC class I binding groove. SIINFEKL/H-2 Kb was incubated with 2 μg of anti-SIINFEKL/H-2 Kb or isotype control antibodies overnight. As detailed in the Materials and Methods, IgG containing material was purified using protein A/G-complexed agarose and resolved by SDS-PAGE under reducing conditions. The presence of SIINFEKL/H-2 Kb was further established through western blot using an anti-mouse 32 microglobulin antibody (FIG. 3B). Overall, these results help further validate the identity of soluble peptide/MHC from CHO cells and establish that these secreted proteins retain ligand binding specificity at the peptide/MHC class I interface.


Multimerization and functional assessment of eukaryotic-derived peptide/MHC. Biotinylated peptide/MHC arguably provides the greatest convenience to users for downstream assays. The inventors, therefore, designed a BirA tail to the terminal end of the peptide/MHC transgene by using a particular BirA tail peptide, GLNDIFEAQKIEWHE (SEQ ID NO: 600), which offers a highly targeted site for enzymatic conjugation of biotin with minimal footprint (Beckett et al., 1999). AC purified peptide/MHC was subjected to BirA ligase activity in the presence of free biotin overnight. Excess biotin and other reaction components were removed by excessive washing in PBS using a 30 MWCO centrifugal unit, and the extent of biotinylation first assessed by western blot and ELISA. In the case of western blot analysis, SDS-PAGE-resolved biotinylated protein was incubated with HRP-conjugated streptavidin to generate a specific peptide/MHC signal (FIG. 4A). Likewise, ELISA determination of biotinylated peptide/MHC clearly confirmed the functionality of the BirA tail region (FIG. 4B). Briefly, wells were coated overnight with streptavidin followed by various concentrations of peptide/MHC and biotinylated peptide/MHC. Detection was finally determined indirectly by MHC class I reactivity using the M1/42 antibody. Biotinylated SIINFEKL/H-2 Kb (as low as 0.25 μg/ml protein) was clearly evident in appropriate wells, with negligible reactivity occurring for conditions containing either unbiotinylated SIINFEKL/H-2 Kb or biotinylated SIINFEKL/H-2 Kb incubated with an isotype control. Next, the ability of immobilized/properly oriented biontinylated peptide/MHC to specifically engage ligands through the MHC class I peptide binding site was confirmed. Streptavidin was covalently attached to PMMA 5 μM beads and incubated with saturating conditions of biotinylated SIINFEKL/H-2 Kb. Beads were washed, incubated with appropriate primary reagents (i.e., anti-SIINFEKL/H-2 Kb and anti-MHC class I agents), and the extent of MHC ligand binding determined by flow cytometry using secondary PE-conjugated antibodies. Ultimately, as initially validated by the immunoprecipitation shown in FIG. 3B, biotinylated peptide/MHC bound streptavidin and specifically interacted with a TCR-like antibody that recapitulates CD8+ T cell interactions (FIG. 4C), indicating no observable functional issues with peptide/MHC post biotinylation and multimerization.


Next, the inventors assessed the ability of fluorescently-labeled multimers to specifically detect antigen-specific CD8+ T cells. Splenocytes and lymph nodes were harvested from wild-type and OT-1 transgenic (i.e., SIINFEKL-reactive) mice and CD8+ T cells subsequently purified through magnetic bead selection. Biotinylated SIINFEKL/H-2 Kb was then incubated with PE-conjugated streptavidin following a 4:1 molar ratio, thereby, generating tetramers. In order to stabilize membrane dynamics of TCRs, CD8+ T cells were exposed to dasatinib (as previously described [Dolton et al., 2015]), followed by incubation with tetramers. After suitable wash steps, cells were specifically labeled with a FITC-conjugated anti-mouse CD8 antibody that displays minimal interference with TCR:MHC binding (Clement et al., 2011). Cells were fixed and double-positive events (CD8+/tetramer+) assessed by flow cytometry. As detailed in FIG. 5, CD8+OT-1 cells clearly bound PE-labeled tetramers, with most cells displaying CD8 and tetramer positivity (in comparison to wild-type mice). Altogether, these data show the overarching strategy (as outlined in FIG. 1B) of stably producing eukaryotic-derived peptide/MHC that can be multimerized and used for immunologically-relevant assays such as CD8+ T cell identification.


Although MHC class I peptide candidates can be easily identified through in silico prediction methods (Andreatta and Nielsen 2016), free peptide occupancy of MHC class I molecules tends to be a rate limiting step in successfully generating stable peptide/MHC molecules from bacteria (Altman and Davis 2016). Considering the vital role MHC plays in human health (Cho and Sprent 2018), an inability to produce certain peptide/MHC reagents may adversely impact efforts on a number of fronts including diagnostics, therapies, and generalized scientific endeavors. For example, the burgeoning field of neoepitope identification for personalized cancer therapy could be stalled by those unique patient epitopes that exhibit high dissociation rates from MHC class I (Hu et al., 2018). One workaround to the issue of peptide occupancy has been in designing and expressing polychain SCTs that ensure full assembly of peptide, p2 microglobulin, and MHC class I heavy chain through flexible linkers (Hansen et al., 2009). SCTs retained on the plasma membrane of eukaryotic cells maintain their native conformation and are highly resistant to exogenous peptide binding (Yu et al., 2002). Additionally, membrane-bound SCTs serve as effective targets for CD8+ T cell priming (Hung et al., 2007) and destruction (Yu et al., 2002). In the case of diagnostic determination of CD8+ T cell frequencies by tetramers, SCTs can be modified for expression/secretion in bacteria and biotinylation by way of an explicit amino acid sequence that directs BirA enzyme function (Mitaksov et al., 2007).


Previously, the present inventors developed a unique protocol to establish eukaryotic cell lines (such as CHO suspension cells) in as little as two weeks that stably secrete peptide/MHC molecules through transposon-directed delivery. Soluble peptide/MHC may then be biotinylated and utilized as multimers (via streptavidin), particularly for CD8+ T cell relevant assays. Currently, CHO cells are an industry standard in producing FDA approved therapeutic recombinant proteins (Kuo et al., 2018). The inventors sought the advantages of the CHO cell line in order to [i] instigate post-translational modifications and [ii] be easily grown at high density under serum-free conditions in suspension cultures. However, other common cell line “protein workhorses” (e.g., HEK-293 cells) are amenable to the expression and characterization techniques outlined.


One advantage of the present invention is the rapid development of stable CHO cells secreting peptide/MHC using the SB transposon system. These studies incorporated the SB transposase SB100X, which has a high gene insertion efficiency at close-to-random chromosomal sites (Mates et al., 2009). The SB approach provides the advantageous properties of viral transduction to insert transgenes without the disadvantages of either maintaining genomic material episomally (e.g., adeno-associated viruses) or near/in proto-oncogenes (e.g., retroviral vectors) (Kebriaei et al., 2017). Additionally, manufacturing high-quality viral particles can be a cumbersome task fraught with regulatory obstacles. The inventors generally experienced minimal difficulty in developing and expanding stable lines from parental cells after transiently transfecting plasmids that propagated the SB transposon system. The protocol is also amenable to freezing material at convenient stopping points. There was no apparent adverse effects to generating multimerized reagents when either cell-free CHO-derived supernatants or biotinylated peptide/MHC was frozen long-term at −80° C. The method of the present invention is compatible with downstream tetramer production with the added benefits of convenient peptide/MHC expression that can incorporate a range of peptide affinities to the MHC peptide binding groove. Traditionally, to circumvent the low intrinsic affinity of the TCR with peptide/IIC, tetravalent multimers have been utilized to increase T cell avidity. However, these soluble peptide/MHC molecules can be utilized for higher order reagents to better discriminate low frequency T cells (or bind “difficult” TCRs) such as fluorochrome-conjugated dextramers since the production process involves incubating biotinylated peptide/MHC with a dextran backbone containing streptavidin (Dolton et al., 2014). Thus, the present invention can be used to reliably produce a range of soluble eukaryotic-derived peptide/MHC molecules for diagnostic, therapeutic, and investigative purposes.









TABLE 1







MHC, Peptide Sequences, and Target.










ALLELE
PEPTIDE
TARGET
SEQ ID NO:













H-2 Db
AAVKNWMTQTL
SIV gag
1


H-2 Db
AGPHNDMEI
p56
2


H-2 Db
AGVDNRECI
L1
3


H-2 Db
AIQGNVTSI
Mycobacterium tuberculosis ESAT-
4




6


H-2 Db
AQLANDVVL
MC-38
5


H-2 Db
ASFRNLTHL
TPBG
6


H-2 Db
ASMTNMELM
MC38 adpgk neoantigen
7


H-2 Db
ASNENMDAM
NP
8


H-2 Db
ASNENMETM
NP
9


H-2 Db
ATFKNWPFL
Murine Survivin
10


H-2 Db
CMTWNQMNL
WT1
11


H-2 Db
CSANNSHHYI
gp
12


H-2 Db
FQPQNGQFI
NP396
13


H-2 Db
FSNSTNDILI
VEGFR2/KDR fragment 1
14


H-2 Db
GAVQNEVTL
HCV NS3
15


H-2 Db
HCIRNKSVI
PSA
16


H-2 Db
HCIRNKSVIL
hPSA
17


H-2 Db
HGIRNASFI
M45
18


H-2 Db
KAVYNFATC
gP
19


H-2 Db
KAVYNFATM
gp33 (C9M)
20


H-2 Db
KCSRNRQYL
miHAg SMCY
21


H-2 Db
KVPRNQDWL
gp100
22


H-2 Db
LGMSNRDFL
West Nile Virus polyprotein
23


H-2 Db
RAHYNIVTF
E7
24


H-2 Db
RMFPNAPYL
WT1
25


H-2 Db
RSPFSRVVHL
MOG precursor
26


H-2 Db
SCLENFRAYV
PolA
27


H-2 Db
SGPSNTPPEI
Ad5 E1A
28


H-2 Db
SGVENPGGYCL
gp
29


H-2 Db
SHLVEALYL
IGF
30


H-2 Db
SQLLNAKYL
Plasmodium berghei ANKA acid
31




phosphatase


H-2 Db
SSLENFRAYV
PolA
32


H-2 Db
VILTNPISM
VEGFR2
33


H-2 Db
WMHHNMDLI
H-Y
34


H-2 Dd
AGPHNDMEI
p56
35


H-2 Dd
AGPPRYSRI
M164
36


H-2 Dd
IGPGRAFYA
HIV-1 US4 gp120
37


H-2 Dd
IPGRAFYA
Env
38


H-2 Dd
LGPISGHVL
pp65
39


H-2 Dd
RGPGRAFVTI
HIV-1 IIIB gp120
40


H-2 Dk
RRLGRTLLL
Middle T antigen
41


H-2 Kb
AGLAYYSM
Polyprotein
42


H-2 Kb
ANYNFTLV
Trypanosoma cruzi SP
43


H-2 Kb
ATLTYRML
Yellow Fever Virus 17D
44




polyprotein


H-2 Kb
DAPIYTNV
Beta-gal
45


H-2 Kb
EVYDFAFRDL
E6
46


H-2 Kb
FAPGNYPAL
NP
47


H-2 Kb
HILIYSDV
MYBPC-2
48


H-2 Kb
HNTQYCNL
MAGE-A5
49


H-2 Kb
ICPMYARV
Beta-gal
50


H-2 Kb
ILSPFLPLL
HBV surface antigen
51


H-2 Kb
IMYNYPAM
TB10.3-4
52


H-2 Kb
IMYNYPAML
Mycobacterium tuberculosis
53




TB10.4


H-2 Kb
ISHNFCNL
gp
54


H-2 Kb
KSPWFTTL
MuLV env
55


H-2 Kb
KVVRFDKL
Ovalbumin (subdominant)
56


H-2 Kb
LTFNYRNL
Histocompatibility antigen 60
57


H-2 Kb
MGLKFRQL
CP
58


H-2 Kb
RGYVYQGL
NP52
59


H-2 Kb
SCLEFWQRV
M57
60


H-2 Kb
SDYYFSWL
muFAP α
61


H-2 Kb
SIINFEKL
OVA
62


H-2 Kb
SIIVFNLL
MC-38
63


H-2 Kb
SIYRYYGL
OVA
64


H-2 Kb
SKYVFENV
MYBPC-2
65


H-2 Kb
SSIEFARL
gp
66


H-2 Kb
STYTFVRT
M38
67


H-2 Kb
SVLAFRRL
tgd057
68


H-2 Kb
SVYDFFVWL
TRP2
69


H-2 Kb
TSINFVKI
P79
70


H-2 Kb
TSYKFESV
INF γ R
71


H-2 Kb
TVSEFLKL
Murine Survivin
72


H-2 Kb
TVYGFCLL
m139
73


H-2 Kb
VGRNFTNL
mTERT
74


H-2 Kb
VIDAFSRL
m141
75


H-2 Kb
VIYIFTVRL
VACCL3_100
76


H-2 Kb
VNHRFTLV
Trypanosoma cruzi ASP-2
77


H-2 Kb
VVYDFLKL
SV40 T antigen
78


H-2 Kb
VWLSVIWM
HBsAg
79


H-2 Kd
AMQMLKDTI
HIV gag p24
80


H-2 Kd
AMQMLKETI
HIV-1 gag p24
81


H-2 Kd
AYIDFEMKI
SART3
82


H-2 Kd
CYYASRTKL
m145
83


H-2 Kd
DYWGQGTEL
Surface IgG (sA20-Ig) of A20
84


H-2 Kd
EYILSLEEL
GPC3
85


H-2 Kd
GYETVITQL
PPE
86


H-2 Kd
GYKDGNEYI
Listeria monocytogenes
87




Listeriolysin


H-2 Kd
HYLSTQSAL
Enhanced Green Fluorescent
88




Protein (eGFP)


H-2 Kd
IYNVGQVSI
Sialidases
89


H-2 Kd
IYSTVASSL
ND
90


H-2 Kd
KYKNAVTEL
RSV A strain F protein
91


H-2 Kd
KYNKANVFL
NRP-V7 superagonist peptide 8.3
92




Tg NOD mouse


H-2 Kd
QYIHSANVL
Erk1
93


H-2 Kd
RYLKNGKETL
HLA-Cw3
94


H-2 Kd
SYIGSINNI
M2-1
95


H-2 Kd
SYIPSAEKI
Plasmodium berghei CSP
96


H-2 Kd
SYMLQALCI
TNP03
97


H-2 Kd
SYVPSAEQI
Plasmodium CSP
98


H-2 Kd
TYLPTNASL
HER2
99


H-2 Kd
TYQRTRALV
Influenza A (PR8) NP
100


H-2 Kd
TYVPANASL
Neu/Her-2/Erbb2 proto-
101




oncoprotein


H-2 Kd
TYWPVVSDI
UL105
102


H-2 Kd
VYAGAMSGL
Mtb85A
103


H-2 Kd
YYIPHQSSL
Plasmodium falciparum Liver
104




stage antigen


H-2 Kk
DYENDIEKKI
CPS
105


H-2 Kk
FETFEAKI
Tyrosine-3-hydroxylase
106


H-2 Kk
TENSGKDI
SMCY
107


H-2 Kk
TEWETGQI
ASP-2
108


H-2 Kk
VESTAGSL
ESAT-6
109


H-2 Kk
YENDIEKKI
PLAM csp
110


H-2 Ld
HPQKVTKFM
KLK3
111


H-2 Ld
IPQSLDSWWTSL
HBV surface antigen
112


H-2 Ld
LPYLGWLVF
P1A
113


H-2 Ld
MPVGGQSSF
Ag85A
114


H-2 Ld
MPYLIDFGL
VSV N
115


H-2 Ld
RPQASGVYM
NP
116


H-2 Ld
SPGAAGYDL
Dutpase
117


H-2 Ld
SPSYVYHQF
EMV-1
118


H-2 Ld
TPHPARIGL
Beta-gal
119


H-2 Ld
YPHFMPTNL
MCMV IE1
120


HLA-A*0101
ATDALMTGF
HCV NS3
121


HLA-A*0101
ATDALMTGY
Polyprotein
122


HLA-A*0101
CTELKLSDY
NP
123


HLA-A*0101
EADPTGHSY
MAGE-1
124


HLA-A*0101
EVDPIGHLY
MAGE-3
125


HLA-A*0101
FTELTLGEF
Survivin
126


HLA-A*0101
IVDCLTEMY
USP9Y
127


HLA-A*0101
KSDICTDEY
Tyrosinase
128


HLA-A*0101
SADNNNSEY
VP1
129


HLA-A*0101
SSDYVIPIGTY
Tyrosinase
130


HLA-A*0101
TDLGQNLLY
AdV 5 Hexon
131


HLA-A*0101
TLDTLTAFY
MSLN
132


HLA-A*0101
TSEKRPFMCAY
WT1
133


HLA-A*0101
VSDGGPNLY
Influenza A PB1
134


HLA-A*0101
VTEHDTLLY
UL44
135


HLA-A*0101
YSEHPTFTSQY
HCMV pp65
136


HLA-A*0201
AILALLPAL
PSCA
137


HLA-A*0201
AIQDLCLAV
NPM1
138


HLA-A*0201
AIQDLCVAV
NPM1
139


HLA-A*0201
AITEVECFL
VP1
140


HLA-A*0201
ALCNTDSPL
iLR1
141


HLA-A*0201
ALDVYNGLL
ACPP
142


HLA-A*0201
ALFDIESKV
PSM P2
143


HLA-A*0201
ALIAPVHAV
Neg. Control
144


HLA-A*0201
ALISAFSGS
K8.1
145


HLA-A*0201
ALKDVEERV
MAGE-C2
146


HLA-A*0201
ALLEIASCL
ID0
147


HLA-A*0201
ALLTSRLRFI
Telomerase
148


HLA-A*0201
ALMEQQHYV
ITGB8
149


HLA-A*0201
ALNVYNGLL
ACPP
150


HLA-A*0201
ALPFGFILV
IL13Ra
151


HLA-A*0201
ALPHIIDEV
ND
152


HLA-A*0201
ALQPGTALL
PSCA
153


HLA-A*0201
ALSPVPPVV
BCL-2
154


HLA-A*0201
ALTPVVVTL
cyclin-dependent kinase 4
155


HLA-A*0201
ALVCYGPGI
FAP α
156


HLA-A*0201
ALVEMGHHA
Vpu
157


HLA-A*0201
ALWALPHAA
IE62
158


HLA-A*0201
ALWGPDPAAA
Insulin
159


HLA-A*0201
ALWPWLLMAT
RNF43
160


HLA-A*0201
ALYDVVTKL
Polyprotein
161


HLA-A*0201
ALYLMELTM
CB9L2
162


HLA-A*0201
ALYVDSLFFL
PRAME
163


HLA-A*0201
AMASTEGNV
ESAT-6
164


HLA-A*0201
AMLVLLAEI
LANA
165


HLA-A*0201
AQCQETIRV
Midkine
166


HLA-A*0201
ATGEALWAL
IE62
167


HLA-A*0201
ATWAENIQV
West Nile virus NY-99
168




polyprotein precursor


HLA-A*0201
AVLDGLLSL
bZIP factor
169


HLA-A*0201
CINGVCWTV
NS3
170


HLA-A*0201
CLGGLLTMV
LMP-2A
171


HLA-A*0201
CLPSPSTPV
BMI1
172


HLA-A*0201
CLWCVPQLR
ABL1
173


HLA-A*0201
CVNGVCWTV
Polyprotein
174


HLA-A*0201
DIWDGIPHV
NRP-2
175


HLA-A*0201
DLMGYIPAV
HCV core
176


HLA-A*0201
DLMGYIPLV
HCV core
177


HLA-A*0201
EIWTHSYKV
FOLR1
178


HLA-A*0201
ELAGIGILTV
MART-1
179


HLA-A*0201
ELSDSLGPV
PASD1
180


HLA-A*0201
ELTLGEFLKL
Survivin
181


HLA-A*0201
ELVDGLLSL
bZIP factor
182


HLA-A*0201
FIDSYICQV
H-Y
183


HLA-A*0201
FILGIIITV
V131
184


HLA-A*0201
FIYDFCIFGV
Lengsin
185


HLA-A*0201
FLAEDALNTV
EDDR1
186


HLA-A*0201
FLAMLKNTV
MAGE-C1
187


HLA-A*0201
FLDKGTYTL
BALF4
188


HLA-A*0201
FLDPRPLTV
CYP190
189


HLA-A*0201
FLFLRNFSL
TARP
190


HLA-A*0201
FLGKIWPS
Gag
191


HLA-A*0201
FLGYLILGV
PAP-3
192


HLA-A*0201
FLLSLFSLWL
ZnT-8
193


HLA-A*0201
FLLSLGIHL
HBV polymerase
194


HLA-A*0201
FLLTRILTI
S protein
195


HLA-A*0201
FLNKCETWV
DLK1
196


HLA-A*0201
FLPSDFFPSI
HBV core
197


HLA-A*0201
FLPSDFFPSV
CP
198


HLA-A*0201
FLPSPLFFFL
TARP 2M
199


HLA-A*0201
FLTPKKLQCV
PSA
200


HLA-A*0201
FLWGPRALV
MAGE-3
201


HLA-A*0201
FLYALALLL
LMP-2A
202


HLA-A*0201
FLYDDNQRV
topII
203


HLA-A*0201
FMNKFIYEI
alfa fetoprotein
204


HLA-A*0201
FVGEFFTDV
Glypican 3
205


HLA-A*0201
GILGFVFTL
MP
206


HLA-A*0201
GILTVSVAV
Mtb 16 kDa
207


HLA-A*0201
GLADQLIHL
Vif
208


HLA-A*0201
GLAPPQHLIRV
p53
209


HLA-A*0201
GLCTLVAML
BMLF1
210


HLA-A*0201
GLFKCGIAV
FAP α
211


HLA-A*0201
GLIQLVEGV
TRAG
212


HLA-A*0201
GLLGASVLGL
Telomerase
213


HLA-A*0201
GLLRFVTAV
NRP-1
214


HLA-A*0201
GLLSLEEEL
bZIP factor
215


HLA-A*0201
GLMEEMSAL
Mena
216


HLA-A*0201
GLPVEYLQV
Mycobacterium bovis antigen 85-A
217


HLA-A*0201
GLQDCTMLV
HCV NS5B
218


HLA-A*0201
GLQHWVPEL
BA46
219


HLA-A*0201
GLSPTVWLSV
S protein
220


HLA-A*0201
GLSRYVARL
Polymerase
221


HLA-A*0201
GLYDGMEHL
MAGE-10
222


HLA-A*0201
GMLGMVSGL
NRP-1
223


HLA-A*0201
GVDPNIRTGV
Polyprotein
224


HLA-A*0201
GVLVGVALI
CEA
225


HLA-A*0201
GVRGRVEEI
BCR-ABL
226


HLA-A*0201
GVYDGREHTV
MAGE-4
227


HLA-A*0201
HIAGSLAVV
ZnT-8
228


HLA-A*0201
HLSTAFARV
G250
229


HLA-A*0201
HLVEALYLV
Insulin
230


HLA-A*0201
ILAKFLHWL
Telomerase
231


HLA-A*0201
ILDDNLYKV
Vaccinia virus Copenhagen
232




Protein G5


HLA-A*0201
ILGFVFTLTV
MP
233


HLA-A*0201
ILGVLTSLV
DLK1
234


HLA-A*0201
ILHDGAYSL
HER2
235


HLA-A*0201
ILHNGAYSL
HER2
236


HLA-A*0201
ILKDFSILL
ZnT-8
237


HLA-A*0201
ILKEPVHGV
RT
238


HLA-A*0201
ILLWEIFTL
PDGFRbeta
239


HLA-A*0201
ILLWQPIPV
PAP-3
240


HLA-A*0201
ILMWEAVTL
VPI
241


HLA-A*0201
ILSLELMKL
HMMR
242


HLA-A*0201
IMDQVPFSV
gp100
243


HLA-A*0201
ITDQVPFSV
gp100
244


HLA-A*0201
KIFGSLAFL
HER2
245


HLA-A*0201
KLCPVQLWV
p53
246


HLA-A*0201
KLDVGNAEV
BAP31
247


HLA-A*0201
KLFGTSGQKT
EGFR
248


HLA-A*0201
KLGEFYNQMM
BNP
249


HLA-A*0201
KLHLYSHPI
Polymerase
250


HLA-A*0201
KLIANNTRV
Mycobacterium bovis antigen 85-A
251


HLA-A*0201
KLMSSNSTDL
HSP105
252


HLA-A*0201
KLPQLCTEL
HPV 16 E6
253


HLA-A*0201
KLQCVDLHV
PSA
254


HLA-A*0201
KLQDASAEV
HM1.24
255


HLA-A*0201
KLQVFLIVL
IAPP
256


HLA-A*0201
KLSGLGINAV
HCV NS3
257


HLA-A*0201
KLTPLCVTL
HIV-1 env gp120 848-856
258


HLA-A*0201
KLVALGINAV
Polyprotein
259


HLA-A*0201
KMLKEMGEV
RSV NP
260


HLA-A*0201
KTWGQYWQV
gp100
261


HLA-A*0201
KVAEELVHFL
MAGE-A3
262


HLA-A*0201
KVAELVHFL
MAGE-A3
263


HLA-A*0201
KVDDTFYYV
Vaccinia virus Host range
264




protein 2


HLA-A*0201
KVLEYVIKV
MAGE-A1
265


HLA-A*0201
KVVEFLAML
MAGE-C1
266


HLA-A*0201
LAALPHSCL
RGS5
267


HLA-A*0201
LIAHNQVRQV
HER2
268


HLA-A*0201
LIDQYLYYL
VP1
269


HLA-A*0201
LILPLLFYL
NG2
270


HLA-A*0201
LLAARAIVAI
Ilr1
271


HLA-A*0201
LLDFVRFMGV
EBNA 3B
272


HLA-A*0201
LLDVPTAAV
Interferon gamma inducible
273




protein (GILT) 30


HLA-A*0201
LLFGLALIEV
MAGE-C2
274


HLA-A*0201
LLFGYPVYV
Tax
275


HLA-A*0201
LLFNILGGWV
HCV NS4b
276


HLA-A*0201
LLGRNSFEV
p53
277


HLA-A*0201
LLHETDSAV
PSMA
278


HLA-A*0201
LLLASIAAGL
LY6K
279


HLA-A*0201
LLLGPLGPL
Heparanase
280


HLA-A*0201
LLLIWFRPV
Large T antigen
281


HLA-A*0201
LLLLTVLTV
Mucin
282


HLA-A*0201
LLLNCLWSV
Spike GP
283


HLA-A*0201
LLLTVLTVV
Mucin
284


HLA-A*0201
LLMGTLGIVC
E7
285


HLA-A*0201
LLMWEAVTV
VP1
286


HLA-A*0201
LLNGWRWRL
ND
287


HLA-A*0201
LLQERGVAYI
PSMA
288


HLA-A*0201
LLTAALWYV
CD105
289


HLA-A*0201
LLVPTCVFLV
TEM1
290


HLA-A*0201
LLWNGPMAV
Polyprotein
291


HLA-A*0201
LMLGEFLKL
Survivin
292


HLA-A*0201
LMWYELSKI
gp
293


HLA-A*0201
LNIDLLWSV
IGRP
294


HLA-A*0201
LTFGWCFKL
HIV-1 Nef
295


HLA-A*0201
LTLGEFLKL
Survivin-3a
296


HLA-A*0201
LVWMACHSA
Nucleocapsid
297


HLA-A*0201
MLAVFLPIV
STEAP1
298


HLA-A*0201
MLDLQPETT
E7
299


HLA-A*0201
MLMAQEALAFL
CAMEL
300


HLA-A*0201
MLNIPSINV
pp65
301


HLA-A*0201
MMNDQLMFL
PSMA
302


HLA-A*0201
MVWESGCTV
IA-2
303


HLA-A*0201
NLFETPVEA
BA46
304


HLA-A*0201
NLVPMVATV
pp65
305


HLA-A*0201
NVWATHACV
Env
306


HLA-A*0201
PLFDFSWLSL
BCL-2
307


HLA-A*0201
QLCPICRAPV
LIVIN
308


HLA-A*0201
QLFEELQEL
H0-1
309


HLA-A*0201
QLFNHTMFI
Non-muscle Myosin
310


HLA-A*0201
QLGEQCWTV
PSCA
311


HLA-A*0201
QLLDGFMITL
PASD1
312


HLA-A*0201
QLLIKAVNL
MPP11
313


HLA-A*0201
QMARLAWEA
LANA
314


HLA-A*0201
QQAHCLWCV
ABL1
315


HLA-A*0201
RILGAVAKV
Vinculin
316


HLA-A*0201
RLAEYQAYI
SART3
317


HLA-A*0201
RLDDDGNFQL
West Nile Virus NY-99
318




polyprotein precursor


HLA-A*0201
RLLGNVLVCV
HBB
319


HLA-A*0201
RLLQETELV
HER2
320


HLA-A*0201
RLLVVYPWT
HBB
321


HLA-A*0201
RLMNDMTAV
HSP105
322


HLA-A*0201
RLNMFTPYI
chlamydia trachomatis MOMP
323


HLA-A*0201
RLSSCVPVA
TGF β
324


HLA-A*0201
RLTPGVHEL
DLK1
325


HLA-A*0201
RLTSRVKAL
Telomerase
326


HLA-A*0201
RLVDDFLLV
Telomerase
327


HLA-A*0201
RLWQELSDI
circadian clock protein PASD1
328


HLA-A*0201
RMFPNAPYL
WT1
329


HLA-A*0201
RMPEAAPPV
p53
330


HLA-A*0201
RTLDKVLEV
HA-8
331


HLA-A*0201
RTLNAWVKV
Gag
332


HLA-A*0201
RVASPTSGV
IRS-2
333


HLA-A*0201
SIDWFMVTV
PLAC1
334


HLA-A*0201
SILLRDAGLV
TRAG
335


HLA-A*0201
SITEVECFL
VPI
336


HLA-A*0201
SLFEPPPPG
PSMA
337


HLA-A*0201
SLFLGILSV
MS4A1
338


HLA-A*0201
SLFNTVATL
Gag
339


HLA-A*0201
SLFNTVATLY
Gag
340


HLA-A*0201
SLGEQQYSV
WT1
341


HLA-A*0201
SLLFLLFSL
MSLN
342


HLA-A*0201
SLLMWITQC
NY-ESO-1
343


HLA-A*0201
SLLMWITQV
NY-ESO-1
344


HLA-A*0201
SLLNATAIAV
Env
345


HLA-A*0201
SLLQHLIGL
PRAME
346


HLA-A*0201
SLNQTVHSL
ND
347


HLA-A*0201
SLPPPGTRV
p53
348


HLA-A*0201
SLSEKTVLL
CD59
349


HLA-A*0201
SLSRFSWGA
Myelin basic protein
350


HLA-A*0201
SLVDVMPWL
Cytochrome p450
351


HLA-A*0201
SLVKHHMYI
Vif
352


HLA-A*0201
SLYNTVATL
Gag
353


HLA-A*0201
SLYNTVATLY
Gag
354


HLA-A*0201
SLYSFPEPEA
PRAME
355


HLA-A*0201
SMYRVFEVGV
H250
356


HLA-A*0201
SQADALKYV
EZH2
357


HLA-A*0201
STLCQVEPV
MPP11
358


HLA-A*0201
STPPPGTRV
p53
359


HLA-A*0201
TLADFDPRV
EphA2
360


HLA-A*0201
TLDYKPLSV
BMRF1
361


HLA-A*0201
TLFWLLLTL
VEGFR1
362


HLA-A*0201
TLFWLLTL
FLT1
363


HLA-A*0201
TLNAWVKVV
Gag
364


HLA-A*0201
TLPGYPPHV
PAX-5
365


HLA-A*0201
TLPPAWQPFL
Survivin
366


HLA-A*0201
TLQDIVYKL
BMI1
367


HLA-A*0201
TLSNLSFPV
NG2
368


HLA-A*0201
TMNGSKSPV
Mena
369


HLA-A*0201
VIFDFLHCI
Large T antigen
370


HLA-A*0201
VIMPCSWWV
Chondromodulin
371


HLA-A*0201
VISNDVCAQV
KLK
372


HLA-A*0201
VIVMLTPLV
IA-2
373


HLA-A*0201
VIYHYVDDL
Pol
374


HLA-A*0201
VLAELVKQI
HCMV IE1
375


HLA-A*0201
VLAGGFFLL
PSMA
376


HLA-A*0201
VLDFAPPGA
WT1
377


HLA-A*0201
VLDGLDVLL
PRAME
378


HLA-A*0201
VLEETSVML
IE-1
379


HLA-A*0201
VLFGLGFAI
IGRP
380


HLA-A*0201
VLHDDLLEA
HA-1
381


HLA-A*0201
VLLGAVCGV
NRP-1
382


HLA-A*0201
VLMIKALEL
Non muscle Myosin-9
383


HLA-A*0201
VLPLTVAEV
MSLN
384


HLA-A*0201
VLQELNVTV
Pr1
385


HLA-A*0201
VLQMKEEDV
iLR1
386


HLA-A*0201
VLSDFKTWL
HCV NS5a
387


HLA-A*0201
VLTDGNPPEV
Mtb 19 kDa
388


HLA-A*0201
VLYRYGSFSV
gp100
389


HLA-A*0201
VMNILLQYVV
GAD65
390


HLA-A*0201
VVTGVLVYL
ZnT-8
391


HLA-A*0201
WLSLKTLLSL
BCL-2
392


HLA-A*0201
WLSLLVPFV
S protein
393


HLA-A*0201
YAYDGKDYIA
HLA-A2
394


HLA-A*0201
YIGEVLVSV
HA-2
395


HLA-A*0201
YLEPGPVTA
gp100
396


HLA-A*0201
YLEPGPVTV
gp100
397


HLA-A*0201
YLFFYRKSV
mTERT
398


HLA-A*0201
YLGSYGFRL
p53
399


HLA-A*0201
YLIELIDRV
TACE
400


HLA-A*0201
YLISGDSPV
CD33
401


HLA-A*0201
YLLEMLWRL
LMP-1
402


HLA-A*0201
YLLPRRGPRL
HCV core
403


HLA-A*0201
YLNDHLEPWI
BCL-X
404


HLA-A*0201
YLNKIQNSL
Plasmodium falciparum CSP
405


HLA-A*0201
YLNRHLHTWI
BCL-2
406


HLA-A*0201
YLNTVQPTCV
EGFR
407


HLA-A*0201
YLQLVFGIEV
MAGE-A2
408


HLA-A*0201
YLQQNWWTL
LMP-1
409


HLA-A*0201
YLQQNWWTL
LMP-1
410


HLA-A*0201
YLQVDLRFL
NRP-2
411


HLA-A*0201
YLQVNSLQTV
Telomerase
412


HLA-A*0201
YLQWIEFSI
Prominin1
413


HLA-A*0201
YLSGADLNL
CEA
414


HLA-A*0201
YLSGANLNL
CEACAM
415


HLA-A*0201
YLVGNVCIL
PASD1
416


HLA-A*0201
YLVSIFLHL
ND
417


HLA-A*0201
YLYQWLGAPV
BGLAP
418


HLA-A*0201
YMCSFLFNL
EZH2
419


HLA-A*0201
YMDGTMSQV
Tyrosinase
420


HLA-A*0201
YMLDLQPETT
E7
421


HLA-A*0201
YMNGTMSQV
Tyrosinase
422


HLA-A*0201
YTCPLCRAPV
SAA
423


HLA-A*0201
YTMDGEYRL
West Nile virus NY-99
424




polyprotein precursoR


HLA-A*0201
YVLDHLIVV
BRLF1
425


HLA-A*0301
AIFQSSMTK
HIV pol
426


HLA-A*0301
ALLAVGATK
gp100
427


HLA-A*0301
ATGFKQSSK
bcr-abl 210 kD fusion protein
428


HLA-A*0301
ILRGSVAHK
Influenza A (PR8) NP
429


HLA-A*0301
KLCLRFLSK
E6
430


HLA-A*0301
KLGGALQAK
IE-1
431


HLA-A*0301
KQSSKALQR
bcr-abl 210 kD fusion protein
432


HLA-A*0301
QVLKKIAQK
HMOX1
433


HLA-A*0301
QVPLRPMTYK
NEF
434


HLA-A*0301
RIAAWMATY
BCL-2L1
435


HLA-A*0301
RISTFKNWPK
Survivin-3a
436


HLA-A*0301
RLGLQVRKNK
RhoC
437


HLA-A*0301
RLLFFAPTR
MCL-1
438


HLA-A*0301
RLRAEAQVK
EMNA 3A
439


HLA-A*0301
RLRPGGKKK
Gag
440


HLA-A*0301
RVCEKMALY
HCV NS5B
441


HLA-A*0301
RVRAYTYSK
BRLF1
442


HLA-A*0301
SVLNYERARR
hTERT
443


HLA-A*0301
VTLTHPITK
Polyprotein
444


HLA-A*0301
YMVPFIPLYR
Tyrosinase
445


HLA-A*1101
ACQGVGGPGHK
HIV gag p24
446


HLA-A*1101
ATIGTAMYK
EBV BRLF1
447


HLA-A*1101
AVDLSHFLK
NEF
448


HLA-A*1101
AVFDRKSDAK
EBNA 3B
449


HLA-A*1101
IVTDFSVIK
EBNA 3B
450


HLA-A*1101
KSMREEYRK
Influenza A MP2
451


HLA-A*1101
NTLEQTVKK
E6
452


HLA-A*1101
RMVLASTTAK
Influenza A MP1
453


HLA-A*1101
SIIPSGPLK
Influenza A MP
454


HLA-A*1101
SSCSSCPLSK
EBV LMP-2
455


HLA-A*1101
YVNVNMGLK
HBV core antigen
456


HLA-A*2301
QYDPVAALF
pp65
457


HLA-A*2402
AFLPWHRLF
Tyrosinase
458


HLA-A*2402
AYACNTSTL
Survivin
459


HLA-A*2402
AYAQKIFKI
IE-1
460


HLA-A*2402
AYQGVQQKV
ESAT-6
461


HLA-A*2402
AYSQQTRGL
HCV NS3
462


HLA-A*2402
CYASGWGSI
PSA
463


HLA-A*2402
CYTWNQMNL
WT1
464


HLA-A*2402
DYCNVLNKEF
BRLF1
465


HLA-A*2402
DYLNEWGSRF
p-Cadherin
466


HLA-A*2402
DYLQYVLQI
BCL-2A1
467


HLA-A*2402
EYCPGGNLF
MELK
468


HLA-A*2402
EYILSLEEL
Glypican 3
469


HLA-A*2402
EYLQLVFGI
MAGEA2
470


HLA-A*2402
EYLVSFGVW
HBV core
471


HLA-A*2402
EYRALQLHL
Carbonic anhydrase
472


HLA-A*2402
EYYELFVNI
DEP DC1
473


HLA-A*2402
GYCTQIGIF
C1orf59
474


HLA-A*2402
IMPKAGLLI
MAGE-A3
475


HLA-A*2402
IYTWIEDHF
FOXM1
476


HLA-A*2402
KLRGEVKQNL
hTOM34p
477


HLA-A*2402
KWLISPVKI
HJURP
478


HLA-A*2402
KYTSFPWLL
HBV polymerase
479


HLA-A*2402
KYYLRVRPLL
KIF20A
480


HLA-A*2402
LYQWLGAPV
BGLAP
481


HLA-A*2402
NYQPVWLCL
RNF43
482


HLA-A*2402
PYLFWLAAI
EBV LMP2
483


HLA-A*2402
QYDPVAALF
pp65
484


HLA-A*2402
RYCNLEGPPI
LY6K
485


HLA-A*2402
RYLKDQQLL
Env
486


HLA-A*2402
RYLRDQQLL
Env
487


HLA-A*2402
RYNAQCQETI
Midkine
488


HLA-A*2402
RYPLTFGW
HIV nef
489


HLA-A*2402
RYPLTFGWCF
NEF
490


HLA-A*2402
SFHSLHLLF
Tax
491


HLA-A*2402
SYRNEIAYL
TTK
492


HLA-A*2402
TFPDLESEF
MAGEA3
493


HLA-A*2402
TYACFVSNL
CEA
494


HLA-A*2402
TYFSLNNKF
AdV 5 Hexon
495


HLA-A*2402
TYGPVFMCL
LMP-2
496


HLA-A*2402
TYGPVFMSL
EBV LMP2
497


HLA-A*2402
TYLPTNASL
HER-2/neu
498


HLA-A*2402
VYALPLKML
pp65
499


HLA-A*2402
VYDFAFRDL
HPV16 E6
500


HLA-A*2402
VYFFLPDHL
gp100
501


HLA-A*2402
VYGFVRACL
hTRT
502


HLA-A*2402
VYGIRLEHF
Nuf2
503


HLA-A*2402
VYLRVRPLL
KIF20A
504


HLA-A*2402
VYYNWQYLL
IL13r
505


HLA-A*2902
IACPIVMRY
BRLF1
506


HLA-A*2902
KEKYIDQEEL
HSP90 alpha
507


HLA-A*2902
KESTLHLVL
Ubiquitin
508


HLA-A*2902
LYNTVATLY
Gag
509


HLA-A*2902
SFDPIPIHY
Env
510


HLA-A*2902
SFNCRGEFFY
Env
511


HLA-A*6801
IVTDFSVIK
EBNA 3B
512


HLA-A*6801
TVSGNILTIR
NY-ESO-1
513


HLA-B*0702
APKKPKEPV
VP1
514


HLA-B*0702
APRGVRMAV
CAMEL
515


HLA-B*0702
APTKRKGEC
VP1
516


HLA-B*0702
DPRRRSRNL
HCV core
517


HLA-B*0702
GPGHKARVL
Gag-pol
518


HLA-B*0702
GPLCKADSL
VP1
519


HLA-B*0702
GPRLGVRAT
HCV core
520


HLA-B*0702
IPRRIRQGL
HIV-1 env gp120
521


HLA-B*0702
KPTLKEYVL
E7
522


HLA-B*0702
KPYSGTAYNAL
AdV Hexon
523


HLA-B*0702
KPYSGTAYNSL
AdV Hexon
524


HLA-B*0702
LPVSCPEDL
bZIP factor
525


HLA-B*0702
LPVSPRLQL
CEACAM
526


HLA-B*0702
LPWHRLFLL
Tyrosinase
527


HLA-B*0702
NPTAQSQVM
VP1
528


HLA-B*0702
QPEWFRNVL
Influenza A PB1
529


HLA-B*0702
QPRAPIRPI
EBNA 6
530


HLA-B*0702
RPHERNGFTVL
pp65
531


HLA-B*0702
RPPIFIRRL
EBNA 3A
532


HLA-B*0702
RPQGGSRPEFVKL
BMRF1
533


HLA-B*0702
RVRFFFPSL
MAGE-A1
534


HLA-B*0702
SPERKMLPC
VP1
535


HLA-B*0702
SPFFLLLLL
Mucin
536


HLA-B*0702
SPIVPSFDM
Influenza A NP
537


HLA-B*0702
SPSVDKARAEL
SMCY
538


HLA-B*0702
TPGPGVRYPL
NEF
539


HLA-B*0702
TPNQRQNVC
P2X5a
540


HLA-B*0702
TPRVTGGGAM
pp65
541


HLA-B*0702
VPQYGYLTL
VP1
542


HLA-B*0801
AAKGRGAAL
Neg. Control
543


HLA-B*0801
APLLRWVL
HMOX1
544


HLA-B*0801
DIYKRWII
Gag
545


HLA-B*0801
EIYKRWII
HIV p24 gag
546


HLA-B*0801
ELKRKMIYM
IE-1
547


HLA-B*0801
ELNRKMIYM
IE-1
548


HLA-B*0801
ELRRKMMYM
IE-1
549


HLA-B*0801
FLKEKGGL
HIV-1 nef
550


HLA-B*0801
FLRGRAYGL
EBNA 3A
551


HLA-B*0801
GEIYKRWII
HIV-1 gag p24
552


HLA-B*0801
GFKQSSKAL
bcr-abl 210 kD fusion protein
553


HLA-B*0801
HSKKKCDEL
Polyprotein
554


HLA-B*0801
LPHNHTDL
TPR-protein
555


HLA-B*0801
QAKWRLQTL
EBV EBNA3A
556


HLA-B*0801
QIKVRVDMV
IE-1
557


HLA-B*0801
RAKFKQLL
BZLF1
558


HLA-B*0801
YLKDQQLL
Env
559


HLA-B*1501
RLRPGGKKKY
HIV-1 p17
560


HLA-B*2705
ARMILMTHF
Polyprotein
561


HLA-B*2705
GRAFVTIGK
Env
562


HLA-B*2705
GRFGLATEK
BRAF 27
563


HLA-B*2705
GRFGLATVK
BRAF 27
564


HLA-B*2705
KRWIILGLNK
Gag
565


HLA-B*2705
KRWIILGLNKI
Gag
566


HLA-B*2705
KRWIILGLNKINR
Gag
567


HLA-B*2705
KRWIILGLNKIVR
Gag
568


HLA-B*2705
KRWIILGLNKIVR
Gag
569


HLA-B*2705
KRWIIMGL
Gag
570


HLA-B*2705
KRWIIMGLNK
HIV-1 Gag p24
571


HLA-B*2705
RMFPNAPYL
WT1
572


HLA-B*2705
RRWIQLGLQK
Gag
573


HLA-B*2705
SRYWAIRTR
Influenza A NP
574


HLA-B*3501
CPNSSIVY
HCV E
575


HLA-B*3501
EAAGIGILTY
MART-1
576


HLA-B*3501
EPDLAQCFY
Survivin-3a
577


HLA-B*3501
EPLPQGQLTAY
BZLF1
578


HLA-B*3501
EPLSQSQITAY
BZLF1
579


HLA-B*3501
HPNIEEVAL
HCV NS3
580


HLA-B*3501
HPVAEADYFEY
EBNA 1
581


HLA-B*3501
HPVGDADYFEY
EBNA 1
582


HLA-B*3501
HPVGEADYFEY
EBNA 1
583


HLA-B*3501
HPVGQADYFEY
EBNA 1
584


HLA-B*3501
IPSINVHHY
pp65
585


HLA-B*3501
IPYLDGTFY
AdV Hexon
586


HLA-B*3501
LPLNVGLPIIGVM
UL138
587


HLA-B*3501
LPSDFFPSV
CP
588


HLA-B*3501
MPFATPMEA
NY-ESO-1
589


HLA-B*3501
NPDIVIYQY
HIV-1 RT
590


HLA-B*3501
VPLDEDFRKY
RT
591


HLA-B*3501
YPLHEQHGM
EBNA 3A
592


HLA-B*4001
IEDPPFNSL
EBV LMP2
593


HLA-B*4001
KEKGGLEGL
HIV-1 Nef
594


HLA-B*4001
REISVPAEIL
HCV NS5a
595


HLA-B*5101
IPFYGKAI
Polyprotein
596


HLA-B*5101
LPSDFFPSV
CP
597


HLA-B*5101
MPFATPMEA
NY-ESO-1
598


HLA-E*0101
VMAPRTLVL
HLA-A leader sequence peptide
599









It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method, kit, reagent, or composition of the invention, and vice versa. Furthermore, compositions of the invention can be used to achieve methods of the invention.


It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims.


All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.


The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.


As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. In embodiments of any of the compositions and methods provided herein, “comprising” may be replaced with “consisting essentially of” or “consisting of”. As used herein, the phrase “consisting essentially of” requires the specified integer(s) or steps as well as those that do not materially affect the character or function of the claimed invention. As used herein, the term “consisting” is used to indicate the presence of the recited integer (e.g., a feature, an element, a characteristic, a property, a method/process step or a limitation) or group of integers (e.g., feature(s), element(s), characteristic(s), property(ies), method/process steps or limitation(s)) only.


The term “or combinations thereof” as used herein refers to all permutations and combinations of the listed items preceding the term. For example, “A, B, C, or combinations thereof” is intended to include at least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, AB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.


As used herein, words of approximation such as, without limitation, “about”, “substantial” or “substantially” refers to a condition that when so modified is understood to not necessarily be absolute or perfect but would be considered close enough to those of ordinary skill in the art to warrant designating the condition as being present. The extent to which the description may vary will depend on how great a change can be instituted and still have one of ordinary skill in the art recognize the modified feature as still having the required characteristics and capabilities of the unmodified feature. In general, but subject to the preceding discussion, a numerical value herein that is modified by a word of approximation such as “about” may vary from the stated value by at least 1, 2, 3, 4, 5, 6, 7, 10, 12 or 15%.


All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.


To aid the Patent Office, and any readers of any patent issued on this application in interpreting the claims appended hereto, applicants wish to note that they do not intend any of the appended claims to invoke paragraph 6 of 35 U.S.C. § 112, U.S.C. § 112 paragraph (f), or equivalent, as it exists on the date of filing hereof unless the words “means for” or “step for” are explicitly used in the particular claim.


For each of the claims, each dependent claim can depend both from the independent claim and from each of the prior dependent claims for each and every claim so long as the prior claim provides a proper antecedent basis for a claim term or element.


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Claims
  • 1. A fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag.
  • 2. (canceled)
  • 3. The fusion protein of claim 1, wherein the MHC is at least one of: a human, mouse, rat, hamster, horse, pig, cow, simian, avian, or chimeric MHC, wherein the MHC is Class I MHC, or wherein the MHC does not include a transmembrane sequence.
  • 4. (canceled)
  • 5. (canceled)
  • 6. The fusion protein of claim 1, wherein the peptide tag is selected from wherein the peptide tag is selected from at least one of: a BirA tail, a myc, a FLAG, a glutathione-S-transferase, a His tag, a maltose binding protein, hemagglutinin (HA)-tag, a V5 tag, a T7 tag, a V9 tag, a NusA-tag, a thioredoxin-tag, or a fluorescent protein-tag, a Her2/neu-tag, a CD20-tag, or a GFP-tag.
  • 7. The fusion protein of claim 1, wherein the first, the second, or both the first and second flexible linkers comprise glycine, serine or both glycine and serine and comprise 5 to 40 residues.
  • 8. (canceled)
  • 9. The fusion protein of claim 1, wherein the peptide is selected from at least one of: an immunogenic peptide epitope: a peptide that is 8 to 16 residues long: ABL1; ACPP; Ad5 ElA; AdV 5 Hexon; AdV Hexon; Ag85A; alfa fetoprotein; ASP-2; BA46; BALF4; BAP31; BCL-2; BCL-2A1; BCL-2L1; BCL-X; BCR-ABL; bcr-abl 210 kD fusion protein; Beta-gal; BGLAP; BMI1; BMLF1; BMRF1; BNP; BRAF 27; BRLF1; bZIP factor; BZLF1; C1orf59; CAMEL; Carbonic anhydrase; CB9L2; CD105; CD33; CD59; CEA; CEACAM; Chondromodulin; circadian clock protein PASD1; CP; CPS; cyclin-dependent kinase 4; CYP190; Cytochrome p450; DEP DC1; DLK1; Dutpase; E6; E7; EBNA 1; EBNA 3A; EBNA 3B; EBNA 6; EBV BRLF1; EBV EBNA3A; EBV LMP2; EDDR1; EGFR; EMNA 3A; EMV-1; Enhanced Green Fluorescent Protein; Env; EphA2; Erkl; ESAT-6; EZH2; FAPPa; FLT1; FOLR1; FOXM1; G250; GAD65; Gag; Gag-pol; Glypican 3; gp; gp100; gp33 (C9M); GPC3; H250; HA-1; HA-2; HA-8; HBB; HBsAg; HBV core; HBV polymerase; HBV surface antigen; HCMV IE1; HCMV pp65; HCV core; HCV E; HCV NS3; HCV NS4b; HCV NS5a; HCV NS5B; Heparanase; HER2; HER-2/neu; Histocompatibility antigen 60; HIV gag p24; HIV nef, HIV pol; HIV-1 env gp120; HIV-1 IIIB gp120; HIV-1 nef, HIV-1 p17; HIV-1 RT; HIV-1 US4 gp120; HJURP; HLA-A leader sequence peptide; HLA-A2; HLA-Cw3; Chlamydia trachomatis MOMP; HM1.24; HMMR; HMOX1; HO-1; hPSA; HPV 16 E6; HSP105; HSP90 alpha; hTERT; hTOM34p; hTRT; H-Y; IA-2; IAPP; IDO; IE-1; IE62; IGF; IGRP; IL13r; IL13Ra; Ilr1; Influenza A (PR8) NP; Influenza A MP; Influenza A MP1; Influenza A MP2; Influenza A NP; Influenza A PB1; INFγR; Insulin; Interferon gamma inducible protein (GILT) 30; IRS-2; ITGB8; K8.1; KIF20A; KLK; KLK3; L1; LANA; Large T antigen; Lengsin; Listeria monocytogenes Listeriolysin; LIVIN; LMP-1; LMP-2; LMP-2A; LMP-2A; LY6K; m139; mi41; m145; M164; M2-1; M38; M45; M57; MAGE-1; MAGE-10; MAGE-3; MAGE-4; MAGE-A1; MAGEA2; MAGEA3; MAGE-A5; MAGE-C1; MAGE-C2; MART-1; MC38 adpgk neoantigen; MC-38; MCL-1; MCMV IE1; MELK; Mena; Middle T antigen; Midkine; miHAg SMCY; MOG precursor; MP; MPP11; MS4A1; MSLN; Mtb 16 kDa; Mtb 19 kDa; Mtb85A; mTERT; Mucin; muFAPα; MuLV env; Murine Survivin; MYBPC-2; Mycobacterium bovis antigen 85-A; Mycobacterium tuberculosis ESAT-6; Mycobacterium tuberculosis TB10.4; Myelin basic protein; ND; NEF; NEF; Neu/Her-2/Erbb2 proto-oncoprotein; NG2; Non muscle Myosin-9; Non-muscle Myosin; NP; NP396; NP52; NPM1; NRP-1; NRP-2; NRP-V7 superagonist peptide 8.3 Tg NOD mouse; NS3; Nucleocapsid; Nuf2; NY-ESO-1; OVA; Ovalbumin (subdominant); PiA; β2X5a; p53; p56; P79; PAP-3; PASD1; PAX-5; p-Cadherin; PDGFRbeta; PLAC1; PLAM csp; Plasmodium berghei ANKA acid phosphatase; Plasmodium berghei CSP; Plasmodium CSP; Plasmodium falciparum CSP; Plasmodium falciparum Liver stage antigen; PolA; Polymerase; Polyprotein; pp65; PPE; Pr1; PRAME; Prominin1; PSA; PSCA; PSM β2; PSMA; RGS5; RhoC; RNF43; RSV A strain F protein; RSV NP; RT; S protein; SAA; SART3; Sialidases; SIV gag; SMCY; Spike GP; STEAPI; Surface IgG (sA20-Ig) of A20; Survivin; Survivin-3a; SV40 T antigen; TACE; TARP; TARP 2M; Tax; TB10.3-4; Telomerase; TEM1; tgd057; TGFβ; TNPO3; topII; TPBG; TPR-protein; TRAG; TRP2; Trypanosoma cruzi ASP-2; Trypanosoma cruzi SP; TTK; Tyrosinase; Tyrosine-3-hydroxylase; Ubiquitin; UL105; UL138; UL44; USP9Y; V131; Vaccinia virus Copenhagen Protein G5; Vaccinia virus Host range protein 2; VACCL3_100; VEGFR1; VEGFR2; VEGFR2/KDR fragment 1; Vif; Vinculin; VP1; Vpu; VSV N; West Nile virus NY-99 polyprotein precursor; West Nile Virus polyprotein; WT1; Yellow Fever Virus 17D polyprotein; or ZnT-8.
  • 10. The fusion protein of claim 1, wherein the MHC is selected from at least one of H-2 Db, H-2 Dd; H-2 Dk; H-2 Kb; H-2 Kd; H-2 Kk; H-2 Ld; HLA-A*0101; HLA-A*0201; HLA-A*0301; HLA-A*1101; HLA-A*2301; HLA-A*2402; HLA-A*2902; HLA-A*6801; HLA-B*0702; HLA-B*0801; HLA-B*1501; HLA-B*2705; HLA-B*3501; HLA-B*4001; HLA-B*5101; or HLA-E*0101.
  • 11. The fusion protein of claim 1, wherein the peptide is at least one of SEQ ID NO:1-599.
  • 12. A nucleic acid that expresses a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag.
  • 13. (canceled)
  • 14. The nucleic acid of claim 12, wherein the MHC is at least one of: a human, mouse, rat, hamster, horse, pig, cow, simian, avian, or chimeric MHC, wherein the MHC is Class I MHC, or wherein the MHC does not include a transmembrane sequence.
  • 15. (canceled)
  • 16. (canceled)
  • 17. The nucleic acid of claim 12, wherein the peptide tag is selected from at least one of: a BirA tail, a myc, a FLAG, a glutathione-S-transferase, a His tag, a maltose binding protein, hemagglutinin (HA)-tag, a V5 tag, a T7 tag, a V9 tag, a NusA-tag, a thioredoxin-tag, or a fluorescent protein-tag, a Her2/neu-tag, a CD20-tag, or a GFP-tag.
  • 18. The nucleic acid of claim 12, wherein the first, the second, or both the first and second flexible linkers comprise glycine, serine or both glycine and serine and comprise 5 to 40 residues.
  • 19. (canceled)
  • 20. The nucleic acid of claim 12, wherein the peptide is selected from at least one of: an immunogenic peptide epitope; a peptide that is 8 to 16 residues long; ABL1; ACPP; Ad5 ElA; AdV 5 Hexon; AdV Hexon; Ag85A; alfa fetoprotein; ASP-2; BA46; BALF4; BAP31; BCL-2; BCL-2A1; BCL-2L1; BCL-X; BCR-ABL; bcr-abl 210 kD fusion protein; Beta-gal; BGLAP; BMI1; BMLF1; BMRF1; BNP; BRAF 27; BRLF1; bZIP factor; BZLF1; C1orf59; CAMEL; Carbonic anhydrase; CB9L2; CD105; CD33; CD59; CEA; CEACAM; Chondromodulin; circadian clock protein PASD1; CP; CPS; cyclin-dependent kinase 4; CYP190; Cytochrome p450; DEP DC1; DLK1; Dutpase; E6; E7; EBNA 1; EBNA 3A; EBNA 3B; EBNA 6; EBV BRLF1; EBV EBNA3A; EBV LMP2; EDDR1; EGFR; EMNA 3A; EMV-1; Enhanced Green Fluorescent Protein; Env; EphA2; Erkl; ESAT-6; EZH2; FAPPa; FLT1; FOLR1; FOXM1; G250; GAD65; Gag; Gag-pol; Glypican 3; gp; gp100; gp33 (C9M); GPC3; H250; HA-1; HA-2; HA-8; HBB; HBsAg; HBV core; HBV polymerase; HBV surface antigen; HCMV IE1; HCMV pp65; HCV core; HCV E; HCV NS3; HCV NS4b; HCV NS5a; HCV NS5B; Heparanase; HER2; HER-2/neu; Histocompatibility antigen 60; HIV gag p24; HIV nef, HIV pol; HIV-1 env gp120; HIV-1 IIIB gp120; HIV-1 nef, HIV-1 p17; HIV-1 RT; HIV-1 US4 gp120; HJURP; HLA-A leader sequence peptide; HLA-A2; HLA-Cw3; Chlamydia trachomatis MOMP; HM1.24; HMMR; HMOX1; HO-1; hPSA; HPV 16 E6; HSP105; HSP90 alpha; hTERT; hTOM34p; hTRT; H-Y; IA-2; IAPP; IDO; IE-1; IE62; IGF; IGRP; IL13r; IL13Ra; Ilr1; Influenza A (PR8) NP; Influenza A MP; Influenza A MP1; Influenza A MP2; Influenza A NP; Influenza A PB1; INFγR; Insulin; Interferon gamma inducible protein (GILT) 30; IRS-2; ITGB8; K8.1; KIF20A; KLK; KLK3; L1; LANA; Large T antigen; Lengsin; Listeria monocytogenes Listeriolysin; LIVIN; LMP-1; LMP-2; LMP-2A; LMP-2A; LY6K; m139; m141; m145; M164; M2-1; M38; M45; M57; MAGE-1; MAGE-10; MAGE-3; MAGE-4; MAGE-A1; MAGEA2; MAGEA3; MAGE-A5; MAGE-C1; MAGE-C2; MART-1; MC38 adpgk neoantigen; MC-38; MCL-1; MCMV IE1; MELK; Mena; Middle T antigen; Midkine; miHAg SMCY; MOG precursor; MP; MPP11; MS4A1; MSLN; Mtb 16 kDa; Mtb 19 kDa; Mtb85A; mTERT; Mucin; muFAPα; MuLV env; Murine Survivin; MYBPC-2; Mycobacterium bovis antigen 85-A; Mycobacterium tuberculosis ESAT-6; Mycobacterium tuberculosis TB10.4; Myelin basic protein; ND; NEF; NEF; Neu/Her-2/Erbb2 proto-oncoprotein; NG2; Non muscle Myosin-9; Non-muscle Myosin; NP; NP396; NP52; NPM1; NRP-1; NRP-2; NRP-V7 superagonist peptide 8.3 Tg NOD mouse; NS3; Nucleocapsid; Nuf2; NY-ESO-1; OVA; Ovalbumin (subdominant); P1A; β2X5a; p53; p56; P79; PAP-3; PASD1; PAX-5; p-Cadherin; PDGFRbeta; PLAC1; PLAM csp; Plasmodium berghei ANKA acid phosphatase; Plasmodium berghei CSP; Plasmodium CSP; Plasmodium falciparum CSP; Plasmodium falciparum Liver stage antigen; PolA; Polymerase; Polyprotein; pp65; PPE; Pr1; PRAME; Prominin1; PSA; PSCA; PSM β2; PSMA; RGS5; RhoC; RNF43; RSV A strain F protein; RSV NP; RT; S protein; SAA; SART3; Sialidases; SIV gag; SMCY; Spike GP; STEAPI; Surface IgG (sA20-Ig) of A20; Survivin; Survivin-3a; SV40 T antigen; TACE; TARP; TARP 2M; Tax; TB10.3-4; Telomerase; TEM1; tgd057; TGFβ; TNPO3; topII; TPBG; TPR-protein; TRAG; TRP2; Trypanosoma cruzi ASP-2; Trypanosoma cruzi SP; TTK; Tyrosinase; Tyrosine-3-hydroxylase; Ubiquitin; UL105; UL138; UL44; USP9Y; V131; Vaccinia virus Copenhagen Protein G5; Vaccinia virus Host range protein 2; VACCL3_100; VEGFR1; VEGFR2; VEGFR2/KDR fragment 1; Vif; Vinculin; VP1; Vpu; VSV N; West Nile virus NY-99 polyprotein precursor; West Nile Virus polyprotein; WT1; Yellow Fever Virus 17D polyprotein; or ZnT-8.
  • 21. The nucleic acid of claim 12, wherein the MHC is selected from at least one of H-2 Db, H-2 Dd; H-2 Dk; H-2 Kb; H-2 Kd; H-2 Kk; H-2 Ld; HLA-A*0101; HLA-A*0201; HLA-A*0301; HLA-A*1101; HLA-A*2301; HLA-A*2402; HLA-A*2902; HLA-A*6801; HLA-B*0702; HLA-B*0801; HLA-B*1501; HLA-B*2705; HLA-B*3501; HLA-B*4001; HLA-B*5101; or HLA-E*0101.
  • 22. The nucleic acid of claim 12, wherein the peptide is SEQ ID NO:1-599.
  • 23. A method of making a soluble eukaryotic-derived peptide/MHC complex comprising: expressing in a cell a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag.
  • 24. The method of claim 23, further comprising isolating the fusion protein from a supernatant.
  • 25. The method of claim 23, further comprising forming dimers, trimers, tetramers, or multimers of the fusion protein by mixing the fusion protein with one or more agents that bind to two or more fusion proteins.
  • 26. The method of claim 25, wherein the agent is selected from an antibody, a cross-linking agent, a ligase, an avidin, a streptavidin, a Protein A, or a J-chain.
  • 27. (canceled)
  • 28. (canceled)
  • 29. (canceled)
  • 30. (canceled)
  • 31. (canceled)
  • 32. (canceled)
  • 33. (canceled)
  • 34. A cell line expressing a fusion protein comprising a fusion protein comprising a peptide, a first flexible linker, a β2-microglobulin domain, a second flexible linker, a soluble major histocompatibility complex (MHC) heavy chain and a peptide tag.
  • 35. The cell line of claim 34, wherein the fusion protein is integrated into the genome by co-transfecting a fusion protein expressing vector with a transposase vector that expresses a transposase and wherein the fusion protein expressing vector, the transposase vector, or both further comprise a selectable marker.
  • 36. (canceled)
  • 37. (canceled)
  • 38. (canceled)
  • 39. (canceled)
  • 40. (canceled)
  • 41. (canceled)
  • 42. (canceled)
CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application Ser. No. 62/746,198, filed Oct. 16, 2018, the entire contents of which are incorporated herein by reference.

STATEMENT OF FEDERALLY FUNDED RESEARCH

This invention was made with government support under R15 CA215874 and W81XWH-18-1-0293 awarded by the National Institutes of Health and the Department of Defense, respectively. The government has certain rights in the invention.

PCT Information
Filing Document Filing Date Country Kind
PCT/US2019/056281 10/15/2019 WO 00
Provisional Applications (1)
Number Date Country
62746198 Oct 2018 US